Sun, 30 Jun 2019

Package missRanger updated to version 2.1.0 with previous version 1.0.5 dated 2019-06-09

Title: Fast Imputation of Missing Values
Description: Alternative implementation of the beautiful 'MissForest' algorithm used to impute mixed-type data sets by chaining random forests, introduced by Stekhoven, D.J. and Buehlmann, P. (2012) <doi:10.1093/bioinformatics/btr597>. Under the hood, it uses the lightning fast random jungle package 'ranger'. Between the iterative model fitting, we offer the option of using predictive mean matching. This firstly avoids imputation with values not already present in the original data (like a value 0.3334 in 0-1 coded variable). Secondly, predictive mean matching tries to raise the variance in the resulting conditional distributions to a realistic level. This would allow e.g. to do multiple imputation when repeating the call to missRanger(). A formula interface allows to control which variables should be imputed by which.
Author: Michael Mayer [aut, cre, cph]
Maintainer: Michael Mayer <mayermichael79@gmail.com>

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Package isni updated to version 1.0 with previous version 0.4 dated 2019-02-04

Title: Index of Local Sensitivity to Nonignorability
Description: The current version provides functions to compute, print and summarize the Index of Sensitivity to Nonignorability (ISNI) in the generalized linear model for independent data, and in the marginal multivariate Gaussian model and the mixed-effects models for continuous and binary longitudinal/clustered data. It allows for arbitrary patterns of missingness in the regression outcomes caused by dropout and/or intermittent missingness. One can compute the sensitivity index without estimating any nonignorable models or positing specific magnitude of nonignorability. Thus ISNI provides a simple quantitative assessment of how robust the standard estimates assuming missing at random is with respect to the assumption of ignorability. For a tutorial, download at <http://huixie.people.uic.edu/Research/ISNI_R_tutorial.pdf>. For more details, see Troxel Ma and Heitjan (2004) and Xie and Heitjan (2004) <doi:10.1191/1740774504cn005oa> and Ma Troxel and Heitjan (2005) <doi:10.1002/sim.2107> and Xie (2008) <doi:10.1002/sim.3117> and Xie (2012) <doi:10.1016/j.csda.2010.11.021> and Xie and Qian (2012) <doi:10.1002/jae.1157>.
Author: Hui Xie <huixie@uic.edu>, Weihua Gao, Baodong Xing, Daniel Heitjan, Donald Hedeker, Chengbo Yuan
Maintainer: Hui Xie <huixie@uic.edu>

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Package tvReg updated to version 0.4.2 with previous version 0.4.1 dated 2019-04-08

Title: Time-Varying Coefficient Linear Regression for Single and Multi-Equations
Description: Fitting time-varying coefficient models both for single and multi-equation regressions, using kernel smoothing techniques.
Author: Isabel Casas [aut, cre], Ruben Fernandez-Casal [aut]
Maintainer: Isabel Casas <casasis@gmail.com>

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Package densratio updated to version 0.2.1 with previous version 0.1.1 dated 2019-05-08

Title: Density Ratio Estimation
Description: Density ratio estimation. The estimated density ratio function can be used in many applications such as anomaly detection, change-point detection, covariate shift adaptation. The implemented methods are uLSIF (Hido et al. (2011) <doi:10.1007/s10115-010-0283-2>), RuLSIF (Yamada et al. (2011) <doi:10.1162/NECO_a_00442>), and KLIEP (Sugiyama et al. (2007) <doi:10.1007/s10463-008-0197-x>).
Author: Koji Makiyama [aut, cre]
Maintainer: Koji Makiyama <hoxo.smile@gmail.com>

Diff between densratio versions 0.1.1 dated 2019-05-08 and 0.2.1 dated 2019-06-30

 densratio-0.1.1/densratio/R/uLSIF_search_sigma_and_lambda.R                               |only
 densratio-0.2.1/densratio/DESCRIPTION                                                     |   11 
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 densratio-0.2.1/densratio/NAMESPACE                                                       |    4 
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Package RProtoBuf updated to version 0.4.14 with previous version 0.4.13 dated 2018-11-03

Title: R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
Description: Protocol Buffers are a way of encoding structured data in an efficient yet extensible format. Google uses Protocol Buffers for almost all of its internal 'RPC' protocols and file formats. Additional documentation is available in two included vignettes one of which corresponds to our 'JSS' paper (2016, <doi:10.18637/jss.v071.i02>. Either version 2 or 3 of the 'Protocol Buffers' 'API' is supported.
Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package googleAuthR updated to version 0.8.0 with previous version 0.7.0 dated 2018-11-16

Title: Authenticate and Create Google APIs
Description: Create R functions that interact with OAuth2 Google APIs <https://developers.google.com/apis-explorer/> easily, with auto-refresh and Shiny compatibility.
Author: Mark Edmondson [aut, cre] (<https://orcid.org/0000-0002-8434-3881>), Jennifer Bryan [ctb], Johann deBoer [ctb], Neal Richardson [ctb], David Kulp [ctb], Joe Cheng [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>

Diff between googleAuthR versions 0.7.0 dated 2018-11-16 and 0.8.0 dated 2019-06-30

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 R/auth.R                                                                         |   14 
 R/auto_auth.R                                                                    |   30 
 R/batch.R                                                                        |   18 
 R/checks.R                                                                       |    7 
 R/debugging.R                                                                    |only
 R/discovery.R                                                                    |    2 
 R/gce.R                                                                          |   75 ++
 R/generator.R                                                                    |   28 
 R/memoise.R                                                                      |    8 
 R/options.R                                                                      |    6 
 R/page_results.R                                                                 |   49 +
 R/set_client.R                                                                   |   17 
 R/shiny-auth.R                                                                   |    2 
 R/shiny-js-signin.R                                                              |    4 
 R/shiny-modifyurl.R                                                              |   35 -
 R/utility.R                                                                      |    2 
 inst/doc/advanced-building.html                                                  |    6 
 inst/doc/building.html                                                           |    4 
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 inst/doc/setup.html                                                              |    4 
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 man/checkTokenAPI.Rd                                                             |    1 
 man/gar_api_generator.Rd                                                         |    4 
 man/gar_api_page.Rd                                                              |    8 
 man/gar_attach_auto_auth.Rd                                                      |    8 
 man/gar_auth.Rd                                                                  |    1 
 man/gar_auth_service.Rd                                                          |    4 
 man/gar_auto_auth.Rd                                                             |    7 
 man/gar_batch.Rd                                                                 |    1 
 man/gar_batch_walk.Rd                                                            |   22 
 man/gar_cache_setup.Rd                                                           |    5 
 man/gar_create_api_objects.Rd                                                    |    1 
 man/gar_create_api_skeleton.Rd                                                   |    1 
 man/gar_create_package.Rd                                                        |    3 
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 man/gar_discovery_api.Rd                                                         |    1 
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 man/gar_gce_auth.Rd                                                              |    1 
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 man/gar_shiny_auth.Rd                                                            |    3 
 man/gar_shiny_auth_url.Rd                                                        |    1 
 man/gar_shiny_login_ui.Rd                                                        |    1 
 man/gar_shiny_ui.Rd                                                              |    1 
 man/gar_token_info.Rd                                                            |    3 
 man/get_google_token.Rd                                                          |    1 
 man/googleAuth.Rd                                                                |    7 
 man/googleAuthUI.Rd                                                              |    1 
 man/silent_auth.Rd                                                               |    1 
 man/token_exists.Rd                                                              |    1 
 man/with_shiny.Rd                                                                |    1 
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Package pksensi updated to version 1.1.2 with previous version 1.1.1 dated 2019-05-29

Title: Global Sensitivity Analysis in Physiologically Based Kinetic Modeling
Description: Applying the global sensitivity analysis workflow to investigate the parameter uncertainty and sensitivity in pharmacokinetic (PK) models, especially the physiologically-based pharmacokinetic (PBPK) model with multivariate outputs. The package also provide some functions to check the sensitivity measures and its convergence of model parameters.
Author: Nan-Hung Hsieh [aut, cre] (<https://orcid.org/0000-0003-0163-2766>), Brad Reisfeld [aut], Weihsueh A. Chiu [aut] (<https://orcid.org/0000-0002-7575-2368>)
Maintainer: Nan-Hung Hsieh <nhsieh@cvm.tamu.edu>

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Package sensitivity updated to version 1.16.1 with previous version 1.16.0 dated 2019-05-25

Title: Global Sensitivity Analysis of Model Outputs
Description: A collection of functions for factor screening, global sensitivity analysis and reliability sensitivity analysis. Most of the functions have to be applied on model with scalar output, but several functions support multi-dimensional outputs.
Author: Bertrand Iooss, Alexandre Janon and Gilles Pujol, with contributions from Baptiste Broto, Khalid Boumhaout, Sebastien Da Veiga, Thibault Delage, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Loic Le Gratiet, Paul Lemaitre, Barry L. Nelson, Filippo Monari, Roelof Oomen, Oldrich Rakovec, Bernardo Ramos, Olivier Roustant, Eunhye Song, Jeremy Staum, Roman Sueur, Taieb Touati, Frank Weber
Maintainer: Bertrand Iooss <biooss@yahoo.fr>

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Package RcppAlgos updated to version 2.3.3 with previous version 2.3.2 dated 2019-04-14

Title: High Performance Tools for Combinatorics and Computational Mathematics
Description: Provides optimized functions implemented in C++ with 'Rcpp' for solving problems in combinatorics and computational mathematics. Utilizes parallel programming via 'RcppThread' for maximal performance. Also makes use of the RMatrix class from the 'RcppParallel' library. There are combination/permutation functions with constraint parameters that allow for generation of all combinations/permutations of a vector meeting specific criteria (e.g. finding all combinations such that the sum is between two bounds). Capable of generating specific combinations/permutations (e.g. retrieve only the nth lexicographical result) which sets up nicely for parallelization as well as random sampling. Gmp support permits exploration where the total number of results is large (e.g. comboSample(10000, 500, n = 4)). Additionally, there are several high performance number theoretic functions that are useful for problems common in computational mathematics. Some of these functions make use of the fast integer division library 'libdivide' by <http://ridiculousfish.com>. The primeSieve function is based on the segmented sieve of Eratosthenes implementation by Kim Walisch. It is also efficient for large numbers by using the cache friendly improvements originally developed by Tomás Oliveira. Finally, there is a prime counting function that implements Legendre's formula based on the algorithm by Kim Walisch.
Author: Joseph Wood
Maintainer: Joseph Wood <jwood000@gmail.com>

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 RcppAlgos-2.3.3/RcppAlgos/src/NthResult.cpp                        |    5 
 RcppAlgos-2.3.3/RcppAlgos/src/PollardRho.cpp                       |  364 ++++--
 RcppAlgos-2.3.3/RcppAlgos/src/Primes.cpp                           |   10 
 RcppAlgos-2.3.3/RcppAlgos/src/RcppExports.cpp                      |   15 
 RcppAlgos-2.3.3/RcppAlgos/src/SampCombPerm.cpp                     |   14 
 RcppAlgos-2.3.3/RcppAlgos/src/importExportMPZ.cpp                  |   10 
 RcppAlgos-2.3.3/RcppAlgos/tests/testthat/testComboGeneral.R        |    7 
 RcppAlgos-2.3.3/RcppAlgos/tests/testthat/testDivisorsSieve.R       |    4 
 RcppAlgos-2.3.3/RcppAlgos/tests/testthat/testEulerPhiSieve.R       |    4 
 RcppAlgos-2.3.3/RcppAlgos/tests/testthat/testIsPrimeRcpp.R         |    2 
 RcppAlgos-2.3.3/RcppAlgos/tests/testthat/testNumDivisorSieve.R     |    4 
 RcppAlgos-2.3.3/RcppAlgos/tests/testthat/testPermuteGeneral.R      |   10 
 RcppAlgos-2.3.3/RcppAlgos/tests/testthat/testPrimeFactorizeSieve.R |    2 
 RcppAlgos-2.3.3/RcppAlgos/tests/testthat/testPrimeSieve.R          |    2 
 RcppAlgos-2.3.3/RcppAlgos/tests/testthat/testSample.R              |    4 
 RcppAlgos-2.3.3/RcppAlgos/tests/testthat/testSpecialSubsetSum.R    |only
 39 files changed, 689 insertions(+), 858 deletions(-)

More information about RcppAlgos at CRAN
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Package openCR updated to version 1.4.1 with previous version 1.4.0 dated 2019-06-15

Title: Open Population Capture-Recapture
Description: Functions for non-spatial and spatial open-population capture-recapture analysis.
Author: Murray Efford [aut, cre] (<https://orcid.org/0000-0001-5231-5184>)
Maintainer: Murray Efford <murray.efford@otago.ac.nz>

Diff between openCR versions 1.4.0 dated 2019-06-15 and 1.4.1 dated 2019-06-30

 DESCRIPTION                   |    8 -
 MD5                           |   33 ++--
 NAMESPACE                     |    2 
 NEWS                          |   16 ++
 R/logliksecr.R                |  110 +++++---------
 R/moving.fit.R                |    6 
 R/openCR.fit.R                |    3 
 R/predict.openCR.R            |    1 
 R/prwi.R                      |only
 R/prwisecr.R                  |  313 ++++++++++++------------------------------
 R/simulate.R                  |   27 +--
 R/summary.openCR.R            |   17 +-
 inst/doc/openCR-vignette.Rmd  |   14 -
 inst/doc/openCR-vignette.pdf  |binary
 man/openCR-internal.Rd        |    6 
 man/openCR-package.Rd         |    4 
 src/prwisecrparallel.cpp      |  119 ++++++++-------
 vignettes/openCR-vignette.Rmd |   14 -
 18 files changed, 287 insertions(+), 406 deletions(-)

More information about openCR at CRAN
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