Title: Computes Proximity in Large Sparse Matrices
Description: Computes proximity between rows or columns of large matrices efficiently in C++.
Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries.
Among several built-in similarity/distance measures, computation of correlation,
cosine similarity and Euclidean distance is particularly fast.
Author: Kohei Watanabe [cre, aut, cph]
(<https://orcid.org/0000-0001-6519-5265>)
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between proxyC versions 0.1.0 dated 2018-12-31 and 0.1.2 dated 2019-04-19
DESCRIPTION | 11 +++---- MD5 | 29 ++++++++++---------- NEWS.md |only R/RcppExports.R | 8 ++--- R/proxy.R | 54 ++++++++++++++++++++++++++------------- README.md | 13 ++++++--- man/images/unnamed-chunk-4-1.png |binary man/images/unnamed-chunk-5-1.png |binary man/images/unnamed-chunk-6-1.png |binary man/simil.Rd | 20 +++++++++----- src/RcppExports.cpp | 18 +++++++------ src/linear.cpp | 13 +++++---- src/pair.cpp | 7 ++--- tests/testthat/test-dist.R | 31 +++++++++++++++------- tests/testthat/test-proxy.R | 10 +++++++ tests/testthat/test-simil.R | 34 ++++++++++++++++++------ 16 files changed, 161 insertions(+), 87 deletions(-)
Title: Straightforward 'NetCDF' Metadata
Description: Extract metadata from 'NetCDF' data sources, these can be files, file handles or
servers. This package leverages and extends the lower level functions of the 'RNetCDF' package
providing a consistent set of functions that all return data frames. We introduce named concepts
of 'grid', 'axis' and 'source' which are all meaningful entities without formal definition in the
'NetCDF' library <https://www.unidata.ucar.edu/software/netcdf/>. 'RNetCDF' matches the library
itself with only the named concepts of 'variables', 'dimensions' and 'attributes'. 'ncmeta'
provides a required framework for the in-development 'tidync' project <https://github.com/hypertidy/tidync>.
Author: Michael Sumner [aut, cre],
Tomas Remenyi [ctb],
Ben Raymond [ctb],
David Blodgett [ctb]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between ncmeta versions 0.0.3 dated 2018-10-26 and 0.0.4 dated 2019-04-19
DESCRIPTION | 16 ++-- MD5 | 52 +++++++++++----- NAMESPACE | 18 +++++ NEWS.md | 8 ++ R/nc-gridmapping.R |only R/nc-prj.R |only R/nc_att.R | 20 +++--- R/nc_axes.R | 6 - R/nc_coord.R |only R/nc_dim.R | 2 R/nc_grid.R | 18 ++++- R/nc_inq_file.R | 2 R/nc_var.R | 2 R/tidync.R |only R/utils.R | 61 +++++++++++++++++-- inst/extdata/avhrr-only-v2.19810901.cdl |only inst/extdata/avhrr-only-v2.19810901_header.nc |only inst/extdata/daymet_sample.cdl |only inst/extdata/daymet_sample.nc |only inst/extdata/guam.nc |only inst/extdata/rasterwise-bad_examples_62-example3.cdl |only inst/extdata/rasterwise-bad_examples_62-example3.nc |only inst/extdata/rasterwise-high-dim-test-1.cdl |only inst/extdata/rasterwise-high-dim-test-1.nc |only inst/extdata/rasterwise-timeseries.cdl |only inst/extdata/rasterwise-timeseries.nc |only man/nc_att.Rd | 3 man/nc_coord_var.Rd |only man/nc_gm_to_prj.Rd |only man/nc_grid_mapping_atts.Rd |only man/nc_grids.Rd | 5 + man/nc_prj_to_gridmapping.Rd |only tests/testthat/test-attributes.R | 17 +++-- tests/testthat/test-coord.R |only tests/testthat/test-grid-var-order.R | 3 tests/testthat/test-gridmapping-prj.R |only tests/testthat/test-utils.R |only tests/testthat/test-vars.R | 4 - 38 files changed, 184 insertions(+), 53 deletions(-)
Title: General Semiparametric Shared Frailty Model
Description: Simulates and fits semiparametric shared frailty models under a
wide range of frailty distributions using a consistent and
asymptotically-normal estimator. Currently supports: gamma, power variance
function, log-normal, and inverse Gaussian frailty models.
Author: Vinnie Monaco [aut, cre],
Malka Gorfine [aut],
Li Hsu [aut]
Maintainer: Vinnie Monaco <contact@vmonaco.com>
Diff between frailtySurv versions 1.3.5 dated 2018-08-28 and 1.3.6 dated 2019-04-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 3 +++ man/genfrail.Rd | 3 +++ 4 files changed, 13 insertions(+), 7 deletions(-)
Title: Times and Dates from S-PLUS
Description: A collection of classes and methods for working with
times and dates. The code was originally available in S-PLUS.
Author: TIBCO Software Inc.
Maintainer: Stephen Kaluzny <skaluzny@tibco.com>
Diff between splusTimeDate versions 2.5.0-141 dated 2018-05-30 and 2.5.0-142 dated 2019-04-19
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 6 +++--- src/timeObj.c | 11 ++++++----- 4 files changed, 14 insertions(+), 13 deletions(-)
Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine
copula modeling based on 'Boost' and 'Eigen'. The 'rvinecopulib'
package implements the core features of the popular 'VineCopula' package, in
particular inference algorithms for both vine copula and bivariate copula
models. Advantages over 'VineCopula' are a sleeker and more modern API,
improved performances, especially in high dimensions, nonparametric and
multi-parameter families. The 'rvinecopulib' package includes 'vinecopulib' as
header-only C++ library (currently version 0.3.1). Thus
users do not need to install 'vinecopulib' itself in order to use
'rvinecopulib'. Since their initial releases, 'vinecopulib' is licensed under
the MIT License, and 'rvinecopulib' is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>
Diff between rvinecopulib versions 0.3.0.1.1 dated 2018-08-22 and 0.3.1.1.0 dated 2019-04-19
DESCRIPTION | 10 MD5 | 220 +++---- NEWS.md | 26 R/RcppExports.R | 4 R/as_rvine_structure.R | 297 +++++----- R/bicop.R | 2 R/bicop_methods.R | 19 R/family_sets.R | 2 R/rvine_structure.R | 266 ++++---- R/rvinecopulib.R | 2 R/tools.R | 15 R/vine.R | 56 - R/vine_methods.R | 2 R/vinecop.R | 6 R/vinecop_methods.R | 15 R/vinecop_plot.R | 2 inst/include/version.hpp | 6 inst/include/vinecopulib.hpp | 2 inst/include/vinecopulib/bicop/abstract.hpp | 2 inst/include/vinecopulib/bicop/archimedean.hpp | 2 inst/include/vinecopulib/bicop/bb1.hpp | 2 inst/include/vinecopulib/bicop/bb6.hpp | 2 inst/include/vinecopulib/bicop/bb7.hpp | 2 inst/include/vinecopulib/bicop/bb8.hpp | 2 inst/include/vinecopulib/bicop/class.hpp | 2 inst/include/vinecopulib/bicop/clayton.hpp | 2 inst/include/vinecopulib/bicop/elliptical.hpp | 2 inst/include/vinecopulib/bicop/family.hpp | 2 inst/include/vinecopulib/bicop/fit_controls.hpp | 2 inst/include/vinecopulib/bicop/frank.hpp | 2 inst/include/vinecopulib/bicop/gaussian.hpp | 2 inst/include/vinecopulib/bicop/gumbel.hpp | 2 inst/include/vinecopulib/bicop/implementation/abstract.ipp | 2 inst/include/vinecopulib/bicop/implementation/archimedean.ipp | 2 inst/include/vinecopulib/bicop/implementation/bb1.ipp | 2 inst/include/vinecopulib/bicop/implementation/bb6.ipp | 2 inst/include/vinecopulib/bicop/implementation/bb7.ipp | 2 inst/include/vinecopulib/bicop/implementation/bb8.ipp | 2 inst/include/vinecopulib/bicop/implementation/class.ipp | 4 inst/include/vinecopulib/bicop/implementation/clayton.ipp | 8 inst/include/vinecopulib/bicop/implementation/elliptical.ipp | 2 inst/include/vinecopulib/bicop/implementation/family.ipp | 2 inst/include/vinecopulib/bicop/implementation/fit_controls.ipp | 2 inst/include/vinecopulib/bicop/implementation/frank.ipp | 2 inst/include/vinecopulib/bicop/implementation/gaussian.ipp | 2 inst/include/vinecopulib/bicop/implementation/gumbel.ipp | 2 inst/include/vinecopulib/bicop/implementation/indep.ipp | 2 inst/include/vinecopulib/bicop/implementation/joe.ipp | 2 inst/include/vinecopulib/bicop/implementation/kernel.ipp | 2 inst/include/vinecopulib/bicop/implementation/parametric.ipp | 14 inst/include/vinecopulib/bicop/implementation/student.ipp | 2 inst/include/vinecopulib/bicop/implementation/tll.ipp | 2 inst/include/vinecopulib/bicop/implementation/tools_select.ipp | 2 inst/include/vinecopulib/bicop/indep.hpp | 2 inst/include/vinecopulib/bicop/joe.hpp | 2 inst/include/vinecopulib/bicop/kernel.hpp | 2 inst/include/vinecopulib/bicop/parametric.hpp | 2 inst/include/vinecopulib/bicop/student.hpp | 2 inst/include/vinecopulib/bicop/tll.hpp | 2 inst/include/vinecopulib/bicop/tools_select.hpp | 2 inst/include/vinecopulib/misc/implementation/tools_eigen.ipp | 2 inst/include/vinecopulib/misc/implementation/tools_interpolation.ipp | 2 inst/include/vinecopulib/misc/implementation/tools_optimization.ipp | 2 inst/include/vinecopulib/misc/implementation/tools_stats.ipp | 2 inst/include/vinecopulib/misc/tools_batch.hpp | 2 inst/include/vinecopulib/misc/tools_bobyqa.hpp | 5 inst/include/vinecopulib/misc/tools_eigen.hpp | 2 inst/include/vinecopulib/misc/tools_integration.hpp | 2 inst/include/vinecopulib/misc/tools_interface.hpp | 2 inst/include/vinecopulib/misc/tools_interpolation.hpp | 2 inst/include/vinecopulib/misc/tools_optimization.hpp | 4 inst/include/vinecopulib/misc/tools_serialization.hpp | 2 inst/include/vinecopulib/misc/tools_stats.hpp | 6 inst/include/vinecopulib/misc/tools_stats_ghalton.hpp | 2 inst/include/vinecopulib/misc/tools_stats_sobol.hpp | 2 inst/include/vinecopulib/misc/tools_stl.hpp | 2 inst/include/vinecopulib/misc/tools_thread.hpp | 2 inst/include/vinecopulib/misc/triangular_array.hpp | 60 +- inst/include/vinecopulib/vinecop/class.hpp | 29 inst/include/vinecopulib/vinecop/fit_controls.hpp | 37 - inst/include/vinecopulib/vinecop/implementation/class.ipp | 238 ++++---- inst/include/vinecopulib/vinecop/implementation/fit_controls.ipp | 62 +- inst/include/vinecopulib/vinecop/implementation/rvine_structure.ipp | 167 +++-- inst/include/vinecopulib/vinecop/implementation/tools_select.ipp | 208 ++++--- inst/include/vinecopulib/vinecop/rvine_structure.hpp | 51 - inst/include/vinecopulib/vinecop/tools_select.hpp | 31 - inst/include/wrappers.hpp | 5 man/as_rvine_structure.Rd | 32 - man/bicop.Rd | 5 man/bicop_methods.Rd | 3 man/getters.Rd | 6 man/mBICV.Rd | 11 man/plot.bicop_dist.Rd | 3 man/plot.vinecop_dist.Rd | 3 man/predict_bicop.Rd | 1 man/predict_vine.Rd | 6 man/predict_vinecop.Rd | 5 man/rosenblatt.Rd | 1 man/rvine_structure.Rd | 65 +- man/rvinecopulib.Rd | 2 man/vine.Rd | 22 man/vine_methods.Rd | 2 man/vinecop.Rd | 8 man/vinecop_methods.Rd | 2 src/Makevars | 4 src/RcppExports.cpp | 14 src/wrappers.cpp | 18 tests/testthat/Rplots.pdf |binary tests/testthat/test_rvine_structure.R | 4 tests/testthat/test_truncate_model.R | 6 tests/testthat/test_vine.R | 10 111 files changed, 1259 insertions(+), 961 deletions(-)
Title: Paired Lasso Regression
Description: Implements sparse regression with paired covariates (Rauschenberger et al. 2019). For the optional shrinkage, install ashr (<https://github.com/stephens999/ashr>) and CorShrink (<https://github.com/kkdey/CorShrink>) from GitHub (see README).
Author: Armin Rauschenberger [aut, cre]
Maintainer: Armin Rauschenberger <a.rauschenberger@vumc.nl>
Diff between palasso versions 0.0.4 dated 2019-03-08 and 0.0.5 dated 2019-04-19
palasso-0.0.4/palasso/R/elastic_net.R |only palasso-0.0.4/palasso/data |only palasso-0.0.4/palasso/man/toydata.Rd |only palasso-0.0.5/palasso/DESCRIPTION | 10 - palasso-0.0.5/palasso/MD5 | 34 ++-- palasso-0.0.5/palasso/NAMESPACE | 1 palasso-0.0.5/palasso/R/function.R | 188 +++++++++++++++++---------- palasso-0.0.5/palasso/R/hidden.R | 139 +++++++++++++++++++ palasso-0.0.5/palasso/R/methods.R | 6 palasso-0.0.5/palasso/README.md | 7 - palasso-0.0.5/palasso/build/vignette.rds |binary palasso-0.0.5/palasso/inst/doc/script.R |only palasso-0.0.5/palasso/inst/doc/script.Rmd |only palasso-0.0.5/palasso/inst/doc/script.html |only palasso-0.0.5/palasso/inst/doc/vignette.R | 33 ++-- palasso-0.0.5/palasso/inst/doc/vignette.Rmd | 5 palasso-0.0.5/palasso/inst/doc/vignette.html | 24 --- palasso-0.0.5/palasso/man/dot-combine.Rd |only palasso-0.0.5/palasso/man/other.Rd | 3 palasso-0.0.5/palasso/man/palasso.Rd | 2 palasso-0.0.5/palasso/vignettes/script.Rmd |only palasso-0.0.5/palasso/vignettes/vignette.Rmd | 5 22 files changed, 321 insertions(+), 136 deletions(-)
Title: Internet Memes for Data Analysts
Description: Generates internet memes that optionally include a superimposed inset plot and other atypical features,
combining the visual impact of an attention-grabbing meme with graphic results of data analysis.
The package differs from related packages that focus on imitating and reproducing standard memes.
Some packages do this by interfacing with online meme generators whereas others achieve this natively.
This package takes the latter approach. It does not interface with online meme generators or require any authentication with external websites.
It reads images directly from local files or via URL and meme generation is done by the package.
While this is similar to the 'meme' package available on CRAN, it differs in that the focus is on
allowing for non-standard meme layouts and hybrids of memes mixed with graphs.
While this package can be used to make basic memes like an online meme generator would produce,
it caters primarily to hybrid graph-meme plots where the meme presentation can be seen as a backdrop highlighting
foreground graphs of data analysis results.
The package also provides support for an arbitrary number of meme text labels with arbitrary size, position and other attributes
rather than restricting to the standard top and/or bottom text placement.
This is useful for proper aesthetic interleaving of plots of data between meme image backgrounds and overlain text labels.
The package offers a selection of templates for graph placement and appearance with respect to the underlying meme.
Graph templates also permit additional template-specific customization.
Animated gif support is provided but this is optional and functional only if the 'magick' package is installed.
'magick' is not required unless gif functionality is desired.
Author: Matthew Leonawicz [aut, cre]
Maintainer: Matthew Leonawicz <matt_leonawicz@esource.com>
Diff between memery versions 0.5.0 dated 2018-05-17 and 0.5.2 dated 2019-04-19
memery-0.5.0/memery/inst/memery.png |only memery-0.5.0/memery/inst/shiny/memeApp/rsconnect |only memery-0.5.2/memery/DESCRIPTION | 14 +-- memery-0.5.2/memery/MD5 | 25 +++--- memery-0.5.2/memery/NEWS.md | 20 +++-- memery-0.5.2/memery/R/meme.R | 54 +++----------- memery-0.5.2/memery/R/memery.R | 4 - memery-0.5.2/memery/build/vignette.rds |binary memery-0.5.2/memery/inst/doc/memery.Rmd | 6 - memery-0.5.2/memery/inst/doc/memery.html | 83 +++++++++++++++-------- memery-0.5.2/memery/man/figures |only memery-0.5.2/memery/man/meme.Rd | 23 +++--- memery-0.5.2/memery/man/memeApp.Rd | 2 memery-0.5.2/memery/tests/testthat/test-meme.R | 2 memery-0.5.2/memery/vignettes/memery.Rmd | 6 - 15 files changed, 121 insertions(+), 118 deletions(-)
Title: Univariate and Multivariate Model-Based Clustering in
Group-Specific Functional Subspaces
Description: The funHDDC algorithm allows to cluster functional univariate (Bouveyron and Jacques, 2011, <doi:10.1007/s11634-011-0095-6>) or multivariate data (Schmutz et al., 2018) by modeling each group within a specific functional subspace.
Author: A Schmutz, J. Jacques & C. Bouveyron
Maintainer: Charles Bouveyron <charles.bouveyron@gmail.com>
Diff between funHDDC versions 2.2.0 dated 2018-10-08 and 2.3.0 dated 2019-04-19
DESCRIPTION | 10 - MD5 | 22 ++-- R/plot.mfpca.R | 268 ++++++++++++++++++++++++------------------------- R/predict.funHDDC.R | 186 +++++++++++++++++----------------- build/vignette.rds |binary inst/doc/funHDDC.html | 68 ++++++------ inst/extdata |only man/funHDDC.Rd | 13 +- man/mfpca.Rd | 91 ++++++++-------- man/plot.mfpca.Rd | 87 ++++++++------- man/predict.funHDDC.Rd | 165 +++++++++++++++--------------- man/slopeHeuristic.Rd | 142 ++++++++++++------------- 12 files changed, 535 insertions(+), 517 deletions(-)
Title: Directional Statistics
Description: A collection of functions for directional data analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). An elliptically symmetric angular Gaussian distribution. Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>, P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2019). Spherical regression models with general covariates and anisotropic errors. Statistics and Computing (to appear). <doi:10.1007/s11222-019-09872-2>.
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Directional versions 3.6 dated 2019-03-25 and 3.7 dated 2019-04-19
DESCRIPTION | 10 ++-- MD5 | 19 +++++---- NAMESPACE | 6 +- R/ESAGmle.R | 33 +++++++++++---- R/cosap.R | 94 +++++++++++++++++++++++---------------------- R/iag.reg.R |only R/rfb.R | 73 +++++++++++++++++++++++++++++----- R/vmf.reg.R |only man/Directional-package.Rd | 4 - man/ESAGmle.Rd | 16 ++++++- man/iag.reg.Rd |only man/spml.reg.Rd | 8 +-- 12 files changed, 173 insertions(+), 90 deletions(-)
Title: Music Chords Extraction
Description: Extracts music chords from the 'CifraClub' website <https://www.cifraclub.com.br/>.
The package also has functions for cleaning the extracted data and
feature extraction.
Author: Bruna Wundervald
Maintainer: Bruna Wundervald <brunadaviesw@gmail.com>
Diff between chorrrds versions 0.1.8 dated 2019-01-28 and 0.1.9 dated 2019-04-19
DESCRIPTION | 12 +-- LICENSE |only MD5 | 15 +++- NAMESPACE | 2 R/chords_bigram.R |only R/feature_extraction.R |only R/utils.R | 3 README.md | 147 ++++++++++++++++++++++++++++++++++++++++++++-- man/chords_ngram.Rd |only man/feature_extraction.Rd |only tests |only 11 files changed, 164 insertions(+), 15 deletions(-)
Title: Anchored Kmedoids for Longitudinal Data Clustering
Description: Advances a novel adaptation of longitudinal k-means clustering technique (Genolini et al. (2015) <doi:10.18637/jss.v065.i04>) for grouping trajectories based on the similarities of their long-term trends and determines the optimal solution based on the Calinski-Harabatz criterion (Calinski and Harabatz (1974) <doi:10.1080/03610927408827101>). Includes functions to extract descriptive statistics and generate a visualisation of the resulting groups, drawing methods from the 'ggplot2' library (Wickham H. (2016) <doi:10.1007/978-3-319-24277-4>). The package also includes a number of other useful functions for exploring and manipulating longitudinal data prior to the clustering process.
Author: Monsuru Adepeju [cre, aut], Samuel Langton [aut], Jon Bannister [aut]
Maintainer: Monsuru Adepeju <monsuur2010@yahoo.com>
Diff between akmedoids versions 0.1.1 dated 2019-04-18 and 0.1.2 dated 2019-04-19
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 15 ++++++--------- README.md | 2 +- build/vignette.rds |binary inst/doc/akmedoids-vignette.Rmd | 2 +- inst/doc/akmedoids-vignette.html | 2 +- vignettes/akmedoids-vignette.Rmd | 2 +- 8 files changed, 21 insertions(+), 24 deletions(-)
Title: Companion Animal Population Management
Description: Quantitative analysis to support companion animal population
management. Some functions assist survey sampling tasks (calculate sample
size for simple and complex designs, select sampling units and estimate
population parameters) while others assist the modelling of population
dynamics. For demographic characterizations and population management
evaluations see: "Baquero, et al." (2018),
<doi:10.1016/j.prevetmed.2018.07.006>. For modelling of
population dynamics see: "Baquero et al." (2016),
<doi:10.1016/j.prevetmed.2015.11.009>. For sampling methods
see: "Levy PS & Lemeshow S" (2013), "ISBN-10: 0470040076";
"Lumley" (2010), "ISBN: 978-0-470-28430-8".
Author: Oswaldo Santos Baquero [aut, cre],
Marcos Amaku [ctb],
Fernando Ferreira [ctb]
Maintainer: Oswaldo Santos Baquero <baquero@usp.br>
Diff between capm versions 0.13.9 dated 2018-11-26 and 0.13.10 dated 2019-04-19
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- NEWS | 5 +++++ R/PlotPopPyramid.R | 6 +++--- R/capm-package.R | 4 ++-- man/Calculate2StageSampleSize.Rd | 4 ++-- man/CalculateStratifiedSampleSize.Rd | 4 ++-- man/GetDataIASA.Rd | 20 +++++++++++--------- man/MapkmlPSU.Rd | 3 ++- man/PlotLocalSens.Rd | 7 ++++--- man/PlotModels.Rd | 6 +++--- man/PlotPopPyramid.Rd | 3 ++- man/SampleSystematic.Rd | 4 ++-- man/SolveIASA.Rd | 7 ++++--- man/capm-package.Rd | 4 ++-- 15 files changed, 63 insertions(+), 52 deletions(-)
Title: Multi-Reader, Multi-Case Analysis Methods (ROC, Agreement, and
Other Metrics)
Description: Do Multi-Reader, Multi-Case (MRMC) analyses of data from imaging studies where clinicians (readers)
evaluate patient images (cases). What does this mean? ... Many imaging studies are designed
so that every reader reads every case in all modalities, a fully-crossed study. In this case, the
data is cross-correlated, and we consider the readers and cases to be cross-correlated random effects.
An MRMC analysis accounts for the variability and correlations from the readers and cases when
estimating variances, confidence intervals, and p-values. The functions in this package can treat
arbitrary study designs and studies with missing data, not just fully-crossed study designs.
The initial package analyzes the reader-average area under the receiver operating characteristic (ROC)
curve with U-statistics according to Gallas, Bandos, Samuelson,
and Wagner 2009 <doi:10.1080/03610920802610084>.
Additional functions analyze other endpoints with U-statistics (binary performance
and score differences) following the work by Gallas, Pennello, and Myers 2007
<doi:10.1364/JOSAA.24.000B70>.
Package development and documentation is at <https://github.com/DIDSR/iMRMC/tree/master>.
Author: Brandon Gallas
Maintainer: Brandon Gallas <Brandon.Gallas@fda.hhs.gov>
Diff between iMRMC versions 1.1.0 dated 2017-12-12 and 1.2.0 dated 2019-04-19
iMRMC-1.1.0/iMRMC/inst/java/iMRMC-v4.0.0.jar |only iMRMC-1.1.0/iMRMC/man/uStat11.jointD.Rd |only iMRMC-1.2.0/iMRMC/DESCRIPTION | 10 iMRMC-1.2.0/iMRMC/MD5 | 62 - iMRMC-1.2.0/iMRMC/NAMESPACE | 8 iMRMC-1.2.0/iMRMC/R/iMRMC.R | 42 - iMRMC-1.2.0/iMRMC/R/limitsOfAgreement.R |only iMRMC-1.2.0/iMRMC/R/simMRMC.R | 195 ++--- iMRMC-1.2.0/iMRMC/R/uStats.R | 68 + iMRMC-1.2.0/iMRMC/R/utils.R | 388 +++++++++- iMRMC-1.2.0/iMRMC/data |only iMRMC-1.2.0/iMRMC/inst/java/iMRMC-v4.0.3.jar |only iMRMC-1.2.0/iMRMC/man/convertDFtoDesignMatrix.Rd | 13 iMRMC-1.2.0/iMRMC/man/convertDFtoScoreMatrix.Rd | 13 iMRMC-1.2.0/iMRMC/man/createGroups.Rd |only iMRMC-1.2.0/iMRMC/man/doIMRMC.Rd | 8 iMRMC-1.2.0/iMRMC/man/extractPairedComparisonsBRBM.Rd |only iMRMC-1.2.0/iMRMC/man/extractPairedComparisonsWRBM.Rd |only iMRMC-1.2.0/iMRMC/man/getMRMCscore.Rd |only iMRMC-1.2.0/iMRMC/man/laBRBM.Rd |only iMRMC-1.2.0/iMRMC/man/laWRBM.Rd |only iMRMC-1.2.0/iMRMC/man/renameCol.Rd |only iMRMC-1.2.0/iMRMC/man/roeMetzConfigs.Rd |only iMRMC-1.2.0/iMRMC/man/sim.gRoeMetz.Rd | 9 iMRMC-1.2.0/iMRMC/man/sim.gRoeMetz.config.Rd | 8 iMRMC-1.2.0/iMRMC/man/simMRMC.Rd | 10 iMRMC-1.2.0/iMRMC/man/simRoeMetz.example.Rd | 7 iMRMC-1.2.0/iMRMC/man/uStat11.Rd |only iMRMC-1.2.0/iMRMC/man/uStat11.diff.Rd | 9 iMRMC-1.2.0/iMRMC/man/uStat11.identity.Rd | 8 iMRMC-1.2.0/iMRMC/tests/testthat/Rplots.pdf |binary iMRMC-1.2.0/iMRMC/tests/testthat/test_createANDundoIMRMCdf.R | 2 iMRMC-1.2.0/iMRMC/tests/testthat/test_doIMRMC.R | 7 iMRMC-1.2.0/iMRMC/tests/testthat/test_doIMRMCfromFile.R | 2 iMRMC-1.2.0/iMRMC/tests/testthat/test_lecuyerRNG.R | 7 iMRMC-1.2.0/iMRMC/tests/testthat/test_simRoeMetz.R | 2 iMRMC-1.2.0/iMRMC/tests/testthat/test_uStat11.R | 4 iMRMC-1.2.0/iMRMC/tests/testthat/test_uStat11.Rdata |binary iMRMC-1.2.0/iMRMC/tests/testthat/test_uStat11_splitPlot.R |only iMRMC-1.2.0/iMRMC/tests/testthat/test_uStat11_splitPlot.Rdata |only 40 files changed, 660 insertions(+), 222 deletions(-)
Title: Computing Essential Biodiversity Variables from Global Forest
Change Data
Description: Metrics of two Essential Biodiversity Variables: forest extents and forest fragmentation indices (O'connor et al., 2015) <doi:10.1002/rse2.4> are computed by processing Global Forest Change data (Hansen et al., 2013) <doi:10.1126/science.1244693>. The Forest Change Data are extracted using either Geographic Administrative Units, see <https://gadm.org/>, or user-defined polygons. Most of the procedures can be understood implementing two functions: FCPolygon() and EBVmetric().
Author: Wilson Lara <wilarhen@temple.edu>, Victor Gutierrez-Velez <victorhugo@temple.edu>
Maintainer: Wilson Lara <wilarhen@temple.edu>
Diff between forestChange versions 0.5 dated 2019-03-26 and 0.6 dated 2019-04-19
DESCRIPTION | 8 - MD5 | 18 ++-- NEWS | 5 + R/FCPolygon.R | 217 +++++++++++++++++++++++++++--------------------------- R/GFCurls.R | 14 +-- R/getGADM.R | 8 - build/partial.rdb |binary man/FCPolygon.Rd | 29 +++---- man/GFCurls.Rd | 20 ++-- man/getGADM.Rd | 16 +-- 10 files changed, 174 insertions(+), 161 deletions(-)
Title: Interface to 'ECMWF' and 'CDS' Data Web Services
Description: Programmatic interface to the European Centre for Medium-Range
Weather Forecasts dataset web services (ECMWF; <https://www.ecmwf.int/>)
and Copernicus's Climate Data Store (CDS;
<https://cds.climate.copernicus.eu>). Allows for easy downloads of weather
forecasts and climate reanalysis data in R.
Author: Koen Hufkens [aut, cre] (<https://orcid.org/0000-0002-5070-8109>),
Reto Stauffer [ctb] (<https://orcid.org/0000-0002-3798-5507>),
Elio Campitelli [ctb] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between ecmwfr versions 1.1.0 dated 2019-02-06 and 1.2.0 dated 2019-04-19
DESCRIPTION | 29 +- MD5 | 71 ++-- NAMESPACE | 2 R/addin.R |only R/methods.R |only R/wf_archetype.R |only R/wf_datasets.R | 6 R/wf_delete.R | 4 R/wf_get_key.R | 13 R/wf_product_info.R | 28 - R/wf_request.R | 53 ++- R/wf_services.R | 2 R/wf_set_key.R | 50 +++ R/wf_transfer.R | 10 R/wf_user_info.R | 2 R/zzz.R | 53 +++ build/vignette.rds |binary inst/CITATION |only inst/doc/advanced_vignette.R |only inst/doc/advanced_vignette.Rmd |only inst/doc/advanced_vignette.html |only inst/doc/cds_vignette.R | 4 inst/doc/cds_vignette.Rmd | 48 +-- inst/doc/cds_vignette.html | 338 ++++------------------- inst/doc/webapi_vignette.R | 42 +- inst/doc/webapi_vignette.Rmd | 39 +- inst/doc/webapi_vignette.html | 471 ++++++++------------------------- inst/rstudio |only man/wf_archetype.Rd |only man/wf_datasets.Rd | 5 man/wf_delete.Rd | 6 man/wf_get_key.Rd | 4 man/wf_product_info.Rd | 15 - man/wf_request.Rd | 23 - man/wf_set_key.Rd | 12 man/wf_transfer.Rd | 13 tests/testthat/test_cds.R | 68 ++++ tests/testthat/test_ecmwf.r | 166 ++++++++++- tests/testthat/test_helper_functions.R |only vignettes/advanced_vignette.Rmd |only vignettes/cds_vignette.Rmd | 48 +-- vignettes/webapi_vignette.Rmd | 39 +- 42 files changed, 778 insertions(+), 886 deletions(-)
Title: Utility Functions for Working with Random Number Generators
Description: Provides a set of functions for working with
Random Number Generators (RNGs). In particular, a generic
S4 framework is defined for getting/setting the current RNG, or RNG data
that are embedded into objects for reproducibility.
Notably, convenient default methods greatly facilitate the way current
RNG settings can be changed.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>
Diff between rngtools versions 1.3.1 dated 2018-05-15 and 1.3.1.1 dated 2019-04-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- tests/testthat/test-format.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: 'tint' is not 'Tufte'
Description: A 'tufte'-alike style for 'rmarkdown'.
A modern take on the 'Tufte' design for pdf and html vignettes,
building on the 'tufte' package with additional contributions
from the 'knitr' and 'ggtufte' package, and also acknowledging
the key influence of 'envisioned css'.
Author: Dirk Eddelbuettel and Jonathan Gilligan
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tint versions 0.1.1 dated 2019-04-01 and 0.1.2 dated 2019-04-19
tint-0.1.1/tint/inst/doc/tintHTML.R |only tint-0.1.1/tint/inst/doc/tintHTML.Rmd |only tint-0.1.1/tint/inst/doc/tintHTML.html |only tint-0.1.1/tint/inst/doc/tintPDF.R |only tint-0.1.1/tint/inst/doc/tintPDF.Rmd |only tint-0.1.1/tint/inst/doc/tintPDF.pdf |only tint-0.1.1/tint/inst/examples/simplePdf.Rmd |only tint-0.1.1/tint/inst/examples/tintPDFGaramond.pdf |only tint-0.1.1/tint/inst/examples/tintPDFLato.pdf |only tint-0.1.1/tint/vignettes/tintHTML.Rmd |only tint-0.1.1/tint/vignettes/tintPDF.Rmd |only tint-0.1.2/tint/ChangeLog | 74 ++++++++ tint-0.1.2/tint/DESCRIPTION | 12 - tint-0.1.2/tint/MD5 | 56 +++--- tint-0.1.2/tint/NAMESPACE | 3 tint-0.1.2/tint/R/html.R | 51 +++-- tint-0.1.2/tint/R/isConnected.R |only tint-0.1.2/tint/R/pdf.R | 89 +++++----- tint-0.1.2/tint/R/theme.R |only tint-0.1.2/tint/R/utils.R | 14 + tint-0.1.2/tint/R/utilsKnitr.R | 7 tint-0.1.2/tint/README.md | 6 tint-0.1.2/tint/build/vignette.rds |binary tint-0.1.2/tint/cleanup |only tint-0.1.2/tint/inst/NEWS.Rd | 9 + tint-0.1.2/tint/inst/doc/tintHtmlIntro.R |only tint-0.1.2/tint/inst/doc/tintHtmlIntro.Rmd |only tint-0.1.2/tint/inst/doc/tintHtmlIntro.html |only tint-0.1.2/tint/inst/doc/tintPdfIntro.R |only tint-0.1.2/tint/inst/doc/tintPdfIntro.Rmd |only tint-0.1.2/tint/inst/doc/tintPdfIntro.pdf |only tint-0.1.2/tint/inst/examples/tintHTML.Rmd |only tint-0.1.2/tint/inst/examples/tintPDF.Rmd |only tint-0.1.2/tint/inst/rmarkdown/templates/tintPdf/resources/tintPdf-template.tex | 3 tint-0.1.2/tint/man/Custom-templates.Rd | 14 - tint-0.1.2/tint/man/YAML-metadata.Rd | 14 - tint-0.1.2/tint/man/theme_tint.Rd |only tint-0.1.2/tint/man/tintHtml.Rd | 40 ++-- tint-0.1.2/tint/tests/simple.R | 15 - tint-0.1.2/tint/vignettes/tint.bib |only tint-0.1.2/tint/vignettes/tintHtmlIntro.Rmd |only tint-0.1.2/tint/vignettes/tintPdfIntro.Rmd |only 42 files changed, 263 insertions(+), 144 deletions(-)
Title: Univariate Bootstrapping and Other Things
Description: Primarily devoted to implementing the Univariate Bootstrap (as well as the Traditional Bootstrap). In addition there are multiple functions for DeFries-Fulker behavioral genetics models. The univariate bootstrapping functions, DeFries-Fulker functions, regression and traditional bootstrapping functions form the original core. Additional features may come online later, however this software is a work in progress. For more information about univariate bootstrapping see: Lee and Rodgers (1998) and Beasley et al (2007) <doi.org/10.1037/1082-989X.12.4.414>.
Author: Patrick O'Keefe
Maintainer: Patrick O'Keefe <patrick.okeefe@vanderbilt.edu>
Diff between Omisc versions 0.1.0 dated 2018-10-14 and 0.1.1 dated 2019-04-19
Omisc-0.1.0/Omisc/R/naiveBoot.R |only Omisc-0.1.1/Omisc/DESCRIPTION | 10 - Omisc-0.1.1/Omisc/MD5 | 36 +++--- Omisc-0.1.1/Omisc/NAMESPACE | 5 Omisc-0.1.1/Omisc/R/BCa.R | 2 Omisc-0.1.1/Omisc/R/BarebonesBetas.R | 21 ++- Omisc-0.1.1/Omisc/R/DFSimulatedChisqnew.R |only Omisc-0.1.1/Omisc/R/NaiveBoot.R |only Omisc-0.1.1/Omisc/R/NaiveBoot_dep.R |only Omisc-0.1.1/Omisc/R/bootsample.R | 3 Omisc-0.1.1/Omisc/R/cholcovs.R |only Omisc-0.1.1/Omisc/R/lbind.R |only Omisc-0.1.1/Omisc/R/standardBootIntervals.R | 8 - Omisc-0.1.1/Omisc/R/uniboot.R | 144 +++++++++++-------------- Omisc-0.1.1/Omisc/R/uniboot_dep.R |only Omisc-0.1.1/Omisc/man/BarebonesBetas.Rd | 6 - Omisc-0.1.1/Omisc/man/DFSimulatedChisqNew.Rd |only Omisc-0.1.1/Omisc/man/NaiveBoot.Rd | 2 Omisc-0.1.1/Omisc/man/NaiveBoot_dep.Rd |only Omisc-0.1.1/Omisc/man/TestData.Rd | 4 Omisc-0.1.1/Omisc/man/cholcovs.Rd |only Omisc-0.1.1/Omisc/man/lbind.Rd |only Omisc-0.1.1/Omisc/man/standardBootIntervals.Rd | 4 Omisc-0.1.1/Omisc/man/uniboot.Rd | 9 + Omisc-0.1.1/Omisc/man/uniboot_dep.Rd |only 25 files changed, 139 insertions(+), 115 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 0.8.0 dated 2019-04-07 and 0.8.1 dated 2019-04-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/timeroc.R | 10 +++++++++- inst/doc/jsmodule.html | 4 ++-- 5 files changed, 23 insertions(+), 11 deletions(-)
Title: Variable Selection for Supervised Classification in High
Dimension
Description: The functions provided in the FADA (Factor Adjusted Discriminant Analysis) package aim at performing supervised classification of high-dimensional and correlated profiles. The procedure combines a decorrelation step based on a
factor modeling of the dependence among covariates and a classification method. The available methods are Lasso regularized logistic model
(see Friedman et al. (2010)), sparse linear discriminant analysis (see
Clemmensen et al. (2011)), shrinkage linear and diagonal discriminant
analysis (see M. Ahdesmaki et al. (2010)). More methods of classification can be used on the decorrelated data provided by the package FADA.
Author: Emeline Perthame (Institut Pasteur, Paris, France), Chloe Friguet
(Universite de Bretagne Sud, Vannes, France) and David Causeur (Agrocampus
Ouest, Rennes, France)
Maintainer: David Causeur <david.causeur@agrocampus-ouest.fr>
Diff between FADA versions 1.3.3 dated 2018-02-07 and 1.3.4 dated 2019-04-19
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/func.R | 6 ++++-- 3 files changed, 11 insertions(+), 9 deletions(-)
Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data analysis,
drake rebuilds intermediate data objects when their dependencies change,
and it skips work when the results are already up to date.
Not every execution starts from scratch,
there is native support for parallel and distributed computing,
and completed projects have tangible evidence
that they are reproducible.
Extensive documentation, from beginner-friendly tutorials
to practical examples and more, is available at the reference website
<https://ropensci.github.io/drake/> and the online manual
<https://ropenscilabs.github.io/drake-manual/>.
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Alex Axthelm [ctb],
Jasper Clarkberg [ctb],
Kirill Müller [ctb],
Ben Bond-Lamberty [ctb] (<https://orcid.org/0000-0001-9525-4633>),
Tristan Mahr [ctb] (<https://orcid.org/0000-0002-8890-5116>),
Miles McBain [ctb] (<https://orcid.org/0000-0003-2865-2548>),
Ben Marwick [rev],
Peter Slaughter [rev],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between drake versions 7.1.0 dated 2019-04-07 and 7.2.0 dated 2019-04-19
drake-7.1.0/drake/man/test_with_dir.Rd |only drake-7.2.0/drake/DESCRIPTION | 14 drake-7.2.0/drake/MD5 | 252 +++++----- drake-7.2.0/drake/NAMESPACE | 3 drake-7.2.0/drake/NEWS.md | 31 + drake-7.2.0/drake/R/api-build.R | 2 drake-7.2.0/drake/R/api-cache.R | 17 drake-7.2.0/drake/R/api-callr.R | 2 drake-7.2.0/drake/R/api-clean.R | 6 drake-7.2.0/drake/R/api-debug.R | 2 drake-7.2.0/drake/R/api-diagnose.R | 2 drake-7.2.0/drake/R/api-dsl.R | 3 drake-7.2.0/drake/R/api-examples.R | 8 drake-7.2.0/drake/R/api-exposeimports.R | 2 drake-7.2.0/drake/R/api-make.R | 6 drake-7.2.0/drake/R/api-outdated.R | 23 drake-7.2.0/drake/R/api-package.R | 4 drake-7.2.0/drake/R/api-plan.R | 10 drake-7.2.0/drake/R/api-predict.R | 25 drake-7.2.0/drake/R/api-progress.R | 6 drake-7.2.0/drake/R/api-read.R | 32 - drake-7.2.0/drake/R/api-times.R | 2 drake-7.2.0/drake/R/backend-clustermq.R | 2 drake-7.2.0/drake/R/backend-future.R | 1 drake-7.2.0/drake/R/backend-loop.R | 2 drake-7.2.0/drake/R/exec-backend.R | 8 drake-7.2.0/drake/R/exec-dependencies.R | 8 drake-7.2.0/drake/R/exec-imports.R | 16 drake-7.2.0/drake/R/exec-queue.R | 14 drake-7.2.0/drake/R/exec-run.R | 2 drake-7.2.0/drake/R/exec-session.R | 10 drake-7.2.0/drake/R/exec-triggers.R | 2 drake-7.2.0/drake/R/preprocess-config.R | 18 drake-7.2.0/drake/R/preprocess-sanitize.R | 6 drake-7.2.0/drake/R/test-dbug.R | 11 drake-7.2.0/drake/R/test-testthat.R | 44 - drake-7.2.0/drake/R/utils-check.R | 23 drake-7.2.0/drake/R/utils-deprecate.R | 2 drake-7.2.0/drake/R/utils-encoding.R | 2 drake-7.2.0/drake/R/utils-graphinfo.R | 74 ++ drake-7.2.0/drake/R/utils-hpc.R | 4 drake-7.2.0/drake/R/utils-knitr.R | 2 drake-7.2.0/drake/R/utils-utils.R | 11 drake-7.2.0/drake/R/vis-console.R | 4 drake-7.2.0/drake/R/vis-ggraph.R | 50 + drake-7.2.0/drake/R/vis-graphinfo.R | 43 - drake-7.2.0/drake/R/vis-sankey.R | 20 drake-7.2.0/drake/R/vis-visnetwork.R | 74 +- drake-7.2.0/drake/README.md | 22 drake-7.2.0/drake/inst/doc/drake.Rmd | 4 drake-7.2.0/drake/inst/doc/drake.html | 13 drake-7.2.0/drake/inst/rmarkdown/templates/drake/skeleton/skeleton.Rmd | 2 drake-7.2.0/drake/man/build_times.Rd | 2 drake-7.2.0/drake/man/cached.Rd | 2 drake-7.2.0/drake/man/clean.Rd | 2 drake-7.2.0/drake/man/clean_mtcars_example.Rd | 2 drake-7.2.0/drake/man/cmq_build.Rd | 2 drake-7.2.0/drake/man/deps_knitr.Rd | 2 drake-7.2.0/drake/man/deps_profile.Rd | 2 drake-7.2.0/drake/man/deps_target.Rd | 2 drake-7.2.0/drake/man/deps_targets.Rd | 2 drake-7.2.0/drake/man/diagnose.Rd | 2 drake-7.2.0/drake/man/do_prework.Rd | 2 drake-7.2.0/drake/man/drake-package.Rd | 2 drake-7.2.0/drake/man/drake_build.Rd | 2 drake-7.2.0/drake/man/drake_cache_log.Rd | 2 drake-7.2.0/drake/man/drake_config.Rd | 6 drake-7.2.0/drake/man/drake_debug.Rd | 2 drake-7.2.0/drake/man/drake_example.Rd | 2 drake-7.2.0/drake/man/drake_examples.Rd | 2 drake-7.2.0/drake/man/drake_gc.Rd | 2 drake-7.2.0/drake/man/drake_get_session_info.Rd | 2 drake-7.2.0/drake/man/drake_ggraph.Rd | 13 drake-7.2.0/drake/man/drake_graph_info.Rd | 18 drake-7.2.0/drake/man/drake_hpc_template_file.Rd | 2 drake-7.2.0/drake/man/drake_hpc_template_files.Rd | 2 drake-7.2.0/drake/man/drake_plan.Rd | 2 drake-7.2.0/drake/man/expose_imports.Rd | 2 drake-7.2.0/drake/man/failed.Rd | 2 drake-7.2.0/drake/man/file_in.Rd | 2 drake-7.2.0/drake/man/file_out.Rd | 2 drake-7.2.0/drake/man/file_store.Rd | 2 drake-7.2.0/drake/man/find_cache.Rd | 2 drake-7.2.0/drake/man/get_cache.Rd | 2 drake-7.2.0/drake/man/ignore.Rd | 2 drake-7.2.0/drake/man/isolate_example.Rd |only drake-7.2.0/drake/man/knitr_in.Rd | 2 drake-7.2.0/drake/man/load_mtcars_example.Rd | 2 drake-7.2.0/drake/man/make.Rd | 8 drake-7.2.0/drake/man/missed.Rd | 2 drake-7.2.0/drake/man/new_cache.Rd | 2 drake-7.2.0/drake/man/outdated.Rd | 6 drake-7.2.0/drake/man/predict_runtime.Rd | 2 drake-7.2.0/drake/man/predict_workers.Rd | 2 drake-7.2.0/drake/man/progress.Rd | 2 drake-7.2.0/drake/man/r_make.Rd | 2 drake-7.2.0/drake/man/readd.Rd | 25 drake-7.2.0/drake/man/render_drake_ggraph.Rd | 8 drake-7.2.0/drake/man/render_drake_graph.Rd | 34 - drake-7.2.0/drake/man/render_sankey_drake_graph.Rd | 11 drake-7.2.0/drake/man/rescue_cache.Rd | 2 drake-7.2.0/drake/man/running.Rd | 2 drake-7.2.0/drake/man/sankey_drake_graph.Rd | 13 drake-7.2.0/drake/man/static_drake_graph.Rd | 4 drake-7.2.0/drake/man/tracked.Rd | 2 drake-7.2.0/drake/man/trigger.Rd | 2 drake-7.2.0/drake/man/vis_drake_graph.Rd | 37 - drake-7.2.0/drake/tests/scenarios/tests-separate.Rout | 8 drake-7.2.0/drake/tests/testthat/test-cache.R | 19 drake-7.2.0/drake/tests/testthat/test-clustermq.R | 2 drake-7.2.0/drake/tests/testthat/test-deprecate.R | 6 drake-7.2.0/drake/tests/testthat/test-dsl.R | 151 +++-- drake-7.2.0/drake/tests/testthat/test-edge-cases.R | 21 drake-7.2.0/drake/tests/testthat/test-examples.R | 25 drake-7.2.0/drake/tests/testthat/test-future.R | 1 drake-7.2.0/drake/tests/testthat/test-graph.R | 29 - drake-7.2.0/drake/tests/testthat/test-import-file.R | 1 drake-7.2.0/drake/tests/testthat/test-intermediate-file.R | 3 drake-7.2.0/drake/tests/testthat/test-lazy-load.R | 2 drake-7.2.0/drake/tests/testthat/test-memory.R | 83 +-- drake-7.2.0/drake/tests/testthat/test-other-features.R | 72 +- drake-7.2.0/drake/tests/testthat/test-plans.R | 70 -- drake-7.2.0/drake/tests/testthat/test-priority-queue.R | 14 drake-7.2.0/drake/tests/testthat/test-random.R | 2 drake-7.2.0/drake/tests/testthat/test-time.R | 2 drake-7.2.0/drake/tests/testthat/test-triggers.R | 32 - drake-7.2.0/drake/tests/testthat/test-wildcards.R | 47 + drake-7.2.0/drake/vignettes/drake.Rmd | 4 128 files changed, 962 insertions(+), 845 deletions(-)
Title: Fix Data and Create Report Tables from Different Objects
Description: Tools for assessing data quality, performing exploratory analysis,
fixing data errors in numerical, factor and date variables and creating report
tables from models and summaries.
Author: Victoria Fornes Ferrer, David Hervas Marin
Maintainer: David Hervas Marin <ddhervas@yahoo.es>
Diff between clickR versions 0.4.20 dated 2018-10-17 and 0.4.32 dated 2019-04-19
DESCRIPTION | 8 ++-- MD5 | 22 ++++++----- NAMESPACE | 2 + NEWS | 7 +++ R/descriptive.R | 84 +++++++++++++++++++++++++++++++++++-------- R/report_model.R | 2 - man/check_quality.Rd | 4 +- man/fix.levels.Rd | 4 +- man/mine.plot.Rd | 4 +- man/report.data.frame.Rd | 4 +- man/report.merModLmerTest.Rd | 4 +- man/search_scripts.Rd |only man/unforge.Rd |only 13 files changed, 106 insertions(+), 39 deletions(-)
Title: Automatic Differentiation of Multivariate Operations
Description: An object that supports automatic differentiation
of matrix- and multidimensional-valued functions with
respect to multidimensional independent variables.
Automatic differentiation is via 'forward accumulation'.
Author: Steven E. Pav [aut, cre] (<https://orcid.org/0000-0002-4197-6195>)
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between madness versions 0.2.5 dated 2018-08-29 and 0.2.6 dated 2019-04-19
ChangeLog | 5 +++++ DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- R/madness_pkg.r | 7 +++++++ R/sums.r | 8 ++++---- inst/doc/introducing_madness.pdf |binary man/NEWS.Rd | 9 +++++++++ man/as.madness.Rd | 1 - man/det.Rd | 1 - man/eigen.Rd | 1 - man/matwise.Rd | 1 - man/max.Rd | 1 - man/norm.Rd | 3 --- man/outer.Rd | 1 - man/todiag.Rd | 1 - man/vec.Rd | 1 - vignettes/common.bib | 5 +++-- 17 files changed, 49 insertions(+), 38 deletions(-)
Title: Geometry Decomposition
Description: Build a map of path-based geometry, this is a simple description of the number
of parts in an object and their basic structure. Translation and restructuring operations for
planar shapes and other hierarchical types require a data model with a record of the underlying
relationships between elements. The gibble() function creates a geometry map, a simple record of
the underlying structure in path-based hierarchical types. There are methods for the planar shape
types in the 'sf' and 'sp' packages and for types in the 'trip' and in-development 'silicate' packages.
Author: Michael Sumner [aut, cre] (<https://orcid.org/0000-0002-2471-7511>)
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between gibble versions 0.1.2 dated 2018-10-31 and 0.2.0 dated 2019-04-19
DESCRIPTION | 12 +-- MD5 | 21 +++--- NAMESPACE | 2 NEWS.md | 6 + R/gibble-silicate.R |only R/gibble.R | 13 --- R/ibble-sf.R | 2 R/sysdata.rda |binary README.md | 5 + man/gibble.Rd | 12 ++- tests/testthat/test-sf.R | 140 ++++++++++++++++++++--------------------- tests/testthat/test-silicate.R | 11 ++- 12 files changed, 117 insertions(+), 107 deletions(-)
Title: Optimal Designs for Nonlinear Models
Description: Finds optimal designs for nonlinear models using a metaheuristic algorithm called imperialist competitive algorithm ICA. See, for details, Masoudi et al. (2017) <doi:10.1016/j.csda.2016.06.014> and Masoudi et al. (2019) <doi:10.1080/10618600.2019.1601097>.
Author: Ehsan Masoudi [aut, cre],
Heinz Holling [aut],
Weng Kee Wong [aut]
Maintainer: Ehsan Masoudi <ehsan.masoudi@wwu.de>
Diff between ICAOD versions 0.9.8 dated 2019-01-14 and 0.9.9 dated 2019-04-19
ICAOD-0.9.8/ICAOD/inst/Rcodes_JGCS |only ICAOD-0.9.8/ICAOD/man/iterate.Rd |only ICAOD-0.9.8/ICAOD/man/iterate.bayes.Rd |only ICAOD-0.9.8/ICAOD/man/iterate.minimax.Rd |only ICAOD-0.9.9/ICAOD/DESCRIPTION | 14 ICAOD-0.9.9/ICAOD/MD5 | 126 +- ICAOD-0.9.9/ICAOD/NAMESPACE | 7 ICAOD-0.9.9/ICAOD/R/1-UserCommonFunctions.R | 96 +- ICAOD-0.9.9/ICAOD/R/10-UserEfficiency.R | 248 ++++- ICAOD-0.9.9/ICAOD/R/2-InternalCommonFunctions.R | 183 +++ ICAOD-0.9.9/ICAOD/R/3-UserMinimaxFunctions.R | 634 +++++++------ ICAOD-0.9.9/ICAOD/R/4-InternalMinimaxFunctions.R | 751 ++++++++++------ ICAOD-0.9.9/ICAOD/R/5-InternalMultipleFunctions.R | 22 ICAOD-0.9.9/ICAOD/R/6-UserBayesFunctions.R | 365 +++---- ICAOD-0.9.9/ICAOD/R/7-InternalBayesFunctions.R | 294 ++++-- ICAOD-0.9.9/ICAOD/R/ICABOD_help_page.R | 64 - ICAOD-0.9.9/ICAOD/build |only ICAOD-0.9.9/ICAOD/inst/JSS_code.R |only ICAOD-0.9.9/ICAOD/inst/JSS_code2.R |only ICAOD-0.9.9/ICAOD/inst/acebayes.R |only ICAOD-0.9.9/ICAOD/inst/doc |only ICAOD-0.9.9/ICAOD/inst/examples/bayes_examples.R | 92 + ICAOD-0.9.9/ICAOD/inst/examples/bayescomp_examples.R | 9 ICAOD-0.9.9/ICAOD/inst/examples/beff_examples.R | 72 - ICAOD-0.9.9/ICAOD/inst/examples/leff_examples.R | 8 ICAOD-0.9.9/ICAOD/inst/examples/locally_examples.R | 129 ++ ICAOD-0.9.9/ICAOD/inst/examples/locallycomp_examples.R | 32 ICAOD-0.9.9/ICAOD/inst/examples/meff_examples.R |only ICAOD-0.9.9/ICAOD/inst/examples/minimax_examples.R | 178 +++ ICAOD-0.9.9/ICAOD/inst/examples/multiple_examples.R | 24 ICAOD-0.9.9/ICAOD/inst/examples/robust_examples.R | 112 ++ ICAOD-0.9.9/ICAOD/inst/examples/sensbayes_examples.R | 10 ICAOD-0.9.9/ICAOD/inst/examples/senslocally_examples.R | 46 ICAOD-0.9.9/ICAOD/inst/examples/sensminimax_examples.R | 71 + ICAOD-0.9.9/ICAOD/inst/examples/sensmultiple_examples.R | 2 ICAOD-0.9.9/ICAOD/inst/examples/sensrobust_examples.R | 30 ICAOD-0.9.9/ICAOD/man/ICA.control.Rd | 2 ICAOD-0.9.9/ICAOD/man/ICAOD.Rd | 61 - ICAOD-0.9.9/ICAOD/man/bayes.Rd | 149 +-- ICAOD-0.9.9/ICAOD/man/bayescomp.Rd | 28 ICAOD-0.9.9/ICAOD/man/beff.Rd | 84 - ICAOD-0.9.9/ICAOD/man/crt.bayes.control.Rd | 19 ICAOD-0.9.9/ICAOD/man/crt.minimax.control.Rd | 6 ICAOD-0.9.9/ICAOD/man/leff.Rd | 32 ICAOD-0.9.9/ICAOD/man/locally.Rd | 140 ++ ICAOD-0.9.9/ICAOD/man/locallycomp.Rd | 38 ICAOD-0.9.9/ICAOD/man/meff.Rd |only ICAOD-0.9.9/ICAOD/man/minimax.Rd | 222 ++++ ICAOD-0.9.9/ICAOD/man/multiple.Rd | 39 ICAOD-0.9.9/ICAOD/man/plot.bayes.Rd | 12 ICAOD-0.9.9/ICAOD/man/plot.minimax.Rd | 7 ICAOD-0.9.9/ICAOD/man/print.bayes.Rd | 4 ICAOD-0.9.9/ICAOD/man/print.minimax.Rd | 4 ICAOD-0.9.9/ICAOD/man/robust.Rd | 123 ++ ICAOD-0.9.9/ICAOD/man/sens.bayes.control.Rd | 65 - ICAOD-0.9.9/ICAOD/man/sens.control.Rd |only ICAOD-0.9.9/ICAOD/man/sens.minimax.control.Rd | 103 -- ICAOD-0.9.9/ICAOD/man/sensbayes.Rd | 40 ICAOD-0.9.9/ICAOD/man/sensbayescomp.Rd | 21 ICAOD-0.9.9/ICAOD/man/senslocally.Rd | 59 + ICAOD-0.9.9/ICAOD/man/senslocallycomp.Rd | 4 ICAOD-0.9.9/ICAOD/man/sensminimax.Rd | 88 + ICAOD-0.9.9/ICAOD/man/sensmultiple.Rd | 9 ICAOD-0.9.9/ICAOD/man/sensrobust.Rd | 43 ICAOD-0.9.9/ICAOD/man/update.bayes.Rd |only ICAOD-0.9.9/ICAOD/man/update.minimax.Rd |only ICAOD-0.9.9/ICAOD/vignettes |only 67 files changed, 3292 insertions(+), 1729 deletions(-)