Thu, 22 Aug 2019

Package MixGHD updated to version 2.3.3 with previous version 2.3.2 dated 2019-04-12

Title: Model Based Clustering, Classification and Discriminant Analysis Using the Mixture of Generalized Hyperbolic Distributions
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution. The first model 'MGHD' (Browne and McNicholas (2015) <doi:10.1002/cjs.11246>) is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' (Tortora et al. (2016) <doi:10.1007/s11634-015-0204-z>) is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD'(Tortora et al. (2016) <arXiv:1403.2332v7>), mixture of multiple scaled generalized hyperbolic distributions. The 'cMSGHD' (Tortora et al. (2016) <arXiv:1403.2332v7>) is a 'MSGHD' with convex contour plots. The 'MCGHD' (Tortora et al. (2016) <arXiv:1403.2332v7>), mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora [aut, cre, cph], Aisha ElSherbiny [com], Ryan P. Browne [aut, cph], Brian C. Franczak [aut, cph], and Paul D. McNicholas [aut, cph], and Donald D. Amos [ctb].
Maintainer: Cristina Tortora <grikris1@gmail.com>

Diff between MixGHD versions 2.3.2 dated 2019-04-12 and 2.3.3 dated 2019-08-22

 MixGHD-2.3.2/MixGHD/data/datalist  |only
 MixGHD-2.3.3/MixGHD/DESCRIPTION    |    8 ++++----
 MixGHD-2.3.3/MixGHD/MD5            |   29 ++++++++++++++---------------
 MixGHD-2.3.3/MixGHD/NAMESPACE      |   25 ++++++++++++++-----------
 MixGHD-2.3.3/MixGHD/R/GHD.R        |   18 +++++++++++-------
 MixGHD-2.3.3/MixGHD/R/MSGHD.R      |   11 ++++++-----
 MixGHD-2.3.3/MixGHD/R/cMSGHD.R     |   11 ++++++-----
 MixGHD-2.3.3/MixGHD/R/rfunctions.R |    2 +-
 MixGHD-2.3.3/MixGHD/man/DA.Rd      |    2 +-
 MixGHD-2.3.3/MixGHD/man/MCGHD.Rd   |    8 ++++----
 MixGHD-2.3.3/MixGHD/man/MGHD.Rd    |    8 ++++----
 MixGHD-2.3.3/MixGHD/man/MGHFA.Rd   |    2 +-
 MixGHD-2.3.3/MixGHD/man/MSGHD.Rd   |    8 ++++----
 MixGHD-2.3.3/MixGHD/man/cMSGHD.Rd  |    8 ++++----
 MixGHD-2.3.3/MixGHD/man/coef.Rd    |   11 +++++++----
 MixGHD-2.3.3/MixGHD/man/predict.Rd |   11 +++++++----
 16 files changed, 88 insertions(+), 74 deletions(-)

More information about MixGHD at CRAN
Permanent link

Package MetaboList updated to version 2.0 with previous version 1.4 dated 2019-06-04

Title: Annotation of Metabolites from Liquid Chromatography-Mass Spectrometry Data
Description: Automatic metabolite annotation from Liquid Chromatography-Mass Spectrometry (LC-MS and LC-MS/MS DIA) analysis.
Author: Manuel David Peris Diaz
Maintainer: Manuel David Peris Diaz <manuel.perisdiaz@uwr.edu.pl>

Diff between MetaboList versions 1.4 dated 2019-06-04 and 2.0 dated 2019-08-22

 DESCRIPTION              |    6 
 MD5                      |   18 +
 R/AIF.R                  |  469 ++++++-----------------------------------------
 R/Filter_AIF.R           |  109 +++-------
 R/FullMS.R               |    9 
 R/Isotopic.R             |only
 R/elemental.formula.R    |only
 man/AIF.rd               |    9 
 man/Filter_AIF.rd        |    9 
 man/FullMS.rd            |   10 -
 man/Isotopic.rd          |only
 man/elemental.formula.rd |only
 12 files changed, 130 insertions(+), 509 deletions(-)

More information about MetaboList at CRAN
Permanent link

Package FPDclustering updated to version 1.3.1 with previous version 1.3 dated 2019-04-12

Title: PD-Clustering and Factor PD-Clustering
Description: Probabilistic distance clustering (PD-clustering) is an iterative, distribution free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership, under the constraint that the product of the probability and the distance of each point to any cluster centre is a constant. PD-clustering is a flexible method that can be used with non-spherical clusters, outliers, or noisy data. PDQ is an extension of the algorithm for clusters of different size. Factor PD-clustering (FPDC) is a recently proposed factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It works on high dimensional datasets.
Author: Cristina Tortora [aut, cre, cph], Noe Vidales [aut], and Paul D. McNicholas [fnd]
Maintainer: Cristina Tortora <grikris1@gmail.com>

Diff between FPDclustering versions 1.3 dated 2019-04-12 and 1.3.1 dated 2019-08-22

 DESCRIPTION   |    8 ++++----
 MD5           |    4 ++--
 data/datalist |    1 -
 3 files changed, 6 insertions(+), 7 deletions(-)

More information about FPDclustering at CRAN
Permanent link

Package pmd updated to version 0.1.5 with previous version 0.1.1 dated 2018-12-02

Title: Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis
Description: Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. A GUI for PMD analysis is also included as a 'shiny' application.
Author: Miao YU [aut, cre] (<https://orcid.org/0000-0002-2804-6014>)
Maintainer: Miao YU <yufreecas@gmail.com>

Diff between pmd versions 0.1.1 dated 2018-12-02 and 0.1.5 dated 2019-08-22

 DESCRIPTION             |   16 
 MD5                     |   61 -
 NAMESPACE               |    9 
 NEWS.md                 |   39 
 R/data.R                |   50 +
 R/pmd.R                 | 1947 +++++++++++++++++++++++++++++-------------------
 R/pmdvis.R              |only
 README.md               |   10 
 build/vignette.rds      |binary
 data/datalist           |only
 data/hmdb.rda           |only
 data/hmdbp.rda          |only
 data/keggrall.rda       |only
 data/omics.rda          |only
 data/spmeinvivo.rda     |binary
 inst/doc/globalstd.R    |   59 +
 inst/doc/globalstd.Rmd  |  110 ++
 inst/doc/globalstd.html |  405 +++++++--
 man/getchain.Rd         |only
 man/getcluster.Rd       |only
 man/getcorcluster.Rd    |only
 man/getpaired.Rd        |   10 
 man/getpmd.Rd           |only
 man/getrda.Rd           |only
 man/getreact.Rd         |only
 man/getsda.Rd           |   11 
 man/getstd.Rd           |    8 
 man/gettarget.Rd        |only
 man/globalstd.Rd        |   10 
 man/hmdb.Rd             |only
 man/hmdbp.Rd            |only
 man/keggrall.Rd         |only
 man/omics.Rd            |only
 man/pcasf.Rd            |only
 man/plotpaired.Rd       |    4 
 man/plotrtg.Rd          |    4 
 man/plotsda.Rd          |only
 man/plotstd.Rd          |    4 
 man/plotstdrt.Rd        |    4 
 man/plotstdsda.Rd       |    4 
 vignettes/globalstd.Rmd |  110 ++
 41 files changed, 1956 insertions(+), 919 deletions(-)

More information about pmd at CRAN
Permanent link

Package nat updated to version 1.8.13 with previous version 1.8.11 dated 2017-11-12

Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Author: Gregory Jefferis [aut, cre] (<https://orcid.org/0000-0002-0587-9355>), James Manton [aut] (<https://orcid.org/0000-0001-9260-3156>)
Maintainer: Gregory Jefferis <jefferis@gmail.com>

Diff between nat versions 1.8.11 dated 2017-11-12 and 1.8.13 dated 2019-08-22

 DESCRIPTION                                   |   26 
 MD5                                           |  222 +-
 NAMESPACE                                     |    4 
 NEWS                                          |   22 
 R/cmtk.R                                      |   57 
 R/cmtkreg.R                                   |    2 
 R/dotprops.R                                  |   14 
 R/nat-package.R                               |  223 +-
 R/neuron-plot.R                               |   44 
 R/neuronlist.R                                |   19 
 R/neuronlistfh.R                              |   17 
 R/summary.R                                   |    7 
 R/vaa3draw-io.R                               |    2 
 README.md                                     |   20 
 build/vignette.rds                            |binary
 inst/doc/Installation.Rmd                     |   20 
 inst/doc/Installation.html                    |  339 +++
 inst/doc/neurons-intro.Rmd                    |   14 
 inst/doc/neurons-intro.html                   | 2439 ++++++++++++++++++++------
 man/Cell07PNs.Rd                              |    1 
 man/MBL.surf.Rd                               |    1 
 man/affmat2cmtkparams.Rd                      |    1 
 man/all.equal.im3d.Rd                         |    4 
 man/all.equal.neuron.Rd                       |    4 
 man/amiramesh-io.Rd                           |    6 
 man/amiratype.Rd                              |    1 
 man/as.hxsurf.Rd                              |    1 
 man/as.im3d.Rd                                |    4 
 man/as.mesh3d.Rd                              |    1 
 man/as.neuronlist.Rd                          |    3 
 man/boundingbox.Rd                            |    7 
 man/cmtk.bindir.Rd                            |   60 
 man/cmtk.dof2mat.Rd                           |    2 
 man/cmtk.extract_affine.Rd                    |    1 
 man/cmtk.mat2dof.Rd                           |    2 
 man/cmtk.targetvolume.Rd                      |    2 
 man/cmtkparams2affmat.Rd                      |    1 
 man/cmtkreg.Rd                                |    2 
 man/coord2ind.Rd                              |    4 
 man/dotprops.Rd                               |    6 
 man/fileformats.Rd                            |    7 
 man/find.neuron.Rd                            |    4 
 man/graph.nodes.Rd                            |    4 
 man/im3d-coords.Rd                            |    1 
 man/im3d-io.Rd                                |    1 
 man/im3d.Rd                                   |    1 
 man/imexpand.grid.Rd                          |    1 
 man/imscalebar.Rd                             |    5 
 man/imslice.Rd                                |    1 
 man/is.amiramesh.Rd                           |    1 
 man/is.im3d.Rd                                |    1 
 man/is.neuronlist.Rd                          |    1 
 man/is.vaa3draw.Rd                            |    2 
 man/kcs20.Rd                                  |    1 
 man/mask.Rd                                   |    1 
 man/materials.Rd                              |    3 
 man/mirror.Rd                                 |    8 
 man/nat-package.Rd                            |  205 +-
 man/ndigest.Rd                                |    4 
 man/neuron.Rd                                 |    1 
 man/neuronlist-arithmetic.Rd                  |    1 
 man/neuronlist-dataframe-methods.Rd           |    2 
 man/neuronlist.Rd                             |    1 
 man/neuronlistfh.Rd                           |    9 
 man/ngraph.Rd                                 |    5 
 man/nlapply.Rd                                |    5 
 man/normalise_swc.Rd                          |   10 
 man/nview3d.Rd                                |only
 man/origin.Rd                                 |    1 
 man/plot.neuron.Rd                            |    8 
 man/plot.neuronlist.Rd                        |    5 
 man/plot3d.hxsurf.Rd                          |    1 
 man/plot3d.neuronlist.Rd                      |    3 
 man/pointsinside.Rd                           |    4 
 man/potential_synapses.Rd                     |    5 
 man/projection.Rd                             |    1 
 man/prune.Rd                                  |    1 
 man/read.cmtk.Rd                              |    1 
 man/read.cmtkreg.Rd                           |    1 
 man/read.hxsurf.Rd                            |    2 
 man/read.neuronlistfh.Rd                      |    1 
 man/read.neurons.Rd                           |    6 
 man/read.nrrd.Rd                              |    5 
 man/read.vaa3draw.Rd                          |    3 
 man/remotesync.Rd                             |    1 
 man/resample.Rd                               |    1 
 man/rootpoints.Rd                             |    3 
 man/scale.neuron.Rd                           |    2 
 man/segmentgraph.Rd                           |    5 
 man/spine.Rd                                  |    5 
 man/sub-.neuronlistfh.Rd                      |    1 
 man/subset.hxsurf.Rd                          |    5 
 man/subset.neuron.Rd                          |    1 
 man/summary.neuron.Rd                         |    3 
 man/threshold.Rd                              |    5 
 man/unmask.Rd                                 |    1 
 man/voxdims.Rd                                |    1 
 man/write.cmtk.Rd                             |    1 
 man/write.cmtkreg.Rd                          |    1 
 man/write.hxsurf.Rd                           |    2 
 man/write.neuronlistfh.Rd                     |    1 
 man/write.neurons.Rd                          |    5 
 man/write.nrrd.Rd                             |    4 
 man/xform.Rd                                  |   13 
 man/xformimage.Rd                             |    4 
 tests/testthat/test-landmarks-io.R            |    2 
 tests/testthat/test-ndigest.R                 |    7 
 tests/testthat/test-ngraph.R                  |    2 
 tests/testthat/test-pop3d.R                   |   10 
 tests/testthat/test-summary.R                 |    3 
 tests/testthat/testdata/summary_cell07pns.rda |only
 vignettes/Installation.Rmd                    |   20 
 vignettes/neurons-intro.Rmd                   |   14 
 113 files changed, 2936 insertions(+), 1126 deletions(-)

More information about nat at CRAN
Permanent link

Package tdthap updated to version 1.1-11 with previous version 1.1-9 dated 2018-06-30

Title: TDT Tests for Extended Haplotypes
Description: Functions and examples are provided for Transmission/disequilibrium tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) "Transmission/disequilibrium tests for extended marker haplotypes". Amer. J. Hum. Genet., 65:1161-1169, <doi:10.1086/302566>.
Author: David Clayton
Maintainer: Jing Hua Zhao <jinghuazhao@hotmail.com>

Diff between tdthap versions 1.1-9 dated 2018-06-30 and 1.1-11 dated 2019-08-22

 ChangeLog                 |    8 ++++++++
 DESCRIPTION               |   10 ++++++----
 MD5                       |   12 ++++++------
 R/tdthap.R                |    2 +-
 build/vignette.rds        |binary
 inst/doc/tdthap-paper.pdf |binary
 src/nuc_fam.c             |    6 +++---
 7 files changed, 24 insertions(+), 14 deletions(-)

More information about tdthap at CRAN
Permanent link

Package GillespieSSA2 updated to version 0.2.5 with previous version 0.2.4 dated 2019-08-05

Title: Gillespie's Stochastic Simulation Algorithm for Impatient People
Description: A fast, scalable, and versatile framework for simulating large systems with Gillespie's Stochastic Simulation Algorithm ('SSA'). This package is the spiritual successor to the 'GillespieSSA' package originally written by Mario Pineda-Krch. Benefits of this package include major speed improvements (>100x), easier to understand documentation, and many unit tests that try to ensure the package works as intended.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

Diff between GillespieSSA2 versions 0.2.4 dated 2019-08-05 and 0.2.5 dated 2019-08-22

 GillespieSSA2-0.2.4/GillespieSSA2/inst/NEWS                                  |only
 GillespieSSA2-0.2.4/GillespieSSA2/inst/NEWS.md                               |only
 GillespieSSA2-0.2.5/GillespieSSA2/DESCRIPTION                                |   20 ++-
 GillespieSSA2-0.2.5/GillespieSSA2/MD5                                        |   55 ++++------
 GillespieSSA2-0.2.5/GillespieSSA2/NAMESPACE                                  |    3 
 GillespieSSA2-0.2.5/GillespieSSA2/NEWS.md                                    |only
 GillespieSSA2-0.2.5/GillespieSSA2/R/RcppExports.R                            |    4 
 GillespieSSA2-0.2.5/GillespieSSA2/R/compile_reactions.R                      |   53 ++-------
 GillespieSSA2-0.2.5/GillespieSSA2/R/ssa_simulation.R                         |    6 -
 GillespieSSA2-0.2.5/GillespieSSA2/README.md                                  |   27 ++--
 GillespieSSA2-0.2.5/GillespieSSA2/build/partial.rdb                          |binary
 GillespieSSA2-0.2.5/GillespieSSA2/inst/doc/an_introduction.html              |    4 
 GillespieSSA2-0.2.5/GillespieSSA2/inst/doc/converting_from_GillespieSSA.Rmd  |    2 
 GillespieSSA2-0.2.5/GillespieSSA2/inst/doc/converting_from_GillespieSSA.html |   10 -
 GillespieSSA2-0.2.5/GillespieSSA2/inst/doc/decaying_dimer.html               |    6 -
 GillespieSSA2-0.2.5/GillespieSSA2/inst/doc/epi_chain.html                    |    6 -
 GillespieSSA2-0.2.5/GillespieSSA2/inst/doc/linear_chain.html                 |    6 -
 GillespieSSA2-0.2.5/GillespieSSA2/inst/doc/logistic_growth.html              |    6 -
 GillespieSSA2-0.2.5/GillespieSSA2/inst/doc/lotka_predator_prey.html          |    6 -
 GillespieSSA2-0.2.5/GillespieSSA2/inst/doc/radioactive_decay.html            |    6 -
 GillespieSSA2-0.2.5/GillespieSSA2/inst/doc/rm_predator_prey.html             |    6 -
 GillespieSSA2-0.2.5/GillespieSSA2/inst/doc/sir.html                          |    6 -
 GillespieSSA2-0.2.5/GillespieSSA2/man/compile_reactions.Rd                   |    8 -
 GillespieSSA2-0.2.5/GillespieSSA2/src/RcppExports.cpp                        |   11 --
 GillespieSSA2-0.2.5/GillespieSSA2/src/ode_em.cpp                             |    2 
 GillespieSSA2-0.2.5/GillespieSSA2/src/ssa_simulation.cpp                     |   14 +-
 GillespieSSA2-0.2.5/GillespieSSA2/src/test_helper_funs.cpp                   |   10 +
 GillespieSSA2-0.2.5/GillespieSSA2/tests/testthat/helper-test_propensity.R    |    3 
 GillespieSSA2-0.2.5/GillespieSSA2/tests/testthat/test-ssa.R                  |    2 
 GillespieSSA2-0.2.5/GillespieSSA2/vignettes/converting_from_GillespieSSA.Rmd |    2 
 30 files changed, 129 insertions(+), 155 deletions(-)

More information about GillespieSSA2 at CRAN
Permanent link

Package esquisse updated to version 0.2.2 with previous version 0.2.1 dated 2019-07-01

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] (Facets support)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between esquisse versions 0.2.1 dated 2019-07-01 and 0.2.2 dated 2019-08-22

 esquisse-0.2.1/esquisse/R/module_filterDF.R                      |only
 esquisse-0.2.2/esquisse/DESCRIPTION                              |    6 
 esquisse-0.2.2/esquisse/MD5                                      |   41 -
 esquisse-0.2.2/esquisse/NAMESPACE                                |    4 
 esquisse-0.2.2/esquisse/NEWS.md                                  |   27 
 esquisse-0.2.2/esquisse/R/esquisser.R                            |    2 
 esquisse-0.2.2/esquisse/R/esquisserUI.R                          |  140 ++++-
 esquisse-0.2.2/esquisse/R/input-colors.R                         |only
 esquisse-0.2.2/esquisse/R/input-dragula.R                        |   80 --
 esquisse-0.2.2/esquisse/R/module-chartControls.R                 |   21 
 esquisse-0.2.2/esquisse/R/module-filterDF.R                      |only
 esquisse-0.2.2/esquisse/R/utils.R                                |   81 ++
 esquisse-0.2.2/esquisse/build/vignette.rds                       |binary
 esquisse-0.2.2/esquisse/inst/doc/get-started.html                |    6 
 esquisse-0.2.2/esquisse/inst/doc/shiny-usage.R                   |  128 +++-
 esquisse-0.2.2/esquisse/inst/doc/shiny-usage.Rmd                 |  171 +++++-
 esquisse-0.2.2/esquisse/inst/doc/shiny-usage.html                |  275 ++++++----
 esquisse-0.2.2/esquisse/man/input-colors.Rd                      |only
 esquisse-0.2.2/esquisse/man/module-esquisse.Rd                   |   77 ++
 esquisse-0.2.2/esquisse/man/module-filterDF.Rd                   |    2 
 esquisse-0.2.2/esquisse/vignettes/figures/input-color.png        |only
 esquisse-0.2.2/esquisse/vignettes/figures/input-palette.png      |only
 esquisse-0.2.2/esquisse/vignettes/figures/shiny-esquisse-out.png |only
 esquisse-0.2.2/esquisse/vignettes/figures/shiny-esquisse.png     |binary
 esquisse-0.2.2/esquisse/vignettes/shiny-usage.Rmd                |  171 +++++-
 25 files changed, 892 insertions(+), 340 deletions(-)

More information about esquisse at CRAN
Permanent link

Package dexter updated to version 1.0.0 with previous version 0.8.5 dated 2019-04-25

Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris, Timo Bechger, Jesse Koops, Ivailo Partchev
Maintainer: Jesse Koops <jesse.koops@cito.nl>

Diff between dexter versions 0.8.5 dated 2019-04-25 and 1.0.0 dated 2019-08-22

 dexter-0.8.5/dexter/R/d3c.R                                   |only
 dexter-0.8.5/dexter/R/shine.R                                 |only
 dexter-0.8.5/dexter/R/zzz.R                                   |only
 dexter-0.8.5/dexter/inst/REFERENCES.bib                       |only
 dexter-0.8.5/dexter/inst/doc/data_management.R                |only
 dexter-0.8.5/dexter/inst/doc/data_management.Rmd              |only
 dexter-0.8.5/dexter/inst/doc/data_management.html             |only
 dexter-0.8.5/dexter/man/add_test3DC.Rd                        |only
 dexter-0.8.5/dexter/man/create3DC.Rd                          |only
 dexter-0.8.5/dexter/man/design_as_network.Rd                  |only
 dexter-0.8.5/dexter/man/get_item_properties.Rd                |only
 dexter-0.8.5/dexter/man/get_person_properties.Rd              |only
 dexter-0.8.5/dexter/man/iModels.Rd                            |only
 dexter-0.8.5/dexter/man/iTIA.Rd                               |only
 dexter-0.8.5/dexter/man/plot3DC.Rd                            |only
 dexter-0.8.5/dexter/src/elsymean.c                            |only
 dexter-0.8.5/dexter/src/elsymean.h                            |only
 dexter-0.8.5/dexter/src/packagename_init.c                    |only
 dexter-0.8.5/dexter/src/pascal.c                              |only
 dexter-0.8.5/dexter/src/roger.c                               |only
 dexter-0.8.5/dexter/src/roger.h                               |only
 dexter-0.8.5/dexter/vignettes/data_management.Rmd             |only
 dexter-1.0.0/dexter/DESCRIPTION                               |   22 
 dexter-1.0.0/dexter/MD5                                       |  255 -
 dexter-1.0.0/dexter/NAMESPACE                                 |  214 
 dexter-1.0.0/dexter/NEWS                                      |  237 -
 dexter-1.0.0/dexter/R/RcppExports.R                           |only
 dexter-1.0.0/dexter/R/ability.R                               |  472 --
 dexter-1.0.0/dexter/R/anon.R                                  |  946 +---
 dexter-1.0.0/dexter/R/anon_calibration.R                      |  985 ++--
 dexter-1.0.0/dexter/R/anon_plausible_values.R                 |  781 +--
 dexter-1.0.0/dexter/R/data_selection.R                        |  717 +--
 dexter-1.0.0/dexter/R/database.R                              |  339 -
 dexter-1.0.0/dexter/R/dexter.R                                | 2334 +++++-----
 dexter-1.0.0/dexter/R/dif.R                                   |  468 --
 dexter-1.0.0/dexter/R/enorm.R                                 | 1374 ++---
 dexter-1.0.0/dexter/R/equating.R                              |  607 +-
 dexter-1.0.0/dexter/R/individual_differences.R                |  190 
 dexter-1.0.0/dexter/R/interaction_model.R                     |  769 +--
 dexter-1.0.0/dexter/R/misc.R                                  | 1083 ++--
 dexter-1.0.0/dexter/R/oplike.R                                |  831 +--
 dexter-1.0.0/dexter/R/plausible_scores.R                      |  335 -
 dexter-1.0.0/dexter/R/plausible_values.R                      |  322 -
 dexter-1.0.0/dexter/R/plots.R                                 |  768 +--
 dexter-1.0.0/dexter/R/predicates.R                            |  665 ++
 dexter-1.0.0/dexter/R/profile_analysis.R                      |  602 +-
 dexter-1.0.0/dexter/R/reparam.R                               |  541 +-
 dexter-1.0.0/dexter/R/resp_data.R                             |only
 dexter-1.0.0/dexter/R/standards.R                             |only
 dexter-1.0.0/dexter/R/suf_stats.R                             |only
 dexter-1.0.0/dexter/R/tia.R                                   |  183 
 dexter-1.0.0/dexter/README.md                                 |  207 
 dexter-1.0.0/dexter/build/vignette.rds                        |binary
 dexter-1.0.0/dexter/data/verbAggrData.rda                     |binary
 dexter-1.0.0/dexter/inst/doc/DIF_vignette.R                   |only
 dexter-1.0.0/dexter/inst/doc/DIF_vignette.Rmd                 |only
 dexter-1.0.0/dexter/inst/doc/DIF_vignette.html                |only
 dexter-1.0.0/dexter/inst/doc/Equating.R                       |  302 -
 dexter-1.0.0/dexter/inst/doc/Equating.Rmd                     |  597 +-
 dexter-1.0.0/dexter/inst/doc/Equating.html                    |  784 ++-
 dexter-1.0.0/dexter/inst/doc/Plausible_Values.R               |  218 
 dexter-1.0.0/dexter/inst/doc/Plausible_Values.Rmd             |  357 -
 dexter-1.0.0/dexter/inst/doc/Plausible_Values.html            |  692 +-
 dexter-1.0.0/dexter/inst/doc/Test_Individual_differences.R    |  113 
 dexter-1.0.0/dexter/inst/doc/Test_Individual_differences.Rmd  |  210 
 dexter-1.0.0/dexter/inst/doc/Test_Individual_differences.html |  594 +-
 dexter-1.0.0/dexter/inst/doc/dexter.R                         |  182 
 dexter-1.0.0/dexter/inst/doc/dexter.Rmd                       |  412 -
 dexter-1.0.0/dexter/inst/doc/dexter.html                      | 1447 +++---
 dexter-1.0.0/dexter/inst/doc/profile-plots.R                  |  255 -
 dexter-1.0.0/dexter/inst/doc/profile-plots.Rmd                |  458 -
 dexter-1.0.0/dexter/inst/doc/profile-plots.html               |  480 +-
 dexter-1.0.0/dexter/inst/extdata/3dc.sql                      |  330 -
 dexter-1.0.0/dexter/inst/extdata/dexter_sqlite.sql            |  160 
 dexter-1.0.0/dexter/inst/extdata/dexter_standard.sql          |  189 
 dexter-1.0.0/dexter/man/DIF.Rd                                |   86 
 dexter-1.0.0/dexter/man/ability.Rd                            |  164 
 dexter-1.0.0/dexter/man/add_booklet.Rd                        |  170 
 dexter-1.0.0/dexter/man/add_item_properties.Rd                |   94 
 dexter-1.0.0/dexter/man/add_person_properties.Rd              |   60 
 dexter-1.0.0/dexter/man/close_project.Rd                      |   28 
 dexter-1.0.0/dexter/man/coef.p2pass.Rd                        |   54 
 dexter-1.0.0/dexter/man/coef.prms.Rd                          |   52 
 dexter-1.0.0/dexter/man/design_info.Rd                        |   58 
 dexter-1.0.0/dexter/man/dexter-package.Rd                     |   58 
 dexter-1.0.0/dexter/man/distractor_plot.Rd                    |   76 
 dexter-1.0.0/dexter/man/fit_domains.Rd                        |   86 
 dexter-1.0.0/dexter/man/fit_enorm.Rd                          |   91 
 dexter-1.0.0/dexter/man/fit_inter.Rd                          |   86 
 dexter-1.0.0/dexter/man/get_booklets.Rd                       |   36 
 dexter-1.0.0/dexter/man/get_design.Rd                         |   65 
 dexter-1.0.0/dexter/man/get_items.Rd                          |   38 
 dexter-1.0.0/dexter/man/get_persons.Rd                        |   38 
 dexter-1.0.0/dexter/man/get_resp_data.Rd                      |only
 dexter-1.0.0/dexter/man/get_responses.Rd                      |  108 
 dexter-1.0.0/dexter/man/get_rules.Rd                          |   34 
 dexter-1.0.0/dexter/man/get_testscores.Rd                     |   38 
 dexter-1.0.0/dexter/man/get_variables.Rd                      |   54 
 dexter-1.0.0/dexter/man/individual_differences.Rd             |   84 
 dexter-1.0.0/dexter/man/information.Rd                        |  144 
 dexter-1.0.0/dexter/man/keys_to_rules.Rd                      |   64 
 dexter-1.0.0/dexter/man/open_project.Rd                       |   36 
 dexter-1.0.0/dexter/man/plausible_scores.Rd                   |   84 
 dexter-1.0.0/dexter/man/plausible_values.Rd                   |  146 
 dexter-1.0.0/dexter/man/plot.DIF_stats.Rd                     |   48 
 dexter-1.0.0/dexter/man/plot.p2pass.Rd                        |   42 
 dexter-1.0.0/dexter/man/plot.prms.Rd                          |   60 
 dexter-1.0.0/dexter/man/plot.rim.Rd                           |   76 
 dexter-1.0.0/dexter/man/probability_to_pass.Rd                |  106 
 dexter-1.0.0/dexter/man/profile_plot.Rd                       |  120 
 dexter-1.0.0/dexter/man/profiles.Rd                           |  107 
 dexter-1.0.0/dexter/man/ratedData.Rd                          |   28 
 dexter-1.0.0/dexter/man/ratedDataProperties.Rd                |   24 
 dexter-1.0.0/dexter/man/ratedDataRules.Rd                     |   22 
 dexter-1.0.0/dexter/man/read_oplm_par.Rd                      |   60 
 dexter-1.0.0/dexter/man/standards_3dc.Rd                      |only
 dexter-1.0.0/dexter/man/standards_db.Rd                       |only
 dexter-1.0.0/dexter/man/start_new_project.Rd                  |   98 
 dexter-1.0.0/dexter/man/start_new_project_from_oplm.Rd        |  130 
 dexter-1.0.0/dexter/man/tia_tables.Rd                         |   58 
 dexter-1.0.0/dexter/man/touch_rules.Rd                        |   81 
 dexter-1.0.0/dexter/man/verbAggrData.Rd                       |   24 
 dexter-1.0.0/dexter/man/verbAggrProperties.Rd                 |   24 
 dexter-1.0.0/dexter/man/verbAggrRules.Rd                      |   24 
 dexter-1.0.0/dexter/src/Makevars                              |only
 dexter-1.0.0/dexter/src/Makevars.win                          |only
 dexter-1.0.0/dexter/src/RcppExports.cpp                       |only
 dexter-1.0.0/dexter/src/data.cpp                              |only
 dexter-1.0.0/dexter/src/elsym.cpp                             |only
 dexter-1.0.0/dexter/src/meanelsym.cpp                         |only
 dexter-1.0.0/dexter/src/pascal.cpp                            |only
 dexter-1.0.0/dexter/src/roger.cpp                             |only
 dexter-1.0.0/dexter/tests/testthat.R                          |   10 
 dexter-1.0.0/dexter/tests/testthat/test_ability.R             |  230 
 dexter-1.0.0/dexter/tests/testthat/test_data_selection.R      |  294 +
 dexter-1.0.0/dexter/tests/testthat/test_database.R            |  321 -
 dexter-1.0.0/dexter/tests/testthat/test_enorm.R               |  182 
 dexter-1.0.0/dexter/tests/testthat/test_interaction.R         |   42 
 dexter-1.0.0/dexter/tests/testthat/test_oplike.r              |  104 
 dexter-1.0.0/dexter/tests/testthat/test_plausible_scores.R    |  100 
 dexter-1.0.0/dexter/tests/testthat/test_plausible_values.R    |   44 
 dexter-1.0.0/dexter/tests/testthat/test_profiles.R            |  133 
 dexter-1.0.0/dexter/vignettes/DIF_vignette.Rmd                |only
 dexter-1.0.0/dexter/vignettes/Equating.Rmd                    |  597 +-
 dexter-1.0.0/dexter/vignettes/Plausible_Values.Rmd            |  357 -
 dexter-1.0.0/dexter/vignettes/Test_Individual_differences.Rmd |  210 
 dexter-1.0.0/dexter/vignettes/dexter.Rmd                      |  412 -
 dexter-1.0.0/dexter/vignettes/dexter.bib                      |  626 +-
 dexter-1.0.0/dexter/vignettes/profile-plots.Rmd               |  458 -
 149 files changed, 16294 insertions(+), 15117 deletions(-)

More information about dexter at CRAN
Permanent link

Package apexcharter updated to version 0.1.2 with previous version 0.1.1 dated 2019-07-28

Title: Create Interactive Chart with the JavaScript 'ApexCharts' Library
Description: Provides an 'htmlwidgets' interface to 'apexcharts.js'. 'Apexcharts' is a modern JavaScript charting library to build interactive charts and visualizations with simple API. 'Apexcharts' examples and documentation are available here: <https://apexcharts.com/>.
Author: Victor Perrier [aut, cre], Fanny Meyer [aut], Juned Chhipa [cph] (apexcharts.js library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between apexcharter versions 0.1.1 dated 2019-07-28 and 0.1.2 dated 2019-08-22

 DESCRIPTION                                           |    6 -
 MD5                                                   |   18 ++--
 NEWS.md                                               |   12 ++
 README.md                                             |    9 +-
 inst/doc/labs.html                                    |   31 ++++---
 inst/doc/lines.html                                   |   51 ++++++------
 inst/doc/starting-with-apexcharts.html                |   75 +++++++++---------
 inst/htmlwidgets/apexcharter.js                       |    3 
 inst/htmlwidgets/apexcharter.yaml                     |    2 
 inst/htmlwidgets/lib/apexcharts-3.8/apexcharts.min.js |    4 
 10 files changed, 119 insertions(+), 92 deletions(-)

More information about apexcharter at CRAN
Permanent link

Package forecast updated to version 8.9 with previous version 8.8 dated 2019-08-02

Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] (<https://orcid.org/0000-0002-2140-5352>), George Athanasopoulos [aut], Christoph Bergmeir [aut] (<https://orcid.org/0000-0002-3665-9021>), Gabriel Caceres [aut], Leanne Chhay [aut], Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>), Fotios Petropoulos [aut] (<https://orcid.org/0000-0003-3039-4955>), Slava Razbash [aut], Earo Wang [aut], Farah Yasmeen [aut] (<https://orcid.org/0000-0002-1479-5401>), R Core Team [ctb, cph], Ross Ihaka [ctb, cph], Daniel Reid [ctb], David Shaub [ctb], Yuan Tang [ctb] (<https://orcid.org/0000-0001-5243-233X>), Zhenyu Zhou [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>

Diff between forecast versions 8.8 dated 2019-08-02 and 8.9 dated 2019-08-22

 DESCRIPTION                                                    |    9 
 MD5                                                            |   34 +--
 NEWS.md                                                        |    6 
 R/ggplot.R                                                     |    2 
 R/mstl.R                                                       |    4 
 R/nnetar.R                                                     |    4 
 R/simulate.R                                                   |    6 
 inst/doc/JSS2008.R                                             |   77 +++++++
 inst/doc/JSS2008.Rmd                                           |   97 +++++++---
 inst/doc/JSS2008.pdf                                           |binary
 man/mstl.Rd                                                    |    4 
 tests/testthat/test-accuracy.R                                 |    5 
 tests/testthat/test-newarima2.R                                |    5 
 vignettes/JSS2008.Rmd                                          |   97 +++++++---
 vignettes/JSS2008_files/figure-latex/arima-auto-fcast-1.pdf    |binary
 vignettes/JSS2008_files/figure-latex/arimaexamples-1.pdf       |binary
 vignettes/JSS2008_files/figure-latex/ets-usnetelec-fcast-1.pdf |binary
 vignettes/JSS2008_files/figure-latex/etsexamples-1.pdf         |binary
 18 files changed, 264 insertions(+), 86 deletions(-)

More information about forecast at CRAN
Permanent link

Package STMotif updated to version 1.0.3 with previous version 1.0.2 dated 2019-02-11

Title: Discovery of Motifs in Spatial-Time Series
Description: Allow to identify motifs in spatial-time series. A motif is a previously unknown subsequence of a (spatial) time series with relevant number of occurrences. For this purpose, the Combined Series Approach (CSA) is used.
Author: Heraldo Borges [aut, cre] (CEFET/RJ), Amin Bazaz [aut] (Polytech'Montpellier), Luciana Escobar [aut] (CEFET/RJ), Esther Pacitti [aut] (CEFET/RJ), Eduardo Ogasawara [aut] (CEFET/RJ)
Maintainer: Heraldo Borges <stmotif@eic.cefet-rj.br>

Diff between STMotif versions 1.0.2 dated 2019-02-11 and 1.0.3 dated 2019-08-22

 DESCRIPTION            |   16 ++++++++++------
 MD5                    |    6 +++---
 README.md              |    5 +++--
 inst/doc/examples.html |    4 ++--
 4 files changed, 18 insertions(+), 13 deletions(-)

More information about STMotif at CRAN
Permanent link

Package nandb updated to version 2.0.5 with previous version 2.0.4 dated 2019-07-08

Title: Number and Brightness Image Analysis
Description: Calculation of molecular number and brightness from fluorescence microscopy image series. The software was published in a 2016 paper <doi:10.1093/bioinformatics/btx434>. The seminal paper for the technique is Digman et al. 2008 <doi:10.1529/biophysj.107.114645>. A review of the technique was published in 2017 <doi:10.1016/j.ymeth.2017.12.001>.
Author: Rory Nolan [aut, cre, cph] (<https://orcid.org/0000-0002-5239-4043>), Luis Alvarez [ctb, cph] (<https://orcid.org/0000-0003-1316-1906>), Sergi Padilla-Parra [ctb, ths, cph] (<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

Diff between nandb versions 2.0.4 dated 2019-07-08 and 2.0.5 dated 2019-08-22

 DESCRIPTION                         |   66 ++++++++++++++++++++----------------
 MD5                                 |   16 ++++----
 NEWS.md                             |    6 +++
 build/partial.rdb                   |binary
 build/vignette.rds                  |binary
 inst/doc/batch-mode.html            |   10 +++--
 inst/doc/brightness-timeseries.html |    8 +++-
 inst/doc/single-images.html         |   12 ++++--
 tests/testthat/test-number.R        |   11 ------
 9 files changed, 73 insertions(+), 56 deletions(-)

More information about nandb at CRAN
Permanent link

Package units updated to version 0.6-4 with previous version 0.6-3 dated 2019-05-03

Title: Measurement Units for R Vectors
Description: Support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. Compatible with the POSIXct, Date and difftime classes. Uses the UNIDATA udunits library and unit database for unit compatibility checking and conversion. Documentation about 'units' is provided in the paper by Pebesma, Mailund & Hiebert (2016, <doi:10.32614/RJ-2016-061>), included in this package as a vignette; see 'citation("units")' for details.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>), Thomas Mailund [aut], Tomasz Kalinowski [aut], James Hiebert [ctb], Iñaki Ucar [ctb] (<https://orcid.org/0000-0001-6403-5550>)
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

Diff between units versions 0.6-3 dated 2019-05-03 and 0.6-4 dated 2019-08-22

 DESCRIPTION                           |    6 -
 MD5                                   |   34 +++++-----
 NAMESPACE                             |    2 
 NEWS.md                               |    8 ++
 R/deprecated.R                        |    2 
 R/make_units.R                        |    8 --
 R/summaries.R                         |    6 +
 R/sysdata.rda                         |binary
 R/user_conversion.R                   |   26 ++++++--
 R/valid_udunits.R                     |   19 ++++-
 build/vignette.rds                    |binary
 configure                             |   18 ++---
 inst/doc/measurement_units_in_R.html  |   14 +---
 inst/doc/units.html                   |  110 +++++++++++++++++-----------------
 tests/testthat/test_misc.R            |    4 -
 tests/testthat/test_summaries.R       |    4 -
 tests/testthat/test_udunits.R         |    1 
 tests/testthat/test_user_conversion.R |   14 ++++
 18 files changed, 165 insertions(+), 111 deletions(-)

More information about units at CRAN
Permanent link

Package radiant.data updated to version 1.0.6 with previous version 1.0.0 dated 2019-07-18

Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

Diff between radiant.data versions 1.0.0 dated 2019-07-18 and 1.0.6 dated 2019-08-22

 DESCRIPTION                                            |   11 +--
 MD5                                                    |   28 ++++----
 NEWS.md                                                |   31 +++++++--
 R/manage.R                                             |   22 +++---
 R/radiant.R                                            |    3 
 inst/app/global.R                                      |   55 +++++++++++++----
 inst/app/init.R                                        |   25 +++----
 inst/app/radiant.R                                     |   53 ++++++++--------
 inst/app/rsconnect/shinyapps.io/vnijs/radiant-data.dcf |    5 -
 inst/app/tools/app/report_r.R                          |    2 
 inst/app/tools/app/report_rmd.R                        |   16 +---
 inst/app/tools/data/manage_ui.R                        |   26 ++++----
 inst/app/tools/data/transform_ui.R                     |    4 -
 inst/app/www/js/run_return.js                          |    7 ++
 man/fix_names.Rd                                       |    4 -
 15 files changed, 178 insertions(+), 114 deletions(-)

More information about radiant.data at CRAN
Permanent link

Package rpart.plot updated to version 3.0.8 with previous version 3.0.7 dated 2019-04-12

Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>

Diff between rpart.plot versions 3.0.7 dated 2019-04-12 and 3.0.8 dated 2019-08-22

 DESCRIPTION                               |    6 
 MD5                                       |   50 +++----
 NEWS                                      |   13 ++
 R/layout.R                                |    1 
 R/node.labs.R                             |    4 
 R/palette.R                               |   26 ++--
 R/rpart.rules.R                           |   38 +++--
 inst/doc/prp.pdf                          |binary
 inst/slowtests/rpart.report.Rout.save     |  193 +++++++++++++++---------------
 inst/slowtests/rpart.report.bat           |    2 
 inst/slowtests/test.describe.col.bat      |    2 
 inst/slowtests/test.imports.bat           |    2 
 inst/slowtests/test.na.bat                |    2 
 inst/slowtests/test.palette.R             |   48 +++++++
 inst/slowtests/test.palette.Rout.save     |   74 +++++++++++
 inst/slowtests/test.palette.bat           |    2 
 inst/slowtests/test.prp.Rout.save         |    4 
 inst/slowtests/test.rpart.plot.Rout.save  |   10 -
 inst/slowtests/test.rpart.plot.bat        |    2 
 inst/slowtests/test.rpart.rules.R         |    2 
 inst/slowtests/test.rpart.rules.Rout.save |  134 +++++++++-----------
 inst/slowtests/test.rpart.rules.bat       |    2 
 inst/slowtests/test.type5.bat             |    2 
 inst/slowtests/usersplits.bat             |    2 
 inst/slowtests/vignette.bat               |    2 
 inst/slowtests/webpage.figs.bat           |    2 
 26 files changed, 387 insertions(+), 238 deletions(-)

More information about rpart.plot at CRAN
Permanent link

Package paws updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-28

Title: Amazon Web Services Software Development Kit
Description: Interface to Amazon Web Services <https://aws.amazon.com>, including storage, database, and compute services, such as 'Simple Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda' functions-as-a-service.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws versions 0.1.3 dated 2019-07-28 and 0.1.4 dated 2019-08-22

 DESCRIPTION |   26 +++++++++++++-------------
 MD5         |    9 +++++----
 NEWS.md     |only
 R/paws.R    |    4 ++--
 man/acm.Rd  |    2 +-
 man/kms.Rd  |    2 +-
 6 files changed, 22 insertions(+), 21 deletions(-)

More information about paws at CRAN
Permanent link

Package enviGCMS updated to version 0.5.7 with previous version 0.5.5 dated 2019-05-14

Title: GC/LC-MS Data Analysis for Environmental Science
Description: Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Author: Miao YU [aut, cre] (<https://orcid.org/0000-0002-2804-6014>), Thanh Wang [ctb] (<https://orcid.org/0000-0002-5729-1908>)
Maintainer: Miao YU <yufreecas@gmail.com>

Diff between enviGCMS versions 0.5.5 dated 2019-05-14 and 0.5.7 dated 2019-08-22

 DESCRIPTION          |    8 +++----
 MD5                  |   45 +++++++++++++++++++++++--------------------
 NAMESPACE            |    2 +
 NEWS.md              |   12 +++++++++++
 R/general.R          |    5 ++--
 R/getmzrt.R          |   10 +++++----
 R/io.R               |    9 ++++----
 R/mda.R              |   53 +++++++++++++++++++++++++++++++++++++++++++--------
 R/plotmzrt.R         |   19 ++++++++++--------
 data/TBBPA.rda       |only
 data/list.rda        |binary
 inst/doc/GCMSDA.html |    8 +++++--
 man/TBBPA.Rd         |only
 man/findmet.Rd       |only
 man/findohc.Rd       |    2 -
 man/getcsv.Rd        |    2 +
 man/getmzrtcsv.Rd    |    2 -
 man/gifmr.Rd         |    2 +
 man/plotden.Rd       |    6 +++--
 man/plothm.Rd        |    2 -
 man/plotpca.Rd       |    2 -
 man/plotridges.Rd    |    2 -
 man/plotrla.Rd       |    2 -
 man/plotrtms.Rd      |    4 ++-
 man/writeMSP.Rd      |    2 +
 25 files changed, 137 insertions(+), 62 deletions(-)

More information about enviGCMS at CRAN
Permanent link

Package Eagle updated to version 1.5.2 with previous version 1.5.1 dated 2019-05-24

Title: Multiple Locus Association Mapping on a Genome-Wide Scale
Description: An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred and outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. For users unfamiliar with R, to perform an analysis, run 'OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.
Author: Andrew George [aut, cre], Joshua Bowden [ctb], Ryan Stephenson [ctb], Hyun Kang [ctb], Noah Zaitlen [ctb], Claire Wade [ctb], Andrew Kirby [ctb], David Heckerman [ctb], Mark Daly [ctb], Eleazar Eskin [ctb]
Maintainer: Andrew George <andrew.george@csiro.au>

Diff between Eagle versions 1.5.1 dated 2019-05-24 and 1.5.2 dated 2019-08-22

 DESCRIPTION                       |    6 +++---
 MD5                               |    8 ++++----
 R/FPR4AM.R                        |    2 +-
 R/onAttach.R                      |    2 +-
 src/calculate_a_and_vara_rcpp.cpp |    8 +++++---
 5 files changed, 14 insertions(+), 12 deletions(-)

More information about Eagle at CRAN
Permanent link

Wed, 21 Aug 2019

Package rdlocrand updated to version 0.5 with previous version 0.4 dated 2019-03-13

Title: Local Randomization Methods for RD Designs
Description: The regression discontinuity (RD) design is a popular quasi-experimental design for causal inference and policy evaluation. Under the local randomization approach, RD designs can be interpreted as randomized experiments inside a window around the cutoff. This package provides tools to perform randomization inference for RD designs under local randomization: rdrandinf() to perform hypothesis testing using randomization inference, rdwinselect() to select a window around the cutoff in which randomization is likely to hold, rdsensitivity() to assess the sensitivity of the results to different window lengths and null hypotheses and rdrbounds() to construct Rosenbaum bounds for sensitivity to unobserved confounders. See Cattaneo, Titiunik and Vazquez-Bare (2016) <https://sites.google.com/site/rdpackages/rdlocrand/Cattaneo-Titiunik-VazquezBare_2016_Stata.pdf> for further methodological details.
Author: Matias D. Cattaneo, Rocio Titiunik, Gonzalo Vazquez-Bare
Maintainer: Gonzalo Vazquez-Bare <gvazquez@econ.ucsb.edu>

Diff between rdlocrand versions 0.4 dated 2019-03-13 and 0.5 dated 2019-08-21

 DESCRIPTION              |   10 +++++-----
 MD5                      |   24 ++++++++++++------------
 R/rdlocrand_fun.R        |    2 +-
 R/rdlocrand_package.R    |    6 +++---
 R/rdrandinf.R            |    6 +++---
 R/rdrbounds.R            |    6 +++---
 R/rdsensitivity.R        |    6 +++---
 R/rdwinselect.R          |    6 +++---
 man/rdlocrand-package.Rd |    6 +++---
 man/rdrandinf.Rd         |   17 +++++++++--------
 man/rdrbounds.Rd         |    6 +++---
 man/rdsensitivity.Rd     |   13 +++++++------
 man/rdwinselect.Rd       |   16 ++++++++--------
 13 files changed, 63 insertions(+), 61 deletions(-)

More information about rdlocrand at CRAN
Permanent link

Package dtw updated to version 1.21-1 with previous version 1.20-1 dated 2018-05-18

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.
Author: Toni Giorgino <toni.giorgino@gmail.com>,
Maintainer: Toni Giorgino <toni.giorgino@gmail.com>

Diff between dtw versions 1.20-1 dated 2018-05-18 and 1.21-1 dated 2019-08-21

 dtw-1.20-1/dtw/R/triangleFixing.R           |only
 dtw-1.20-1/dtw/R/zzz.R                      |only
 dtw-1.20-1/dtw/build/partial.rdb            |only
 dtw-1.20-1/dtw/man/triangleFixing.Rd        |only
 dtw-1.21-1/dtw/DESCRIPTION                  |   10 
 dtw-1.21-1/dtw/MD5                          |   84 ++----
 dtw-1.21-1/dtw/NAMESPACE                    |   89 ++----
 dtw-1.21-1/dtw/R/backtrack.R                |    2 
 dtw-1.21-1/dtw/R/countPaths.R               |   33 ++
 dtw-1.21-1/dtw/R/data.R                     |only
 dtw-1.21-1/dtw/R/dtw-internal.R             |   17 +
 dtw-1.21-1/dtw/R/dtw-package.R              |only
 dtw-1.21-1/dtw/R/dtw.R                      |  246 +++++++++++++++++
 dtw-1.21-1/dtw/R/dtwDist.R                  |  111 +++++++
 dtw-1.21-1/dtw/R/globalCostMatrix.R         |    4 
 dtw-1.21-1/dtw/R/mvm.R                      |   64 ++++
 dtw-1.21-1/dtw/R/plot.dtw.R                 |  256 +++++++++++++++++-
 dtw-1.21-1/dtw/R/stepPattern.R              |  269 ++++++++++++++++++-
 dtw-1.21-1/dtw/R/warp.R                     |   74 +++++
 dtw-1.21-1/dtw/R/warpArea.R                 |   45 +++
 dtw-1.21-1/dtw/R/window.R                   |  104 +++++++
 dtw-1.21-1/dtw/build/vignette.rds           |binary
 dtw-1.21-1/dtw/demo/dtw.R                   |    2 
 dtw-1.21-1/dtw/inst/ChangeLog               |    3 
 dtw-1.21-1/dtw/inst/doc/dtw.R               |    1 
 dtw-1.21-1/dtw/inst/doc/dtw.Rnw             |    7 
 dtw-1.21-1/dtw/inst/doc/dtw.pdf             |binary
 dtw-1.21-1/dtw/man/aami.Rd                  |   77 ++---
 dtw-1.21-1/dtw/man/countPaths.Rd            |   46 +--
 dtw-1.21-1/dtw/man/dtw-internal.Rd          |   12 
 dtw-1.21-1/dtw/man/dtw-package.Rd           |  138 ++++-----
 dtw-1.21-1/dtw/man/dtw.Rd                   |  348 ++++++++++--------------
 dtw-1.21-1/dtw/man/dtwDist.Rd               |   96 +++---
 dtw-1.21-1/dtw/man/dtwPlot.Rd               |  129 +++------
 dtw-1.21-1/dtw/man/dtwPlotThreeWay.Rd       |  117 +++-----
 dtw-1.21-1/dtw/man/dtwPlotTwoWay.Rd         |  118 +++-----
 dtw-1.21-1/dtw/man/dtwWindowingFunctions.Rd |  182 +++++--------
 dtw-1.21-1/dtw/man/mvm.Rd                   |   76 ++---
 dtw-1.21-1/dtw/man/stepPattern.Rd           |  391 ++++++++++++----------------
 dtw-1.21-1/dtw/man/warp.Rd                  |   60 ++--
 dtw-1.21-1/dtw/man/warpArea.Rd              |   49 +--
 dtw-1.21-1/dtw/src/Makevars                 |    2 
 dtw-1.21-1/dtw/src/computeCM.c              |    2 
 dtw-1.21-1/dtw/src/init.c                   |    8 
 dtw-1.21-1/dtw/src/triangleFixing.c         |    2 
 dtw-1.21-1/dtw/vignettes/dtw.Rnw            |    7 
 46 files changed, 2119 insertions(+), 1162 deletions(-)

More information about dtw at CRAN
Permanent link

Package DataSpaceR updated to version 0.7.2 with previous version 0.6.3 dated 2019-04-05

Title: Interface to 'the CAVD DataSpace'
Description: Provides a convenient API interface to access immunological data within 'the CAVD DataSpace'(<https://dataspace.cavd.org>), a data sharing and discovery tool that facilitates exploration of HIV immunological data from pre-clinical and clinical HIV vaccine studies.
Author: Ju Yeong Kim [aut, cre, cph], Sean Hughes [rev] (Sean reviewed the package for ropensci, see <https://github.com/ropensci/software-review/issues/261>), Jason Taylor [aut]
Maintainer: Ju Yeong Kim <jkim2345@fredhutch.org>

Diff between DataSpaceR versions 0.6.3 dated 2019-04-05 and 0.7.2 dated 2019-08-21

 DESCRIPTION                                     |   14 
 MD5                                             |   35 -
 NAMESPACE                                       |    2 
 NEWS.md                                         |   12 
 R/DataSpaceConnection.R                         |  214 +++++++
 R/DataSpaceMab.R                                |only
 R/helpers.R                                     |   30 +
 README.md                                       |  205 ++++---
 build/vignette.rds                              |binary
 inst/doc/Accessing_Monoconal_Antibody_Data.R    |only
 inst/doc/Accessing_Monoconal_Antibody_Data.Rmd  |only
 inst/doc/Accessing_Monoconal_Antibody_Data.html |only
 inst/doc/Intro_to_DataSpaceR.R                  |    3 
 inst/doc/Intro_to_DataSpaceR.Rmd                |   25 
 inst/doc/Intro_to_DataSpaceR.html               |  661 +++++++++++++++++-------
 man/DataSpaceConnection.Rd                      |   22 
 man/DataSpaceMab.Rd                             |only
 tests/testthat/test-connection.R                |   89 +++
 tests/testthat/test-mab.R                       |only
 tests/testthat/test-study.R                     |    6 
 vignettes/Accessing_Monoconal_Antibody_Data.Rmd |only
 vignettes/Intro_to_DataSpaceR.Rmd               |   25 
 22 files changed, 1062 insertions(+), 281 deletions(-)

More information about DataSpaceR at CRAN
Permanent link

Package burnr updated to version 0.5.0 with previous version 0.4.0 dated 2019-07-09

Title: Forest Fire History Analysis
Description: Tools to read, write, parse, and analyze forest fire history data (e.g. FHX). Described in Malevich et al. (2018) <doi:10.1016/j.dendro.2018.02.005>.
Author: Steven Malevich [aut, cre] (<https://orcid.org/0000-0002-4752-8190>), Christopher Guiterman [ctb] (<https://orcid.org/0000-0002-9706-9332>), Ellis Margolis [ctb] (<https://orcid.org/0000-0002-0595-9005>)
Maintainer: Steven Malevich <sbmalev@gmail.com>

Diff between burnr versions 0.4.0 dated 2019-07-09 and 0.5.0 dated 2019-08-21

 burnr-0.4.0/burnr/man/check_duplicates.Rd         |only
 burnr-0.4.0/burnr/man/find_recording.Rd           |only
 burnr-0.4.0/burnr/man/get_ggplot.Rd               |only
 burnr-0.4.0/burnr/man/list_filestrings.Rd         |only
 burnr-0.4.0/burnr/man/run_sea.Rd                  |only
 burnr-0.4.0/burnr/man/site_stats.Rd               |only
 burnr-0.4.0/burnr/tests/testthat/test-empty.R     |only
 burnr-0.5.0/burnr/DESCRIPTION                     |   24 
 burnr-0.5.0/burnr/MD5                             |  155 +-
 burnr-0.5.0/burnr/NAMESPACE                       |    8 
 burnr-0.5.0/burnr/NEWS.md                         |   27 
 burnr-0.5.0/burnr/R/data.R                        |   93 +
 burnr-0.5.0/burnr/R/intervals.R                   |  267 ++--
 burnr-0.5.0/burnr/R/io.R                          |  276 ++--
 burnr-0.5.0/burnr/R/plotting.R                    |  413 ++++--
 burnr-0.5.0/burnr/R/sea.R                         |  445 ++++--
 burnr-0.5.0/burnr/R/stats.R                       |  350 ++---
 burnr-0.5.0/burnr/R/sysdata.rda                   |only
 burnr-0.5.0/burnr/R/utils.R                       |  673 +++++++---
 burnr-0.5.0/burnr/README.md                       |   11 
 burnr-0.5.0/burnr/inst/CITATION                   |only
 burnr-0.5.0/burnr/inst/doc/introduction.Rmd       |    2 
 burnr-0.5.0/burnr/inst/doc/introduction.html      |  714 +++++------
 burnr-0.5.0/burnr/man/as.fhx.Rd                   |only
 burnr-0.5.0/burnr/man/as_fhx.Rd                   |only
 burnr-0.5.0/burnr/man/composite.Rd                |   44 
 burnr-0.5.0/burnr/man/count_event_position.Rd     |   54 
 burnr-0.5.0/burnr/man/count_injury.Rd             |   14 
 burnr-0.5.0/burnr/man/count_recording.Rd          |   14 
 burnr-0.5.0/burnr/man/count_scar.Rd               |   14 
 burnr-0.5.0/burnr/man/count_year_span.Rd          |   16 
 burnr-0.5.0/burnr/man/delete.Rd                   |   27 
 burnr-0.5.0/burnr/man/fhx.Rd                      |   57 
 burnr-0.5.0/burnr/man/first_year.Rd               |   14 
 burnr-0.5.0/burnr/man/get_event_years.Rd          |   37 
 burnr-0.5.0/burnr/man/get_series.Rd               |   21 
 burnr-0.5.0/burnr/man/get_year.Rd                 |   18 
 burnr-0.5.0/burnr/man/inner_type.Rd               |   15 
 burnr-0.5.0/burnr/man/intervals.Rd                |   40 
 burnr-0.5.0/burnr/man/is.fhx.Rd                   |   17 
 burnr-0.5.0/burnr/man/is.intervals.Rd             |    9 
 burnr-0.5.0/burnr/man/is.sea.Rd                   |    9 
 burnr-0.5.0/burnr/man/is_fhx.Rd                   |only
 burnr-0.5.0/burnr/man/is_intervals.Rd             |only
 burnr-0.5.0/burnr/man/is_sea.Rd                   |only
 burnr-0.5.0/burnr/man/last_year.Rd                |   15 
 burnr-0.5.0/burnr/man/lgr2.Rd                     |    7 
 burnr-0.5.0/burnr/man/lgr2_meta.Rd                |   12 
 burnr-0.5.0/burnr/man/make_rec_type.Rd            |   20 
 burnr-0.5.0/burnr/man/max.intervals.Rd            |   18 
 burnr-0.5.0/burnr/man/mean.intervals.Rd           |   18 
 burnr-0.5.0/burnr/man/median.intervals.Rd         |   18 
 burnr-0.5.0/burnr/man/min.intervals.Rd            |   18 
 burnr-0.5.0/burnr/man/outer_type.Rd               |   15 
 burnr-0.5.0/burnr/man/percent_scarred.Rd          |   23 
 burnr-0.5.0/burnr/man/pgm.Rd                      |   16 
 burnr-0.5.0/burnr/man/pgm_meta.Rd                 |   27 
 burnr-0.5.0/burnr/man/pgm_pdsi.Rd                 |   21 
 burnr-0.5.0/burnr/man/plot.fhx.Rd                 |   36 
 burnr-0.5.0/burnr/man/plot.intervals.Rd           |    9 
 burnr-0.5.0/burnr/man/plot.sea.Rd                 |   15 
 burnr-0.5.0/burnr/man/plot_demograph.Rd           |  132 +-
 burnr-0.5.0/burnr/man/plot_intervals_dist.Rd      |   30 
 burnr-0.5.0/burnr/man/plot_sealags.Rd             |   30 
 burnr-0.5.0/burnr/man/plus-.fhx.Rd                |   21 
 burnr-0.5.0/burnr/man/print.intervals.Rd          |   18 
 burnr-0.5.0/burnr/man/print.sea.Rd                |   39 
 burnr-0.5.0/burnr/man/quantile.intervals.Rd       |   21 
 burnr-0.5.0/burnr/man/read_fhx.Rd                 |   22 
 burnr-0.5.0/burnr/man/sample_depth.Rd             |   11 
 burnr-0.5.0/burnr/man/sea.Rd                      |  118 +
 burnr-0.5.0/burnr/man/series_mean_interval.Rd     |   16 
 burnr-0.5.0/burnr/man/series_names.Rd             |   20 
 burnr-0.5.0/burnr/man/series_stats.Rd             |   40 
 burnr-0.5.0/burnr/man/sort.fhx.Rd                 |   20 
 burnr-0.5.0/burnr/man/summary.fhx.Rd              |   13 
 burnr-0.5.0/burnr/man/write_fhx.Rd                |   14 
 burnr-0.5.0/burnr/man/year_range.Rd               |   21 
 burnr-0.5.0/burnr/man/yearly_recording.Rd         |   11 
 burnr-0.5.0/burnr/tests/testthat/test-intervals.R |   16 
 burnr-0.5.0/burnr/tests/testthat/test-io.R        | 1404 +++++++++++-----------
 burnr-0.5.0/burnr/tests/testthat/test-plotting.R  |only
 burnr-0.5.0/burnr/tests/testthat/test-sea.R       |   25 
 burnr-0.5.0/burnr/tests/testthat/test-stats.R     |   36 
 burnr-0.5.0/burnr/tests/testthat/test-utils.R     |  214 ++-
 burnr-0.5.0/burnr/vignettes/introduction.Rmd      |    2 
 86 files changed, 3981 insertions(+), 2479 deletions(-)

More information about burnr at CRAN
Permanent link

Package pccc updated to version 1.0.3 with previous version 1.0.2 dated 2018-07-02

Title: Pediatric Complex Chronic Conditions
Description: An implementation of the pediatric complex chronic conditions (CCC) classification system using R and C++.
Author: Peter DeWitt [aut], Tell Bennett [aut], James Feinstein [aut], Seth Russell [aut, cre]
Maintainer: Seth Russell <seth.russell@ucdenver.edu>

Diff between pccc versions 1.0.2 dated 2018-07-02 and 1.0.3 dated 2019-08-21

 DESCRIPTION                     |    8 
 MD5                             |   22 
 NEWS.md                         |    6 
 build/vignette.rds              |binary
 inst/doc/pccc-example.html      |  325 ++++----
 inst/doc/pccc-icd-codes.html    | 1603 ++++++++++++++++++++--------------------
 inst/doc/pccc-overview.html     |  225 +++--
 src/get_codes.cpp               |   52 -
 tests/testthat/test_ccc.R       |   14 
 tests/testthat/test_ccc_icd10.R |    2 
 tests/testthat/test_ccc_icd9.R  |    2 
 tests/testthat/test_get_codes.R |    5 
 12 files changed, 1179 insertions(+), 1085 deletions(-)

More information about pccc at CRAN
Permanent link

Package ICD10gm updated to version 1.0.4 with previous version 1.0.3 dated 2019-02-12

Title: Metadata Processing for the German Modification of the ICD-10 Coding System
Description: Provides convenient access to the German modification of the International Classification of Diagnoses, 10th revision (ICD-10-GM). It provides functionality to aid in the identification, specification and historisation of ICD-10 codes. Its intended use is the analysis of routinely collected data in the context of epidemiology, medical research and health services research. The underlying metadata are released by the German Institute for Medical Documentation and Information <https://www.dimdi.de>, and are redistributed in accordance with their license.
Author: Ewan Donnachie [aut, cre] (<https://orcid.org/0000-0002-0668-0049>)
Maintainer: Ewan Donnachie <ewan@donnachie.net>

Diff between ICD10gm versions 1.0.3 dated 2019-02-12 and 1.0.4 dated 2019-08-21

 DESCRIPTION                  |   11 -
 MD5                          |   24 +-
 NAMESPACE                    |    2 
 NEWS.md                      |    4 
 R/icd_expand.R               |   26 +-
 R/icd_history.R              |    2 
 README.md                    |   10 
 build/vignette.rds           |binary
 data/icd_meta_blocks.rda     |binary
 data/icd_meta_chapters.rda   |binary
 data/icd_meta_codes.rda      |binary
 data/icd_meta_transition.rda |binary
 inst/doc/icd10gm_intro.html  |  439 ++++++++++++++++++++++++++++++++-----------
 13 files changed, 372 insertions(+), 146 deletions(-)

More information about ICD10gm at CRAN
Permanent link

Package DTRreg updated to version 1.4 with previous version 1.3 dated 2017-08-30

Title: DTR Estimation and Inference via G-Estimation, Dynamic WOLS, Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
Description: Dynamic treatment regime estimation and inference via G-estimation, dynamic weighted ordinary least squares (dWOLS) and Q-learning. Inference via bootstrap and (for G-estimation) recursive sandwich estimation. Estimation and inference for survival outcomes via Dynamic Weighted Survival Modeling (DWSurv).
Author: Michael Wallace, Erica E M Moodie, David A Stephens and Gabrielle Simoneau
Maintainer: Michael Wallace <michael.wallace@uwaterloo.ca>

Diff between DTRreg versions 1.3 dated 2017-08-30 and 1.4 dated 2019-08-21

 DTRreg-1.3/DTRreg/inst                  |only
 DTRreg-1.3/DTRreg/man/chooseM.DTRreg.Rd |only
 DTRreg-1.4/DTRreg/DESCRIPTION           |   20 
 DTRreg-1.4/DTRreg/MD5                   |   17 
 DTRreg-1.4/DTRreg/NAMESPACE             |   30 
 DTRreg-1.4/DTRreg/R/DTRreg.R            | 1929 +++++++++++++++++++-------------
 DTRreg-1.4/DTRreg/man/DTRreg.Rd         |   18 
 DTRreg-1.4/DTRreg/man/DWSurv.Rd         |only
 DTRreg-1.4/DTRreg/man/chooseM.Rd        |only
 DTRreg-1.4/DTRreg/man/confint.DTRreg.Rd |only
 DTRreg-1.4/DTRreg/man/plot.DTRreg.Rd    |  137 +-
 DTRreg-1.4/DTRreg/man/predict.DTRreg.Rd |  136 +-
 12 files changed, 1345 insertions(+), 942 deletions(-)

More information about DTRreg at CRAN
Permanent link

Package DClusterm updated to version 1.0-0 with previous version 0.2-1 dated 2018-05-28

Title: Model-Based Detection of Disease Clusters
Description: Model-based methods for the detection of disease clusters using GLMs, GLMMs and zero-inflated models. These methods are described in 'V. Gómez-Rubio et al.' (2019) <doi:10.18637/jss.v090.i14> and 'V. Gómez-Rubio et al.' (2018) <doi:10.1007/978-3-030-01584-8_1>.
Author: Virgilio Gomez-Rubio, Paula Esther Moraga Serrano, Barry Rowlingson
Maintainer: Virgilio Gomez-Rubio <virgilio.gomez@uclm.es>

Diff between DClusterm versions 0.2-1 dated 2018-05-28 and 1.0-0 dated 2019-08-21

 DClusterm-0.2-1/DClusterm/vignettes/jsslogo.jpg             |only
 DClusterm-1.0-0/DClusterm/DESCRIPTION                       |   15 
 DClusterm-1.0-0/DClusterm/MD5                               |   38 
 DClusterm-1.0-0/DClusterm/R/Functions1.R                    |   22 
 DClusterm-1.0-0/DClusterm/build/vignette.rds                |binary
 DClusterm-1.0-0/DClusterm/data/NY8.RData                    |binary
 DClusterm-1.0-0/DClusterm/data/NY8_clusters.RData           |binary
 DClusterm-1.0-0/DClusterm/data/Navarre.RData                |binary
 DClusterm-1.0-0/DClusterm/data/brainNM.RData                |binary
 DClusterm-1.0-0/DClusterm/data/brainNM_clusters.RData       |binary
 DClusterm-1.0-0/DClusterm/inst/CITATION                     |only
 DClusterm-1.0-0/DClusterm/inst/doc/DClusterm.R              |  113 -
 DClusterm-1.0-0/DClusterm/inst/doc/DClusterm.Rnw            |  165 +-
 DClusterm-1.0-0/DClusterm/inst/doc/DClusterm.pdf            |binary
 DClusterm-1.0-0/DClusterm/man/CalcStatClusterGivenCenter.Rd |    4 
 DClusterm-1.0-0/DClusterm/man/CalcStatsAllClusters.Rd       |    4 
 DClusterm-1.0-0/DClusterm/man/DetectClustersModel.Rd        |   14 
 DClusterm-1.0-0/DClusterm/man/glmAndZIP.iscluster.Rd        |    4 
 DClusterm-1.0-0/DClusterm/vignettes/DClusterm.Rnw           |  165 +-
 DClusterm-1.0-0/DClusterm/vignettes/DClusterm.bib           |  756 +++++-------
 DClusterm-1.0-0/DClusterm/vignettes/Makefile                |    2 
 21 files changed, 628 insertions(+), 674 deletions(-)

More information about DClusterm at CRAN
Permanent link

Package NetworkToolbox updated to version 1.3.0 with previous version 1.2.3 dated 2019-01-31

Title: Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis
Description: Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershogoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.
Author: Alexander Christensen [aut, cre], Guido Previde Massara [ctb]
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>

Diff between NetworkToolbox versions 1.2.3 dated 2019-01-31 and 1.3.0 dated 2019-08-21

 NetworkToolbox-1.2.3/NetworkToolbox/R/centlist.R                  |only
 NetworkToolbox-1.2.3/NetworkToolbox/R/cpmEV.R                     |only
 NetworkToolbox-1.2.3/NetworkToolbox/R/cpmFP.R                     |only
 NetworkToolbox-1.2.3/NetworkToolbox/R/cpmFPperm.R                 |only
 NetworkToolbox-1.2.3/NetworkToolbox/R/cpmIV.R                     |only
 NetworkToolbox-1.2.3/NetworkToolbox/R/nams.R                      |only
 NetworkToolbox-1.2.3/NetworkToolbox/man/centlist.Rd               |only
 NetworkToolbox-1.2.3/NetworkToolbox/man/cpmEV.Rd                  |only
 NetworkToolbox-1.2.3/NetworkToolbox/man/cpmFP.Rd                  |only
 NetworkToolbox-1.2.3/NetworkToolbox/man/cpmFPperm.Rd              |only
 NetworkToolbox-1.2.3/NetworkToolbox/man/cpmIV.Rd                  |only
 NetworkToolbox-1.2.3/NetworkToolbox/man/nams.Rd                   |only
 NetworkToolbox-1.3.0/NetworkToolbox/DESCRIPTION                   |   17 
 NetworkToolbox-1.3.0/NetworkToolbox/MD5                           |  147 ++++---
 NetworkToolbox-1.3.0/NetworkToolbox/NAMESPACE                     |   21 -
 NetworkToolbox-1.3.0/NetworkToolbox/NEWS                          |   28 +
 NetworkToolbox-1.3.0/NetworkToolbox/R/LoGo.R                      |    8 
 NetworkToolbox-1.3.0/NetworkToolbox/R/MFCF.R                      |only
 NetworkToolbox-1.3.0/NetworkToolbox/R/NetworkToolbox.R            |    4 
 NetworkToolbox-1.3.0/NetworkToolbox/R/TMFG.R                      |  185 ++++++----
 NetworkToolbox-1.3.0/NetworkToolbox/R/betweenness.R               |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/R/binarize.R                  |    4 
 NetworkToolbox-1.3.0/NetworkToolbox/R/closeness.R                 |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/R/clustcoeff.R                |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/R/comcat.R                    |  123 +++---
 NetworkToolbox-1.3.0/NetworkToolbox/R/comm.close.R                |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/R/comm.eigen.R                |    1 
 NetworkToolbox-1.3.0/NetworkToolbox/R/comm.str.R                  |   54 ++
 NetworkToolbox-1.3.0/NetworkToolbox/R/convert2igraph.R            |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/R/cpm.R                       |only
 NetworkToolbox-1.3.0/NetworkToolbox/R/depend.R                    |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/R/depna.R                     |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/R/desc.R                      |    4 
 NetworkToolbox-1.3.0/NetworkToolbox/R/desc.all.R                  |   28 +
 NetworkToolbox-1.3.0/NetworkToolbox/R/diversity.R                 |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/R/edgerep.R                   |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/R/gain.functions.R            |only
 NetworkToolbox-1.3.0/NetworkToolbox/R/impact.R                    |    3 
 NetworkToolbox-1.3.0/NetworkToolbox/R/kld.R                       |    7 
 NetworkToolbox-1.3.0/NetworkToolbox/R/leverage.R                  |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/R/net.coverage.R              |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/R/node.multidimensional.R     |only
 NetworkToolbox-1.3.0/NetworkToolbox/R/node.redundant.R            |only
 NetworkToolbox-1.3.0/NetworkToolbox/R/pathlengths.R               |    9 
 NetworkToolbox-1.3.0/NetworkToolbox/R/reg.R                       |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/R/rmse.R                      |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/R/rspbc.R                     |   30 +
 NetworkToolbox-1.3.0/NetworkToolbox/R/sim.chordal.R               |only
 NetworkToolbox-1.3.0/NetworkToolbox/R/sim.swn.R                   |   49 +-
 NetworkToolbox-1.3.0/NetworkToolbox/R/smallworldness.R            |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/R/stable.R                    |   24 -
 NetworkToolbox-1.3.0/NetworkToolbox/R/strength.R                  |    9 
 NetworkToolbox-1.3.0/NetworkToolbox/R/zzz.R                       |only
 NetworkToolbox-1.3.0/NetworkToolbox/inst/CITATION                 |   11 
 NetworkToolbox-1.3.0/NetworkToolbox/man/LoGo.Rd                   |    7 
 NetworkToolbox-1.3.0/NetworkToolbox/man/MFCF.Rd                   |only
 NetworkToolbox-1.3.0/NetworkToolbox/man/NetworkToolbox-package.Rd |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/TMFG.Rd                   |   33 +
 NetworkToolbox-1.3.0/NetworkToolbox/man/betweenness.Rd            |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/binarize.Rd               |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/closeness.Rd              |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/clustcoeff.Rd             |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/comcat.Rd                 |   10 
 NetworkToolbox-1.3.0/NetworkToolbox/man/comm.close.Rd             |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/comm.str.Rd               |   29 +
 NetworkToolbox-1.3.0/NetworkToolbox/man/convert2igraph.Rd         |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/cpm.Rd                    |only
 NetworkToolbox-1.3.0/NetworkToolbox/man/depend.Rd                 |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/depna.Rd                  |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/desc.Rd                   |    4 
 NetworkToolbox-1.3.0/NetworkToolbox/man/desc.all.Rd               |    4 
 NetworkToolbox-1.3.0/NetworkToolbox/man/edgerep.Rd                |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/gain.functions.Rd         |only
 NetworkToolbox-1.3.0/NetworkToolbox/man/impact.Rd                 |    3 
 NetworkToolbox-1.3.0/NetworkToolbox/man/kld.Rd                    |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/leverage.Rd               |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/net.coverage.Rd           |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/node.multidimensional.Rd  |only
 NetworkToolbox-1.3.0/NetworkToolbox/man/node.redundant.Rd         |only
 NetworkToolbox-1.3.0/NetworkToolbox/man/reg.Rd                    |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/rmse.Rd                   |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/rspbc.Rd                  |    9 
 NetworkToolbox-1.3.0/NetworkToolbox/man/sim.chordal.Rd            |only
 NetworkToolbox-1.3.0/NetworkToolbox/man/sim.swn.Rd                |   13 
 NetworkToolbox-1.3.0/NetworkToolbox/man/smallworldness.Rd         |    2 
 NetworkToolbox-1.3.0/NetworkToolbox/man/stable.Rd                 |   10 
 NetworkToolbox-1.3.0/NetworkToolbox/man/strength.Rd               |    6 
 87 files changed, 628 insertions(+), 326 deletions(-)

More information about NetworkToolbox at CRAN
Permanent link

Package pagedown updated to version 0.4 with previous version 0.3 dated 2019-07-15

Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript library 'paged.js' to split the content of an HTML document into discrete pages. Each page can have its page size, page numbers, margin boxes, and running headers, etc. Applications of this package include books, letters, reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Romain Lesur [aut, cph] (<https://orcid.org/0000-0002-0721-5595>), Brent Thorne [aut] (<https://orcid.org/0000-0002-1099-3857>), Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>), Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), RStudio, Inc. [cph], Adam Hyde [ctb] (paged.js in resources/js/), Min-Zhong Lu [ctb] (resume.css in resources/css/), Zulko [ctb] (poster-relaxed.css in resources/css/)
Maintainer: Yihui Xie <xie@yihui.name>

Diff between pagedown versions 0.3 dated 2019-07-15 and 0.4 dated 2019-08-21

 DESCRIPTION                                                 |    8 
 MD5                                                         |   24 
 NEWS.md                                                     |    8 
 R/paged.R                                                   |   19 
 README.md                                                   |    4 
 inst/resources/html/jss_paged.html                          |    9 
 inst/resources/html/paged.html                              |   45 
 inst/resources/html/poster-jacobs.html                      |    5 
 inst/resources/html/poster-relaxed.html                     |    5 
 inst/resources/html/thesis.html                             |   45 
 inst/resources/js/config.js                                 |   53 -
 inst/resources/js/hooks.js                                  |  554 ++++++------
 inst/rmarkdown/templates/thesis-paged/skeleton/skeleton.Rmd |   23 
 13 files changed, 434 insertions(+), 368 deletions(-)

More information about pagedown at CRAN
Permanent link

Package circlize updated to version 0.4.7 with previous version 0.4.6 dated 2019-04-03

Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>

Diff between circlize versions 0.4.6 dated 2019-04-03 and 0.4.7 dated 2019-08-21

 DESCRIPTION                          |   10 
 LICENSE                              |    2 
 MD5                                  |   50 +--
 NEWS                                 |   12 
 R/chordDiagram.R                     |  124 ++++---
 R/circos.arrow.R                     |    4 
 R/circos.nested.R                    |   69 ++--
 R/genomic.R                          |  169 +++++++---
 R/genomic_utils.R                    |   26 +
 R/global.R                           |   38 +-
 R/plot.R                             |  555 ++++++++++++++++++-----------------
 R/raster.R                           |    2 
 R/utils.R                            |   74 +++-
 build/vignette.rds                   |binary
 man/circos.dendrogram.rd             |    4 
 man/circos.genomicAxis.rd            |    5 
 man/circos.initializeWithIdeogram.rd |    2 
 man/circos.points.rd                 |    2 
 man/circos.segments.rd               |    2 
 man/circos.text.rd                   |    2 
 man/circos.trackHist.rd              |    2 
 man/circos.trackPlotRegion.rd        |    8 
 man/circos.trackPoints.rd            |    2 
 man/circos.updatePlotRegion.rd       |    2 
 man/read.chromInfo.rd                |    4 
 man/read.cytoband.rd                 |    4 
 26 files changed, 679 insertions(+), 495 deletions(-)

More information about circlize at CRAN
Permanent link

Package shinylogs updated to version 0.1.7 with previous version 0.1.6 dated 2019-07-18

Title: Record Everything that Happens in a 'Shiny' Application
Description: Track and record the use of applications and the user's interactions with 'Shiny' inputs. Allow to save inputs clicked, output generated and eventually errors.
Author: Fanny Meyer [aut], Victor Perrier [aut, cre], Silex Technologies [fnd] (https://www.silex-ip.com), iamkun [cph] (dayjs library), Mozilla [cph] (localForage library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between shinylogs versions 0.1.6 dated 2019-07-18 and 0.1.7 dated 2019-08-21

 DESCRIPTION                             |    6 +++---
 MD5                                     |    6 +++---
 NEWS.md                                 |    6 ++++++
 inst/assets/js/shinylogs-localForage.js |   19 ++++++++++++++++---
 4 files changed, 28 insertions(+), 9 deletions(-)

More information about shinylogs at CRAN
Permanent link

Package ggimage updated to version 0.2.2 with previous version 0.2.1 dated 2019-01-16

Title: Use Image in 'ggplot2'
Description: Supports image files and graphic objects to be visualized in 'ggplot2' graphic system.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

Diff between ggimage versions 0.2.1 dated 2019-01-16 and 0.2.2 dated 2019-08-21

 DESCRIPTION              |    6 
 MD5                      |   90 +++---
 NAMESPACE                |  121 ++++----
 NEWS.md                  |  200 +++++++-------
 R/color_image.R          |   38 +-
 R/draw_key.R             |  128 ++++-----
 R/geom_bgimage.R         |only
 R/geom_emoji.R           |   34 +-
 R/geom_flag.R            |  198 +++++++-------
 R/geom_icon.R            |   54 +--
 R/geom_image.R           |  648 +++++++++++++++++++++++------------------------
 R/geom_phylopic.R        |  148 +++++-----
 R/geom_pokemon.R         |   76 ++---
 R/geom_subview.R         |  188 ++++++-------
 R/geom_twitchemote.R     |   60 ++--
 R/ggbackground.R         |   36 +-
 R/image_read2.R          |   98 +++----
 R/reexport.R             |   14 -
 R/theme.R                |   86 +++---
 README.md                |   94 +++---
 build/vignette.rds       |binary
 inst/doc/ggimage.R       |  176 ++++++------
 inst/doc/ggimage.Rmd     |  274 +++++++++----------
 inst/doc/ggimage.html    |  520 +++++++++++++++++++------------------
 inst/extdata/medals.txt  |   62 ++--
 man/draw_key.Rd          |   44 +--
 man/geom_bgimage.Rd      |only
 man/geom_emoji.Rd        |   62 ++--
 man/geom_flag.Rd         |   62 ++--
 man/geom_icon.Rd         |   62 ++--
 man/geom_image.Rd        |  100 +++----
 man/geom_phylopic.Rd     |   66 ++--
 man/geom_pokemon.Rd      |   62 ++--
 man/geom_subview.Rd      |   66 ++--
 man/geom_twitchemote.Rd  |   62 ++--
 man/geom_worldcup2018.Rd |   62 ++--
 man/ggbackground.Rd      |   48 +--
 man/image_read2.Rd       |   48 +--
 man/list.flag.Rd         |   34 +-
 man/list.icon.Rd         |   34 +-
 man/list.pokemon.Rd      |   34 +-
 man/list.worldcup2018.Rd |   34 +-
 man/phylopic_uid.Rd      |   40 +-
 man/reexports.Rd         |   34 +-
 man/theme_nothing.Rd     |   44 +--
 man/theme_transparent.Rd |   40 +-
 vignettes/ggimage.Rmd    |  274 +++++++++----------
 47 files changed, 2349 insertions(+), 2312 deletions(-)

More information about ggimage at CRAN
Permanent link

Package GENEAclassify updated to version 1.4.18 with previous version 1.4.17 dated 2019-05-14

Title: Segmentation and Classification of Accelerometer Data
Description: Segmentation and classification procedures for data from the 'Activinsights GENEActiv' <https://www.activinsights.com/products/geneactiv/> accelerometer that provides the user with a model to guess behaviour from test data where behaviour is missing. Includes a step counting algorithm, a function to create segmented data with custom features and a function to use recursive partitioning provided in the function rpart() of the 'rpart' package to create classification models.
Author: Chris Campbell [aut], Aimee Gott [aut], Joss Langford [aut], Charles Sweetland [aut, cre], Activinsights Ltd [cph]
Maintainer: Charles Sweetland <charles@sweetland-solutions.co.uk>

Diff between GENEAclassify versions 1.4.17 dated 2019-05-14 and 1.4.18 dated 2019-08-21

 DESCRIPTION                     |    8 +++---
 MD5                             |   28 ++++++++++++------------
 R/classifyGENEA.R               |   13 +++++++----
 R/createGENEAmodel.R            |   28 ++++++++++++++++++------
 R/dataImport.R                  |   46 ++++++++++++++++++++++++++++------------
 R/getGENEAsegments.R            |   31 +++++++++++++++-----------
 R/segmentation.R                |    6 +++--
 build/vignette.rds              |binary
 inst/doc/GENEAclassifyDemo.html |    6 ++++-
 man/GENEAclassify-package.Rd    |    1 
 man/classifyGENEA.Rd            |    6 +++--
 man/createGENEAmodel.Rd         |   15 +++++++++----
 man/dataImport.Rd               |   12 ++++++----
 man/getGENEAsegments.Rd         |   13 +++++++----
 man/segmentation.Rd             |    5 +++-
 15 files changed, 144 insertions(+), 74 deletions(-)

More information about GENEAclassify at CRAN
Permanent link

Package circumplex updated to version 0.3.2 with previous version 0.3.1 dated 2019-05-15

Title: Analysis and Visualization of Circular Data
Description: Tools for analyzing and visualizing circular data, including scoring functions for relevant instruments and a generalization of the bootstrapped structural summary method from Zimmermann & Wright (2017) <doi:10.1177/1073191115621795> and functions for creating publication-ready tables and figures from the results. Future versions will include tools for circular fit and reliability analyses, as well as visualization enhancements.
Author: Jeffrey Girard [aut, cre] (<https://orcid.org/0000-0002-7359-3746>), Johannes Zimmermann [aut] (<https://orcid.org/0000-0001-6975-2356>), Aidan Wright [aut] (<https://orcid.org/0000-0002-2369-0601>)
Maintainer: Jeffrey Girard <me@jmgirard.com>

Diff between circumplex versions 0.3.1 dated 2019-05-15 and 0.3.2 dated 2019-08-21

 DESCRIPTION                                |    7 -
 MD5                                        |   40 +++----
 NAMESPACE                                  |    7 -
 NEWS.md                                    |  154 ++++++++++++++++-------------
 R/assertions.R                             |    7 -
 R/circumplex.R                             |    3 
 R/instrument_data.R                        |   10 +
 R/instrument_oop.R                         |   13 +-
 R/ssm_analysis.R                           |  138 ++++++++++++-------------
 R/ssm_bootstrap.R                          |   41 ++++---
 R/ssm_visualization.R                      |   18 +--
 README.md                                  |    3 
 build/vignette.rds                         |binary
 data/iitc.rda                              |only
 inst/doc/intermediate-ssm-analysis.html    |    6 -
 inst/doc/introduction-to-ssm-analysis.html |    6 -
 inst/doc/using-instruments.html            |   18 ++-
 man/iitc.Rd                                |only
 man/ssm_analyze.Rd                         |    4 
 tests/testthat/test-assertions.R           |   25 ++++
 tests/testthat/test-instrument_oop.R       |    2 
 tests/testthat/test-ssm_analysis.R         |   14 --
 22 files changed, 292 insertions(+), 224 deletions(-)

More information about circumplex at CRAN
Permanent link

Package lumberjack updated to version 1.0.2 with previous version 0.3.0 dated 2018-07-20

Title: Track Changes in Data
Description: A framework that allows for easy logging of changes in data. Main features: start tracking changes by adding a single line of code to an existing script. Track changes in multiple datasets, using multiple loggers. Add custom-built loggers or use loggers offered by other packages.
Author: Mark van der Loo [aut, cre] (<https://orcid.org/0000-0002-9807-4686>)
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>

Diff between lumberjack versions 0.3.0 dated 2018-07-20 and 1.0.2 dated 2019-08-21

 lumberjack-0.3.0/lumberjack/inst/doc/extending.R                           |only
 lumberjack-0.3.0/lumberjack/inst/doc/extending.Rmd                         |only
 lumberjack-0.3.0/lumberjack/inst/doc/extending.html                        |only
 lumberjack-0.3.0/lumberjack/inst/doc/intro.R                               |only
 lumberjack-0.3.0/lumberjack/inst/doc/intro.Rmd                             |only
 lumberjack-0.3.0/lumberjack/inst/doc/intro.html                            |only
 lumberjack-0.3.0/lumberjack/tests/testthat                                 |only
 lumberjack-0.3.0/lumberjack/tests/testthat.R                               |only
 lumberjack-0.3.0/lumberjack/vignettes/extending.Rmd                        |only
 lumberjack-0.3.0/lumberjack/vignettes/intro.Rmd                            |only
 lumberjack-1.0.2/lumberjack/DESCRIPTION                                    |   24 -
 lumberjack-1.0.2/lumberjack/MD5                                            |   77 +--
 lumberjack-1.0.2/lumberjack/NAMESPACE                                      |    1 
 lumberjack-1.0.2/lumberjack/NEWS                                           |   14 
 lumberjack-1.0.2/lumberjack/R/cellwise.R                                   |   49 +-
 lumberjack-1.0.2/lumberjack/R/expression_logger.R                          |   63 +-
 lumberjack-1.0.2/lumberjack/R/filedump.R                                   |   45 +
 lumberjack-1.0.2/lumberjack/R/lumberjack.R                                 |  234 +++++++---
 lumberjack-1.0.2/lumberjack/R/run.R                                        |only
 lumberjack-1.0.2/lumberjack/R/simple.R                                     |   25 -
 lumberjack-1.0.2/lumberjack/README.md                                      |only
 lumberjack-1.0.2/lumberjack/build/vignette.rds                             |binary
 lumberjack-1.0.2/lumberjack/inst/doc/using_lumberjack.R                    |only
 lumberjack-1.0.2/lumberjack/inst/doc/using_lumberjack.Rnw                  |only
 lumberjack-1.0.2/lumberjack/inst/doc/using_lumberjack.pdf                  |only
 lumberjack-1.0.2/lumberjack/inst/tinytest                                  |only
 lumberjack-1.0.2/lumberjack/man/cellwise.Rd                                |   41 +
 lumberjack-1.0.2/lumberjack/man/dump_log.Rd                                |   36 +
 lumberjack-1.0.2/lumberjack/man/expression_logger.Rd                       |   31 -
 lumberjack-1.0.2/lumberjack/man/filedump.Rd                                |   34 +
 lumberjack-1.0.2/lumberjack/man/get_log.Rd                                 |   13 
 lumberjack-1.0.2/lumberjack/man/grapes-greater-than-greater-than-grapes.Rd |   11 
 lumberjack-1.0.2/lumberjack/man/lumberjack.Rd                              |   29 -
 lumberjack-1.0.2/lumberjack/man/run_file.Rd                                |only
 lumberjack-1.0.2/lumberjack/man/simple.Rd                                  |   18 
 lumberjack-1.0.2/lumberjack/man/start_log.Rd                               |   45 +
 lumberjack-1.0.2/lumberjack/man/stop_log.Rd                                |   27 +
 lumberjack-1.0.2/lumberjack/tests/tinytest.R                               |only
 lumberjack-1.0.2/lumberjack/vignettes/datastep2.pdf                        |only
 lumberjack-1.0.2/lumberjack/vignettes/extending.html                       |only
 lumberjack-1.0.2/lumberjack/vignettes/process.R                            |only
 lumberjack-1.0.2/lumberjack/vignettes/using_lumberjack.Rnw                 |only
 42 files changed, 571 insertions(+), 246 deletions(-)

More information about lumberjack at CRAN
Permanent link

Package av updated to version 0.3 with previous version 0.2 dated 2018-09-30

Title: Working with Audio and Video
Description: Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with audio and video in R. Generate high quality videos files by capturing images from the R graphics device combined with custom audio stream. Also offers tools to convert between countless audio / video formats, or convert images to video and vice versa. 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 0.2 dated 2018-09-30 and 0.3 dated 2019-08-21

 av-0.2/av/R/util.R                    |only
 av-0.2/av/man/av_encode_video.Rd      |only
 av-0.2/av/src/util.c                  |only
 av-0.3/av/DESCRIPTION                 |   23 -
 av-0.3/av/MD5                         |   36 +-
 av-0.3/av/NAMESPACE                   |    7 
 av-0.3/av/NEWS                        |only
 av-0.3/av/R/capture.R                 |    2 
 av-0.3/av/R/demo.R                    |    4 
 av-0.3/av/R/encode.R                  |   74 +++--
 av-0.3/av/R/images.R                  |only
 av-0.3/av/R/info.R                    |    1 
 av-0.3/av/R/logging.R                 |    5 
 av-0.3/av/configure                   |    2 
 av-0.3/av/man/av_video_images.Rd      |only
 av-0.3/av/man/capturing.Rd            |    6 
 av-0.3/av/man/demo.Rd                 |    2 
 av-0.3/av/man/encoding.Rd             |only
 av-0.3/av/man/info.Rd                 |    1 
 av-0.3/av/src/init.c                  |   28 +-
 av-0.3/av/src/video.c                 |  476 ++++++++++++++++++++--------------
 av-0.3/av/tests/testthat/test-audio.R |only
 av-0.3/av/tests/testthat/test-video.R |   53 +++
 23 files changed, 453 insertions(+), 267 deletions(-)

More information about av at CRAN
Permanent link

Package ludic updated to version 0.1.7 with previous version 0.1.6 dated 2018-01-28

Title: Linkage Using Diagnosis Codes
Description: Probabilistic record linkage without direct identifiers using only diagnosis codes. Method is detailed in: Hejblum, Weber, Liao, Palmer, Churchill, Szolovits, Murphy, Kohane & Cai (2019) <doi: 10.1038/sdata.2018.298>.
Author: Boris P Hejblum [aut, cre], Tianxi Cai [aut]
Maintainer: Boris P Hejblum <boris.hejblum@u-bordeaux.fr>

Diff between ludic versions 0.1.6 dated 2018-01-28 and 0.1.7 dated 2019-08-21

 DESCRIPTION            |   27 ++++++++++++++++++---------
 MD5                    |   42 ++++++++++++++++++++++--------------------
 NAMESPACE              |    7 +++++++
 NEWS.md                |    7 +++++++
 R/RA.R                 |    2 +-
 R/RcppExports.R        |   30 +++++++++++++++---------------
 R/em_winkler.R         |    8 +++++---
 R/ludic-package.R      |    4 ++--
 R/recordLink.R         |    2 +-
 R/test_combine.R       |only
 README.md              |   42 ++++++++++++++++++++++++++++--------------
 inst/CITATION          |   23 ++++++++++++-----------
 man/RA.Rd              |    2 +-
 man/agree_C.Rd         |    3 ---
 man/em_winkler.Rd      |    8 +++-----
 man/loglikC_bin.Rd     |    3 ---
 man/ludic-package.Rd   |    4 ++--
 man/matchingScore_C.Rd |    2 --
 man/recordLink.Rd      |    9 +++++----
 man/test_combine.Rd    |only
 src/Makevars           |   18 +++++++++++++-----
 src/Makevars.win       |   14 +++++++++++++-
 src/RcppExports.cpp    |   26 +++++++++++++-------------
 23 files changed, 168 insertions(+), 115 deletions(-)

More information about ludic at CRAN
Permanent link

Package bookdown updated to version 0.13 with previous version 0.12 dated 2019-07-11

Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), JJ Allaire [ctb], Albert Kim [ctb], Alessandro Samuel-Rosa [ctb], Andrzej Oles [ctb], Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), Aust Frederik [ctb] (<https://orcid.org/0000-0003-4900-788X>), Bastiaan Quast [ctb], Ben Marwick [ctb], Chester Ismay [ctb], Christophe Dervieux [ctb], Clifton Franklund [ctb], Daniel Emaasit [ctb], David Shuman [ctb], Dean Attali [ctb], Drew Tyre [ctb], Ellis Valentiner [ctb], Frans van Dunne [ctb], Hadley Wickham [ctb], Jeff Allen [ctb], Jennifer Bryan [ctb], Jonathan McPhers [ctb], Junwen Huang [ctb], Kevin Cheung [ctb], Kevin Ushey [ctb], Kim Seonghyun [ctb], Kirill Muller [ctb], Luciano Selzer [ctb], Matthew Lincoln [ctb], Maximilian Held [ctb], Michael Sachs [ctb], Michal Bojanowski [ctb], Noam Ross [ctb], Peter Hickey [ctb], Sahir Bhatnagar [ctb], Steve Simpson [ctb], Thierry Onkelinx [ctb] (<https://orcid.org/0000-0001-8804-4216>), Vincent Fulco [ctb], Yixuan Qiu [ctb], Zhuoer Dong [ctb], RStudio Inc [cph], Bartek Szopka [ctb] (The jQuery Highlight plugin), jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/resources/AUTHORS), MathQuill contributors [ctb] (The MathQuill library; authors listed in inst/resources/AUTHORS), FriendCode Inc [cph, ctb] (The gitbook style, with modifications)
Maintainer: Yihui Xie <xie@yihui.name>

Diff between bookdown versions 0.12 dated 2019-07-11 and 0.13 dated 2019-08-21

 DESCRIPTION                 |    6 +++---
 MD5                         |   16 ++++++++--------
 NAMESPACE                   |    3 +++
 R/gitbook.R                 |    4 ++--
 R/html.R                    |    4 +++-
 R/word.R                    |   27 ++++++++++++++++++++++++---
 inst/templates/gitbook.html |    5 +++--
 man/bookdown-package.Rd     |    1 +
 man/html_document2.Rd       |   21 ++++++++++++++++-----
 9 files changed, 63 insertions(+), 24 deletions(-)

More information about bookdown at CRAN
Permanent link

Package sys updated to version 3.3 with previous version 3.2 dated 2019-04-23

Title: Powerful and Reliable Tools for Running System Commands in R
Description: Drop-in replacements for the base system2() function with fine control and consistent behavior across platforms. Supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. Arguments on Windows automatically get encoded and quoted to work on different locales.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), Gábor Csárdi [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between sys versions 3.2 dated 2019-04-23 and 3.3 dated 2019-08-21

 DESCRIPTION                    |    8 ++++----
 MD5                            |   10 +++++-----
 NEWS                           |    4 ++++
 R/exec.R                       |    3 +++
 tests/testthat/test-encoding.R |    8 ++++++--
 tests/testthat/test-timeout.R  |    6 ++++--
 6 files changed, 26 insertions(+), 13 deletions(-)

More information about sys at CRAN
Permanent link

Package geometry updated to version 0.4.3 with previous version 0.4.2 dated 2019-07-12

Title: Mesh Generation and Surface Tessellation
Description: Makes the 'Qhull' library <http://www.qhull.org> available in R, in a similar manner as in Octave and MATLAB. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2D, 3D, 4D, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this.
Author: Jean-Romain Roussel [cph, ctb] (wrote tsearch function with QuadTrees), C. B. Barber [cph], Kai Habel [cph, aut], Raoul Grasman [cph, aut], Robert B. Gramacy [cph, aut], Pavlo Mozharovskyi [cph, aut], David C. Sterratt [cph, aut, cre] (<https://orcid.org/0000-0001-9092-9099>)
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>

Diff between geometry versions 0.4.2 dated 2019-07-12 and 0.4.3 dated 2019-08-21

 DESCRIPTION                     |    8 +--
 MD5                             |   40 ++++++++---------
 NEWS                            |   39 ++++++++++++++++
 R/convhulln.R                   |   14 ++----
 R/delaunayn.R                   |   12 +----
 R/halfspacen.R                  |   12 +----
 inst/doc/qhull-eg.pdf           |binary
 src/QuadTree.cpp                |   92 +++++++++++++++++++---------------------
 src/QuadTree.h                  |   20 ++++----
 src/Rconvhulln.c                |    8 +--
 src/Rdelaunayn.c                |   10 ++--
 src/Rgeometry.c                 |   17 ++++---
 src/Rgeometry.h                 |    5 +-
 src/Rhalfspacen.c               |    8 +--
 src/Rtsearch.cpp                |   10 ++--
 src/Rtsearchn.c                 |    5 +-
 src/geometry_init.c             |   12 ++---
 tests/testthat/test-convhulln.R |    3 -
 tests/testthat/test-delaunayn.R |    2 
 tests/testthat/test-tsearch.R   |   41 +++++++++++++++++
 tests/testthat/test-tsearchn.R  |    2 
 21 files changed, 218 insertions(+), 142 deletions(-)

More information about geometry at CRAN
Permanent link

Package GD updated to version 1.7 with previous version 1.6 dated 2018-07-02

Title: Geographical Detectors
Description: Geographical detectors for measuring spatial stratified heterogeneity, as described in Jinfeng Wang (2010) <doi:10.1080/13658810802443457> and Jinfeng Wang (2016) <doi:10.1016/j.ecolind.2016.02.052>. Includes the optimal discretization of continuous data, four primary functions of geographical detectors, comparison of size effects of spatial unit and the visualizations of results. The descriptions of the package, methods and case datasets refer to the citation information below.
Author: Yongze Song [aut, cre] (<https://orcid.org/0000-0003-3420-9622>)
Maintainer: Yongze Song <yongze.song@postgrad.curtin.edu.au>

Diff between GD versions 1.6 dated 2018-07-02 and 1.7 dated 2019-08-21

 GD-1.6/GD/R/citv.R         |only
 GD-1.6/GD/R/stra.R         |only
 GD-1.6/GD/R/stra2v.R       |only
 GD-1.6/GD/man/citv.Rd      |only
 GD-1.6/GD/man/stra.Rd      |only
 GD-1.6/GD/man/stra2v.Rd    |only
 GD-1.7/GD/DESCRIPTION      |   10 -
 GD-1.7/GD/INDEX            |    3 
 GD-1.7/GD/MD5              |   60 +++++------
 GD-1.7/GD/NAMESPACE        |   40 ++-----
 GD-1.7/GD/R/disc.R         |  129 +++++++++++++++++--------
 GD-1.7/GD/R/gd.R           |  126 ++++++++++++------------
 GD-1.7/GD/R/gdeco.R        |  126 +++++++++++-------------
 GD-1.7/GD/R/gdinteract.R   |  139 +++++++++++++++------------
 GD-1.7/GD/R/gdm.R          |  109 ++++++++-------------
 GD-1.7/GD/R/gdrisk.R       |  184 ++++++++++++++++--------------------
 GD-1.7/GD/R/optidisc.R     |  228 ++++++++++++++++++++++-----------------------
 GD-1.7/GD/R/riskmean.R     |   97 +++++++------------
 GD-1.7/GD/R/sesu.R         |   80 +++++++--------
 GD-1.7/GD/data/ndvi_10.rda |binary
 GD-1.7/GD/data/ndvi_20.rda |binary
 GD-1.7/GD/data/ndvi_30.rda |binary
 GD-1.7/GD/data/ndvi_40.rda |binary
 GD-1.7/GD/data/ndvi_5.rda  |binary
 GD-1.7/GD/data/ndvi_50.rda |binary
 GD-1.7/GD/data/road_GD.rda |binary
 GD-1.7/GD/inst/doc/GD.R    |   73 ++++++--------
 GD-1.7/GD/inst/doc/GD.Rmd  |   73 ++++++--------
 GD-1.7/GD/inst/doc/GD.html |  109 +++++++++------------
 GD-1.7/GD/man/gd.Rd        |   13 +-
 GD-1.7/GD/man/gdm.Rd       |   15 --
 GD-1.7/GD/man/optidisc.Rd  |   13 +-
 GD-1.7/GD/man/sesu.Rd      |   17 ---
 GD-1.7/GD/vignettes/GD.Rmd |   73 ++++++--------
 34 files changed, 816 insertions(+), 901 deletions(-)

More information about GD at CRAN
Permanent link

Package AzureAuth updated to version 1.2.0 with previous version 1.1.1 dated 2019-06-07

Title: Authentication Services for Azure Active Directory
Description: Provides Azure Active Directory (AAD) authentication functionality for R users of Microsoft's 'Azure' cloud <https://azure.microsoft.com/>. Use this package to obtain 'OAuth' 2.0 tokens for services including Azure Resource Manager, Azure Storage and others. It supports both AAD v1.0 and v2.0, as well as multiple authentication methods, including device code and resource owner grant. Tokens are cached in a user-specific directory obtained using the 'rappdirs' package. The interface is based on the 'OAuth' framework in the 'httr' package, but customised and streamlined for Azure. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre], httr development team [ctb] (Original OAuth listener code), Scott Holden [ctb] (Advice on AAD authentication), Chris Stone [ctb] (Advice on AAD authentication), Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>

Diff between AzureAuth versions 1.1.1 dated 2019-06-07 and 1.2.0 dated 2019-08-21

 AzureAuth-1.1.1/AzureAuth/man/decode_jwt.Rd                     |only
 AzureAuth-1.1.1/AzureAuth/tests/testthat/test01_v1_token.R      |only
 AzureAuth-1.1.1/AzureAuth/tests/testthat/test02_v2_token.R      |only
 AzureAuth-1.2.0/AzureAuth/DESCRIPTION                           |    8 
 AzureAuth-1.2.0/AzureAuth/MD5                                   |   55 +-
 AzureAuth-1.2.0/AzureAuth/NAMESPACE                             |   17 
 AzureAuth-1.2.0/AzureAuth/NEWS.md                               |   10 
 AzureAuth-1.2.0/AzureAuth/R/AzureToken.R                        |  202 +++-------
 AzureAuth-1.2.0/AzureAuth/R/cert_creds.R                        |    4 
 AzureAuth-1.2.0/AzureAuth/R/classes.R                           |only
 AzureAuth-1.2.0/AzureAuth/R/flow_init.R                         |only
 AzureAuth-1.2.0/AzureAuth/R/format.R                            |    2 
 AzureAuth-1.2.0/AzureAuth/R/initfuncs.R                         |   94 ----
 AzureAuth-1.2.0/AzureAuth/R/jwt.R                               |only
 AzureAuth-1.2.0/AzureAuth/R/managed_token.R                     |    7 
 AzureAuth-1.2.0/AzureAuth/R/normalize.R                         |   16 
 AzureAuth-1.2.0/AzureAuth/R/token.R                             |  175 ++++----
 AzureAuth-1.2.0/AzureAuth/R/utils.R                             |  128 ++----
 AzureAuth-1.2.0/AzureAuth/README.md                             |   31 +
 AzureAuth-1.2.0/AzureAuth/build/vignette.rds                    |binary
 AzureAuth-1.2.0/AzureAuth/inst/doc/shiny.Rmd                    |only
 AzureAuth-1.2.0/AzureAuth/inst/doc/shiny.html                   |only
 AzureAuth-1.2.0/AzureAuth/inst/doc/token.Rmd                    |   18 
 AzureAuth-1.2.0/AzureAuth/inst/doc/token.html                   |   30 +
 AzureAuth-1.2.0/AzureAuth/man/AzureToken.Rd                     |   26 -
 AzureAuth-1.2.0/AzureAuth/man/authorization.Rd                  |only
 AzureAuth-1.2.0/AzureAuth/man/cert_assertion.Rd                 |    2 
 AzureAuth-1.2.0/AzureAuth/man/figures                           |only
 AzureAuth-1.2.0/AzureAuth/man/get_azure_token.Rd                |   70 ++-
 AzureAuth-1.2.0/AzureAuth/man/jwt.Rd                            |only
 AzureAuth-1.2.0/AzureAuth/tests/testthat/test02_jwt.R           |only
 AzureAuth-1.2.0/AzureAuth/tests/testthat/test10_v1_token.R      |only
 AzureAuth-1.2.0/AzureAuth/tests/testthat/test11_v1_token_misc.R |only
 AzureAuth-1.2.0/AzureAuth/tests/testthat/test20_v2_token.R      |only
 AzureAuth-1.2.0/AzureAuth/tests/testthat/test21_v2_token_misc.R |only
 AzureAuth-1.2.0/AzureAuth/vignettes/shiny.Rmd                   |only
 AzureAuth-1.2.0/AzureAuth/vignettes/token.Rmd                   |   18 
 37 files changed, 459 insertions(+), 454 deletions(-)

More information about AzureAuth at CRAN
Permanent link

Package denvax updated to version 0.1.1 with previous version 0.1.0 dated 2019-07-19

Title: Simple Dengue Test and Vaccinate Cost Thresholds
Description: Provides the mathematical model described by "Serostatus Testing & Dengue Vaccine Cost-Benefit Thresholds" in <doi:10.1098/rsif.2019.0234>. Using the functions in the package, that analysis can be repeated using sample life histories, either synthesized from local seroprevalence data using other functions in this package (as in the manuscript) or from some other source. The package provides a vignette which walks through the analysis in the publication, as well as a function to generate a project skeleton for such an analysis.
Author: Carl A. B. Pearson [aut, cre] (<https://orcid.org/0000-0003-0701-7860>), Kaja M. Abbas [aut] (<https://orcid.org/0000-0003-0563-1576>), Samuel Clifford [aut] (<https://orcid.org/0000-0002-3774-3882>), Stefan Flasche [aut] (<https://orcid.org/0000-0002-5808-2606>), Thomas J. Hladish [aut] (<https://orcid.org/0000-0003-1819-6235>)
Maintainer: Carl A. B. Pearson <carl.pearson@lshtm.ac.uk>

Diff between denvax versions 0.1.0 dated 2019-07-19 and 0.1.1 dated 2019-08-21

 DESCRIPTION                      |   25 ++++++++++++++++++-------
 MD5                              |   20 ++++++++++----------
 R/main.R                         |    4 ++--
 inst/doc/published-analysis.Rmd  |    2 +-
 inst/doc/published-analysis.html |    2 +-
 inst/extdata/pub/Makefile        |    8 ++++----
 inst/extdata/pub/Rplots.pdf      |binary
 inst/extdata/pub/fig-ntests.R    |   14 +++++++++++++-
 man/denvax.Rd                    |    2 +-
 man/nPxA.Rd                      |    2 +-
 vignettes/published-analysis.Rmd |    2 +-
 11 files changed, 52 insertions(+), 29 deletions(-)

More information about denvax at CRAN
Permanent link

Package billboarder updated to version 0.2.7 with previous version 0.2.6 dated 2019-05-07

Title: Create Interactive Chart with the JavaScript 'Billboard' Library
Description: Provides an 'htmlwidgets' interface to 'billboard.js', a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts. All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in 'shiny' apps.
Author: Victor Perrier [aut, cre], Fanny Meyer [aut], NAVER Corp [cph] (billboard library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between billboarder versions 0.2.6 dated 2019-05-07 and 0.2.7 dated 2019-08-21

 billboarder-0.2.6/billboarder/inst/htmlwidgets/lib/billboard-1.6  |only
 billboarder-0.2.6/billboarder/inst/htmlwidgets/lib/billboard-1.7  |only
 billboarder-0.2.6/billboarder/inst/htmlwidgets/lib/billboard-1.8  |only
 billboarder-0.2.7/billboarder/DESCRIPTION                         |    6 
 billboarder-0.2.7/billboarder/MD5                                 |   64 +-
 billboarder-0.2.7/billboarder/NAMESPACE                           |    1 
 billboarder-0.2.7/billboarder/NEWS.md                             |   12 
 billboarder-0.2.7/billboarder/R/bauge.R                           |   11 
 billboarder-0.2.7/billboarder/R/bb_helpers.R                      |  133 +---
 billboarder-0.2.7/billboarder/R/bb_utils.R                        |   15 
 billboarder-0.2.7/billboarder/R/billboarder-package.R             |    6 
 billboarder-0.2.7/billboarder/R/billboarder.R                     |   43 -
 billboarder-0.2.7/billboarder/R/theme.R                           |only
 billboarder-0.2.7/billboarder/build/vignette.rds                  |binary
 billboarder-0.2.7/billboarder/inst/doc/billboarder-intro.html     |  283 +++++-----
 billboarder-0.2.7/billboarder/inst/doc/billboarder-mapping.html   |  114 ++--
 billboarder-0.2.7/billboarder/inst/doc/billboarder-options.html   |  154 ++---
 billboarder-0.2.7/billboarder/inst/doc/billboarder.R              |    3 
 billboarder-0.2.7/billboarder/inst/doc/billboarder.Rmd            |    3 
 billboarder-0.2.7/billboarder/inst/doc/billboarder.html           |   98 +--
 billboarder-0.2.7/billboarder/inst/htmlwidgets/bauge.yaml         |    4 
 billboarder-0.2.7/billboarder/inst/htmlwidgets/billboarder.js     |   19 
 billboarder-0.2.7/billboarder/inst/htmlwidgets/billboarder.yaml   |    4 
 billboarder-0.2.7/billboarder/inst/htmlwidgets/lib/billboard-1.10 |only
 billboarder-0.2.7/billboarder/inst/htmlwidgets/lib/billboard-1.9  |only
 billboarder-0.2.7/billboarder/man/bb_bubble.Rd                    |   15 
 billboarder-0.2.7/billboarder/man/bb_scatterplot.Rd               |    9 
 billboarder-0.2.7/billboarder/man/billboarder-exports.Rd          |    1 
 billboarder-0.2.7/billboarder/man/set_theme.Rd                    |    2 
 billboarder-0.2.7/billboarder/vignettes/billboarder.Rmd           |    3 
 30 files changed, 464 insertions(+), 539 deletions(-)

More information about billboarder at CRAN
Permanent link

Package xfun updated to version 0.9 with previous version 0.8 dated 2019-06-25

Title: Miscellaneous Functions by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>), Daijiang Li [ctb], Xianying Tan [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between xfun versions 0.8 dated 2019-06-25 and 0.9 dated 2019-08-21

 DESCRIPTION        |    6 +++---
 MD5                |   15 ++++++++-------
 NAMESPACE          |    1 +
 NEWS.md            |    6 ++++++
 R/paths.R          |   40 ++++++++++++++++++++++++++++++++++++++++
 R/revcheck.R       |    2 +-
 build/vignette.rds |binary
 inst/doc/xfun.html |   27 +++++++--------------------
 man/rename_seq.Rd  |only
 9 files changed, 66 insertions(+), 31 deletions(-)

More information about xfun at CRAN
Permanent link

Package webutils updated to version 1.0 with previous version 0.6 dated 2017-06-23

Title: Utility Functions for Developing Web Applications
Description: Parses http request data in application/json, multipart/form-data, or application/x-www-form-urlencoded format. Includes example of hosting and parsing html form data in R using either 'httpuv' or 'Rhttpd'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

Diff between webutils versions 0.6 dated 2017-06-23 and 1.0 dated 2019-08-21

 DESCRIPTION                |   15 ++++++++-------
 MD5                        |   12 ++++++------
 NEWS                       |    5 +++++
 R/get_boundary.R           |    4 ++--
 man/demo_httpuv.Rd         |    1 +
 man/demo_rhttpd.Rd         |    1 +
 tests/testthat/test-echo.R |   12 ++++++++----
 7 files changed, 31 insertions(+), 19 deletions(-)

More information about webutils at CRAN
Permanent link

Package umap updated to version 0.2.3.1 with previous version 0.2.3 dated 2019-08-19

Title: Uniform Manifold Approximation and Projection
Description: Uniform manifold approximation and projection is a technique for dimension reduction. The algorithm was described by McInnes and Healy (2018) in <arXiv:1802.03426>. This package provides an interface for two implementations. One is written from scratch, including components for nearest-neighbor search and for embedding. The second implementation is a wrapper for 'python' package 'umap-learn' (requires separate installation, see vignette for more details).
Author: Tomasz Konopka [aut, cre]
Maintainer: Tomasz Konopka <tokonopka@gmail.com>

Diff between umap versions 0.2.3 dated 2019-08-19 and 0.2.3.1 dated 2019-08-21

 DESCRIPTION                 |    6 +++---
 MD5                         |   10 +++++-----
 inst/doc/umap.html          |    4 ++--
 inst/doc/umap_learn.html    |    2 +-
 tests/testthat/synthetic.R  |    3 +--
 tests/testthat/test_naive.R |   43 +++++++++++++++++++++++++++----------------
 6 files changed, 39 insertions(+), 29 deletions(-)

More information about umap at CRAN
Permanent link

Package gdalcubes updated to version 0.2.1 with previous version 0.2.0 dated 2019-08-08

Title: Earth Observation Data Cubes from Satellite Image Collections
Description: Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time, applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values, exporting data cubes as 'netCDF' or 'GeoTIFF' files, and plotting. The package implements lazy evaluation and multithreading. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries. See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Author: Marius Appel [aut, cre] (<https://orcid.org/0000-0001-5281-3896>), Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>), Roger Bivand [ctb], Lewis Van Winkle [cph], Ole Christian Eidheim [cph], Niels Lohmann [cph], Howard Hinnant [cph], Adrian Colomitchi [cph], Florian Dang [cph], Paul Thompson [cph], Tomasz Kamiński [cph]
Maintainer: Marius Appel <marius.appel@uni-muenster.de>

Diff between gdalcubes versions 0.2.0 dated 2019-08-08 and 0.2.1 dated 2019-08-21

 DESCRIPTION                                    |    8 
 MD5                                            |   19 -
 NEWS.md                                        |    7 
 inst/doc/MODIS.html                            |  355 +++++++++++++++++++------
 inst/formats/PlanetScope_3B_AnalyticMS_SR.json |only
 src/gdalcubes/src/build_info.h                 |    4 
 src/gdalcubes/src/cube.cpp                     |   10 
 src/gdalcubes/src/cube.h                       |   16 -
 src/gdalcubes/src/image_collection_cube.cpp    |   58 +---
 src/gdalcubes/src/image_collection_ops.cpp     |    1 
 src/gdalcubes/src/progress.h                   |    2 
 11 files changed, 333 insertions(+), 147 deletions(-)

More information about gdalcubes at CRAN
Permanent link

Package spANOVA updated to version 0.99.1 with previous version 0.99.0 dated 2019-07-02

Title: Spatial Analysis of Field Trials Experiments using Geostatistics and Spatial Autoregressive Model
Description: Perform analysis of variance when the experimental units are spatially correlated. There are two methods to deal with spatial dependence: Spatial autoregressive models (see Rossoni, D. F., & Lima, R. R. (2019) <doi:10.28951/rbb.v37i2.388>) and geostatistics (see Pontes, J. M., & Oliveira, M. S. D. (2004) <doi:10.1590/S1413-70542004000100018>). For both methods, there are three multicomparison procedure available: Tukey, multivariate T, and Scott-Knott.
Author: Lucas Roberto de Castro, Renato Ribeiro de Lima, Diogo Francisco Rossoni, Cristina Henriques Nogueira
Maintainer: Lucas Roberto de Castro <lrcastro@estudante.ufla.br>

Diff between spANOVA versions 0.99.0 dated 2019-07-02 and 0.99.1 dated 2019-08-21

 DESCRIPTION                    |   12 
 MD5                            |   43 +--
 NAMESPACE                      |    4 
 NEWS.md                        |only
 R/aovGeo.R                     |   20 -
 R/aovSar.crd.R                 |    9 
 R/aovSar.gen.R                 |  506 ++++++++++++++++++------------------
 R/aovSar.rcbd.R                |  564 ++++++++++++++++++++---------------------
 R/spANOVAapp.R                 |    2 
 R/spMVT.R                      |    2 
 R/spScottKnott.R               |    2 
 R/spTukey.R                    |   41 +-
 README.md                      |   12 
 inst/shiny/spANOVAapp/global.R |    2 
 inst/shiny/spANOVAapp/server.R |    4 
 inst/shiny/spANOVAapp/ui.R     |    4 
 man/aovGeo.Rd                  |    4 
 man/aovSar.crd.Rd              |    9 
 man/aovSar.gen.Rd              |    4 
 man/aovSar.rcbd.Rd             |    4 
 man/spMVT.Rd                   |    2 
 man/spScottKnott.Rd            |    2 
 man/spTukey.Rd                 |    9 
 23 files changed, 632 insertions(+), 629 deletions(-)

More information about spANOVA at CRAN
Permanent link

Package qs updated to version 0.18.3 with previous version 0.17.3 dated 2019-07-08

Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd and lz4 code), Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled zstd code), Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled code), Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd bundled code), Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled code), Romain Francois [ctb, cph] (Derived example/tutorials for Alt-Rep structures), Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc library)
Maintainer: Travers Ching <traversc@gmail.com>

Diff between qs versions 0.17.3 dated 2019-07-08 and 0.18.3 dated 2019-08-21

 qs-0.17.3/qs/src/qs_inspect.h                |only
 qs-0.18.3/qs/ChangeLog                       |   16 
 qs-0.18.3/qs/DESCRIPTION                     |   13 
 qs-0.18.3/qs/LICENSE                         |  844 +++++----------------------
 qs-0.18.3/qs/MD5                             |   65 +-
 qs-0.18.3/qs/NAMESPACE                       |   25 
 qs-0.18.3/qs/R/RcppExports.R                 |   74 ++
 qs-0.18.3/qs/R/help_files.R                  |  151 ++++
 qs-0.18.3/qs/R/zzz.R                         |only
 qs-0.18.3/qs/README.md                       |   13 
 qs-0.18.3/qs/build/vignette.rds              |binary
 qs-0.18.3/qs/configure                       |   14 
 qs-0.18.3/qs/data/starnames.rda              |binary
 qs-0.18.3/qs/inst/doc/vignette.R             |    8 
 qs-0.18.3/qs/inst/doc/vignette.html          |   86 +-
 qs-0.18.3/qs/inst/doc/vignette.rmd           |   10 
 qs-0.18.3/qs/man/convertToAlt.Rd             |    3 
 qs-0.18.3/qs/man/qdeserialize.Rd             |only
 qs-0.18.3/qs/man/qread.Rd                    |    4 
 qs-0.18.3/qs/man/qread_fd.Rd                 |only
 qs-0.18.3/qs/man/qread_handle.Rd             |only
 qs-0.18.3/qs/man/qread_ptr.Rd                |only
 qs-0.18.3/qs/man/qsave.Rd                    |    7 
 qs-0.18.3/qs/man/qsave_fd.Rd                 |only
 qs-0.18.3/qs/man/qsave_handle.Rd             |only
 qs-0.18.3/qs/man/qserialize.Rd               |only
 qs-0.18.3/qs/src/Makevars.in                 |    2 
 qs-0.18.3/qs/src/Makevars.win                |    2 
 qs-0.18.3/qs/src/RcppExports.cpp             |  254 +++++++-
 qs-0.18.3/qs/src/qs_common.h                 |  668 ++++++++++++++++++---
 qs-0.18.3/qs/src/qs_deserialization.h        |   40 -
 qs-0.18.3/qs/src/qs_deserialization_stream.h |  350 ++++++++---
 qs-0.18.3/qs/src/qs_functions.cpp            |  625 ++++++++++++++++---
 qs-0.18.3/qs/src/qs_mt_deserialization.h     |   17 
 qs-0.18.3/qs/src/qs_mt_serialization.h       |   14 
 qs-0.18.3/qs/src/qs_serialization.h          |   24 
 qs-0.18.3/qs/src/qs_serialization_stream.h   |   66 +-
 qs-0.18.3/qs/vignettes/vignette.rmd          |   10 
 38 files changed, 2246 insertions(+), 1159 deletions(-)

More information about qs at CRAN
Permanent link

Package durmod updated to version 1.1-2 with previous version 1.1-1 dated 2019-07-25

Title: Mixed Proportional Hazard Competing Risk Model
Description: Estimation of piecewise constant mixed proportional hazard competing risk model with NPMLE. The model is described in S. Gaure et al. (2007) <doi:10.1016/j.jeconom.2007.01.015>, J. Heckman and B. Singer (1984) <doi:10.2307/1911491>, and B.G. Lindsay (1983) <doi:10.1214/aos/1176346059>.
Author: Simen Gaure [aut, cre] (<https://orcid.org/0000-0001-7251-8747>)
Maintainer: Simen Gaure <simen@gaure.no>

Diff between durmod versions 1.1-1 dated 2019-07-25 and 1.1-2 dated 2019-08-21

 DESCRIPTION               |    8 ++++----
 MD5                       |   26 +++++++++++++-------------
 NAMESPACE                 |    1 +
 R/duration.R              |   29 +++++++++++++++++------------
 R/durmod-package.R        |   32 +++++++++++++++++++++++++++++++-
 R/utils.R                 |   19 +++++++++++++++++++
 inst/NEWS.Rd              |    8 ++++++++
 inst/doc/whatmph.Rnw      |    3 +--
 inst/doc/whatmph.pdf      |binary
 man/durmod-package.Rd     |   31 ++++++++++++++++++++++++++++++-
 man/mphdist.Rd            |    5 +++++
 src/cfunctions.cpp        |   32 +++++++++++++++++++++++++-------
 tests/sometests.Rout.save |   10 +++++-----
 vignettes/whatmph.Rnw     |    3 +--
 14 files changed, 160 insertions(+), 47 deletions(-)

More information about durmod at CRAN
Permanent link

Package Countr updated to version 3.5.4 with previous version 3.5.2 dated 2018-10-04

Title: Flexible Univariate Count Models Based on Renewal Processes
Description: Flexible univariate count models based on renewal processes. The models may include covariates and can be specified with familiar formula syntax as in glm() and package 'flexsurv'. The methodology is described in a forthcoming paper in the Journal of Statistical Software <10.18637/jss.v090.i13> (included as vignette 'Countr_guide' in the package).
Author: Tarak Kharrat [aut, cre], Georgi N. Boshnakov [aut]
Maintainer: Tarak Kharrat <Tarak.Kharrat@liverpool.ac.uk>

Diff between Countr versions 3.5.2 dated 2018-10-04 and 3.5.4 dated 2019-08-21

 Countr-3.5.2/Countr/man/Countr.Rd                            |only
 Countr-3.5.4/Countr/DESCRIPTION                              |   18 +
 Countr-3.5.4/Countr/MD5                                      |  106 +++++------
 Countr-3.5.4/Countr/NEWS.md                                  |   17 +
 Countr-3.5.4/Countr/R/Countr-package.R                       |   23 +-
 Countr-3.5.4/Countr/R/coefnames.R                            |    4 
 Countr-3.5.4/Countr/R/renewal_cstr.R                         |   34 +++
 Countr-3.5.4/Countr/R/renewal_tools.R                        |   41 ++--
 Countr-3.5.4/Countr/README.md                                |only
 Countr-3.5.4/Countr/build/partial.rdb                        |binary
 Countr-3.5.4/Countr/build/vignette.rds                       |binary
 Countr-3.5.4/Countr/inst/CITATION                            |only
 Countr-3.5.4/Countr/inst/REFERENCES.bib                      |   11 +
 Countr-3.5.4/Countr/inst/doc/ComputationalPerformance.pdf    |binary
 Countr-3.5.4/Countr/inst/doc/Countr_guide.pdf                |binary
 Countr-3.5.4/Countr/inst/doc/ModelSelectionAndComparison.pdf |binary
 Countr-3.5.4/Countr/inst/doc/Rnw/CountrJSSArticle.bib        |only
 Countr-3.5.4/Countr/inst/doc/Rnw/Countr_guide_paper.Rnw      |   12 -
 Countr-3.5.4/Countr/inst/doc/VarianceCovariance.pdf          |binary
 Countr-3.5.4/Countr/inst/doc/exampleFertility.pdf            |binary
 Countr-3.5.4/Countr/inst/doc/exampleFootball.pdf             |binary
 Countr-3.5.4/Countr/inst/doc/index.html                      |   48 ++--
 Countr-3.5.4/Countr/inst/doc/org/fertility.bib               |   11 +
 Countr-3.5.4/Countr/inst/doc/org/fertility.org               |   36 ++-
 Countr-3.5.4/Countr/inst/doc/org/football.bib                |   13 +
 Countr-3.5.4/Countr/inst/doc/org/football.org                |    3 
 Countr-3.5.4/Countr/inst/doc/org/perf.bib                    |   13 +
 Countr-3.5.4/Countr/inst/doc/org/perf.org                    |    3 
 Countr-3.5.4/Countr/inst/doc/org/quine.bib                   |   11 +
 Countr-3.5.4/Countr/inst/doc/org/quine.org                   |    3 
 Countr-3.5.4/Countr/inst/doc/org/var_covar.bib               |   13 +
 Countr-3.5.4/Countr/inst/doc/org/var_covar.org               |   35 +--
 Countr-3.5.4/Countr/inst/examples/example-jss.R              |only
 Countr-3.5.4/Countr/inst/include/Countr_RcppExports.h        |   28 ++
 Countr-3.5.4/Countr/man/Countr-package.Rd                    |only
 Countr-3.5.4/Countr/man/dCount_conv_bi.Rd                    |    6 
 Countr-3.5.4/Countr/man/dCount_conv_loglik_bi.Rd             |   13 -
 Countr-3.5.4/Countr/man/dCount_naive_bi.Rd                   |    8 
 Countr-3.5.4/Countr/man/dWeibullCount.Rd                     |   15 -
 Countr-3.5.4/Countr/man/dWeibullCount_mat.Rd                 |    9 
 Countr-3.5.4/Countr/man/dWeibullgammaCount.Rd                |    9 
 Countr-3.5.4/Countr/man/evCount_conv_bi.Rd                   |    5 
 Countr-3.5.4/Countr/man/predict.renewal.Rd                   |    4 
 Countr-3.5.4/Countr/man/renewal.Rd                           |    1 
 Countr-3.5.4/Countr/man/renewalCoef.Rd                       |    3 
 Countr-3.5.4/Countr/man/renewalCount.Rd                      |   19 +
 Countr-3.5.4/Countr/man/renewal_methods.Rd                   |   13 -
 Countr-3.5.4/Countr/man/se.coef.Rd                           |    3 
 Countr-3.5.4/Countr/src/RcppExports.cpp                      |   56 +++++
 Countr-3.5.4/Countr/tests/testthat.R                         |    8 
 Countr-3.5.4/Countr/tests/testthat/test-hess.R               |only
 Countr-3.5.4/Countr/tests/testthat/test-issue_1.R            |only
 Countr-3.5.4/Countr/vignettes/Countr_guide_paper.pdf         |binary
 Countr-3.5.4/Countr/vignettes/fertility.pdf                  |binary
 Countr-3.5.4/Countr/vignettes/football.pdf                   |binary
 Countr-3.5.4/Countr/vignettes/perf.pdf                       |binary
 Countr-3.5.4/Countr/vignettes/quine.pdf                      |binary
 Countr-3.5.4/Countr/vignettes/var_covar.pdf                  |binary
 58 files changed, 456 insertions(+), 199 deletions(-)

More information about Countr at CRAN
Permanent link

Package clustree updated to version 0.4.1 with previous version 0.4.0 dated 2019-04-18

Title: Visualise Clusterings at Different Resolutions
Description: Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualisation for interrogating clusterings as resolution increases.
Author: Luke Zappia [aut, cre] (<https://orcid.org/0000-0001-7744-8565>), Alicia Oshlack [aut] (<https://orcid.org/0000-0001-9788-5690>), Andrea Rau [ctb], Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>)
Maintainer: Luke Zappia <luke@lazappi.id.au>

Diff between clustree versions 0.4.0 dated 2019-04-18 and 0.4.1 dated 2019-08-21

 DESCRIPTION                    |   12 ++--
 MD5                            |   24 ++++----
 NEWS.md                        |   28 +++++++++
 R/clustree.R                   |    5 -
 R/clustree_overlay.R           |   11 ++-
 R/graph.R                      |   13 +++-
 README.md                      |    2 
 build/vignette.rds             |binary
 inst/WORDLIST                  |    4 +
 inst/doc/clustree.Rmd          |    2 
 inst/doc/clustree.html         |  115 ++++++++++++++++++++---------------------
 tests/testthat/test-clustree.R |   11 ++-
 vignettes/clustree.Rmd         |    2 
 13 files changed, 135 insertions(+), 94 deletions(-)

More information about clustree at CRAN
Permanent link

Package splot updated to version 0.5.0 with previous version 0.4.2 dated 2019-04-28

Title: Split Plot
Description: Automates common plotting tasks to ease data exploration. Makes density plots (potentially overlaid on histograms), scatter plots with prediction lines, or bar or line plots with error bars. For each type, y, or x and y variables can be plotted at levels of other variables, all with minimal specification.
Author: Micah Iserman
Maintainer: Micah Iserman <micah.iserman@ttu.edu>

Diff between splot versions 0.4.2 dated 2019-04-28 and 0.5.0 dated 2019-08-21

 DESCRIPTION            |    6 
 MD5                    |   15 -
 NAMESPACE              |    2 
 R/splot.R              |  532 ++++++++++++++++++++++++++++---------------------
 R/utils.R              |  129 +++++++----
 inst/NEWS.Rd           |   32 ++
 man/splot.Rd           |   76 +++----
 man/splot.color.Rd     |    5 
 man/splot.colormean.Rd |only
 9 files changed, 476 insertions(+), 321 deletions(-)

More information about splot at CRAN
Permanent link

Package rmarkdown updated to version 1.15 with previous version 1.14 dated 2019-07-12

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>), Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), Barret Schloerke [ctb], Christophe Dervieux [ctb], Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>), Jeff Allen [ctb], Malcolm Barrett [ctb], Rob Hyndman [ctb], Romain Lesur [ctb], Roy Storey [ctb], Ruben Arslan [ctb], RStudio, Inc. [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs)
Maintainer: Yihui Xie <xie@yihui.name>

Diff between rmarkdown versions 1.14 dated 2019-07-12 and 1.15 dated 2019-08-21

 DESCRIPTION                              |    8 +++++---
 MD5                                      |   14 +++++++-------
 NEWS.md                                  |    9 +++++++++
 R/pdf_document.R                         |   25 +++++++++++++------------
 R/render_site.R                          |   10 ++++++++--
 R/util.R                                 |    3 ++-
 inst/rmd/h/default.html                  |    1 -
 inst/rmd/h/navigation-1.1/codefolding.js |    2 +-
 8 files changed, 45 insertions(+), 27 deletions(-)

More information about rmarkdown at CRAN
Permanent link

Package paws.storage updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-28

Title: Amazon Web Services Storage APIs
Description: Interface to Amazon Web Services storage APIs, including 'Simple Storage Service' ('S3') and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.storage versions 0.1.3 dated 2019-07-28 and 0.1.4 dated 2019-08-21

 DESCRIPTION                |   13 +++++++------
 MD5                        |   18 +++++++++---------
 R/backup_service.R         |    2 +-
 R/dlm_service.R            |    2 +-
 R/efs_service.R            |    2 +-
 R/fsx_service.R            |    2 +-
 R/glacier_service.R        |    2 +-
 R/s3_service.R             |    2 +-
 R/s3control_service.R      |    2 +-
 R/storagegateway_service.R |    2 +-
 10 files changed, 24 insertions(+), 23 deletions(-)

More information about paws.storage at CRAN
Permanent link

Package paws.security.identity updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-28

Title: Amazon Web Services Security, Identity, & Compliance APIs
Description: Interface to Amazon Web Services security, identity, and compliance APIs, including the 'Identity & Access Management' ('IAM') service for managing access to services and resources, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.security.identity versions 0.1.3 dated 2019-07-28 and 0.1.4 dated 2019-08-21

 DESCRIPTION                                     |   16 +++---
 MD5                                             |   58 ++++++++++++------------
 R/acm_service.R                                 |    4 -
 R/acmpca_service.R                              |    2 
 R/clouddirectory_service.R                      |    2 
 R/cloudhsm_service.R                            |    2 
 R/cloudhsmv2_service.R                          |    2 
 R/cognitoidentity_service.R                     |    2 
 R/cognitoidentityprovider_operations.R          |    6 +-
 R/cognitoidentityprovider_service.R             |    2 
 R/cognitosync_service.R                         |    2 
 R/directoryservice_service.R                    |    2 
 R/fms_service.R                                 |    2 
 R/guardduty_service.R                           |    2 
 R/iam_service.R                                 |    2 
 R/inspector_service.R                           |    2 
 R/kms_service.R                                 |    4 -
 R/macie_service.R                               |    2 
 R/ram_service.R                                 |    2 
 R/secretsmanager_operations.R                   |    5 +-
 R/secretsmanager_service.R                      |    2 
 R/securityhub_service.R                         |    2 
 R/shield_service.R                              |    2 
 R/sts_service.R                                 |    2 
 R/waf_service.R                                 |    2 
 R/wafregional_service.R                         |    2 
 man/acm.Rd                                      |    2 
 man/cognitoidentityprovider_create_user_pool.Rd |    6 +-
 man/kms.Rd                                      |    2 
 man/secretsmanager_rotate_secret.Rd             |    5 +-
 30 files changed, 77 insertions(+), 71 deletions(-)

More information about paws.security.identity at CRAN
Permanent link

Package paws.networking updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-28

Title: Amazon Web Services Networking & Content Delivery APIs
Description: Interface to Amazon Web Services networking and content delivery APIs, including 'Route 53' Domain Name System service, 'CloudFront' content delivery, load balancing, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.networking versions 0.1.3 dated 2019-07-28 and 0.1.4 dated 2019-08-21

 DESCRIPTION                         |   14 +++++++-------
 MD5                                 |   28 ++++++++++++++--------------
 R/apigateway_service.R              |    2 +-
 R/apigatewaymanagementapi_service.R |    2 +-
 R/apigatewayv2_service.R            |    2 +-
 R/appmesh_service.R                 |    2 +-
 R/cloudfront_service.R              |    2 +-
 R/directconnect_service.R           |    2 +-
 R/elb_service.R                     |    2 +-
 R/elbv2_service.R                   |    2 +-
 R/globalaccelerator_service.R       |    2 +-
 R/route53_service.R                 |    2 +-
 R/route53domains_service.R          |    2 +-
 R/route53resolver_service.R         |    2 +-
 R/servicediscovery_service.R        |    2 +-
 15 files changed, 34 insertions(+), 34 deletions(-)

More information about paws.networking at CRAN
Permanent link

Package paws.management updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-28

Title: Amazon Web Services Management & Governance APIs
Description: Interface to Amazon Web Services management and governance APIs, including 'CloudWatch' application and infrastructure monitoring, 'Auto Scaling' for automatically scaling resources, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.management versions 0.1.3 dated 2019-07-28 and 0.1.4 dated 2019-08-21

 DESCRIPTION                          |   12 ++++----
 MD5                                  |   48 +++++++++++++++++------------------
 R/applicationautoscaling_service.R   |    2 -
 R/applicationinsights_service.R      |    2 -
 R/autoscaling_service.R              |    2 -
 R/autoscalingplans_service.R         |    2 -
 R/cloudformation_service.R           |    2 -
 R/cloudtrail_service.R               |    2 -
 R/cloudwatch_service.R               |    2 -
 R/cloudwatchevents_service.R         |    2 -
 R/cloudwatchlogs_service.R           |    2 -
 R/configservice_service.R            |    2 -
 R/health_service.R                   |    2 -
 R/licensemanager_service.R           |    2 -
 R/opsworks_service.R                 |    2 -
 R/opsworkscm_service.R               |    2 -
 R/organizations_service.R            |    2 -
 R/pi_service.R                       |    2 -
 R/resourcegroups_service.R           |    2 -
 R/resourcegroupstaggingapi_service.R |    2 -
 R/servicecatalog_service.R           |    2 -
 R/servicequotas_service.R            |    2 -
 R/ssm_operations.R                   |    2 -
 R/ssm_service.R                      |    2 -
 R/support_service.R                  |    2 -
 25 files changed, 53 insertions(+), 53 deletions(-)

More information about paws.management at CRAN
Permanent link

Package paws.machine.learning updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-28

Title: Amazon Web Services Machine Learning APIs
Description: Interface to Amazon Web Services machine learning APIs, including 'SageMaker' managed machine learning service, natural language processing, speech recognition, translation, and more <https://aws.amazon.com/machine-learning/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.machine.learning versions 0.1.3 dated 2019-07-28 and 0.1.4 dated 2019-08-21

 DESCRIPTION                         |   12 ++++++------
 MD5                                 |   32 ++++++++++++++++----------------
 R/comprehend_service.R              |    2 +-
 R/comprehendmedical_service.R       |    2 +-
 R/lexmodelbuildingservice_service.R |    2 +-
 R/lexruntimeservice_service.R       |    2 +-
 R/machinelearning_service.R         |    2 +-
 R/personalize_service.R             |    2 +-
 R/personalizeevents_service.R       |    2 +-
 R/personalizeruntime_service.R      |    2 +-
 R/polly_service.R                   |    2 +-
 R/rekognition_service.R             |    2 +-
 R/sagemaker_service.R               |    2 +-
 R/sagemakerruntime_service.R        |    2 +-
 R/textract_service.R                |    2 +-
 R/transcribeservice_service.R       |    2 +-
 R/translate_service.R               |    2 +-
 17 files changed, 37 insertions(+), 37 deletions(-)

More information about paws.machine.learning at CRAN
Permanent link

Package paws.database updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-27

Title: Amazon Web Services Database APIs
Description: Interface to Amazon Web Services database APIs, including 'Relational Database Service' ('RDS'), 'DynamoDB' 'NoSQL' database, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.database versions 0.1.3 dated 2019-07-27 and 0.1.4 dated 2019-08-21

 DESCRIPTION                 |   14 +++++++-------
 MD5                         |   20 ++++++++++----------
 R/dax_service.R             |    2 +-
 R/dynamodb_service.R        |    2 +-
 R/dynamodbstreams_service.R |    2 +-
 R/elasticache_service.R     |    2 +-
 R/neptune_service.R         |    2 +-
 R/rds_service.R             |    2 +-
 R/rdsdataservice_service.R  |    2 +-
 R/redshift_service.R        |    2 +-
 R/simpledb_service.R        |    2 +-
 11 files changed, 26 insertions(+), 26 deletions(-)

More information about paws.database at CRAN
Permanent link

Package paws.customer.engagement updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-28

Title: Amazon Web Services Customer Engagement APIs
Description: Interface to Amazon Web Services customer engagement APIs, including 'Simple Email Service', 'Connect' contact center service, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.customer.engagement versions 0.1.3 dated 2019-07-28 and 0.1.4 dated 2019-08-21

 DESCRIPTION                  |   14 +++++++-------
 MD5                          |   12 ++++++------
 R/connect_service.R          |    2 +-
 R/pinpoint_service.R         |    2 +-
 R/pinpointemail_service.R    |    2 +-
 R/pinpointsmsvoice_service.R |    2 +-
 R/ses_service.R              |    2 +-
 7 files changed, 18 insertions(+), 18 deletions(-)

More information about paws.customer.engagement at CRAN
Permanent link

Package paws.cost.management updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-27

Title: Amazon Web Services Cost Management APIs
Description: Interface to Amazon Web Services cost management APIs, including cost and usage reports, budgets, pricing, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.cost.management versions 0.1.3 dated 2019-07-27 and 0.1.4 dated 2019-08-21

 DESCRIPTION                               |   12 ++++++------
 MD5                                       |   16 ++++++++--------
 R/budgets_service.R                       |    2 +-
 R/costandusagereportservice_service.R     |    2 +-
 R/costexplorer_service.R                  |    2 +-
 R/marketplacecommerceanalytics_service.R  |    2 +-
 R/marketplaceentitlementservice_service.R |    2 +-
 R/marketplacemetering_service.R           |    2 +-
 R/pricing_service.R                       |    2 +-
 9 files changed, 21 insertions(+), 21 deletions(-)

More information about paws.cost.management at CRAN
Permanent link

Package paws.compute updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-27

Title: Amazon Web Services Compute APIs
Description: Interface to Amazon Web Services compute APIs, including 'Elastic Compute Cloud' ('EC2'), 'Lambda' functions-as-a-service, containers, batch processing, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.compute versions 0.1.3 dated 2019-07-27 and 0.1.4 dated 2019-08-21

 DESCRIPTION                                 |   15 ++++++++-------
 MD5                                         |   22 +++++++++++-----------
 R/batch_service.R                           |    2 +-
 R/ec2_service.R                             |    2 +-
 R/ec2instanceconnect_service.R              |    2 +-
 R/ecr_service.R                             |    2 +-
 R/ecs_service.R                             |    2 +-
 R/eks_service.R                             |    2 +-
 R/elasticbeanstalk_service.R                |    2 +-
 R/lambda_service.R                          |    2 +-
 R/lightsail_service.R                       |    2 +-
 R/serverlessapplicationrepository_service.R |    2 +-
 12 files changed, 29 insertions(+), 28 deletions(-)

More information about paws.compute at CRAN
Permanent link

Package paws.application.integration updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-27

Title: Amazon Web Services Application Integration APIs
Description: Interface to Amazon Web Services application integration APIs, including 'Simple Queue Service' ('SQS') message queue, 'Simple Notification Service' ('SNS') publish/subscribe messaging, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.application.integration versions 0.1.3 dated 2019-07-27 and 0.1.4 dated 2019-08-21

 DESCRIPTION             |   16 ++++++++--------
 MD5                     |   14 +++++++-------
 R/eventbridge_service.R |    2 +-
 R/mq_service.R          |    2 +-
 R/sfn_service.R         |    2 +-
 R/sns_service.R         |    2 +-
 R/sqs_service.R         |    2 +-
 R/swf_service.R         |    2 +-
 8 files changed, 21 insertions(+), 21 deletions(-)

More information about paws.application.integration at CRAN
Permanent link

Package paws.analytics updated to version 0.1.4 with previous version 0.1.3 dated 2019-07-27

Title: Amazon Web Services Analytics APIs
Description: Interface to Amazon Web Services analytics APIs, including 'Elastic MapReduce' 'Hadoop' and 'Spark' big data service, 'Elasticsearch' search engine, and more <https://aws.amazon.com/>.
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.analytics versions 0.1.3 dated 2019-07-27 and 0.1.4 dated 2019-08-21

 DESCRIPTION                      |   12 ++++++------
 MD5                              |   30 +++++++++++++++---------------
 R/athena_service.R               |    2 +-
 R/cloudsearch_service.R          |    2 +-
 R/cloudsearchdomain_service.R    |    2 +-
 R/datapipeline_service.R         |    2 +-
 R/elasticsearchservice_service.R |    2 +-
 R/emr_service.R                  |    2 +-
 R/firehose_service.R             |    2 +-
 R/glue_service.R                 |    2 +-
 R/kafka_service.R                |    2 +-
 R/kinesis_service.R              |    2 +-
 R/kinesisanalytics_service.R     |    2 +-
 R/kinesisanalyticsv2_service.R   |    2 +-
 R/mturk_service.R                |    2 +-
 R/quicksight_service.R           |    2 +-
 16 files changed, 35 insertions(+), 35 deletions(-)

More information about paws.analytics at CRAN
Permanent link

Package optionstrat updated to version 1.4.0 with previous version 1.3.0 dated 2019-06-20

Title: Utilizes the Black-Scholes Option Pricing Model to Perform Strategic Option Analysis and Plot Option Strategies
Description: Utilizes the Black-Scholes-Merton option pricing model to calculate key option analytics and perform graphical analysis of various option strategies. Provides functions to calculate the option premium and option greeks of European-style options.
Author: John T. Buynak [aut, cre]
Maintainer: John T. Buynak <jbuynak94@gmail.com>

Diff between optionstrat versions 1.3.0 dated 2019-06-20 and 1.4.0 dated 2019-08-21

 DESCRIPTION                        |    8 ++++----
 MD5                                |   18 +++++++++---------
 R/optionstrat.R                    |   32 +++++++++++++++++++-------------
 inst/doc/optionstrat_vignette.html |    4 ++--
 man/plotbearcall.Rd                |    4 +++-
 man/plotbearput.Rd                 |    4 +++-
 man/plotbullcall.Rd                |    4 +++-
 man/plotbullput.Rd                 |    4 +++-
 man/plotdv.Rd                      |    4 +++-
 man/plotvertical.Rd                |    4 +++-
 10 files changed, 52 insertions(+), 34 deletions(-)

More information about optionstrat at CRAN
Permanent link

Package deTestSet updated to version 1.1.6 with previous version 1.1.5 dated 2017-01-19

Title: Test Set for Differential Equations
Description: Solvers and test set for stiff and non-stiff differential equations, and differential algebraic equations. 'Mazzia, F., Cash, J.R. and K. Soetaert, 2012. DOI: 10.1016/j.cam.2012.03.014'.
Author: Karline Soetaert [aut, cre], Jeff Cash [aut], Francesca Mazzia [aut], LAPACK authors [cph]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>

Diff between deTestSet versions 1.1.5 dated 2017-01-19 and 1.1.6 dated 2019-08-21

 DESCRIPTION            |   21 
 MD5                    |   79 
 NAMESPACE              |    3 
 R/bimd.R               |    4 
 R/forcings.R           |   39 
 R/gam.R                |  530 +-
 R/mebdfi.R             |    4 
 build/vignette.rds     |binary
 inst/CITATION          |only
 inst/doc/deTestSet.pdf |binary
 man/deTestSet.Rd       |  155 
 man/ex_E5.Rd           |  155 
 man/ex_andrews.Rd      |    2 
 man/ex_beam.Rd         |    2 
 man/ex_caraxis.Rd      |    2 
 man/ex_crank.Rd        |    2 
 man/ex_emep.Rd         |    2 
 man/ex_fekete.Rd       |    2 
 man/ex_hires.Rd        |    2 
 man/ex_nand.Rd         |    3 
 man/ex_orego.Rd        |  153 
 man/ex_pleiades.Rd     |    2 
 man/ex_pollution.Rd    |    2 
 man/ex_reference.Rd    |   68 
 man/ex_ring.Rd         |    2 
 man/ex_rober.Rd        |  161 
 man/ex_transistor.Rd   |    3 
 man/ex_tube.Rd         |    3 
 man/ex_twobit.Rd       |    3 
 man/ex_vdpol.Rd        |  159 
 man/ex_wheelset.Rd     |    2 
 src/call_dopri.c       |   71 
 src/call_gam.c         |   74 
 src/call_mebdfi.c      |   66 
 src/cashkarp.f         |    4 
 src/de.h               |    6 
 src/deTestSetMethods.c |only
 src/de_utils.c         |  122 
 src/errmsg.f           |  113 
 src/forcings.c         |    8 
 src/gamd.f90           |11414 ++++++++++++++++++++++++-------------------------
 src/rprintf.c          |only
 42 files changed, 6674 insertions(+), 6769 deletions(-)

More information about deTestSet at CRAN
Permanent link

Package d3r updated to version 0.8.7 with previous version 0.8.6 dated 2019-07-23

Title: 'd3.js' Utilities for R
Description: Provides a suite of functions to help ease the use of 'd3.js' in R. These helpers include 'htmltools::htmlDependency' functions, hierarchy builders, and conversion tools for 'partykit', 'igraph,' 'table', and 'data.frame' R objects into the 'JSON' that 'd3.js' expects.
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib, http://d3js.org), Kent Russell [aut, cre] (R interface), Gregor Aisch [aut, cph] (d3-jetpack creator, https://github.com/gka/d3-jetpack), Adam Pearce [aut] (core contributor to d3-jetpack), Ben Ortiz [ctb]
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>

Diff between d3r versions 0.8.6 dated 2019-07-23 and 0.8.7 dated 2019-08-21

 DESCRIPTION                   |   10 +++----
 MD5                           |   16 ++++++------
 NEWS.md                       |    5 +++
 R/dependencies.R              |    4 +--
 R/hierarchy.R                 |   55 +++++++++++++++++++++++++++++-------------
 inst/www/d3/v5/CHANGES.md     |   16 ++++++------
 inst/www/d3/v5/dist/d3.min.js |    4 +--
 tests/testthat/test_deps.R    |    1 
 tests/testthat/test_v8.R      |    2 -
 9 files changed, 71 insertions(+), 42 deletions(-)

More information about d3r at CRAN
Permanent link

Package Chaos01 updated to version 1.2.1 with previous version 1.2.0 dated 2019-08-02

Title: 0-1 Test for Chaos
Description: Computes and visualize the results of the 0-1 test for chaos proposed by Gottwald and Melbourne (2004) <DOI:10.1137/080718851>. The algorithm is available in parallel for the independent values of parameter c. Additionally, fast RQA is added to distinguish chaos from noise.
Author: Tomas Martinovic [aut, cre]
Maintainer: Tomas Martinovic <tomas.martinovic@vsb.cz>

Diff between Chaos01 versions 1.2.0 dated 2019-08-02 and 1.2.1 dated 2019-08-21

 DESCRIPTION  |    6 +++---
 MD5          |    6 +++---
 NEWS         |    7 +++++++
 R/rqa_diag.R |    2 +-
 4 files changed, 14 insertions(+), 7 deletions(-)

More information about Chaos01 at CRAN
Permanent link

Package longitudinalcascade updated to version 0.3.2.1 with previous version 0.3.1.1 dated 2019-06-13

Title: Longitudinal Cascade
Description: Creates a series of set of graphics and statistics related to the longitudinal cascade, all included in a single object. The longitudinal cascade inputs longitudinal data to identify gaps in the HIV and related cascades by observing differences using time to event and survival methods. The stage definitions are set by the user, with default standard options. Outputs include graphics, datasets, and formal statistical tests.
Author: Noah Haber [aut, cre]
Maintainer: Noah Haber <noahhaber@gmail.com>

Diff between longitudinalcascade versions 0.3.1.1 dated 2019-06-13 and 0.3.2.1 dated 2019-08-21

 DESCRIPTION             |    6 +++---
 MD5                     |    4 ++--
 R/longitudinalcascade.R |   15 +++++++--------
 3 files changed, 12 insertions(+), 13 deletions(-)

More information about longitudinalcascade at CRAN
Permanent link

Package heuristica updated to version 1.0.2 with previous version 1.0.1 dated 2016-07-17

Title: Heuristics Including Take the Best and Unit-Weight Linear
Description: Implements various heuristics like Take The Best and unit-weight linear, which do two-alternative choice: which of two objects will have a higher criterion? Also offers functions to assess performance, e.g. percent correct across all row pairs in a data set and finding row pairs where models disagree. New models can be added by implementing a fit and predict function-- see vignette.
Author: Jean Whitmore [aut, cre], Daniel Barkoczi [aut]
Maintainer: Jean Whitmore <jeanimal@gmail.com>

Diff between heuristica versions 1.0.1 dated 2016-07-17 and 1.0.2 dated 2019-08-21

 DESCRIPTION                                  |   12 
 LICENSE                                      |    2 
 MD5                                          |  146 ++++----
 NEWS.md                                      |    5 
 R/heuristics.R                               |   36 ++
 README.md                                    |    2 
 build/vignette.rds                           |binary
 inst/doc/README.Rmd                          |    2 
 inst/doc/README.html                         |  375 +++++++++++++++++----
 inst/doc/confusion-matrix.Rmd                |    2 
 inst/doc/confusion-matrix.html               |  429 ++++++++++++++++++------
 inst/doc/cross-validation.R                  |   15 
 inst/doc/cross-validation.Rmd                |   18 -
 inst/doc/cross-validation.html               |  475 ++++++++++++++++++++------
 inst/doc/how-to-make-heuristic.html          |  479 ++++++++++++++++++++-------
 inst/doc/reproducing-results.R               |   61 +++
 inst/doc/reproducing-results.Rmd             |   80 ++++
 inst/doc/reproducing-results.html            |  417 ++++++++++++++++++++---
 man/accuracyFromConfusionMatrix3x3.Rd        |    1 
 man/city_population.Rd                       |    1 
 man/city_population_original.Rd              |    1 
 man/collapseConfusionMatrix3x3To2x2.Rd       |    1 
 man/conditionalCueValidityComplete.Rd        |    1 
 man/confusionMatrixFor_Neg1_0_1.Rd           |    1 
 man/correctGreater.Rd                        |    1 
 man/createFunction.Rd                        |    1 
 man/createFunction.heuristics.Rd             |    1 
 man/cueAccuracy.Rd                           |    1 
 man/cueValidity.Rd                           |    1 
 man/cueValidityAppliedToColumns.Rd           |    1 
 man/cueValidityComplete.Rd                   |    5 
 man/distributeGuessAsExpectedValue.Rd        |    1 
 man/heuristics.Rd                            |    1 
 man/heuristicsList.Rd                        |    1 
 man/heuristicsProb.Rd                        |    1 
 man/highschool_dropout.Rd                    |    1 
 man/lmWrapper.Rd                             |    4 
 man/logRegModel.Rd                           |    1 
 man/minModel.Rd                              |    1 
 man/oneRow.Rd                                |    1 
 man/pairMatrix.Rd                            |    1 
 man/percentCorrect.Rd                        |    1 
 man/percentCorrectList.Rd                    |    1 
 man/percentCorrectListNonSymmetric.Rd        |    1 
 man/percentCorrectListReturnMatrix.Rd        |    1 
 man/predictPair.Rd                           |    1 
 man/predictPairInternal.Rd                   |    1 
 man/predictPairProb.Rd                       |    1 
 man/predictPairSummary.Rd                    |    1 
 man/predictProbInternal.Rd                   |    1 
 man/probGreater.Rd                           |    1 
 man/regInterceptModel.Rd                     |    1 
 man/regModel.Rd                              |    1 
 man/reverseRowsAndReverseColumns.Rd          |    1 
 man/rowIndexes.Rd                            |    1 
 man/rowPairApply.Rd                          |    1 
 man/rowPairApply2Rows.Rd                     |    1 
 man/rowPairApplyList.Rd                      |    1 
 man/singleCueModel.Rd                        |    5 
 man/statsFromConfusionMatrix.Rd              |    1 
 man/ttbGreedyModel.Rd                        |    1 
 man/ttbModel.Rd                              |    1 
 man/unitWeightModel.Rd                       |    5 
 man/validityWeightModel.Rd                   |    1 
 man/zzDocumentationStubFormulaModelParams.Rd |    4 
 man/zzDocumentationStubModelParams.Rd        |    1 
 man/zzDocumentationStubReverseCues.Rd        |    1 
 tests/testthat/test-aggregators.R            |   91 ++---
 tests/testthat/test-heuristics.R             |   65 +++
 tests/testthat/test-heuristics_benchmark.R   |   11 
 vignettes/README.Rmd                         |    2 
 vignettes/confusion-matrix.Rmd               |    2 
 vignettes/cross-validation.Rmd               |   18 -
 vignettes/reproducing-results.Rmd            |   80 ++++
 74 files changed, 2213 insertions(+), 679 deletions(-)

More information about heuristica at CRAN
Permanent link

Package rticles updated to version 0.10 with previous version 0.9 dated 2019-07-12

Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.
Author: JJ Allaire [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), R Foundation [aut, cph], Hadley Wickham [aut], Journal of Statistical Software [aut, cph], RStudio [cph], Ramnath Vaidyanathan [aut, cph], Association for Computing Machinery [aut, cph], Carl Boettiger [aut, cph], Elsevier [aut, cph], Karl Broman [aut, cph], Kirill Mueller [aut, cph], Bastiaan Quast [aut, cph], Randall Pruim [aut, cph], Ben Marwick [aut, cph], Charlotte Wickham [aut, cph], Oliver Keyes [aut, cph], Miao Yu [aut, cph], Daniel Emaasit [aut, cph], Thierry Onkelinx [aut, cph], Alessandro Gasparini [aut, cph] (<https://orcid.org/0000-0002-8319-7624>), Marc-Andre Desautels [aut, cph], Dominik Leutnant [aut, cph] (<https://orcid.org/0000-0003-3293-2315>), MDPI [aut, cph], Taylor and Francis [aut, cph], Oğuzhan Öğreden [aut] (<https://orcid.org/0000-0002-9949-3348>), Dalton Hance [aut], Daniel Nüst [aut, cph] (<https://orcid.org/0000-0002-0024-5046>), Petter Uvesten [aut, cph], Elio Campitelli [aut, cph] (<https://orcid.org/0000-0002-7742-9230>), John Muschelli [aut, cph] (<https://orcid.org/0000-0001-6469-1750>), Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>)
Maintainer: Yihui Xie <xie@yihui.name>

Diff between rticles versions 0.9 dated 2019-07-12 and 0.10 dated 2019-08-21

 DESCRIPTION                                                        |   12 +++++-----
 MD5                                                                |   12 +++++-----
 NEWS.md                                                            |    5 ++++
 README.md                                                          |    2 -
 inst/rmarkdown/templates/copernicus_article/resources/template.tex |    1 
 inst/rmarkdown/templates/peerj_article/resources/template.tex      |    6 +++++
 tests/testit/test-formats.R                                        |    1 
 7 files changed, 27 insertions(+), 12 deletions(-)

More information about rticles at CRAN
Permanent link

Package NPP updated to version 0.2.0 with previous version 0.1.0 dated 2019-07-11

Title: Normalized Power Prior Bayesian Analysis
Description: Posterior sampling in several commonly used distributions using normalized power prior as described in Duan, Ye and Smith (2006) <doi:10.1002/env.752> and Ibrahim et.al. (2015) <doi:10.1002/sim.6728>. Sampling of the power parameter is achieved via either independence Metropolis-Hastings or random walk Metropolis-Hastings based on transformation.
Author: Zifei Han, Tianyu Bai and Keying Ye
Maintainer: Zifei Han <hanzifei1@gmail.com>

Diff between NPP versions 0.1.0 dated 2019-07-11 and 0.2.0 dated 2019-08-21

 DESCRIPTION               |    6 
 MD5                       |   15 +-
 NAMESPACE                 |    2 
 R/LMNPP.R                 |only
 R/NormalNPP.R             |  218 +++++++++++++++---------------
 R/PosteriorModeNPP.R      |  331 ++++++++++++++++++++++++++++------------------
 man/LMNPP.Rd              |only
 man/ModeDeltaLMNPP.Rd     |only
 man/ModeDeltaNormalNPP.Rd |   10 -
 man/NormalNPP.Rd          |    7 
 10 files changed, 338 insertions(+), 251 deletions(-)

More information about NPP at CRAN
Permanent link

Package CBPS updated to version 0.21 with previous version 0.20 dated 2019-03-22

Title: Covariate Balancing Propensity Score
Description: Implements the covariate balancing propensity score (CBPS) proposed by Imai and Ratkovic (2014) <DOI:10.1111/rssb.12027>. The propensity score is estimated such that it maximizes the resulting covariate balance as well as the prediction of treatment assignment. The method, therefore, avoids an iteration between model fitting and balance checking. The package also implements optimal CBPS from Fan et al. (2016) <https://imai.fas.harvard.edu/research/CBPStheory.html>, several extensions of the CBPS beyond the cross-sectional, binary treatment setting. They include the CBPS for longitudinal settings so that it can be used in conjunction with marginal structural models from Imai and Ratkovic (2015) <DOI:10.1080/01621459.2014.956872>, treatments with three- and four-valued treatment variables, continuous-valued treatments from Fong, Hazlett, and Imai (2018) <DOI:10.1214/17-AOAS1101>, propensity score estimation with a large number of covariates from Ning, Peng, and Imai (2018) <arXiv:1812.08683>, and the situation with multiple distinct binary treatments administered simultaneously. In the future it will be extended to other settings including the generalization of experimental and instrumental variable estimates.
Author: Christian Fong [aut, cre], Marc Ratkovic [aut], Kosuke Imai [aut], Chad Hazlett [ctb], Xiaolin Yang [ctb], Sida Peng [ctb]
Maintainer: Christian Fong <cjfong@umich.edu>

Diff between CBPS versions 0.20 dated 2019-03-22 and 0.21 dated 2019-08-21

 ChangeLog         |    1 +
 DESCRIPTION       |   14 +++++++-------
 MD5               |   16 ++++++++--------
 R/CBPSMain.R      |   11 +++++++----
 man/CBMSM.Rd      |   15 ++++++++-------
 man/CBMSM.fit.Rd  |    4 ++--
 man/CBPS.Rd       |   15 +++++++++------
 man/plot.CBMSM.Rd |    4 ++--
 man/plot.CBPS.Rd  |    3 ++-
 9 files changed, 46 insertions(+), 37 deletions(-)

More information about CBPS at CRAN
Permanent link

Package bnviewer updated to version 0.1.4 with previous version 0.1.3 dated 2019-06-08

Title: Interactive Visualization of Bayesian Networks
Description: Bayesian networks provide an intuitive framework for probabilistic reasoning and its graphical nature can be interpreted quite clearly. Graph based methods of machine learning are becoming more popular because they offer a richer model of knowledge that can be understood by a human in a graphical format. The 'bnviewer' is an R Package that allows the interactive visualization of Bayesian Networks. The aim of this package is to improve the Bayesian Networks visualization over the basic and static views offered by existing packages.
Author: Robson Fernandes
Maintainer: Robson Fernandes <robson.fernandes@usp.br>

Diff between bnviewer versions 0.1.3 dated 2019-06-08 and 0.1.4 dated 2019-08-21

 DESCRIPTION             |    8 +-
 MD5                     |    9 +-
 R/bnviewer.R            |  156 +++++++++++++++++++++++++++++++++++++++++-------
 man/bnviewer-package.Rd |    6 -
 man/viewer.Rd           |  106 +++++++++++++++++++++++++-------
 tests/clusters.R        |only
 6 files changed, 231 insertions(+), 54 deletions(-)

More information about bnviewer at CRAN
Permanent link

Package blogdown updated to version 0.15 with previous version 0.14 dated 2019-07-13

Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package supports the static site generator 'Hugo' (<https://gohugo.io>) best, and it also supports 'Jekyll' (<http://jekyllrb.com>) and 'Hexo' (<https://hexo.io>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Beilei Bian [ctb], Forest Fang [ctb], Garrick Aden-Buie [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], JJ Allaire [ctb], Kevin Ushey [ctb], Leonardo Collado-Torres [ctb], Xianying Tan [ctb], Raniere Silva [ctb], Jozef Hajnala [ctb], RStudio Inc [cph]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between blogdown versions 0.14 dated 2019-07-13 and 0.15 dated 2019-08-21

 DESCRIPTION                 |    6 +++---
 MD5                         |    9 +++++----
 NEWS.md                     |    6 ++++++
 R/install.R                 |    1 +
 inst/scripts/insert_image.R |    2 +-
 tests/testit/test-addin.R   |only
 6 files changed, 16 insertions(+), 8 deletions(-)

More information about blogdown at CRAN
Permanent link

Package apcluster updated to version 1.4.8 with previous version 1.4.7 dated 2018-05-29

Title: Affinity Propagation Clustering
Description: Implements Affinity Propagation clustering introduced by Frey and Dueck (2007) <DOI:10.1126/science.1136800>. The algorithms are largely analogous to the 'Matlab' code published by Frey and Dueck. The package further provides leveraged affinity propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.
Author: Ulrich Bodenhofer, Johannes Palme, Chrats Melkonian, Andreas Kothmeier, Nikola Kostic
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>

Diff between apcluster versions 1.4.7 dated 2018-05-29 and 1.4.8 dated 2019-08-21

 apcluster-1.4.7/apcluster/man/ch22Promoters.Rd      |only
 apcluster-1.4.8/apcluster/DESCRIPTION               |    8 +++----
 apcluster-1.4.8/apcluster/MD5                       |   21 +++++++++-----------
 apcluster-1.4.8/apcluster/build/vignette.rds        |binary
 apcluster-1.4.8/apcluster/inst/NEWS                 |    6 +++++
 apcluster-1.4.8/apcluster/inst/doc/apcluster.Rnw    |   11 ++++++++--
 apcluster-1.4.8/apcluster/inst/doc/apcluster.pdf    |binary
 apcluster-1.4.8/apcluster/man/apcluster-methods.Rd  |    2 -
 apcluster-1.4.8/apcluster/man/apclusterK-methods.Rd |    2 -
 apcluster-1.4.8/apcluster/man/apclusterL-methods.Rd |    2 -
 apcluster-1.4.8/apcluster/src/aggExClusterC.cpp     |    9 +++++---
 apcluster-1.4.8/apcluster/vignettes/apcluster.Rnw   |   11 ++++++++--
 12 files changed, 47 insertions(+), 25 deletions(-)

More information about apcluster at CRAN
Permanent link

Tue, 20 Aug 2019

Package visualR updated to version 2.0.2 with previous version 2.0.1 dated 2019-05-05

Title: 3D Visualization of Option Greeks and Volatility Skew
Description: Generates a 3D graph which plots the volatility skew of a stock or a selected stock option parameter over time. The default setting plots the net parameter position of a double vertical spread over time.
Author: John T. Buynak
Maintainer: John T. Buynak <jbuynak94@gmail.com>

Diff between visualR versions 2.0.1 dated 2019-05-05 and 2.0.2 dated 2019-08-20

 DESCRIPTION           |    9 ++++-----
 MD5                   |   14 +++++++-------
 R/visualize.R         |    4 ++--
 build/vignette.rds    |binary
 inst/doc/visualr.Rmd  |    2 +-
 inst/doc/visualr.html |    4 ++--
 man/visualize.Rd      |   13 +++++++------
 vignettes/visualr.Rmd |    2 +-
 8 files changed, 24 insertions(+), 24 deletions(-)

More information about visualR at CRAN
Permanent link

Package scoringRules updated to version 1.0.0 with previous version 0.9.6 dated 2019-05-27

Title: Scoring Rules for Parametric and Simulated Distribution Forecasts
Description: Dictionary-like reference for computing scoring rules in a wide range of situations. Covers both parametric forecast distributions (such as mixtures of Gaussians) and distributions generated via simulation.
Author: Alexander Jordan, Fabian Krueger, Sebastian Lerch
Maintainer: Fabian Krueger <Fabian.Krueger83@gmail.com>

Diff between scoringRules versions 0.9.6 dated 2019-05-27 and 1.0.0 dated 2019-08-20

 DESCRIPTION                  |   11 ++++++-----
 MD5                          |   20 ++++++++++----------
 build/vignette.rds           |binary
 inst/CITATION                |   31 +++++++++++++++++++------------
 inst/doc/article.Rnw         |   19 +++++++++----------
 inst/doc/article.pdf         |binary
 inst/doc/gettingstarted.html |    4 ++--
 man/ar_ms.Rd                 |    7 ++++---
 man/run_mcstudy.Rd           |    4 ++--
 vignettes/article.Rnw        |   19 +++++++++----------
 vignettes/bibliography.bib   |   36 ++++++++++++++++++++++++------------
 11 files changed, 85 insertions(+), 66 deletions(-)

More information about scoringRules at CRAN
Permanent link

Package clustrd updated to version 1.3.4 with previous version 1.3.2 dated 2019-07-11

Title: Methods for Joint Dimension Reduction and Clustering
Description: A class of methods that combine dimension reduction and clustering of continuous, categorical or mixed-type data. For continuous data, the package contains implementations of factorial K-means (Vichi and Kiers 2001; <DOI:10.1016/S0167-9473(00)00064-5>) and reduced K-means (De Soete and Carroll 1994; <DOI:10.1007/978-3-642-51175-2_24>); both methods that combine principal component analysis with K-means clustering. For categorical data, the package provides MCA K-means (Hwang, Dillon and Takane 2006; <DOI:10.1007/s11336-004-1173-x>), i-FCB (Iodice D'Enza and Palumbo 2013, <DOI:10.1007/s00180-012-0329-x>) and Cluster Correspondence Analysis (van de Velden, Iodice D'Enza and Palumbo 2017; <DOI:10.1007/s11336-016-9514-0>), which combine multiple correspondence analysis with K-means. For mixed-type data, it provides mixed Reduced K-means and mixed Factorial K-means (van de Velden, Iodice D'Enza and Markos 2019; <DOI:10.1002/wics.1456>), which combine PCA for mixed-type data with K-means.
Author: Angelos Markos [aut, cre], Alfonso Iodice D'Enza [aut], Michel van de Velden [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>

Diff between clustrd versions 1.3.2 dated 2019-07-11 and 1.3.4 dated 2019-08-20

 DESCRIPTION            |    8 ++++----
 MD5                    |   20 ++++++++++----------
 R/clu_means.R          |    2 +-
 R/clusmca.R            |    4 ++--
 R/outOfIndependence.r  |   13 ++++++++-----
 R/plot.clusmca.R       |   31 +++++++++++++++++++++++++------
 R/plot.cluspca.R       |    8 ++++----
 R/plot.cluspcamix.R    |    8 ++++----
 man/plot.clusmca.Rd    |    4 +++-
 man/plot.cluspca.Rd    |    4 +++-
 man/plot.cluspcamix.Rd |    3 ++-
 11 files changed, 66 insertions(+), 39 deletions(-)

More information about clustrd at CRAN
Permanent link

Package xlink updated to version 1.0.1 with previous version 1.0.0 dated 2019-07-03

Title: Genetic Association Models for X-Chromosome SNPS on Continuous, Binary and Survival Outcomes
Description: The expression of X-chromosome undergoes three possible biological processes: X-chromosome inactivation (XCI), escape of the X-chromosome inactivation (XCI-E),and skewed X-chromosome inactivation (XCI-S). To analyze the X-linked genetic association for phenotype such as continuous, binary, and time-to-event outcomes with the actual process unknown, we propose a unified approach of maximizing the likelihood or partial likelihood over all of the potential biological processes. The methods are described in Wei Xu, Meiling Hao (2017) <doi:10.1002/gepi.22097>. And also see Dongxiao Han, Meiling Hao, Lianqiang Qu, Wei Xu (2019) <doi:10.1177/0962280219859037>.
Author: Wei Xu [aut], Meiling Hao [aut], Yi Zhu [cre]
Maintainer: Yi Zhu <yizhu87@gmail.com>

Diff between xlink versions 1.0.0 dated 2019-07-03 and 1.0.1 dated 2019-08-20

 DESCRIPTION          |    9 +-
 MD5                  |   20 ++---
 NEWS.md              |    7 +
 R/MAF.R              |    8 +-
 R/select_output.R    |  188 ++++++++++++++++++++++++++++-----------------------
 R/xlink_fit.R        |   47 ++++++------
 inst/doc/xlink.Rmd   |   15 ----
 inst/doc/xlink.html  |   25 ++++--
 man/select_output.Rd |    2 
 man/xlink_fit.Rd     |    2 
 vignettes/xlink.Rmd  |   15 ----
 11 files changed, 178 insertions(+), 160 deletions(-)

More information about xlink at CRAN
Permanent link

Package Seurat updated to version 3.1.0 with previous version 3.0.2 dated 2019-06-14

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 Butler A and Satija R (2017) <doi:10.1101/164889> 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 3.0.2 dated 2019-06-14 and 3.1.0 dated 2019-08-20

 DESCRIPTION                             |   23 
 MD5                                     |  108 +-
 NAMESPACE                               |   20 
 NEWS.md                                 |   30 
 R/RcppExports.R                         |    4 
 R/clustering.R                          |  276 ++++-
 R/convenience.R                         |    3 
 R/differential_expression.R             |   25 
 R/dimensional_reduction.R               |  176 ++-
 R/generics.R                            |   23 
 R/integration.R                         | 1483 +++++++++++++++++++++++++-------
 R/objects.R                             |  354 +++++++
 R/preprocessing.R                       |  371 ++++++--
 R/tree.R                                |    7 
 R/utilities.R                           |  229 +++-
 R/visualization.R                       |  511 ++++++++---
 R/zzz.R                                 |   16 
 README.md                               |    9 
 man/ALRAChooseKPlot.Rd                  |    4 
 man/AnchorSet-class.Rd                  |    2 
 man/Assays.Rd                           |only
 man/BuildClusterTree.Rd                 |    8 
 man/CellScatter.Rd                      |    4 
 man/CollapseEmbeddingOutliers.Rd        |only
 man/ColorDimSplit.Rd                    |only
 man/DietSeurat.Rd                       |    8 
 man/DoHeatmap.Rd                        |   11 
 man/DotPlot.Rd                          |    4 
 man/FeaturePlot.Rd                      |   20 
 man/FeatureScatter.Rd                   |    4 
 man/FindClusters.Rd                     |    7 
 man/FindIntegrationAnchors.Rd           |   60 -
 man/FindNeighbors.Rd                    |   21 
 man/FindTransferAnchors.Rd              |   18 
 man/GetResidual.Rd                      |   12 
 man/IntegrateData.Rd                    |   14 
 man/LogNormalize.Rd                     |    4 
 man/MapQuery.Rd                         |only
 man/MixingMetric.Rd                     |   11 
 man/PairwiseIntegrateReference.Rd       |only
 man/PrepSCTIntegration.Rd               |only
 man/Reductions.Rd                       |only
 man/RelativeCounts.Rd                   |    4 
 man/RunALRA.Rd                          |   31 
 man/RunCCA.Rd                           |    8 
 man/RunLSI.Rd                           |    6 
 man/RunUMAP.Rd                          |   31 
 man/SelectIntegrationFeatures.Rd        |   10 
 man/Seurat-package.Rd                   |   11 
 man/SplitObject.Rd                      |    4 
 man/TransferData.Rd                     |   19 
 man/VizDimLoadings.Rd                   |   13 
 src/RcppExports.cpp                     |   13 
 src/data_manipulation.cpp               |    7 
 src/data_manipulation.h                 |    1 
 tests/testthat/test_data_manipulation.R |   14 
 tests/testthat/test_objects.R           |   30 
 tests/testthat/test_preprocessing.R     |   19 
 tests/testthat/test_visualization.R     |only
 59 files changed, 3185 insertions(+), 916 deletions(-)

More information about Seurat at CRAN
Permanent link

Package orthoDr updated to version 0.6.2 with previous version 0.5 dated 2018-03-25

Title: Semi-Parametric Dimension Reduction Models Using Orthogonality Constrained Optimization
Description: Utilize an orthogonality constrained optimization algorithm of Wen & Yin (2013) <DOI:10.1007/s10107-012-0584-1> to solve a variety of dimension reduction problems in the semiparametric framework, such as Ma & Zhu (2012) <DOI:10.1080/01621459.2011.646925>, Ma & Zhu (2013) <DOI:10.1214/12-AOS1072>, Sun, Zhu, Wang & Zeng (2017) <arXiv:1704.05046> and Zhou & Zhu (2018+) <arXiv:1802.06156>. It also serves as a general purpose optimization solver for problems with orthogonality constraints. Parallel computing for approximating the gradient is enabled through `OpenMP'.
Author: Ruilin Zhao, Ruoqing Zhu, Jiyang Zhang, Wenzhuo Zhou and Peng Xu
Maintainer: Ruoqing Zhu <teazrq@gmail.com>

Diff between orthoDr versions 0.5 dated 2018-03-25 and 0.6.2 dated 2019-08-20

 orthoDr-0.5/orthoDr/man/predict.Rd                 |only
 orthoDr-0.6.2/orthoDr/DESCRIPTION                  |   16 -
 orthoDr-0.6.2/orthoDr/MD5                          |   93 ++++---
 orthoDr-0.6.2/orthoDr/NAMESPACE                    |    2 
 orthoDr-0.6.2/orthoDr/R/RcppExports.R              |   76 ++++++
 orthoDr-0.6.2/orthoDr/R/distance.r                 |   13 -
 orthoDr-0.6.2/orthoDr/R/orthoDr_pdose.r            |only
 orthoDr-0.6.2/orthoDr/R/orthoDr_reg.r              |    8 
 orthoDr-0.6.2/orthoDr/R/orthoDr_surv.r             |    4 
 orthoDr-0.6.2/orthoDr/R/ortho_optim.r              |  245 ++++++++++-----------
 orthoDr-0.6.2/orthoDr/R/pSAVE.r                    |only
 orthoDr-0.6.2/orthoDr/R/predict.r                  |  100 +++++++-
 orthoDr-0.6.2/orthoDr/R/print.r                    |   12 -
 orthoDr-0.6.2/orthoDr/R/skcm.r                     |    2 
 orthoDr-0.6.2/orthoDr/inst/CITATION                |   68 +++--
 orthoDr-0.6.2/orthoDr/inst/NEWS                    |   12 +
 orthoDr-0.6.2/orthoDr/man/distance.Rd              |    2 
 orthoDr-0.6.2/orthoDr/man/dosepred.Rd              |only
 orthoDr-0.6.2/orthoDr/man/gen_solver.Rd            |    4 
 orthoDr-0.6.2/orthoDr/man/orthoDr_pdose.Rd         |only
 orthoDr-0.6.2/orthoDr/man/orthoDr_reg.Rd           |    6 
 orthoDr-0.6.2/orthoDr/man/orthoDr_surv.Rd          |    4 
 orthoDr-0.6.2/orthoDr/man/ortho_optim.Rd           |    4 
 orthoDr-0.6.2/orthoDr/man/pSAVE.Rd                 |only
 orthoDr-0.6.2/orthoDr/man/pdose_direct_solver.Rd   |only
 orthoDr-0.6.2/orthoDr/man/pdose_semi_solver.Rd     |only
 orthoDr-0.6.2/orthoDr/man/phd_solver.Rd            |    4 
 orthoDr-0.6.2/orthoDr/man/predict.orthoDr.Rd       |only
 orthoDr-0.6.2/orthoDr/man/predict_orthoDr_pdose.Rd |only
 orthoDr-0.6.2/orthoDr/man/predict_orthoDr_reg.Rd   |    2 
 orthoDr-0.6.2/orthoDr/man/predict_orthoDr_surv.Rd  |    2 
 orthoDr-0.6.2/orthoDr/man/save_solver.Rd           |    4 
 orthoDr-0.6.2/orthoDr/man/sir_solver.Rd            |    4 
 orthoDr-0.6.2/orthoDr/man/skcm.melgene.Rd          |    2 
 orthoDr-0.6.2/orthoDr/man/surv_dm_solver.Rd        |    4 
 orthoDr-0.6.2/orthoDr/man/surv_dn_solver.Rd        |    4 
 orthoDr-0.6.2/orthoDr/man/surv_forward_solver.Rd   |    4 
 orthoDr-0.6.2/orthoDr/src/Makevars                 |    2 
 orthoDr-0.6.2/orthoDr/src/Makevars.win             |    4 
 orthoDr-0.6.2/orthoDr/src/RcppExports.cpp          |   76 ++++++
 orthoDr-0.6.2/orthoDr/src/gen_solver.cpp           |   34 ++
 orthoDr-0.6.2/orthoDr/src/orthoDr_gen.h            |only
 orthoDr-0.6.2/orthoDr/src/orthoDr_pdose.h          |only
 orthoDr-0.6.2/orthoDr/src/orthoDr_reg.h            |only
 orthoDr-0.6.2/orthoDr/src/orthoDr_surv.h           |only
 orthoDr-0.6.2/orthoDr/src/pdose_direct_solver.cpp  |only
 orthoDr-0.6.2/orthoDr/src/pdose_kernel_dose.cpp    |only
 orthoDr-0.6.2/orthoDr/src/pdose_semi_solver.cpp    |only
 orthoDr-0.6.2/orthoDr/src/reg_local_solver.cpp     |   52 ++++
 orthoDr-0.6.2/orthoDr/src/reg_phd_solver.cpp       |   25 ++
 orthoDr-0.6.2/orthoDr/src/reg_save_solver.cpp      |   31 ++
 orthoDr-0.6.2/orthoDr/src/reg_seff_solver.cpp      |   27 ++
 orthoDr-0.6.2/orthoDr/src/reg_sir_solver.cpp       |   25 ++
 orthoDr-0.6.2/orthoDr/src/surv_dm_solver.cpp       |    3 
 orthoDr-0.6.2/orthoDr/src/surv_dn_solver.cpp       |    3 
 orthoDr-0.6.2/orthoDr/src/surv_forward_solver.cpp  |    3 
 56 files changed, 719 insertions(+), 267 deletions(-)

More information about orthoDr at CRAN
Permanent link

Package kernscr updated to version 1.0.5 with previous version 1.0.3 dated 2016-06-28

Title: Kernel Machine Score Test for Semi-Competing Risks
Description: Kernel Machine Score Test for Pathway Analysis in the Presence of Semi-Competing Risks. Method is detailed in: Neykov, Hejblum & Sinnott (2018) <doi: 10.1177/0962280216653427>.
Author: Matey Neykov [aut], Boris P Hejblum [aut, cre], Jennifer A Sinnot [aut]
Maintainer: Boris P Hejblum <boris.hejblum@u-bordeaux.fr>

Diff between kernscr versions 1.0.3 dated 2016-06-28 and 1.0.5 dated 2019-08-20

 kernscr-1.0.3/kernscr/README                   |only
 kernscr-1.0.5/kernscr/DESCRIPTION              |   27 
 kernscr-1.0.5/kernscr/LICENSE                  |  678 ++++++++++++-------------
 kernscr-1.0.5/kernscr/MD5                      |   70 +-
 kernscr-1.0.5/kernscr/NEWS                     |    4 
 kernscr-1.0.5/kernscr/R/Ahat.R                 |   48 -
 kernscr-1.0.5/kernscr/R/M_vec.R                |  148 ++---
 kernscr-1.0.5/kernscr/R/PI_0.R                 |   34 -
 kernscr-1.0.5/kernscr/R/PI_1.R                 |   36 -
 kernscr-1.0.5/kernscr/R/PI_2.R                 |   48 -
 kernscr-1.0.5/kernscr/R/VTM.R                  |   26 
 kernscr-1.0.5/kernscr/R/compute_all_tests.R    |  552 ++++++++++----------
 kernscr-1.0.5/kernscr/R/dM.R                   |   22 
 kernscr-1.0.5/kernscr/R/findRhoInterval.R      |  206 +++----
 kernscr-1.0.5/kernscr/R/kerneval.R             |  266 ++++-----
 kernscr-1.0.5/kernscr/R/kernscr-package.R      |    8 
 kernscr-1.0.5/kernscr/R/lambda.R               |  114 ++--
 kernscr-1.0.5/kernscr/R/plot_kernscr.R         |  296 +++++-----
 kernscr-1.0.5/kernscr/R/sim_SCR_data.R         |  152 ++---
 kernscr-1.0.5/kernscr/R/vijver.R               |   18 
 kernscr-1.0.5/kernscr/README.md                |only
 kernscr-1.0.5/kernscr/inst/CITATION            |   21 
 kernscr-1.0.5/kernscr/man/Ahat.Rd              |    5 
 kernscr-1.0.5/kernscr/man/M_vec.Rd             |    1 
 kernscr-1.0.5/kernscr/man/PI_0.Rd              |    1 
 kernscr-1.0.5/kernscr/man/PI_1.Rd              |    1 
 kernscr-1.0.5/kernscr/man/PI_2.Rd              |    1 
 kernscr-1.0.5/kernscr/man/VTM.Rd               |    1 
 kernscr-1.0.5/kernscr/man/cancer_pathways.Rd   |   19 
 kernscr-1.0.5/kernscr/man/compute_all_tests.Rd |   17 
 kernscr-1.0.5/kernscr/man/dM.Rd                |    5 
 kernscr-1.0.5/kernscr/man/findRhoInterval.Rd   |   11 
 kernscr-1.0.5/kernscr/man/kernelEval.Rd        |    7 
 kernscr-1.0.5/kernscr/man/kernscr-package.Rd   |   17 
 kernscr-1.0.5/kernscr/man/lambda.Rd            |    1 
 kernscr-1.0.5/kernscr/man/plot_kernscr.Rd      |    3 
 kernscr-1.0.5/kernscr/man/sim_SCR_data.Rd      |    5 
 37 files changed, 1433 insertions(+), 1436 deletions(-)

More information about kernscr at CRAN
Permanent link

Package gtsummary updated to version 1.2.1 with previous version 1.2.0 dated 2019-08-19

Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers. The package is enhanced when the 'gt' package is installed. Use this code to install: 'remotes::install_github("rstudio/gt")'.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>), Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>), Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>), Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>), Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>), Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>), Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

Diff between gtsummary versions 1.2.0 dated 2019-08-19 and 1.2.1 dated 2019-08-20

 DESCRIPTION                  |    6 
 MD5                          |   30 +--
 NEWS.md                      |    8 
 R/add_p.R                    |   46 ++--
 R/utils-add_p.R              |   41 +++-
 inst/doc/tbl_regression.R    |    3 
 inst/doc/tbl_regression.Rmd  |    6 
 inst/doc/tbl_regression.html |  351 +++++++++++++++++------------------
 inst/doc/tbl_summary.R       |    3 
 inst/doc/tbl_summary.Rmd     |    6 
 inst/doc/tbl_summary.html    |  421 +++++++++++++++++++++----------------------
 man/add_p.Rd                 |   14 -
 man/figures/add_p_ex2.png    |binary
 tests/testthat/test-add_p.R  |   10 +
 vignettes/tbl_regression.Rmd |    6 
 vignettes/tbl_summary.Rmd    |    6 
 16 files changed, 496 insertions(+), 461 deletions(-)

More information about gtsummary at CRAN
Permanent link

Package dlsem updated to version 2.4.3 with previous version 2.4.2 dated 2019-05-27

Title: Distributed-Lag Linear Structural Equation Models
Description: Inference functionalities for distributed-lag linear structural equation models (DLSEMs). DLSEMs are Markovian structural causal models where each factor of the joint probability distribution is a distributed-lag linear regression (Magrini, 2018 <doi:10.2478/bile-2018-0012>; Magrini et al., 2019 <doi:10.1007/s11135-019-00855-z>). DLSEMs account for temporal delays in the dependence relationships among the variables and allow to perform dynamic causal inference by assessing causal effects at different time lags. Endpoint-constrained quadratic, quadratic decreasing and gamma lag shapes are available.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <alessandro.magrini@unifi.it>

Diff between dlsem versions 2.4.2 dated 2019-05-27 and 2.4.3 dated 2019-08-20

 Changelog                    |   52 
 DESCRIPTION                  |   10 
 MD5                          |   39 
 NAMESPACE                    |   11 
 R/dlsem.r                    | 2329 ++++++++++++++++++++++++-------------------
 build/vignette.rds           |binary
 inst/doc/dlsem_vignette.R    |   38 
 inst/doc/dlsem_vignette.Rnw  |  119 +-
 inst/doc/dlsem_vignette.pdf  |binary
 man/as.graphNEL.Rd           |    4 
 man/auto.lagPlot.Rd          |    5 
 man/autoCode.Rd              |only
 man/causalEff.Rd             |    2 
 man/dlsem-package.Rd         |   10 
 man/dlsem.Rd                 |  159 +-
 man/isIndep.Rd               |    4 
 man/lagPlot.Rd               |    8 
 man/lagShapes.Rd             |only
 man/quec.lag.Rd              |   16 
 man/residualPlot.Rd          |only
 man/unirootTest.Rd           |   20 
 vignettes/dlsem_vignette.Rnw |  119 +-
 22 files changed, 1683 insertions(+), 1262 deletions(-)

More information about dlsem at CRAN
Permanent link

Package bestNormalize updated to version 1.4.2 with previous version 1.4.0 dated 2019-05-13

Title: Normalizing Transformation Functions
Description: Estimate a suite of normalizing transformations, including a new adaptation of a technique based on ranks which can guarantee normally distributed transformed data if there are no ties: ordered quantile normalization (ORQ). ORQ normalization combines a rank-mapping approach with a shifted logit approximation that allows the transformation to work on data outside the original domain. It is also able to handle new data within the original domain via linear interpolation. The package is built to estimate the best normalizing transformation for a vector consistently and accurately. It implements the Box-Cox transformation, the Yeo-Johnson transformation, three types of Lambert WxF transformations, and the ordered quantile normalization transformation. It also estimates the normalization efficacy of other commonly used transformations.
Author: Ryan Andrew Peterson [aut, cre]
Maintainer: Ryan Andrew Peterson <ryan.a.peterson@cuanschutz.edu>

Diff between bestNormalize versions 1.4.0 dated 2019-05-13 and 1.4.2 dated 2019-08-20

 DESCRIPTION                         |   12 
 MD5                                 |  106 +-
 NAMESPACE                           |  124 +--
 NEWS.md                             |  131 +--
 R/arcsinh_x.R                       |  200 ++--
 R/bestNormalize-package.R           |   22 
 R/bestNormalize.R                   |  892 ++++++++++-----------
 R/binarize.R                        |  214 ++---
 R/boxcox.R                          |  324 +++----
 R/data.R                            |   36 
 R/exp_x.R                           |  218 ++---
 R/lambert.R                         |  314 +++----
 R/log_x.R                           |  256 +++---
 R/no_transform.R                    |  220 ++---
 R/orderNorm.R                       |  460 +++++------
 R/plots.R                           |  262 +++---
 R/sqrt_x.R                          |  228 ++---
 R/yeojohnson.R                      |  384 ++++-----
 README.md                           |  294 +++----
 build/vignette.rds                  |binary
 inst/CITATION                       |   27 
 inst/doc/bestNormalize.R            |  436 +++++-----
 inst/doc/bestNormalize.Rmd          |  796 +++++++++----------
 inst/doc/bestNormalize.html         | 1484 ++++++++++++++++++------------------
 man/arcsinh_x.Rd                    |  128 +--
 man/autotrader.Rd                   |   58 -
 man/bestNormalize-package.Rd        |   52 -
 man/bestNormalize.Rd                |  320 +++----
 man/binarize.Rd                     |  124 +--
 man/boxcox.Rd                       |  146 +--
 man/exp_x.Rd                        |  126 +--
 man/lambert.Rd                      |  186 ++--
 man/log_x.Rd                        |  150 +--
 man/no_transform.Rd                 |  132 +--
 man/orderNorm.Rd                    |  202 ++--
 man/plot.bestNormalize.Rd           |  100 +-
 man/sqrt_x.Rd                       |  134 +--
 man/yeojohnson.Rd                   |  162 +--
 tests/testthat.R                    |    8 
 tests/testthat/test_arcsinh_x.R     |  126 +--
 tests/testthat/test_bestNormalize.R |  212 ++---
 tests/testthat/test_binarize.R      |  112 +-
 tests/testthat/test_bn_parallel.R   |   84 +-
 tests/testthat/test_boxcox.R        |  140 +--
 tests/testthat/test_exp_x.R         |  126 +--
 tests/testthat/test_lambert.R       |  190 ++--
 tests/testthat/test_log_x.R         |  170 ++--
 tests/testthat/test_no_transform.R  |  126 +--
 tests/testthat/test_orderNorm.R     |   64 -
 tests/testthat/test_plot_methods.R  |   76 -
 tests/testthat/test_print_methods.R |  110 +-
 tests/testthat/test_sqrt_x.R        |  146 +--
 tests/testthat/test_yeojohnson.R    |  130 +--
 vignettes/bestNormalize.Rmd         |  796 +++++++++----------
 54 files changed, 6042 insertions(+), 6034 deletions(-)

More information about bestNormalize at CRAN
Permanent link

Package BallMapper updated to version 0.2.0 with previous version 0.1.0 dated 2019-07-26

Title: The Ball Mapper Algorithm
Description: The core algorithm is described in "Ball mapper: a shape summary for topological data analysis" by Pawel Dlotko, (2019) <arXiv:1901.07410>. Please consult the following youtube video <https://www.youtube.com/watch?v=M9Dm1nl_zSQfor> the idea of functionality. Ball Mapper provide a topologically accurate summary of a data in a form of an abstract graph. To create it, please provide the coordinates of points (in the points array), values of a function of interest at those points (can be initialized randomly if you do not have it) and the value epsilon which is the radius of the ball in the Ball Mapper construction. It can be understood as the minimal resolution on which we use to create the model of the data.
Author: Pawel Dlotko [aut, cre]
Maintainer: Pawel Dlotko <pdlotko@gmail.com>

Diff between BallMapper versions 0.1.0 dated 2019-07-26 and 0.2.0 dated 2019-08-20

 DESCRIPTION                                                     |   11 
 MD5                                                             |   26 
 NAMESPACE                                                       |   12 
 R/BallMapper.R                                                  |  519 +++++++++-
 R/test_BallMapper.R                                             |   46 
 man/ColorIgraphPlot.Rd                                          |   17 
 man/GrayscaleIgraphPlot.Rd                                      |   14 
 man/colorByAllVariables.Rd                                      |only
 man/colorByAverageValueOfOtherVariable.Rd                       |only
 man/colorByStDevValueOfOtherVariable.Rd                         |only
 man/color_by_distance_to_reference_points.Rd                    |only
 man/coordinates_of_points_in_subcollection.Rd                   |only
 man/find_dominant_difference_using_averages.Rd                  |only
 man/find_dominant_difference_using_averages_normalized_by_sd.Rd |only
 man/normalize_to_average_0_stdev_1.Rd                           |only
 man/normalize_to_min_0_max_1.Rd                                 |only
 man/pointToBallList.Rd                                          |    4 
 man/points_covered_by_landmarks.Rd                              |only
 man/readBallMapperGraphFromFile.Rd                              |only
 man/storeBallMapperGraphInFile.Rd                               |only
 20 files changed, 619 insertions(+), 30 deletions(-)

More information about BallMapper at CRAN
Permanent link

Package vcr updated to version 0.3.0 with previous version 0.2.6 dated 2019-02-12

Title: Record 'HTTP' Calls to Disk
Description: Record test suite 'HTTP' requests and replays them during future runs. A port of the Ruby gem of the same name (<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr' R package for matching 'HTTP' requests by various rules ('HTTP' method, 'URL', query parameters, headers, body, etc.), and then caching real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests matching any previous requests in the same 'cassette' use a cached 'HTTP' response.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <sckott@protonmail.com>

Diff between vcr versions 0.2.6 dated 2019-02-12 and 0.3.0 dated 2019-08-20

 vcr-0.2.6/vcr/inst/doc/vcr_vignette.R                               |only
 vcr-0.2.6/vcr/inst/doc/vcr_vignette.Rmd                             |only
 vcr-0.2.6/vcr/inst/doc/vcr_vignette.html                            |only
 vcr-0.2.6/vcr/vignettes/vcr_vignette.Rmd                            |only
 vcr-0.3.0/vcr/DESCRIPTION                                           |   10 
 vcr-0.3.0/vcr/MD5                                                   |   76 +++---
 vcr-0.3.0/vcr/NEWS.md                                               |   21 +
 vcr-0.3.0/vcr/R/cassette_class.R                                    |  119 ++++++++-
 vcr-0.3.0/vcr/R/error_suggestions.R                                 |   18 -
 vcr-0.3.0/vcr/R/errors.R                                            |    4 
 vcr-0.3.0/vcr/R/http_interaction_list.R                             |   12 -
 vcr-0.3.0/vcr/R/insert_cassette.R                                   |    7 
 vcr-0.3.0/vcr/R/request_handler-crul.R                              |   50 ++++
 vcr-0.3.0/vcr/R/request_handler-httr.R                              |   42 +++
 vcr-0.3.0/vcr/R/request_handler.R                                   |   29 ++
 vcr-0.3.0/vcr/R/request_matcher_registry.R                          |    2 
 vcr-0.3.0/vcr/R/use_cassette.R                                      |   11 
 vcr-0.3.0/vcr/R/vcr-package.R                                       |    2 
 vcr-0.3.0/vcr/R/vcr_setup.R                                         |    2 
 vcr-0.3.0/vcr/R/zzz.R                                               |    6 
 vcr-0.3.0/vcr/README.md                                             |   10 
 vcr-0.3.0/vcr/build/vignette.rds                                    |binary
 vcr-0.3.0/vcr/inst/doc/configuration.Rmd                            |    2 
 vcr-0.3.0/vcr/inst/doc/configuration.html                           |  120 +++++-----
 vcr-0.3.0/vcr/inst/doc/request_matching.Rmd                         |    2 
 vcr-0.3.0/vcr/inst/doc/request_matching.html                        |  120 +++++-----
 vcr-0.3.0/vcr/inst/doc/vcr.R                                        |only
 vcr-0.3.0/vcr/inst/doc/vcr.Rmd                                      |only
 vcr-0.3.0/vcr/inst/doc/vcr.html                                     |only
 vcr-0.3.0/vcr/man/Cassette.Rd                                       |    5 
 vcr-0.3.0/vcr/man/RequestHandler.Rd                                 |    2 
 vcr-0.3.0/vcr/man/RequestHandlerCrul.Rd                             |   50 ++++
 vcr-0.3.0/vcr/man/RequestHandlerHttr.Rd                             |   21 +
 vcr-0.3.0/vcr/man/insert_cassette.Rd                                |    9 
 vcr-0.3.0/vcr/man/use_cassette.Rd                                   |    9 
 vcr-0.3.0/vcr/man/vcr.Rd                                            |    2 
 vcr-0.3.0/vcr/tests/testthat/test-Cassette.R                        |    3 
 vcr-0.3.0/vcr/tests/testthat/test-RequestHandler.R                  |only
 vcr-0.3.0/vcr/tests/testthat/test-ause_cassette_match_requests_on.R |only
 vcr-0.3.0/vcr/tests/testthat/test-ause_cassette_re_record.R         |only
 vcr-0.3.0/vcr/tests/testthat/test-cassette_options.R                |only
 vcr-0.3.0/vcr/tests/testthat/test-errors.R                          |   14 +
 vcr-0.3.0/vcr/vignettes/configuration.Rmd                           |    2 
 vcr-0.3.0/vcr/vignettes/request_matching.Rmd                        |    2 
 vcr-0.3.0/vcr/vignettes/vcr.Rmd                                     |only
 45 files changed, 569 insertions(+), 215 deletions(-)

More information about vcr at CRAN
Permanent link

Package MazamaCoreUtils updated to version 0.3.1 with previous version 0.2.0 dated 2019-07-18

Title: Utility Functions for Production R Code
Description: A suite of utility functions providing functionality commonly needed for production level projects such as logging, error handling, and cache management.
Author: Jonathan Callahan [aut, cre], Spencer Pease [aut], Thomas Bergamaschi [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>

Diff between MazamaCoreUtils versions 0.2.0 dated 2019-07-18 and 0.3.1 dated 2019-08-20

 MazamaCoreUtils-0.2.0/MazamaCoreUtils/R/utils-time.R                          |only
 MazamaCoreUtils-0.2.0/MazamaCoreUtils/tests/testthat/index.html               |only
 MazamaCoreUtils-0.2.0/MazamaCoreUtils/tests/testthat/test-logging.R           |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/DESCRIPTION                             |   11 -
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/MD5                                     |   50 ++++--
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/NAMESPACE                               |    5 
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/NEWS.md                                 |   55 ++++++-
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/R/cacheManagement.R                     |   60 +++----
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/R/data.R                                |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/R/dateRange.R                           |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/R/functionArgument_linting.R            |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/R/initializeLogging.R                   |    5 
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/R/parseDatetime.R                       |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/R/timeRange.R                           |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/R/utils-tidyeval-data.R                 |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/README.md                               |    5 
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/build/vignette.rds                      |binary
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/data                                    |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/inst/doc/date-parsing.R                 |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/inst/doc/date-parsing.Rmd               |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/inst/doc/date-parsing.html              |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/inst/doc/error-handling.html            |   10 -
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/inst/doc/logging.html                   |   32 ++--
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/man/dateRange.Rd                        |   78 ++++++----
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/man/lintFunctionArgs.Rd                 |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/man/manageCache.Rd                      |    8 -
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/man/parseDatetime.Rd                    |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/man/tidyeval-data.Rd                    |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/man/timeRange.Rd                        |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/man/timezoneLintRules.Rd                |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/tests/testthat/test-cacheManagement.R   |   70 +++++---
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/tests/testthat/test-dateRange.R         |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/tests/testthat/test-errorHandling.R     |   33 +---
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/tests/testthat/test-initializeLogging.R |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/tests/testthat/test-parseDatetime.R     |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/tests/testthat/test-pylogger.R          |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/tests/testthat/test-timeRange.R         |only
 MazamaCoreUtils-0.3.1/MazamaCoreUtils/vignettes/date-parsing.Rmd              |only
 38 files changed, 267 insertions(+), 155 deletions(-)

More information about MazamaCoreUtils at CRAN
Permanent link

Package RCzechia updated to version 1.4.2 with previous version 1.4.1 dated 2019-07-01

Title: Spatial Objects of the Czech Republic
Description: Administrative regions and other spatial objects of the Czech Republic.
Author: Jindra Lacko
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>

Diff between RCzechia versions 1.4.1 dated 2019-07-01 and 1.4.2 dated 2019-08-20

 DESCRIPTION                             |   12 ++--
 MD5                                     |   26 +++++-----
 NAMESPACE                               |    1 
 NEWS.md                                 |    5 ++
 R/KFME_grid.R                           |only
 R/geocode.R                             |    1 
 R/sysdata.rda                           |binary
 README.md                               |   13 +++++
 build/vignette.rds                      |binary
 inst/doc/vignette.R                     |   47 ++++++++++++++-----
 inst/doc/vignette.Rmd                   |   67 +++++++++++++++++++++------
 inst/doc/vignette.html                  |   78 ++++++++++++++++++++++++--------
 man/KFME_grid.Rd                        |only
 tests/testthat/test-1-data-structures.R |   46 ++++++++++++++++++
 vignettes/vignette.Rmd                  |   67 +++++++++++++++++++++------
 15 files changed, 287 insertions(+), 76 deletions(-)

More information about RCzechia at CRAN
Permanent link

Package GENEAread updated to version 2.0.7 with previous version 2.0.6 dated 2018-11-16

Title: Package for Reading Binary Files
Description: Functions and analytics for GENEA-compatible accelerometer data into R objects. See topic 'GENEAread' for an introduction to the package.
Author: Zhou Fang [aut], Joss Langford [aut], Charles Sweetland [aut, cre]
Maintainer: Charles Sweetland <charles@sweetland-solutions.co.uk>

Diff between GENEAread versions 2.0.6 dated 2018-11-16 and 2.0.7 dated 2019-08-20

 GENEAread-2.0.6/GENEAread/man/Convert.time.Rd     |only
 GENEAread-2.0.6/GENEAread/man/Recalibrate.Rd      |only
 GENEAread-2.0.7/GENEAread/DESCRIPTION             |   10 ++---
 GENEAread-2.0.7/GENEAread/MD5                     |   22 ++++++------
 GENEAread-2.0.7/GENEAread/NAMESPACE               |    2 -
 GENEAread-2.0.7/GENEAread/R/AccData.r             |    2 -
 GENEAread-2.0.7/GENEAread/R/GENEActiv.calibrate.r |   20 +++++------
 GENEAread-2.0.7/GENEAread/R/Recalibrate.R         |   39 +++++++++++++---------
 GENEAread-2.0.7/GENEAread/R/convert.time.R        |    4 +-
 GENEAread-2.0.7/GENEAread/R/header.info.R         |   29 ++++++++++++----
 GENEAread-2.0.7/GENEAread/R/read.bin.R            |    6 +--
 GENEAread-2.0.7/GENEAread/man/AccData.Rd          |    2 -
 GENEAread-2.0.7/GENEAread/man/convert.time.Rd     |only
 GENEAread-2.0.7/GENEAread/man/recalibrate.Rd      |only
 14 files changed, 79 insertions(+), 57 deletions(-)

More information about GENEAread at CRAN
Permanent link

Package blackbox updated to version 1.1.27 with previous version 1.1.25 dated 2018-06-08

Title: Black Box Optimization and Exploration of Parameter Space
Description: Performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. Includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (Rousset and Leblois, 2012 <doi:10.1093/molbev/MSR262>; Leblois et al., 2014 <doi:10.1093/molbev/msu212>; and see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary Kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.
Author: François Rousset [aut, cre, cph] (<https://orcid.org/0000-0003-4670-0371>), Raphaël Leblois [ctb] (<https://orcid.org/0000-0002-3051-4497>)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>

Diff between blackbox versions 1.1.25 dated 2018-06-08 and 1.1.27 dated 2019-08-20

 DESCRIPTION                                                                          |   19 -
 MD5                                                                                  |   22 -
 R/blackbox.R                                                                         |    4 
 R/volTriangulation.R                                                                 |   19 -
 inst/NEWS.Rd                                                                         |   10 
 tests/test-all.R                                                                     |    2 
 tests/tests_private/IVCP/nextpoints_1.txt                                            |  176 +++++-----
 tests/tests_private/IVCP/output_1.txt                                                |    8 
 tests/tests_private/IVCP/results_1.txt                                               |    4 
 tests/tests_private/Test_OnePop_ISM+SMM_ISstrict_Genepop+NexusFiles/nextpoints_1.txt |   68 +--
 tests/tests_private/Test_OnePop_ISM+SMM_ISstrict_Genepop+NexusFiles/output_1.txt     |    2 
 tests/tests_private/Test_OnePop_ISM+SMM_ISstrict_Genepop+NexusFiles/results_1.txt    |    4 
 12 files changed, 165 insertions(+), 173 deletions(-)

More information about blackbox at CRAN
Permanent link

Package overlapping updated to version 1.5.4 with previous version 1.5.3 dated 2019-05-28

Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more kernel density estimations from empirical data.
Author: Massimiliano Pastore
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>

Diff between overlapping versions 1.5.3 dated 2019-05-28 and 1.5.4 dated 2019-08-20

 DESCRIPTION         |    8 +--
 MD5                 |   10 ++--
 NEWS                |    5 ++
 R/boot.overlap.R    |   16 +++++-
 inst/CITATION       |   16 ++++++
 man/boot.overlap.Rd |  130 ++++++++++++++++++++++++++--------------------------
 6 files changed, 109 insertions(+), 76 deletions(-)

More information about overlapping at CRAN
Permanent link

Package mDAG updated to version 1.2.2 with previous version 1.2 dated 2019-03-13

Title: Inferring Causal Network from Mixed Observational Data Using a Directed Acyclic Graph
Description: Learning a mixed directed acyclic graph based on both continuous and categorical data.
Author: Wujuan Zhong, Li Dong, Quefeng Li, Xiaojing Zheng
Maintainer: Wujuan Zhong <zhongwujuan@gmail.com>

Diff between mDAG versions 1.2 dated 2019-03-13 and 1.2.2 dated 2019-08-20

 DESCRIPTION           |   10 +++++-----
 MD5                   |   16 ++++++++--------
 R/RcppExports.R       |   12 ++++++------
 R/mDAG.R              |    9 +++++----
 R/main.R              |    9 ++++++---
 R/multinom_BIC.R      |    2 +-
 man/mDAG.Rd           |   10 ++++++----
 src/Greedy_Search.cpp |   49 +++++++++++++++++++++++++++----------------------
 src/RcppExports.cpp   |   27 +++++++++++++++------------
 9 files changed, 79 insertions(+), 65 deletions(-)

More information about mDAG at CRAN
Permanent link

Package lgr updated to version 0.3.2 with previous version 0.3.1 dated 2019-06-13

Title: A Fully Featured Logging Framework
Description: A flexible, feature-rich yet light-weight logging framework based on 'R6' classes. It supports hierarchical loggers, custom log levels, arbitrary data fields in log events, logging to plaintext, 'JSON', (rotating) files, memory buffers, and databases, as well as email and push notifications. For a full list of features with examples please refer to the package vignette.
Author: Stefan Fleck [aut, cre] (<https://orcid.org/0000-0003-3344-9851>)
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>

Diff between lgr versions 0.3.1 dated 2019-06-13 and 0.3.2 dated 2019-08-20

 lgr-0.3.1/lgr/inst/benchmarks/benchmarks.html |only
 lgr-0.3.2/lgr/DESCRIPTION                     |   10 -
 lgr-0.3.2/lgr/MD5                             |   54 ++++----
 lgr-0.3.2/lgr/NAMESPACE                       |    1 
 lgr-0.3.2/lgr/NEWS.md                         |    6 
 lgr-0.3.2/lgr/R/Appender.R                    |  148 ++++++++++++++++++++++
 lgr-0.3.2/lgr/R/basic_config.R                |    2 
 lgr-0.3.2/lgr/R/log_levels.R                  |    2 
 lgr-0.3.2/lgr/build/vignette.rds              |binary
 lgr-0.3.2/lgr/inst/WORDLIST                   |    4 
 lgr-0.3.2/lgr/inst/doc/lgr.R                  |    6 
 lgr-0.3.2/lgr/inst/doc/lgr.Rmd                |   10 +
 lgr-0.3.2/lgr/inst/doc/lgr.html               |  168 +++++++++++++-------------
 lgr-0.3.2/lgr/man/Appender.Rd                 |    2 
 lgr-0.3.2/lgr/man/AppenderBuffer.Rd           |    1 
 lgr-0.3.2/lgr/man/AppenderConsole.Rd          |    1 
 lgr-0.3.2/lgr/man/AppenderDbi.Rd              |    1 
 lgr-0.3.2/lgr/man/AppenderFile.Rd             |    1 
 lgr-0.3.2/lgr/man/AppenderFileRotating.Rd     |    1 
 lgr-0.3.2/lgr/man/AppenderGmail.Rd            |    1 
 lgr-0.3.2/lgr/man/AppenderJson.Rd             |    1 
 lgr-0.3.2/lgr/man/AppenderPushbullet.Rd       |    1 
 lgr-0.3.2/lgr/man/AppenderRjdbc.Rd            |    1 
 lgr-0.3.2/lgr/man/AppenderSendmail.Rd         |    5 
 lgr-0.3.2/lgr/man/AppenderSyslog.Rd           |only
 lgr-0.3.2/lgr/man/AppenderTable.Rd            |    3 
 lgr-0.3.2/lgr/man/basic_config.Rd             |    2 
 lgr-0.3.2/lgr/tests/testthat/test_Appender.R  |   36 +++++
 lgr-0.3.2/lgr/vignettes/lgr.Rmd               |   10 +
 29 files changed, 347 insertions(+), 131 deletions(-)

More information about lgr at CRAN
Permanent link

Package bioacoustics updated to version 0.2.1 with previous version 0.2.0.1 dated 2019-06-09

Title: Analyse Audio Recordings and Automatically Extract Animal Vocalizations
Description: Contains all the necessary tools to process audio recordings of various formats (e.g., WAV, WAC, MP3, ZC), filter noisy files, display audio signals, detect and extract automatically acoustic features for further analysis such as classification.
Author: Jean Marchal [aut, cre], Francois Fabianek [aut], Christopher Scott [aut], Chris Corben [ctb, cph] (Read ZC files, original C code), David Riggs [ctb, cph] (Read GUANO metadata, original R code), Peter Wilson [ctb, cph] (Read ZC files, original R code), Wildlife Acoustics, inc. [ctb, cph] (Read WAC files, original C code), WavX, inc. [cph]
Maintainer: Jean Marchal <jean.marchal@wavx.ca>

Diff between bioacoustics versions 0.2.0.1 dated 2019-06-09 and 0.2.1 dated 2019-08-20

 bioacoustics-0.2.0.1/bioacoustics/R/metadata_zc.R           |only
 bioacoustics-0.2.0.1/bioacoustics/man/metadata_zc.Rd        |only
 bioacoustics-0.2.1/bioacoustics/DESCRIPTION                 |    6 
 bioacoustics-0.2.1/bioacoustics/MD5                         |  102 -
 bioacoustics-0.2.1/bioacoustics/NAMESPACE                   |   88 
 bioacoustics-0.2.1/bioacoustics/NEWS.md                     |  126 -
 bioacoustics-0.2.1/bioacoustics/R/BatBioacoustics.R         |  694 +++----
 bioacoustics-0.2.1/bioacoustics/R/BatClassify.R             |  460 ++--
 bioacoustics-0.2.1/bioacoustics/R/RcppExports.R             |   46 
 bioacoustics-0.2.1/bioacoustics/R/bioacoustics.R            |    4 
 bioacoustics-0.2.1/bioacoustics/R/metadata.R                |  140 -
 bioacoustics-0.2.1/bioacoustics/R/myotis-data.R             |   28 
 bioacoustics-0.2.1/bioacoustics/R/read_audio.R              |  544 ++---
 bioacoustics-0.2.1/bioacoustics/R/zc-data.R                 |   26 
 bioacoustics-0.2.1/bioacoustics/build/vignette.rds          |binary
 bioacoustics-0.2.1/bioacoustics/configure                   |   32 
 bioacoustics-0.2.1/bioacoustics/configure.ac                |    2 
 bioacoustics-0.2.1/bioacoustics/data/myotis.rda             |binary
 bioacoustics-0.2.1/bioacoustics/data/zc.rda                 |binary
 bioacoustics-0.2.1/bioacoustics/inst/doc/introduction.Rmd   |  678 +++----
 bioacoustics-0.2.1/bioacoustics/inst/doc/introduction.html  |    4 
 bioacoustics-0.2.1/bioacoustics/inst/doc/tutorial.R         |   95 -
 bioacoustics-0.2.1/bioacoustics/inst/doc/tutorial.Rmd       | 1106 ++++++------
 bioacoustics-0.2.1/bioacoustics/inst/doc/tutorial.html      |  106 -
 bioacoustics-0.2.1/bioacoustics/man/bioacoustics-package.Rd |  102 -
 bioacoustics-0.2.1/bioacoustics/man/blob_detection.Rd       |  190 +-
 bioacoustics-0.2.1/bioacoustics/man/dot-parse.timestamp.Rd  |   30 
 bioacoustics-0.2.1/bioacoustics/man/file_checks.Rd          |   30 
 bioacoustics-0.2.1/bioacoustics/man/file_type_guess.Rd      |   30 
 bioacoustics-0.2.1/bioacoustics/man/fspec.Rd                |  100 -
 bioacoustics-0.2.1/bioacoustics/man/guano_md.Rd             |   34 
 bioacoustics-0.2.1/bioacoustics/man/metadata.Rd             |   71 
 bioacoustics-0.2.1/bioacoustics/man/mp3_to_wav.Rd           |   38 
 bioacoustics-0.2.1/bioacoustics/man/myotis.Rd               |   54 
 bioacoustics-0.2.1/bioacoustics/man/plot_zc.Rd              |   88 
 bioacoustics-0.2.1/bioacoustics/man/read_audio.Rd           |   66 
 bioacoustics-0.2.1/bioacoustics/man/read_mp3.Rd             |   58 
 bioacoustics-0.2.1/bioacoustics/man/read_wac.Rd             |   62 
 bioacoustics-0.2.1/bioacoustics/man/read_wav.Rd             |   62 
 bioacoustics-0.2.1/bioacoustics/man/read_zc.Rd              |   46 
 bioacoustics-0.2.1/bioacoustics/man/resample.Rd             |   50 
 bioacoustics-0.2.1/bioacoustics/man/rotate90.Rd             |   24 
 bioacoustics-0.2.1/bioacoustics/man/spectro.Rd              |   96 -
 bioacoustics-0.2.1/bioacoustics/man/threshold_detection.Rd  |  238 +-
 bioacoustics-0.2.1/bioacoustics/man/to_dB.Rd                |   34 
 bioacoustics-0.2.1/bioacoustics/man/write_zc.Rd             |   44 
 bioacoustics-0.2.1/bioacoustics/src/Makevars.in             |    1 
 bioacoustics-0.2.1/bioacoustics/src/Makevars.win            |    1 
 bioacoustics-0.2.1/bioacoustics/src/bb_extract.cpp          |    2 
 bioacoustics-0.2.1/bioacoustics/src/bb_tools.h              |    2 
 bioacoustics-0.2.1/bioacoustics/src/read_wac.cpp            |    4 
 bioacoustics-0.2.1/bioacoustics/vignettes/introduction.Rmd  |  678 +++----
 bioacoustics-0.2.1/bioacoustics/vignettes/tutorial.Rmd      | 1106 ++++++------
 53 files changed, 3856 insertions(+), 3772 deletions(-)

More information about bioacoustics at CRAN
Permanent link

Package ssizeRNA updated to version 1.3.2 with previous version 1.3.1 dated 2019-02-19

Title: Sample Size Calculation for RNA-Seq Experimental Design
Description: We propose a procedure for sample size calculation while controlling false discovery rate for RNA-seq experimental design. Our procedure depends on the Voom method proposed for RNA-seq data analysis by Law et al. (2014) <DOI:10.1186/gb-2014-15-2-r29> and the sample size calculation method proposed for microarray experiments by Liu and Hwang (2007) <DOI:10.1093/bioinformatics/btl664>. We develop a set of functions that calculates appropriate sample sizes for two-sample t-test for RNA-seq experiments with fixed or varied set of parameters. The outputs also contain a plot of power versus sample size, a table of power at different sample sizes, and a table of critical test values at different sample sizes. To install this package, please use 'source("http://bioconductor.org/biocLite.R"); biocLite("ssizeRNA")'. For R version 3.5 or greater, please use 'if(!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")}; BiocManager::install("ssizeRNA")'.
Author: Ran Bi [aut, cre], Peng Liu [aut], Tim Triche [ctb]
Maintainer: Ran Bi <biranpier@gmail.com>

Diff between ssizeRNA versions 1.3.1 dated 2019-02-19 and 1.3.2 dated 2019-08-20

 DESCRIPTION                   |   14 ++++++++------
 MD5                           |   18 +++++++++---------
 build/vignette.rds            |binary
 inst/NEWS.txt                 |    5 +++++
 inst/doc/ssizeRNA.pdf         |binary
 man/check.power.Rd            |    9 ++++-----
 man/sim.counts.Rd             |    1 -
 man/ssize.twoSampVaryDelta.Rd |   15 +++++++--------
 man/ssizeRNA_single.Rd        |    9 ++++-----
 man/ssizeRNA_vary.Rd          |    9 ++++-----
 10 files changed, 41 insertions(+), 39 deletions(-)

More information about ssizeRNA at CRAN
Permanent link

Package comorbidity updated to version 0.5.0 with previous version 0.4.1 dated 2019-06-27

Title: Computing Comorbidity Scores
Description: Computing comorbidity scores such as the weighted Charlson score (Charlson, 1987 <doi:10.1016/0021-9681(87)90171-8>) and the Elixhauser comorbidity score (Elixhauser, 1998 <doi:10.1097/00005650-199801000-00004>) using ICD-9-CM or ICD-10 codes (Quan, 2005 <doi:10.1097/01.mlr.0000182534.19832.83>).
Author: Alessandro Gasparini [aut, cre] (<https://orcid.org/0000-0002-8319-7624>), Hojjat Salmasian [ctb] (ICD-9-CM scores), Jonathan Williman [ctb] (<https://orcid.org/0000-0001-5080-4435>)
Maintainer: Alessandro Gasparini <ag475@leicester.ac.uk>

Diff between comorbidity versions 0.4.1 dated 2019-06-27 and 0.5.0 dated 2019-08-20

 comorbidity-0.4.1/comorbidity/R/detect.R                        |only
 comorbidity-0.4.1/comorbidity/R/scores.R                        |only
 comorbidity-0.5.0/comorbidity/DESCRIPTION                       |   20 -
 comorbidity-0.5.0/comorbidity/MD5                               |   32 -
 comorbidity-0.5.0/comorbidity/NAMESPACE                         |    2 
 comorbidity-0.5.0/comorbidity/NEWS.md                           |    8 
 comorbidity-0.5.0/comorbidity/R/comorbidity-package.R           |    4 
 comorbidity-0.5.0/comorbidity/R/comorbidity.R                   |   42 +-
 comorbidity-0.5.0/comorbidity/R/data.R                          |    2 
 comorbidity-0.5.0/comorbidity/README.md                         |    2 
 comorbidity-0.5.0/comorbidity/build/partial.rdb                 |binary
 comorbidity-0.5.0/comorbidity/build/vignette.rds                |binary
 comorbidity-0.5.0/comorbidity/inst/doc/comorbidityscores.Rmd    |    2 
 comorbidity-0.5.0/comorbidity/inst/doc/comorbidityscores.html   |  194 +++++-----
 comorbidity-0.5.0/comorbidity/man/australia10.Rd                |    2 
 comorbidity-0.5.0/comorbidity/man/comorbidity.Rd                |    8 
 comorbidity-0.5.0/comorbidity/tests/testthat/test-comorbidity.R |   54 --
 comorbidity-0.5.0/comorbidity/vignettes/comorbidityscores.Rmd   |    2 
 18 files changed, 175 insertions(+), 199 deletions(-)

More information about comorbidity at CRAN
Permanent link

Package sugarbag updated to version 0.1.1 with previous version 0.1.0 dated 2019-06-14

Title: Create Tessellated Hexagon Maps
Description: Create a hexagon tilegram from spatial polygons. Each polygon is represented by a hexagon tile, placed as close to it's original centroid as possible, with a focus on maintaining spatial relationship to a focal point. Developed to aid visualisation and analysis of spatial distributions across Australia, which can be challenging due to the concentration of the population on the coast and wide open interior.
Author: Stephanie Kobakian [aut, cre], Dianne Cook [aut, ths]
Maintainer: Stephanie Kobakian <stephanie.kobakian@gmail.com>

Diff between sugarbag versions 0.1.0 dated 2019-06-14 and 0.1.1 dated 2019-08-20

 DESCRIPTION                              |   13 +--
 MD5                                      |   49 +++++++-----
 NAMESPACE                                |    1 
 NEWS.md                                  |only
 R/allocate.R                             |   44 +++++------
 R/closest_focal_point.R                  |   14 ++-
 R/create_centroids.R                     |    4 -
 R/create_hexmap.R                        |    6 -
 R/data.R                                 |   28 +++++++
 R/filter_grid_points.R                   |   24 +++---
 R/fortify_hexagon.R                      |    5 -
 R/fortify_sfc.R                          |    2 
 R/global.R                               |    4 -
 R/utils.R                                |only
 README.md                                |  121 +++++++++++++++++++++++--------
 build/vignette.rds                       |binary
 data/fp19.rda                            |only
 inst/doc/abs-data.html                   |    8 +-
 inst/doc/tasmania.R                      |    7 +
 inst/doc/tasmania.Rmd                    |    9 +-
 inst/doc/tasmania.html                   |   99 +++++++++++++------------
 man/allocate.Rd                          |    2 
 man/create_hexmap.Rd                     |    2 
 man/figures/README-animated-1.gif        |only
 man/figures/README-plot_facet-1.png      |binary
 man/figures/README-unnamed-chunk-2-1.gif |only
 man/figures/README-unnamed-chunk-7-1.gif |only
 man/fp19.Rd                              |only
 vignettes/tasmania.Rmd                   |    9 +-
 29 files changed, 288 insertions(+), 163 deletions(-)

More information about sugarbag at CRAN
Permanent link

Package suddengains updated to version 0.3.0 with previous version 0.2.1 dated 2019-05-21

Title: Identify Sudden Gains in Longitudinal Data
Description: Identify sudden gains based on the three criteria outlined by Tang and DeRubeis (1999) <doi:10.1037/0022-006X.67.6.894> to a selection of repeated measures. Sudden losses, defined as the opposite of sudden gains can also be identified. Two different datasets can be created, one including all sudden gains/losses and one including one selected sudden gain/loss for each case. It can extract scores around sudden gains/losses. It can plot the average change around sudden gains/losses and trajectories of individual cases.
Author: Milan Wiedemann [aut, cre] (<https://orcid.org/0000-0003-1991-282X>), Graham M Thew [ctb] (<https://orcid.org/0000-0003-2851-1315>), Richard Stott [ctb] (<https://orcid.org/0000-0003-2533-5504>), Anke Ehlers [ctb, ths] (<https://orcid.org/0000-0002-8742-0192>)
Maintainer: Milan Wiedemann <milan.wiedemann@gmail.com>

Diff between suddengains versions 0.2.1 dated 2019-05-21 and 0.3.0 dated 2019-08-20

 suddengains-0.2.1/suddengains/man/dotdotequal.Rd                 |only
 suddengains-0.3.0/suddengains/DESCRIPTION                        |    8 
 suddengains-0.3.0/suddengains/MD5                                |   25 
 suddengains-0.3.0/suddengains/NAMESPACE                          |    2 
 suddengains-0.3.0/suddengains/NEWS.md                            |    4 
 suddengains-0.3.0/suddengains/R/check_interval.R                 |only
 suddengains-0.3.0/suddengains/R/magrittrpipeoperator.R           |   11 
 suddengains-0.3.0/suddengains/R/write_bysg.R                     |    1 
 suddengains-0.3.0/suddengains/README.md                          |   41 
 suddengains-0.3.0/suddengains/build/vignette.rds                 |binary
 suddengains-0.3.0/suddengains/inst/doc/suddengains-tutorial.R    |   41 
 suddengains-0.3.0/suddengains/inst/doc/suddengains-tutorial.Rmd  |   47 
 suddengains-0.3.0/suddengains/inst/doc/suddengains-tutorial.html |  789 +++++-----
 suddengains-0.3.0/suddengains/man/check_interval.Rd              |only
 suddengains-0.3.0/suddengains/vignettes/suddengains-tutorial.Rmd |   47 
 15 files changed, 633 insertions(+), 383 deletions(-)

More information about suddengains at CRAN
Permanent link

Package RgoogleMaps updated to version 1.4.4 with previous version 1.4.3 dated 2018-11-07

Title: Overlays on Static Maps
Description: Serves two purposes: (i) Provide a comfortable R interface to query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R. This requires proper coordinate scaling.
Author: Markus Loecher
Maintainer: Markus Loecher <markus.loecher@gmail.com>

Diff between RgoogleMaps versions 1.4.3 dated 2018-11-07 and 1.4.4 dated 2019-08-20

 RgoogleMaps-1.4.3/RgoogleMaps/README                           |only
 RgoogleMaps-1.4.3/RgoogleMaps/inst/doc                         |only
 RgoogleMaps-1.4.4/RgoogleMaps/DESCRIPTION                      |    8 
 RgoogleMaps-1.4.4/RgoogleMaps/MD5                              |   48 -
 RgoogleMaps-1.4.4/RgoogleMaps/R/GetMap.R                       |  238 ++++-----
 RgoogleMaps-1.4.4/RgoogleMaps/R/GetMap.bbox.R                  |    4 
 RgoogleMaps-1.4.4/RgoogleMaps/R/GetMapTiles.R                  |   29 -
 RgoogleMaps-1.4.4/RgoogleMaps/R/NumTiles.R                     |only
 RgoogleMaps-1.4.4/RgoogleMaps/R/genStaticMap.R                 |only
 RgoogleMaps-1.4.4/RgoogleMaps/R/qbbox.R                        |    7 
 RgoogleMaps-1.4.4/RgoogleMaps/man/ColorMap.Rd                  |    9 
 RgoogleMaps-1.4.4/RgoogleMaps/man/DF2SpatialPointsDataFrame.Rd |    3 
 RgoogleMaps-1.4.4/RgoogleMaps/man/GetBingMap.Rd                |   12 
 RgoogleMaps-1.4.4/RgoogleMaps/man/GetMap.Rd                    |   24 
 RgoogleMaps-1.4.4/RgoogleMaps/man/GetMap.bbox.Rd               |   10 
 RgoogleMaps-1.4.4/RgoogleMaps/man/GetMapTiles.Rd               |  264 ++++++----
 RgoogleMaps-1.4.4/RgoogleMaps/man/GetOsmMap.Rd                 |    6 
 RgoogleMaps-1.4.4/RgoogleMaps/man/MapBackground.Rd             |    7 
 RgoogleMaps-1.4.4/RgoogleMaps/man/NumTiles.Rd                  |only
 RgoogleMaps-1.4.4/RgoogleMaps/man/PlotArrowsOnStaticMap.Rd     |    6 
 RgoogleMaps-1.4.4/RgoogleMaps/man/PlotOnMapTiles.Rd            |    5 
 RgoogleMaps-1.4.4/RgoogleMaps/man/PlotOnStaticMap.Rd           |  176 ++----
 RgoogleMaps-1.4.4/RgoogleMaps/man/PlotPolysOnStaticMap.Rd      |    5 
 RgoogleMaps-1.4.4/RgoogleMaps/man/TextOnStaticMap.Rd           |    5 
 RgoogleMaps-1.4.4/RgoogleMaps/man/bubbleMap.Rd                 |    8 
 RgoogleMaps-1.4.4/RgoogleMaps/man/genStaticMap.Rd              |only
 RgoogleMaps-1.4.4/RgoogleMaps/man/plotmap.Rd                   |   10 
 RgoogleMaps-1.4.4/RgoogleMaps/man/qbbox.Rd                     |   13 
 28 files changed, 495 insertions(+), 402 deletions(-)

More information about RgoogleMaps at CRAN
Permanent link

Package highfrequency updated to version 0.6.0 with previous version 0.5.3 dated 2018-03-03

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], Jonathan Cornelissen [aut], Scott Payseur [aut], Giang Nguyen [ctb], Onno Kleen [ctb] (<https://orcid.org/0000-0003-4731-4640>)
Maintainer: Kris Boudt <Kris.Boudt@econ.kuleuven.be>

Diff between highfrequency versions 0.5.3 dated 2018-03-03 and 0.6.0 dated 2019-08-20

 highfrequency-0.5.3/highfrequency/R/AJjumptest.R                        |only
 highfrequency-0.5.3/highfrequency/R/BNSjumptest.R                       |only
 highfrequency-0.5.3/highfrequency/R/JOjumptest.R                        |only
 highfrequency-0.5.3/highfrequency/R/heavyModelC.R                       |only
 highfrequency-0.5.3/highfrequency/R/highfrequencyGSOC.R                 |only
 highfrequency-0.5.3/highfrequency/R/quantmod_patch.R                    |only
 highfrequency-0.5.3/highfrequency/R/realized.R                          |only
 highfrequency-0.5.3/highfrequency/R/spotvol.r                           |only
 highfrequency-0.5.3/highfrequency/data/lltc.xts.rda                     |only
 highfrequency-0.5.3/highfrequency/data/sbux.xts.rda                     |only
 highfrequency-0.5.3/highfrequency/inst/doc/highfrequency.pdf            |only
 highfrequency-0.5.3/highfrequency/man/ExchangeHoursOnly.Rd              |only
 highfrequency-0.5.3/highfrequency/man/RKurt.Rd                          |only
 highfrequency-0.5.3/highfrequency/man/RQPVar.Rd                         |only
 highfrequency-0.5.3/highfrequency/man/RQuar.Rd                          |only
 highfrequency-0.5.3/highfrequency/man/RSkew.Rd                          |only
 highfrequency-0.5.3/highfrequency/man/RTPVar.Rd                         |only
 highfrequency-0.5.3/highfrequency/man/RsV.Rd                            |only
 highfrequency-0.5.3/highfrequency/man/TAQload.Rd                        |only
 highfrequency-0.5.3/highfrequency/man/convert.Rd                        |only
 highfrequency-0.5.3/highfrequency/man/has.Qty.Rd                        |only
 highfrequency-0.5.3/highfrequency/man/heavyModelC.Rd                    |only
 highfrequency-0.5.3/highfrequency/man/lltc.xts.Rd                       |only
 highfrequency-0.5.3/highfrequency/man/mergequotessametimestamp.Rd       |only
 highfrequency-0.5.3/highfrequency/man/nozeroprices.Rd                   |only
 highfrequency-0.5.3/highfrequency/man/nozeroquotes.Rd                   |only
 highfrequency-0.5.3/highfrequency/man/previoustick.Rd                   |only
 highfrequency-0.5.3/highfrequency/man/quotescleanup.Rd                  |only
 highfrequency-0.5.3/highfrequency/man/rAccumulation.Rd                  |only
 highfrequency-0.5.3/highfrequency/man/rCumSum.Rd                        |only
 highfrequency-0.5.3/highfrequency/man/rKernel.available.Rd              |only
 highfrequency-0.5.3/highfrequency/man/rMarginal.Rd                      |only
 highfrequency-0.5.3/highfrequency/man/rRTSCov.rd                        |only
 highfrequency-0.5.3/highfrequency/man/rScatterReturns.Rd                |only
 highfrequency-0.5.3/highfrequency/man/rTSCov.rd                         |only
 highfrequency-0.5.3/highfrequency/man/rZero.Rd                          |only
 highfrequency-0.5.3/highfrequency/man/rmlargespread.Rd                  |only
 highfrequency-0.5.3/highfrequency/man/rmoutliers.Rd                     |only
 highfrequency-0.5.3/highfrequency/man/rmtradeoutliers.Rd                |only
 highfrequency-0.5.3/highfrequency/man/sbux.xts.Rd                       |only
 highfrequency-0.5.3/highfrequency/man/selectexchange.Rd                 |only
 highfrequency-0.5.3/highfrequency/man/tqLiquidity.Rd                    |only
 highfrequency-0.5.3/highfrequency/man/tradesCleanupFinal.Rd             |only
 highfrequency-0.5.3/highfrequency/man/tradescleanup.Rd                  |only
 highfrequency-0.5.3/highfrequency/src/highfrequency.c                   |only
 highfrequency-0.5.3/highfrequency/src/highfrequency.h                   |only
 highfrequency-0.6.0/highfrequency/DESCRIPTION                           |   35 
 highfrequency-0.6.0/highfrequency/MD5                                   |  228 +--
 highfrequency-0.6.0/highfrequency/NAMESPACE                             |  238 ++-
 highfrequency-0.6.0/highfrequency/R/RcppExports.R                       |only
 highfrequency-0.6.0/highfrequency/R/data.R                              |only
 highfrequency-0.6.0/highfrequency/R/data_handling.R                     |only
 highfrequency-0.6.0/highfrequency/R/har_model.R                         |only
 highfrequency-0.6.0/highfrequency/R/heavy_model.R                       |only
 highfrequency-0.6.0/highfrequency/R/highfrequency.R                     |only
 highfrequency-0.6.0/highfrequency/R/internal.R                          |only
 highfrequency-0.6.0/highfrequency/R/internal_data_handling.R            |only
 highfrequency-0.6.0/highfrequency/R/internal_jump_tests.R               |only
 highfrequency-0.6.0/highfrequency/R/internal_preavering_estimators.R    |only
 highfrequency-0.6.0/highfrequency/R/internal_realized_measures.R        |only
 highfrequency-0.6.0/highfrequency/R/internal_spot_vol_and_drift.R       |only
 highfrequency-0.6.0/highfrequency/R/jump_tests.R                        |only
 highfrequency-0.6.0/highfrequency/R/liquidity_measures.R                |only
 highfrequency-0.6.0/highfrequency/R/rcpp_dynlib_call.R                  |only
 highfrequency-0.6.0/highfrequency/R/realized_measures.R                 |only
 highfrequency-0.6.0/highfrequency/R/realized_measures_inference.R       |only
 highfrequency-0.6.0/highfrequency/R/spot_vol_and_drift.R                |only
 highfrequency-0.6.0/highfrequency/build                                 |only
 highfrequency-0.6.0/highfrequency/data/SP500RM.rda                      |only
 highfrequency-0.6.0/highfrequency/data/datalist                         |only
 highfrequency-0.6.0/highfrequency/data/lltc.RData                       |only
 highfrequency-0.6.0/highfrequency/data/realized_library.rda             |binary
 highfrequency-0.6.0/highfrequency/data/sample_qdata_microseconds.rda    |only
 highfrequency-0.6.0/highfrequency/data/sample_qdataraw.rda              |binary
 highfrequency-0.6.0/highfrequency/data/sample_qdataraw_microseconds.rda |only
 highfrequency-0.6.0/highfrequency/data/sample_real5minprices.rda        |binary
 highfrequency-0.6.0/highfrequency/data/sample_tdata_microseconds.rda    |only
 highfrequency-0.6.0/highfrequency/data/sample_tdataraw.rda              |binary
 highfrequency-0.6.0/highfrequency/data/sample_tdataraw_microseconds.rda |only
 highfrequency-0.6.0/highfrequency/data/sbux.RData                       |only
 highfrequency-0.6.0/highfrequency/inst/doc/data_handing.R               |only
 highfrequency-0.6.0/highfrequency/inst/doc/data_handing.Rmd             |only
 highfrequency-0.6.0/highfrequency/inst/doc/data_handing.html            |only
 highfrequency-0.6.0/highfrequency/man/AJjumptest.Rd                     |  215 +-
 highfrequency-0.6.0/highfrequency/man/BNSjumptest.Rd                    |  169 +-
 highfrequency-0.6.0/highfrequency/man/JOjumptest.Rd                     |  166 +-
 highfrequency-0.6.0/highfrequency/man/MRC.Rd                            |  159 +-
 highfrequency-0.6.0/highfrequency/man/RTQ.Rd                            |only
 highfrequency-0.6.0/highfrequency/man/RV.Rd                             |only
 highfrequency-0.6.0/highfrequency/man/SP500RM.Rd                        |only
 highfrequency-0.6.0/highfrequency/man/TSCov_bi.Rd                       |only
 highfrequency-0.6.0/highfrequency/man/aggregatePrice.Rd                 |  110 -
 highfrequency-0.6.0/highfrequency/man/aggregateQuotes.Rd                |  108 -
 highfrequency-0.6.0/highfrequency/man/aggregateTrades.Rd                |  113 -
 highfrequency-0.6.0/highfrequency/man/aggregatets.Rd                    |  140 -
 highfrequency-0.6.0/highfrequency/man/autoSelectExchangeQuotes.Rd       |   90 -
 highfrequency-0.6.0/highfrequency/man/autoSelectExchangeTrades.Rd       |   90 -
 highfrequency-0.6.0/highfrequency/man/exchangeHoursOnly.Rd              |only
 highfrequency-0.6.0/highfrequency/man/getLiquidityMeasures.Rd           |only
 highfrequency-0.6.0/highfrequency/man/getPrice.Rd                       |   51 
 highfrequency-0.6.0/highfrequency/man/getTradeDirection.Rd              |   79 -
 highfrequency-0.6.0/highfrequency/man/harModel.Rd                       |  233 ++-
 highfrequency-0.6.0/highfrequency/man/hasQty.Rd                         |only
 highfrequency-0.6.0/highfrequency/man/heavyModel.Rd                     |  173 +-
 highfrequency-0.6.0/highfrequency/man/highfrequency-package.Rd          |   66 
 highfrequency-0.6.0/highfrequency/man/ivInference.Rd                    |  160 +-
 highfrequency-0.6.0/highfrequency/man/listAvailableKernels.Rd           |only
 highfrequency-0.6.0/highfrequency/man/lltc.Rd                           |only
 highfrequency-0.6.0/highfrequency/man/makePsd.Rd                        |   90 -
 highfrequency-0.6.0/highfrequency/man/makeReturns.Rd                    |   60 
 highfrequency-0.6.0/highfrequency/man/matchTradesQuotes.Rd              |   78 -
 highfrequency-0.6.0/highfrequency/man/medRQ.Rd                          |   92 -
 highfrequency-0.6.0/highfrequency/man/medRV.Rd                          |  125 -
 highfrequency-0.6.0/highfrequency/man/mergeQuotesSameTimestamp.Rd       |only
 highfrequency-0.6.0/highfrequency/man/mergeTradesSameTimestamp.Rd       |   69 
 highfrequency-0.6.0/highfrequency/man/minRQ.Rd                          |   91 -
 highfrequency-0.6.0/highfrequency/man/minRV.Rd                          |   94 -
 highfrequency-0.6.0/highfrequency/man/mukp.Rd                           |only
 highfrequency-0.6.0/highfrequency/man/noZeroPrices.Rd                   |only
 highfrequency-0.6.0/highfrequency/man/noZeroQuotes.Rd                   |only
 highfrequency-0.6.0/highfrequency/man/quotesCleanup.Rd                  |only
 highfrequency-0.6.0/highfrequency/man/rAVGCov.Rd                        |  104 -
 highfrequency-0.6.0/highfrequency/man/rBPCov.Rd                         |  137 -
 highfrequency-0.6.0/highfrequency/man/rBeta.Rd                          |  135 -
 highfrequency-0.6.0/highfrequency/man/rCov.Rd                           |  110 -
 highfrequency-0.6.0/highfrequency/man/rHYCov.Rd                         |   79 -
 highfrequency-0.6.0/highfrequency/man/rKernelCov.Rd                     |  127 -
 highfrequency-0.6.0/highfrequency/man/rKurt.Rd                          |only
 highfrequency-0.6.0/highfrequency/man/rMPV.Rd                           |  121 -
 highfrequency-0.6.0/highfrequency/man/rOWCov.Rd                         |  186 +-
 highfrequency-0.6.0/highfrequency/man/rQPVar.Rd                         |only
 highfrequency-0.6.0/highfrequency/man/rQuar.Rd                          |only
 highfrequency-0.6.0/highfrequency/man/rRTSCov.Rd                        |only
 highfrequency-0.6.0/highfrequency/man/rSV.Rd                            |only
 highfrequency-0.6.0/highfrequency/man/rSkew.Rd                          |only
 highfrequency-0.6.0/highfrequency/man/rTPVar.Rd                         |only
 highfrequency-0.6.0/highfrequency/man/rTSCov.Rd                         |only
 highfrequency-0.6.0/highfrequency/man/rThresholdCov.Rd                  |  124 -
 highfrequency-0.6.0/highfrequency/man/realized_library.Rd               |   42 
 highfrequency-0.6.0/highfrequency/man/refreshTime.Rd                    |   93 -
 highfrequency-0.6.0/highfrequency/man/rmLargeSpread.Rd                  |only
 highfrequency-0.6.0/highfrequency/man/rmNegativeSpread.Rd               |   50 
 highfrequency-0.6.0/highfrequency/man/rmOutliersQuotes.Rd               |only
 highfrequency-0.6.0/highfrequency/man/rmTradeOutliers.Rd                |only
 highfrequency-0.6.0/highfrequency/man/rmTradeOutliersUsingQuotes.Rd     |only
 highfrequency-0.6.0/highfrequency/man/salesCondition.Rd                 |   50 
 highfrequency-0.6.0/highfrequency/man/sample_5minprices.Rd              |   55 
 highfrequency-0.6.0/highfrequency/man/sample_5minprices_jumps.Rd        |   64 
 highfrequency-0.6.0/highfrequency/man/sample_qdata.Rd                   |   24 
 highfrequency-0.6.0/highfrequency/man/sample_qdata_microseconds.Rd      |only
 highfrequency-0.6.0/highfrequency/man/sample_qdataraw.Rd                |   25 
 highfrequency-0.6.0/highfrequency/man/sample_qdataraw_microseconds.Rd   |only
 highfrequency-0.6.0/highfrequency/man/sample_real5minprices.Rd          |   26 
 highfrequency-0.6.0/highfrequency/man/sample_returns_5min.Rd            |   26 
 highfrequency-0.6.0/highfrequency/man/sample_tdata.Rd                   |   26 
 highfrequency-0.6.0/highfrequency/man/sample_tdata_microseconds.Rd      |only
 highfrequency-0.6.0/highfrequency/man/sample_tdataraw.Rd                |   25 
 highfrequency-0.6.0/highfrequency/man/sample_tdataraw_microseconds.Rd   |only
 highfrequency-0.6.0/highfrequency/man/sbux.Rd                           |only
 highfrequency-0.6.0/highfrequency/man/selectExchange.Rd                 |only
 highfrequency-0.6.0/highfrequency/man/spotDrift.Rd                      |only
 highfrequency-0.6.0/highfrequency/man/spotvol.Rd                        |  720 ++++------
 highfrequency-0.6.0/highfrequency/man/tradesCleanup.Rd                  |only
 highfrequency-0.6.0/highfrequency/man/tradesCleanupUsingQuotes.Rd       |only
 highfrequency-0.6.0/highfrequency/src/RcppExports.cpp                   |only
 highfrequency-0.6.0/highfrequency/src/har_model.cpp                     |only
 highfrequency-0.6.0/highfrequency/src/heavy_model.cpp                   |only
 highfrequency-0.6.0/highfrequency/src/realized_measures.cpp             |only
 highfrequency-0.6.0/highfrequency/tests                                 |only
 highfrequency-0.6.0/highfrequency/vignettes                             |only
 170 files changed, 2875 insertions(+), 2796 deletions(-)

More information about highfrequency at CRAN
Permanent link

Package difNLR updated to version 1.3.0 with previous version 1.2.2 dated 2018-05-06

Title: DIF and DDF Detection by Non-Linear Regression Models
Description: Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression procedures based on generalized logistic regression models (Drabinova and Martinkova, 2017, doi:10.1111/jedm.12158).
Author: Adela Hladka [aut, cre], Patricia Martinkova [aut], Karel Zvara [ctb]
Maintainer: Adela Hladka <hladka@cs.cas.cz>

Diff between difNLR versions 1.2.2 dated 2018-05-06 and 1.3.0 dated 2019-08-20

 DESCRIPTION                  |   28 +-
 MD5                          |   97 ++++---
 NAMESPACE                    |   16 +
 NEWS                         |  145 +++++++++++
 R/GMAT.R                     |    4 
 R/GMAT2.R                    |    4 
 R/GMAT2key.R                 |    4 
 R/GMAT2test.R                |    4 
 R/GMATkey.R                  |    4 
 R/GMATtest.R                 |    4 
 R/MLR.R                      |  270 +++++++++++++++------
 R/MSATB.R                    |    4 
 R/MSATBkey.R                 |    4 
 R/MSATBtest.R                |    4 
 R/NLR.R                      |   29 +-
 R/ORD.R                      |only
 R/checkInterval.R            |    6 
 R/ddfMLR.R                   |  483 +++++++++++++++++++++++---------------
 R/ddfORD.R                   |only
 R/difNLR-package.R           |   27 +-
 R/difNLR.R                   |  536 ++++++++++++++++++++++++-------------------
 R/estimNLR.R                 |    4 
 R/formulaNLR.R               |    4 
 R/genNLR.R                   |  143 ++++++-----
 R/startNLR.R                 |    6 
 README.md                    |   26 +-
 inst/CITATION                |   12 
 inst/DDF_CLRM_category.png   |only
 inst/DDF_CLRM_cumulative.png |only
 inst/DIF_NLR.png             |only
 man/GMAT.Rd                  |    4 
 man/GMAT2.Rd                 |    4 
 man/GMAT2key.Rd              |    4 
 man/GMAT2test.Rd             |    4 
 man/GMATkey.Rd               |    4 
 man/GMATtest.Rd              |    4 
 man/MLR.Rd                   |   32 +-
 man/MSATB.Rd                 |    4 
 man/MSATBkey.Rd              |    4 
 man/MSATBtest.Rd             |    4 
 man/NLR.Rd                   |   19 -
 man/ORD.Rd                   |only
 man/checkInterval.Rd         |    5 
 man/ddfMLR.Rd                |   95 ++++---
 man/ddfORD.Rd                |only
 man/difNLR-package.Rd        |   24 +
 man/difNLR.Rd                |   38 +--
 man/estimNLR.Rd              |    4 
 man/formulaNLR.Rd            |    4 
 man/genNLR.Rd                |   47 ++-
 man/plot.difNLR.Rd           |   12 
 man/predict.difNLR.Rd        |    5 
 man/startNLR.Rd              |    5 
 53 files changed, 1368 insertions(+), 826 deletions(-)

More information about difNLR at CRAN
Permanent link

Package cbsodataR updated to version 0.3.4 with previous version 0.3.2 dated 2019-02-21

Title: Statistics Netherlands (CBS) Open Data API Client
Description: The data and meta data from Statistics Netherlands (<https://www.cbs.nl>) can be browsed and downloaded. The client uses the open data API of Statistics Netherlands.
Author: Edwin de Jonge [aut, cre], Sara Houweling [ctb]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>

Diff between cbsodataR versions 0.3.2 dated 2019-02-21 and 0.3.4 dated 2019-08-20

 cbsodataR-0.3.2/cbsodataR/man/download_table.Rd            |only
 cbsodataR-0.3.2/cbsodataR/man/get_data.Rd                  |only
 cbsodataR-0.3.2/cbsodataR/man/get_meta.Rd                  |only
 cbsodataR-0.3.4/cbsodataR/DESCRIPTION                      |   15 +-
 cbsodataR-0.3.4/cbsodataR/MD5                              |   89 ++++++-------
 cbsodataR-0.3.4/cbsodataR/NAMESPACE                        |    3 
 cbsodataR-0.3.4/cbsodataR/NEWS.md                          |   70 ++++++----
 cbsodataR-0.3.4/cbsodataR/R/cbs_add_date_column.R          |   17 +-
 cbsodataR-0.3.4/cbsodataR/R/cbs_add_label_columns.R        |   24 ++-
 cbsodataR-0.3.4/cbsodataR/R/cbs_default_selection.R        |    4 
 cbsodataR-0.3.4/cbsodataR/R/cbs_download_data.R            |    7 -
 cbsodataR-0.3.4/cbsodataR/R/cbs_download_meta.R            |    6 
 cbsodataR-0.3.4/cbsodataR/R/cbs_download_table.R           |   22 ++-
 cbsodataR-0.3.4/cbsodataR/R/cbs_extract_table_id.R         |    7 -
 cbsodataR-0.3.4/cbsodataR/R/cbs_get_data.R                 |   36 +++--
 cbsodataR-0.3.4/cbsodataR/R/cbs_get_data_from_link.R       |    4 
 cbsodataR-0.3.4/cbsodataR/R/cbs_get_meta.R                 |   30 +++-
 cbsodataR-0.3.4/cbsodataR/R/cbs_get_themes.R               |   14 +-
 cbsodataR-0.3.4/cbsodataR/R/cbs_get_toc.R                  |   18 +-
 cbsodataR-0.3.4/cbsodataR/R/cbsopendata.R                  |   33 ++++
 cbsodataR-0.3.4/cbsodataR/R/deeplink.R                     |    1 
 cbsodataR-0.3.4/cbsodataR/R/download-data.R                |   12 -
 cbsodataR-0.3.4/cbsodataR/R/download-meta.R                |   13 -
 cbsodataR-0.3.4/cbsodataR/R/download-table.R               |   22 ---
 cbsodataR-0.3.4/cbsodataR/R/filter.R                       |    2 
 cbsodataR-0.3.4/cbsodataR/R/get-data.R                     |   32 ----
 cbsodataR-0.3.4/cbsodataR/R/get-meta.R                     |   18 --
 cbsodataR-0.3.4/cbsodataR/R/get-table-list.R               |   10 -
 cbsodataR-0.3.4/cbsodataR/R/get-themes.R                   |   14 +-
 cbsodataR-0.3.4/cbsodataR/build/vignette.rds               |binary
 cbsodataR-0.3.4/cbsodataR/inst/doc/cbsodataR.Rmd           |    2 
 cbsodataR-0.3.4/cbsodataR/inst/doc/cbsodataR.html          |   27 ++-
 cbsodataR-0.3.4/cbsodataR/man/cbs_add_date_column.Rd       |   25 ++-
 cbsodataR-0.3.4/cbsodataR/man/cbs_add_label_columns.Rd     |   35 ++++-
 cbsodataR-0.3.4/cbsodataR/man/cbs_download_data.Rd         |   15 ++
 cbsodataR-0.3.4/cbsodataR/man/cbs_download_meta.Rd         |   14 +-
 cbsodataR-0.3.4/cbsodataR/man/cbs_download_table.Rd        |   29 ++--
 cbsodataR-0.3.4/cbsodataR/man/cbs_extract_table_id.Rd      |    8 +
 cbsodataR-0.3.4/cbsodataR/man/cbs_get_data.Rd              |   34 +++-
 cbsodataR-0.3.4/cbsodataR/man/cbs_get_data_from_link.Rd    |   12 +
 cbsodataR-0.3.4/cbsodataR/man/cbs_get_meta.Rd              |   30 +++-
 cbsodataR-0.3.4/cbsodataR/man/cbsodataR-package.Rd         |only
 cbsodataR-0.3.4/cbsodataR/man/download_data-deprecated.Rd  |   14 +-
 cbsodataR-0.3.4/cbsodataR/man/download_meta-deprecated.Rd  |   14 +-
 cbsodataR-0.3.4/cbsodataR/man/download_table-deprecated.Rd |only
 cbsodataR-0.3.4/cbsodataR/man/get_data-deprecated.Rd       |only
 cbsodataR-0.3.4/cbsodataR/man/get_meta-deprecated.Rd       |only
 cbsodataR-0.3.4/cbsodataR/man/get_table_list.Rd            |    7 -
 cbsodataR-0.3.4/cbsodataR/vignettes/cbsodataR.Rmd          |    2 
 49 files changed, 497 insertions(+), 294 deletions(-)

More information about cbsodataR at CRAN
Permanent link

Package semPlot updated to version 1.1.2 with previous version 1.1.1 dated 2019-04-05

Title: Path Diagrams and Visual Analysis of Various SEM Packages' Output
Description: Path diagrams and visual analysis of various SEM packages' output.
Author: Sacha Epskamp [aut, cre], Simon Stuber [ctb], Jason Nak [ctb], Myrthe Veenman [ctb], Terrence D. Jorgensen [ctb] (<https://orcid.org/0000-0001-5111-6773>)
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

Diff between semPlot versions 1.1.1 dated 2019-04-05 and 1.1.2 dated 2019-08-20

 DESCRIPTION            |   14 ++-
 MD5                    |   10 +-
 NAMESPACE              |    2 
 R/OpenMx.R             |  172 ++++++++++++++++++++++++++++++++++++++++++++-----
 R/semPathsHelperFuns.R |    2 
 man/regsemplot.Rd      |   27 +++----
 6 files changed, 187 insertions(+), 40 deletions(-)

More information about semPlot at CRAN
Permanent link

Package Peptides updated to version 2.4.1 with previous version 2.4 dated 2018-06-08

Title: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences
Description: Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.
Author: Daniel Osorio [aut, cre], Paola Rondon-Villarreal [aut, ths], Rodrigo Torres [aut, ths], J. Sebastian Paez [ctb]
Maintainer: Daniel Osorio <dcosorioh@tamu.edu>

Diff between Peptides versions 2.4 dated 2018-06-08 and 2.4.1 dated 2019-08-20

 Peptides-2.4.1/Peptides/DESCRIPTION                   |   12 ++++-----
 Peptides-2.4.1/Peptides/MD5                           |   20 +++++++--------
 Peptides-2.4.1/Peptides/NEWS.md                       |    9 +++++--
 Peptides-2.4.1/Peptides/R/aaCheck.R                   |    2 -
 Peptides-2.4.1/Peptides/R/readXVG.R                   |   23 +++++++++---------
 Peptides-2.4.1/Peptides/data/AAdata.RData             |binary
 Peptides-2.4.1/Peptides/data/pepdata.RData            |binary
 Peptides-2.4.1/Peptides/man/aacomp.Rd                 |only
 Peptides-2.4.1/Peptides/man/aindex.Rd                 |only
 Peptides-2.4.1/Peptides/man/instaindex.Rd             |only
 Peptides-2.4.1/Peptides/tests/testthat/test.aacheck.R |    5 +++
 Peptides-2.4/Peptides/man/aIndex.Rd                   |only
 Peptides-2.4/Peptides/man/aaComp.Rd                   |only
 Peptides-2.4/Peptides/man/instaIndex.Rd               |only
 14 files changed, 41 insertions(+), 30 deletions(-)

More information about Peptides at CRAN
Permanent link

Package hutilscpp updated to version 0.2.0 with previous version 0.1.0 dated 2019-02-03

Title: Miscellaneous Functions in C++
Description: Provides utility functions that are simply, frequently used, but may require higher performance that what can be obtained from base R. Incidentally provides support for 'reverse geocoding', such as matching a point with its nearest neighbour in another array. Used as a complement to package 'hutils' by sacrificing compilation or installation time for higher running speeds. The name is a portmanteau of the author and 'Rcpp'.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>

Diff between hutilscpp versions 0.1.0 dated 2019-02-03 and 0.2.0 dated 2019-08-20

 hutilscpp-0.1.0/hutilscpp/man/AnyWhich.Rd                            |only
 hutilscpp-0.2.0/hutilscpp/DESCRIPTION                                |    8 
 hutilscpp-0.2.0/hutilscpp/MD5                                        |  100 -
 hutilscpp-0.2.0/hutilscpp/NAMESPACE                                  |    8 
 hutilscpp-0.2.0/hutilscpp/NEWS.md                                    |only
 hutilscpp-0.2.0/hutilscpp/R/RcppExports.R                            |  150 +-
 hutilscpp-0.2.0/hutilscpp/R/as_integer_if_safe.R                     |only
 hutilscpp-0.2.0/hutilscpp/R/hutilscpp-package.R                      |    1 
 hutilscpp-0.2.0/hutilscpp/R/is_constant.R                            |only
 hutilscpp-0.2.0/hutilscpp/R/is_sorted.R                              |only
 hutilscpp-0.2.0/hutilscpp/R/logical3.R                               |only
 hutilscpp-0.2.0/hutilscpp/R/match_nrst_haversine.R                   |    2 
 hutilscpp-0.2.0/hutilscpp/R/pmaxC.R                                  |  377 ++---
 hutilscpp-0.2.0/hutilscpp/R/pminC.R                                  |  307 ++--
 hutilscpp-0.2.0/hutilscpp/R/seqN_by.R                                |only
 hutilscpp-0.2.0/hutilscpp/R/sum_isna.R                               |only
 hutilscpp-0.2.0/hutilscpp/R/utils.R                                  |  173 +-
 hutilscpp-0.2.0/hutilscpp/R/which3.R                                 |only
 hutilscpp-0.2.0/hutilscpp/R/which_first.R                            |  368 +++--
 hutilscpp-0.2.0/hutilscpp/R/which_true_onwards.R                     |    6 
 hutilscpp-0.2.0/hutilscpp/man/as_integer_if_safe.Rd                  |only
 hutilscpp-0.2.0/hutilscpp/man/is_constant.Rd                         |only
 hutilscpp-0.2.0/hutilscpp/man/logical3.Rd                            |only
 hutilscpp-0.2.0/hutilscpp/man/match_nrst_haversine.Rd                |    2 
 hutilscpp-0.2.0/hutilscpp/man/pmaxC.Rd                               |   11 
 hutilscpp-0.2.0/hutilscpp/man/pminC.Rd                               |    2 
 hutilscpp-0.2.0/hutilscpp/man/sum_isna.Rd                            |only
 hutilscpp-0.2.0/hutilscpp/man/which3.Rd                              |only
 hutilscpp-0.2.0/hutilscpp/src/AnyCharMatch.cpp                       |   29 
 hutilscpp-0.2.0/hutilscpp/src/AnyWhich.cpp                           |   42 
 hutilscpp-0.2.0/hutilscpp/src/Implies.cpp                            |   12 
 hutilscpp-0.2.0/hutilscpp/src/RcppExports.cpp                        |  481 ++++++
 hutilscpp-0.2.0/hutilscpp/src/anyOutside.cpp                         |   16 
 hutilscpp-0.2.0/hutilscpp/src/do_cumsum_reset.cpp                    |   46 
 hutilscpp-0.2.0/hutilscpp/src/do_even.cpp                            |   12 
 hutilscpp-0.2.0/hutilscpp/src/do_range.cpp                           |   18 
 hutilscpp-0.2.0/hutilscpp/src/do_which_first.cpp                     |   20 
 hutilscpp-0.2.0/hutilscpp/src/haversineDistance.cpp                  |   47 
 hutilscpp-0.2.0/hutilscpp/src/is_safe2int.cpp                        |only
 hutilscpp-0.2.0/hutilscpp/src/is_sorted.cpp                          |only
 hutilscpp-0.2.0/hutilscpp/src/logical3.cpp                           |only
 hutilscpp-0.2.0/hutilscpp/src/pmax0.cpp                              |only
 hutilscpp-0.2.0/hutilscpp/src/pmaxC.cpp                              |   29 
 hutilscpp-0.2.0/hutilscpp/src/pmaxV.cpp                              |   32 
 hutilscpp-0.2.0/hutilscpp/src/pminC.cpp                              |   25 
 hutilscpp-0.2.0/hutilscpp/src/pminV.cpp                              |    8 
 hutilscpp-0.2.0/hutilscpp/src/squish.cpp                             |    8 
 hutilscpp-0.2.0/hutilscpp/src/sum_isna.cpp                           |only
 hutilscpp-0.2.0/hutilscpp/src/summary3.cpp                           |   12 
 hutilscpp-0.2.0/hutilscpp/src/texParse.cpp                           |    4 
 hutilscpp-0.2.0/hutilscpp/src/which_true_onwards.cpp                 |    6 
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-AnyCharMatch.R         |only
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-and3.R                 |only
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-as_integer_if_safe.R   |only
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-cpp-haversine.R        |  724 +++++-----
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-do_duplicated_sorted.R |only
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-is_constant.R          |only
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-is_sorted.R            |only
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-or3.R                  |only
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-pmax0.R                |only
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-pmax_friends.R         |  512 +++----
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-pmin.R                 |   19 
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-seqN_by.R              |only
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-sum_isna.R             |only
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-which3.R               |only
 hutilscpp-0.2.0/hutilscpp/tests/testthat/test-which_first.R          |  121 +
 66 files changed, 2375 insertions(+), 1363 deletions(-)

More information about hutilscpp at CRAN
Permanent link

Package graphlayouts updated to version 0.5.0 with previous version 0.2.0 dated 2019-07-04

Title: Additional Layout Algorithms for Network Visualizations
Description: Several new layout algorithms to visualize networks are provided which are not part of 'igraph'. Most are based on the concept of stress majorization by Gansner et al. (2004) <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to emphasize hidden group structures in networks or focus on specific nodes.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david.schoch@manchester.ac.uk>

Diff between graphlayouts versions 0.2.0 dated 2019-07-04 and 0.5.0 dated 2019-08-20

 graphlayouts-0.2.0/graphlayouts/R/backbone_function.R               |only
 graphlayouts-0.2.0/graphlayouts/R/manipulate_graph.R                |only
 graphlayouts-0.2.0/graphlayouts/R/manipulate_layout.R               |only
 graphlayouts-0.2.0/graphlayouts/R/spectral_function.R               |only
 graphlayouts-0.2.0/graphlayouts/R/stress_function.R                 |only
 graphlayouts-0.2.0/graphlayouts/build                               |only
 graphlayouts-0.2.0/graphlayouts/inst                                |only
 graphlayouts-0.2.0/graphlayouts/man/backbone_layout.Rd              |only
 graphlayouts-0.2.0/graphlayouts/man/centrality_layout.Rd            |only
 graphlayouts-0.2.0/graphlayouts/man/focal_layout.Rd                 |only
 graphlayouts-0.2.0/graphlayouts/man/qgraph.Rd                       |only
 graphlayouts-0.2.0/graphlayouts/man/spectral_layout.Rd              |only
 graphlayouts-0.2.0/graphlayouts/man/stress_layout.Rd                |only
 graphlayouts-0.2.0/graphlayouts/vignettes                           |only
 graphlayouts-0.5.0/graphlayouts/DESCRIPTION                         |   15 -
 graphlayouts-0.5.0/graphlayouts/MD5                                 |   66 ++---
 graphlayouts-0.5.0/graphlayouts/NAMESPACE                           |    8 
 graphlayouts-0.5.0/graphlayouts/NEWS.md                             |   11 
 graphlayouts-0.5.0/graphlayouts/R/RcppExports.R                     |   14 -
 graphlayouts-0.5.0/graphlayouts/R/annotate_functions.R              |   17 -
 graphlayouts-0.5.0/graphlayouts/R/graph_manipulate.R                |only
 graphlayouts-0.5.0/graphlayouts/R/graphlayouts.R                    |    5 
 graphlayouts-0.5.0/graphlayouts/R/layout_backbone.R                 |only
 graphlayouts-0.5.0/graphlayouts/R/layout_dynamic.R                  |only
 graphlayouts-0.5.0/graphlayouts/R/layout_large_graphs.R             |only
 graphlayouts-0.5.0/graphlayouts/R/layout_manipulate.R               |only
 graphlayouts-0.5.0/graphlayouts/R/layout_spectral.R                 |only
 graphlayouts-0.5.0/graphlayouts/R/layout_stress.R                   |only
 graphlayouts-0.5.0/graphlayouts/R/layouts.R                         |   62 +++--
 graphlayouts-0.5.0/graphlayouts/README.md                           |  116 +++++++---
 graphlayouts-0.5.0/graphlayouts/man/annotate_circle.Rd              |    5 
 graphlayouts-0.5.0/graphlayouts/man/draw_circle.Rd                  |    9 
 graphlayouts-0.5.0/graphlayouts/man/figures/README-example_un-2.png |binary
 graphlayouts-0.5.0/graphlayouts/man/figures/README-flex_cent-1.png  |binary
 graphlayouts-0.5.0/graphlayouts/man/figures/dynamic_ex.png          |only
 graphlayouts-0.5.0/graphlayouts/man/figures/rt-net.png              |only
 graphlayouts-0.5.0/graphlayouts/man/graph_manipulate.Rd             |   17 -
 graphlayouts-0.5.0/graphlayouts/man/graphlayouts.Rd                 |    6 
 graphlayouts-0.5.0/graphlayouts/man/layout_backbone.Rd              |only
 graphlayouts-0.5.0/graphlayouts/man/layout_centrality.Rd            |only
 graphlayouts-0.5.0/graphlayouts/man/layout_dynamic.Rd               |only
 graphlayouts-0.5.0/graphlayouts/man/layout_focus.Rd                 |only
 graphlayouts-0.5.0/graphlayouts/man/layout_manipulate.Rd            |    6 
 graphlayouts-0.5.0/graphlayouts/man/layout_pmds.Rd                  |only
 graphlayouts-0.5.0/graphlayouts/man/layout_sparse_stress.Rd         |only
 graphlayouts-0.5.0/graphlayouts/man/layout_spectral.Rd              |only
 graphlayouts-0.5.0/graphlayouts/man/layout_stress.Rd                |only
 graphlayouts-0.5.0/graphlayouts/src/RcppExports.cpp                 |   18 +
 graphlayouts-0.5.0/graphlayouts/src/sparseStress.cpp                |only
 49 files changed, 247 insertions(+), 128 deletions(-)

More information about graphlayouts at CRAN
Permanent link

Package dtpcrm updated to version 0.1.1 with previous version 0.1.0 dated 2019-04-10

Title: Dose Transition Pathways for Continual Reassessment Method
Description: Provides the dose transition pathways (DTP) to project in advance the doses recommended by a model-based design for subsequent patients (stay, escalate, deescalate or stop early) using all the accumulated toxicity information; See Yap et al (2017) <doi: 10.1158/1078-0432.CCR-17-0582>. DTP can be used as a design and an operational tool and can be displayed as a table or flow diagram. The 'dtpcrm' package also provides the modified continual reassessment method (CRM) and time-to-event CRM (TITE-CRM) with added practical considerations to allow stopping early when there is sufficient evidence that the lowest dose is too toxic and/or there is a sufficient number of patients dosed at the maximum tolerated dose.
Author: Christina Yap [aut, cre], Daniel Slade [aut], Kristian Brock [aut], Yi Pan [aut]
Maintainer: Christina Yap <yapchristina17@gmail.com>

Diff between dtpcrm versions 0.1.0 dated 2019-04-10 and 0.1.1 dated 2019-08-20

 DESCRIPTION                      |    6 
 MD5                              |   12 
 R/stopping_delegates.R           |    4 
 inst/doc/dtpcrm_vignettev02.R    |   21 -
 inst/doc/dtpcrm_vignettev02.Rmd  |   25 +
 inst/doc/dtpcrm_vignettev02.html |  634 ++++++++++++++++++++++++++++++---------
 vignettes/dtpcrm_vignettev02.Rmd |   25 +
 7 files changed, 549 insertions(+), 178 deletions(-)

More information about dtpcrm at CRAN
Permanent link

Package DataVisualizations updated to version 1.1.8 with previous version 1.1.6 dated 2019-03-08

Title: Visualizations of High-Dimensional Data
Description: Gives access to data visualisation methods that are relevant from the data scientist's point of view. The flagship idea of 'DataVisualizations' is the mirrored density plot (MD-plot) for either classified or non-classified multivariate data presented in Thrun et al. (2019) <arXiv:1908.06081>. The MD-plot outperforms the box-and-whisker diagram (box plot) and bean plot. Furthermore, a collection of various visualization methods for univariate data is provided. In the case of exploratory data analysis, 'DataVisualizations' makes it possible to inspect the distribution of each feature of a dataset visually through a combination of four methods. One of these methods is the Pareto density estimation (PDE) of the probability density function (pdf). Additionally, visualizations of the distribution of distances using PDE, the scatter-density plot using PDE for two variables as well as the Shepard density plot and the Bland-Altman plot are presented here. Pertaining to classified high-dimensional data, a number of visualizations are described, such as f.ex. the heat map and silhouette plot. A political map of the world or Germany can be visualized with the additional information defined by a classification of countries or regions. By extending the political map further, an uncomplicated function for a Choropleth map can be used which is useful for measurements across a geographic area. For categorical features, the Pie charts, slope charts and fan plots, improved by the ABC analysis, become usable. More detailed explanations are found in the book by Thrun, M.C.: "Projection-Based Clustering through Self-Organization and Swarm Intelligence" (2018) <doi:10.1007/978-3-658-20540-9>.
Author: Michael Thrun [aut, cre, cph] (<https://orcid.org/0000-0001-9542-5543>), Felix Pape [aut, rev], Onno Hansen-Goos [ctr, ctb], Alfred Ultsch [dtc, ctb]
Maintainer: Michael Thrun <m.thrun@gmx.net>

Diff between DataVisualizations versions 1.1.6 dated 2019-03-08 and 1.1.8 dated 2019-08-20

 DESCRIPTION                       |   21 
 MD5                               |   86 +
 NAMESPACE                         |    5 
 R/ABCbarplot.R                    |only
 R/ClassBoxPlot.R                  |   32 
 R/ClassMDplot.R                   |    4 
 R/ClassPDEplot.R                  |    6 
 R/ClassPDEplotMaxLikeli.R         |   24 
 R/DualaxisLinechart.R             |    2 
 R/Fanplot.R                       |    2 
 R/Heatmap.R                       |   11 
 R/InspectScatterplots.R           |    3 
 R/InspectVariable.R               |    7 
 R/MDplot.R                        |   53 -
 R/OptimalNoBinsV2.R               |only
 R/PDEplot.R                       |    4 
 R/ParetoDensityEstimationV2.R     |only
 R/ParetoRadiusV2.R                |only
 R/Piechart.R                      |    2 
 R/PlotMissingvalues.R             |    2 
 R/QQplot.R                        |    4 
 R/Silhouetteplot.R                |    2 
 R/Slopechart.R                    |    2 
 R/checkCls.R                      |   14 
 R/inPSphere2D.R                   |    2 
 R/stat_pde_density.R              |    2 
 build/partial.rdb                 |binary
 build/vignette.rds                |binary
 data/FundamentalData_Q1_2018.rda  |only
 inst/doc/DataVisualizations.Rmd   |    7 
 inst/doc/DataVisualizations.html  | 1677 +++++++++++++++++++++++++++++++++-----
 man/ABCbarplot.Rd                 |only
 man/ClassBoxPlot.Rd               |    5 
 man/ClassMDplot.Rd                |   14 
 man/ClassPDEplot.Rd               |    9 
 man/ClassPDEplotMaxLikeli.Rd      |   14 
 man/DataVisualizations-package.Rd |    6 
 man/DualaxisLinechart.Rd          |    2 
 man/FundamentalData_Q1_2018.Rd    |only
 man/Heatmap.Rd                    |    2 
 man/InspectVariable.Rd            |   11 
 man/MDplot.Rd                     |   17 
 man/MDplot4multiplevectors.Rd     |   16 
 man/OptimalNoBinsV2.Rd            |only
 man/ParetoDensityEstimationV2.Rd  |only
 man/ParetoRadiusV2.Rd             |only
 man/Plot3D.Rd                     |    2 
 man/SignedLog.Rd                  |    8 
 vignettes/DataVisualizations.Rmd  |    7 
 49 files changed, 1742 insertions(+), 345 deletions(-)

More information about DataVisualizations at CRAN
Permanent link

Package clean updated to version 1.1.0 with previous version 1.0.0 dated 2019-07-28

Title: Fast and Easy Data Cleaning
Description: Data cleaning functions for classes 'logical', 'factor', 'numeric', 'character', 'currency' and 'Date' to make data cleaning fast and easy. Relying on very few dependencies, it provides smart guessing, but with user options to override anything if needed.
Author: Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>)
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>

Diff between clean versions 1.0.0 dated 2019-07-28 and 1.1.0 dated 2019-08-20

 DESCRIPTION                    |   14 +-
 MD5                            |   21 ++--
 NAMESPACE                      |   36 ++++++
 NEWS.md                        |   11 ++
 R/clean.R                      |   81 ++++++++++++++-
 R/currency.R                   |only
 R/freq.R                       |  213 +++++++++++++++++++++++------------------
 R/helpers.R                    |   17 ++-
 README.md                      |   74 ++++++++++++--
 man/clean.Rd                   |   32 +++++-
 man/currency.Rd                |only
 man/freq.Rd                    |   26 ++---
 tests/testthat/test-currency.R |only
 13 files changed, 380 insertions(+), 145 deletions(-)

More information about clean at CRAN
Permanent link

Package bvartools updated to version 0.0.2 with previous version 0.0.1 dated 2019-06-11

Title: Bayesian Inference of Vector Autoregressive Models
Description: Assists in the set-up of algorithms for Bayesian inference of vector autoregressive (VAR) models. Functions for posterior simulation, forecasting, impulse response analysis and forecast error variance decomposition are largely based on the introductory texts of Koop and Korobilis (2010) <doi:10.1561/0800000013> and Luetkepohl (2007, ISBN: 9783540262398).
Author: Franz X. Mohr [aut, cre]
Maintainer: Franz X. Mohr <bvartools@outlook.com>

Diff between bvartools versions 0.0.1 dated 2019-06-11 and 0.0.2 dated 2019-08-20

 DESCRIPTION                |   10 ++---
 MD5                        |   69 +++++++++++++++++++++------------------
 NAMESPACE                  |    2 +
 NEWS.md                    |only
 R/RcppExports.R            |   11 ++++--
 R/bvar.R                   |   11 ++++--
 R/bvec_to_bvar.R           |    6 ++-
 R/fevd.R                   |    2 -
 R/gen_var.R                |   41 +++++++++++++++++------
 R/gen_vec.R                |   41 +++++++++++++++++++++--
 R/irf.R                    |    6 ++-
 R/minnesota_prior.R        |only
 R/plot.bvarfevd.R          |    8 +++-
 R/predict.bvar.R           |   38 +++++++++++++++++----
 R/ssvs_prior.R             |only
 build/vignette.rds         |binary
 inst/doc/bsvar.Rmd         |    1 
 inst/doc/bsvar.html        |   12 ++++--
 inst/doc/bvartools.Rmd     |    6 ++-
 inst/doc/bvartools.html    |   17 ++++++---
 inst/doc/bvec.R            |    1 
 inst/doc/bvec.Rmd          |    1 
 inst/doc/bvec.html         |   13 ++++---
 inst/doc/ssvs.R            |   10 +----
 inst/doc/ssvs.Rmd          |   10 +----
 inst/doc/ssvs.html         |   78 ++++++++++++++++++++++-----------------------
 man/minnesota_prior.Rd     |only
 man/post_coint_kls.Rd      |    2 -
 man/post_coint_kls_sur.Rd  |    9 +++--
 man/ssvs_prior.Rd          |only
 src/kalman_dk.cpp          |    4 +-
 src/post_coint_kls.cpp     |   27 +++++++++------
 src/post_coint_kls_sur.cpp |   39 +++++++++++++++-------
 src/post_normal_sur.cpp    |    2 -
 vignettes/bsvar.Rmd        |    1 
 vignettes/bvartools.Rmd    |    6 ++-
 vignettes/bvec.Rmd         |    1 
 vignettes/ssvs.Rmd         |   10 +----
 38 files changed, 309 insertions(+), 186 deletions(-)

More information about bvartools at CRAN
Permanent link

Package qrandom updated to version 1.2 with previous version 1.1 dated 2019-02-14

Title: True Random Numbers using the ANU Quantum Random Numbers Server
Description: The ANU Quantum Random Number Generator provided by the Australian National University generates true random numbers in real-time by measuring the quantum fluctuations of the vacuum. This package offers an interface using their API. The electromagnetic field of the vacuum exhibits random fluctuations in phase and amplitude at all frequencies. By carefully measuring these fluctuations, one is able to generate ultra-high bandwidth random numbers. The quantum Random Number Generator is based on the papers by Symul et al., (2011) <doi:10.1063/1.3597793> and Haw, et al. (2015) <doi:10.1103/PhysRevApplied.3.054004>. The package offers functions to retrieve a sequence of random integers or hexadecimals and true random samples from a normal or uniform distribution.
Author: Siegfried Köstlmeier [aut, cre] (<https://orcid.org/0000-0002-7221-6981>), Boris Steipe [ctb] (<https://orcid.org/0000-0002-1134-6758>)
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>

Diff between qrandom versions 1.1 dated 2019-02-14 and 1.2 dated 2019-08-20

 DESCRIPTION                         |    9 
 LICENSE                             |  678 ++++++++++++++++++------------------
 MD5                                 |   40 +-
 NAMESPACE                           |   32 -
 R/qUUID.R                           |  152 ++++----
 R/qrandom.R                         |  664 +++++++++++++++++------------------
 R/qrandommaxint.R                   |  118 +++---
 THANKS                              |    7 
 build/partial.rdb                   |binary
 man/qRandomSeq.Rd                   |   54 +-
 man/qUUID.Rd                        |  108 ++---
 man/qrandom.Rd                      |  158 ++++----
 man/qrandommaxint.Rd                |  108 ++---
 man/qrandomnorm.Rd                  |  206 +++++-----
 man/qrandomunif.Rd                  |  134 +++----
 tests/testthat.R                    |   20 -
 tests/testthat/test-qUUID.R         |   56 +-
 tests/testthat/test-qrandom.R       |   56 +-
 tests/testthat/test-qrandommaxint.R |   46 +-
 tests/testthat/test-qrandomnorm.R   |   32 -
 tests/testthat/test-qrandomunif.R   |   38 +-
 21 files changed, 1361 insertions(+), 1355 deletions(-)

More information about qrandom at CRAN
Permanent link

Package metadynminer updated to version 0.1.6 with previous version 0.1.5 dated 2019-07-18

Title: Tools to Read, Analyze and Visualize Metadynamics HILLS Files from 'Plumed'
Description: Metadynamics is a state of the art biomolecular simulation technique. 'Plumed' Tribello, G.A. et al. (2014) <doi:10.1016/j.cpc.2013.09.018> program makes it possible to perform metadynamics using various simulation codes. The results of metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package 'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package. It uses a fast algorithm by Hosek, P. and Spiwok, V. (2016) <doi:10.1016/j.cpc.2015.08.037> to calculate a free energy surface from hills. Minima can be located and plotted on the free energy surface. Transition states can be analyzed by Nudged Elastic Band method by Henkelman, G. and Jonsson, H. (2000) <doi:10.1063/1.1323224>. Free energy surfaces, minima and transition paths can be plotted to produce publication quality images.
Author: Vojtech Spiwok [aut, cre] (<https://orcid.org/0000-0001-8108-2033>)
Maintainer: Vojtech Spiwok <spiwokv@vscht.cz>

Diff between metadynminer versions 0.1.5 dated 2019-07-18 and 0.1.6 dated 2019-08-20

 DESCRIPTION        |    8 +++----
 MD5                |   11 +++++-----
 NAMESPACE          |    1 
 R/minimaandpaths.R |   12 +++++++++--
 R/nebs.R           |    4 +++
 R/readingandfes.R  |   54 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 man/prob.Rd        |only
 7 files changed, 79 insertions(+), 11 deletions(-)

More information about metadynminer at CRAN
Permanent link

Package HiCblock updated to version 1.5 with previous version 1.4 dated 2018-04-18

Title: Systematic Analysis of Architectural Proteins and Functional Elements in Blocking Long-Range Contacts Between Loci
Description: Here we propose a model to systematically analyze the roles of architectural proteins and functional elements in blocking long-range contacts between loci. The proposed model does not rely on topologically associating domain (TAD) mapping from Hi-C data. Instead of testing the enrichment or influence of protein binding at TAD borders, the model directly estimates the blocking effect of proteins on long-range contacts between flanking loci, making the model intuitive and biologically meaningful.
Author: Raphael Mourad
Maintainer: Raphael Mourad <raphael.mourad@ibcg.biotoul.fr>

Diff between HiCblock versions 1.4 dated 2018-04-18 and 1.5 dated 2019-08-20

 DESCRIPTION             |    8 ++++----
 MD5                     |   10 +++++-----
 R/HiCblockMiscFun.R     |    2 +-
 build/partial.rdb       |binary
 data/dataExample.RData  |binary
 man/HiCblock-package.Rd |    4 ++++
 6 files changed, 14 insertions(+), 10 deletions(-)

More information about HiCblock at CRAN
Permanent link

Package dexterMST updated to version 0.1.2 with previous version 0.1.1 dated 2018-10-29

Title: CML Calibration of Multi Stage Tests
Description: Conditional Maximum Likelihood Calibration and data management of multistage tests. Functions for calibration of the Extended Nominal Response and the Interaction models, DIF and profile analysis. See Robert J. Zwitser and Gunter Maris (2015)<doi:10.1007/s11336-013-9369-6>.
Author: Timo Bechger [aut, cre], Jesse Koops [aut], Ivailo Partchev [aut], Gunter Maris [aut], Robert Zwitser [ctb]
Maintainer: Timo Bechger <tmbechger@gmail.com>

Diff between dexterMST versions 0.1.1 dated 2018-10-29 and 0.1.2 dated 2019-08-20

 dexterMST-0.1.1/dexterMST/tests/Rversions.R                     |only
 dexterMST-0.1.2/dexterMST/DESCRIPTION                           |   10 
 dexterMST-0.1.2/dexterMST/MD5                                   |   29 
 dexterMST-0.1.2/dexterMST/NEWS                                  |    8 
 dexterMST-0.1.2/dexterMST/R/anon.R                              |    2 
 dexterMST-0.1.2/dexterMST/R/data_selection.R                    |    8 
 dexterMST-0.1.2/dexterMST/R/misc.R                              |    4 
 dexterMST-0.1.2/dexterMST/R/mst.R                               |    5 
 dexterMST-0.1.2/dexterMST/R/profile_analysis.R                  |    4 
 dexterMST-0.1.2/dexterMST/inst/doc/multistage_fundamentals.R    |   15 
 dexterMST-0.1.2/dexterMST/inst/doc/multistage_fundamentals.Rmd  |   15 
 dexterMST-0.1.2/dexterMST/inst/doc/multistage_fundamentals.html |  558 ++++++----
 dexterMST-0.1.2/dexterMST/man/reexports.Rd                      |    2 
 dexterMST-0.1.2/dexterMST/src/misc.cpp                          |    2 
 dexterMST-0.1.2/dexterMST/tests/testthat/test_inputs.R          |    9 
 dexterMST-0.1.2/dexterMST/vignettes/multistage_fundamentals.Rmd |   15 
 16 files changed, 451 insertions(+), 235 deletions(-)

More information about dexterMST at CRAN
Permanent link

Package monotonicity updated to version 1.3 with previous version 1.2 dated 2019-02-14

Title: Test for Monotonicity in Expected Asset Returns, Sorted by Portfolios
Description: Test for monotonicity in financial variables sorted by portfolios. It is conventional practice in empirical research to form portfolios of assets ranked by a certain sort variable. A t-test is then used to consider the mean return spread between the portfolios with the highest and lowest values of the sort variable. Yet comparing only the average returns on the top and bottom portfolios does not provide a sufficient way to test for a monotonic relation between expected returns and the sort variable. This package provides nonparametric tests for the full set of monotonic patterns by Patton, A. and Timmermann, A. (2010) <doi:10.1016/j.jfineco.2010.06.006> and compares the proposed results with extant alternatives such as t-tests, Bonferroni bounds, and multivariate inequality tests through empirical applications and simulations.
Author: Siegfried Köstlmeier [aut, cre, trl] (<https://orcid.org/0000-0002-7221-6981>)
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>

Diff between monotonicity versions 1.2 dated 2019-02-14 and 1.3 dated 2019-08-20

 DESCRIPTION                             |   10 
 LICENSE                                 |   14 -
 MD5                                     |   60 ++---
 NAMESPACE                               |   34 +--
 R/SB_variance.R                         |   84 +++----
 R/matrix_conversion.R                   |   64 ++---
 R/monoBonferroni.R                      |  102 ++++-----
 R/monoRelation.R                        |  342 ++++++++++++++++----------------
 R/monoSummary.R                         |  194 +++++++++---------
 R/monoUpDown.R                          |  226 ++++++++++-----------
 R/newey_west.R                          |   56 ++---
 R/specify_decimal.R                     |    6 
 R/statBootstrap.R                       |  106 ++++-----
 R/wolak.R                               |  266 ++++++++++++------------
 THANKS                                  |    7 
 build/partial.rdb                       |binary
 man/demo_returns.Rd                     |   56 ++---
 man/monoBonferroni.Rd                   |  116 +++++-----
 man/monoRelation.Rd                     |  112 +++++-----
 man/monoSummary.Rd                      |  143 +++++++------
 man/monoUpDown.Rd                       |   92 ++++----
 man/statBootstrap.Rd                    |   74 +++---
 man/wolak.Rd                            |  147 +++++++------
 tests/testthat.R                        |   24 +-
 tests/testthat/test-matrix_conversion.R |only
 tests/testthat/test-monoBonferroni.R    |   23 +-
 tests/testthat/test-monoRelation.R      |   65 +++---
 tests/testthat/test-monoSummary.R       |   74 ++++--
 tests/testthat/test-monoUpDown.R        |   59 +++--
 tests/testthat/test-specify_decimal.R   |   36 +--
 tests/testthat/test-statBootstrap.R     |only
 tests/testthat/test-wolak.R             |   46 ++--
 32 files changed, 1360 insertions(+), 1278 deletions(-)

More information about monotonicity at CRAN
Permanent link

Package ggforce updated to version 0.3.1 with previous version 0.3.0 dated 2019-08-09

Title: Accelerating 'ggplot2'
Description: The aim of 'ggplot2' is to aid in visual data investigations. This focus has led to a lack of facilities for composing specialised plots. 'ggforce' aims to be a collection of mainly new stats and geoms that fills this gap. All additional functionality is aimed to come through the official extension system so using 'ggforce' should be a stable experience.
Author: Thomas Lin Pedersen [cre, aut] (<https://orcid.org/0000-0002-5147-4711>), RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

Diff between ggforce versions 0.3.0 dated 2019-08-09 and 0.3.1 dated 2019-08-20

 DESCRIPTION        |    6 ++---
 MD5                |   36 ++++++++++++++++-----------------
 NEWS.md            |    4 +++
 R/arc_bar.R        |    5 ++--
 R/bezier.R         |   57 ++++++++++++++++++++++++++++++++++++++++++++++++-----
 R/bspline.R        |    3 ++
 R/bspline_closed.R |    3 ++
 R/diagonal.R       |   16 +++++++-------
 R/diagonal_wide.R  |    4 +--
 R/ellipse.R        |    8 +++----
 R/link.R           |   25 ++++++++++++++++++++++-
 R/mark_circle.R    |    4 ++-
 R/mark_ellipse.R   |    4 ++-
 R/mark_hull.R      |    4 ++-
 R/mark_rect.R      |    4 ++-
 R/regon.R          |    2 -
 R/spiro.R          |   14 ++++++-------
 R/voronoi.R        |    4 +--
 README.md          |    9 +++-----
 19 files changed, 150 insertions(+), 62 deletions(-)

More information about ggforce at CRAN
Permanent link

Package crseEventStudy updated to version 1.2 with previous version 1.1 dated 2019-02-13

Title: A Robust and Powerful Test of Abnormal Stock Returns in Long-Horizon Event Studies
Description: Based on Dutta et al. (2018) <doi:10.1016/j.jempfin.2018.02.004>, this package provides their standardized test for abnormal returns in long-horizon event studies. The methods used improve the major weaknesses of size, power, and robustness of long-run statistical tests described in Kothari/Warner (2007) <doi:10.1016/B978-0-444-53265-7.50015-9>. Abnormal returns are weighted by their statistical precision (i.e., standard deviation), resulting in abnormal standardized returns. This procedure efficiently captures the heteroskedasticity problem. Clustering techniques following Cameron et al. (2011) <10.1198/jbes.2010.07136> are adopted for computing cross-sectional correlation robust standard errors. The statistical tests in this package therefore accounts for potential biases arising from returns' cross-sectional correlation, autocorrelation, and volatility clustering without power loss.
Author: Siegfried Köstlmeier [aut, cre] (<https://orcid.org/0000-0002-7221-6981>), Seppo Pynnonen [aut]
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>

Diff between crseEventStudy versions 1.1 dated 2019-02-13 and 1.2 dated 2019-08-20

 DESCRIPTION                      |    8 -
 LICENSE                          |   14 +-
 MD5                              |   37 ++---
 NAMESPACE                        |   20 +-
 R/asr.R                          |   72 +++++-----
 R/check_data.R                   |   40 ++---
 R/crseEvent.R                    |  262 +++++++++++++++++++--------------------
 R/sar.R                          |   68 +++++-----
 THANKS                           |    6 
 build/partial.rdb                |binary
 man/asr.Rd                       |   84 ++++++------
 man/crseEvent.Rd                 |  170 ++++++++++++-------------
 man/demo_returns.Rd              |   42 +++---
 man/demo_share_repurchases.Rd    |   54 ++++----
 man/sar.Rd                       |   86 ++++++------
 tests/testthat.R                 |   17 +-
 tests/testthat/test-asr.R        |   33 ++--
 tests/testthat/test-check_data.R |only
 tests/testthat/test-crseEvent.R  |   58 +++++---
 tests/testthat/test-sar.R        |   33 ++--
 20 files changed, 565 insertions(+), 539 deletions(-)

More information about crseEventStudy at CRAN
Permanent link

Package birdring updated to version 1.4 with previous version 1.3 dated 2015-10-13

Title: Methods to Analyse Ring Re-Encounter Data
Description: R functions to read EURING data and analyse re-encounter data of birds marked by metal rings. For a tutorial, go to <http://www.tandfonline.com/doi/full/10.1080/03078698.2014.933053>.
Author: Fraenzi Korner-Nievergelt, Rob Robinson
Maintainer: Fraenzi Korner-Nievergelt <fraenzi.korner@vogelwarte.ch>

Diff between birdring versions 1.3 dated 2015-10-13 and 1.4 dated 2019-08-20

 DESCRIPTION        |   10 +++++-----
 MD5                |    4 ++--
 man/draw.recmap.Rd |    3 +++
 3 files changed, 10 insertions(+), 7 deletions(-)

More information about birdring at CRAN
Permanent link

Package readabs updated to version 0.4.1 with previous version 0.4.0 dated 2019-06-07

Title: Download and Tidy Time Series Data from the Australian Bureau of Statistics
Description: Downloads, imports, and tidies time series data from the Australian Bureau of Statistics <https://www.abs.gov.au/>.
Author: Matt Cowgill [aut, cre], Zoe Meers [aut], Jaron Lee [aut], David Diviny [ctb]
Maintainer: Matt Cowgill <mattcowgill@gmail.com>

Diff between readabs versions 0.4.0 dated 2019-06-07 and 0.4.1 dated 2019-08-20

 DESCRIPTION                    |   10 ++--
 MD5                            |   31 +++++++-------
 NAMESPACE                      |    1 
 NEWS.md                        |    3 +
 R/download_abs.R               |    3 -
 R/get_abs_xml_metadata.R       |    8 ++-
 R/get_xml_df.R                 |    3 -
 R/separate_series.R            |   39 +++++++++++++++---
 README.md                      |   33 +++++++++------
 build/vignette.rds             |binary
 inst/doc/readabs_vignette.Rmd  |    8 ++-
 inst/doc/readabs_vignette.html |   64 +++++++++++++++---------------
 man/read_cpi.Rd                |    2 
 man/separate_series.Rd         |   11 +++--
 tests/testdata/640101.xls      |only
 tests/testthat/test_readabs.R  |   87 +++++++++++++++++++++++++++--------------
 vignettes/readabs_vignette.Rmd |    8 ++-
 17 files changed, 196 insertions(+), 115 deletions(-)

More information about readabs at CRAN
Permanent link

Package pksensi updated to version 1.1.3 with previous version 1.1.2 dated 2019-06-30

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>

Diff between pksensi versions 1.1.2 dated 2019-06-30 and 1.1.3 dated 2019-08-20

 DESCRIPTION             |    6 +++---
 MD5                     |   24 ++++++++++++------------
 NEWS.md                 |    5 +++++
 R/install.R             |    2 +-
 R/solve_fun.R           |   24 ++++++++++--------------
 inst/doc/pbpk_apap.Rmd  |   14 +++++++-------
 inst/doc/pbpk_apap.html |   32 ++++++++++++++++----------------
 inst/doc/pbtk1cpt.Rmd   |    2 +-
 inst/doc/pbtk1cpt.html  |   10 +++++-----
 man/mcsim.Rd            |    2 +-
 man/solve_fun.Rd        |    2 +-
 vignettes/pbpk_apap.Rmd |   14 +++++++-------
 vignettes/pbtk1cpt.Rmd  |    2 +-
 13 files changed, 70 insertions(+), 69 deletions(-)

More information about pksensi at CRAN
Permanent link

Package photobiologyInOut updated to version 0.4.21 with previous version 0.4.20 dated 2019-06-15

Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files containing spectral data from spectrometers and their associated software, output from daylight simulation models in common use, and some spectral data repositories. As well as functions for exchange of spectral data with other R packages. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>), Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

Diff between photobiologyInOut versions 0.4.20 dated 2019-06-15 and 0.4.21 dated 2019-08-20

 DESCRIPTION              |   18 +-
 MD5                      |   28 +--
 NEWS                     |    6 
 R/foreign-conversion.r   |  362 ++++++++++++++++++++++++++++-------------------
 R/read-avaspec-csv.r     |    9 -
 R/read-tuv-file.r        |    4 
 build/vignette.rds       |binary
 inst/doc/user-guide.R    |   53 +++---
 inst/doc/user-guide.Rmd  |   73 +++++----
 inst/doc/user-guide.html |  131 +++++++++--------
 man/as.colorSpec.Rd      |    3 
 man/colorSpec2mspct.Rd   |   14 +
 man/hyperSpec2mspct.Rd   |   18 +-
 man/rspec2mspct.Rd       |   26 +--
 vignettes/user-guide.Rmd |   73 +++++----
 15 files changed, 468 insertions(+), 350 deletions(-)

More information about photobiologyInOut at CRAN
Permanent link

Package paws.common updated to version 0.2.0 with previous version 0.1.2 dated 2019-08-08

Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services <https://aws.amazon.com>. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build higher-level interfaces to individual services, such as Simple Storage Service (S3).
Author: David Kretch [aut, cre], Adam Banker [aut], Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>

Diff between paws.common versions 0.1.2 dated 2019-08-08 and 0.2.0 dated 2019-08-20

 DESCRIPTION                   |    6 +++---
 MD5                           |   16 ++++++++--------
 NEWS.md                       |    7 +++++++
 R/client.R                    |   27 ++++++++++++++++++++-------
 R/config.R                    |    9 +++------
 R/service.R                   |    4 ++--
 man/new_service.Rd            |    4 ++--
 tests/testthat/test_client.R  |   27 +++++++++++++++++++++------
 tests/testthat/test_service.R |    4 ++--
 9 files changed, 68 insertions(+), 36 deletions(-)

More information about paws.common at CRAN
Permanent link

Package icarus updated to version 0.3.1 with previous version 0.3.0 dated 2017-03-04

Title: Calibrates and Reweights Units in Samples
Description: Provides user-friendly tools for calibration in survey sampling. The package is production-oriented, and its interface is inspired by the famous popular macro 'Calmar' for SAS, so that 'Calmar' users can quickly get used to 'icarus'. In addition to calibration (with linear, raking and logit methods), 'icarus' features functions for calibration on tight bounds and penalized calibration.
Author: Antoine Rebecq [aut, cre]
Maintainer: Antoine Rebecq <antoine.rebecq@m4x.org>

Diff between icarus versions 0.3.0 dated 2017-03-04 and 0.3.1 dated 2019-08-20

 icarus-0.3.0/icarus/data/ex2.RData                                  |only
 icarus-0.3.0/icarus/man/calWeights_ex2.Rd                           |only
 icarus-0.3.0/icarus/man/data_ex2.Rd                                 |only
 icarus-0.3.1/icarus/DESCRIPTION                                     |   10 -
 icarus-0.3.1/icarus/MD5                                             |   61 +++----
 icarus-0.3.1/icarus/NAMESPACE                                       |    1 
 icarus-0.3.1/icarus/R/calibration.R                                 |   23 +-
 icarus-0.3.1/icarus/R/calmarFunctions.R                             |    5 
 icarus-0.3.1/icarus/R/datasets.R                                    |   12 -
 icarus-0.3.1/icarus/R/margins.R                                     |   27 +++
 icarus-0.3.1/icarus/R/modalities_functions.R                        |    4 
 icarus-0.3.1/icarus/README.md                                       |   18 +-
 icarus-0.3.1/icarus/data/data_employees.RData                       |only
 icarus-0.3.1/icarus/data/datalist                                   |    2 
 icarus-0.3.1/icarus/man/HTmean.Rd                                   |    1 
 icarus-0.3.1/icarus/man/HTtotal.Rd                                  |    1 
 icarus-0.3.1/icarus/man/addMargin.Rd                                |    1 
 icarus-0.3.1/icarus/man/calWeights_movies.Rd                        |only
 icarus-0.3.1/icarus/man/calibration.Rd                              |   31 ++-
 icarus-0.3.1/icarus/man/calibrationMarginStats.Rd                   |   10 -
 icarus-0.3.1/icarus/man/colToDummies.Rd                             |    1 
 icarus-0.3.1/icarus/man/dataPop.Rd                                  |    7 
 icarus-0.3.1/icarus/man/data_employees.Rd                           |only
 icarus-0.3.1/icarus/man/marginStats.Rd                              |    9 -
 icarus-0.3.1/icarus/man/newMarginMatrix.Rd                          |only
 icarus-0.3.1/icarus/man/poptest_calmar.Rd                           |    7 
 icarus-0.3.1/icarus/man/poptest_calmar_nr.Rd                        |    7 
 icarus-0.3.1/icarus/man/regroupCalibrationModalities.Rd             |    4 
 icarus-0.3.1/icarus/man/regroupModalities.Rd                        |    3 
 icarus-0.3.1/icarus/man/table_margins_1.Rd                          |    1 
 icarus-0.3.1/icarus/man/table_margins_2.Rd                          |    1 
 icarus-0.3.1/icarus/man/weightedMean.Rd                             |    1 
 icarus-0.3.1/icarus/man/weightedTotal.Rd                            |    1 
 icarus-0.3.1/icarus/tests/testthat/test_calibration.R               |   84 +++++-----
 icarus-0.3.1/icarus/tests/testthat/test_calibration_small_dataset.R |   72 +++-----
 35 files changed, 208 insertions(+), 197 deletions(-)

More information about icarus at CRAN
Permanent link

Package dst updated to version 1.4.0 with previous version 1.3.0 dated 2018-12-05

Title: Using the Theory of Belief Functions
Description: Using the Theory of Belief Functions for evidence calculus. Basic probability assignments, or mass functions, can be defined on the subsets of a set of possible values and combined. A mass function can be extended to a larger frame. Marginalization, i.e. reduction to a smaller frame can also be done. These features can be combined to analyze small belief networks and take into account situations where information cannot be satisfactorily described by probability distributions.
Author: Claude Boivin, Stat.ASSQ <webapp.cb@gmail.com>
Maintainer: Claude Boivin <webapp.cb@gmail.com>

Diff between dst versions 1.3.0 dated 2018-12-05 and 1.4.0 dated 2019-08-20

 DESCRIPTION                      |    8 -
 MD5                              |   26 ++---
 NEWS                             |    7 +
 R/bcaRel.R                       |    1 
 R/dsrwon.R                       |    1 
 R/extmin.R                       |    4 
 R/productSpace.R                 |    8 -
 build/vignette.rds               |binary
 inst/doc/Monty-hall-Example.R    |    6 -
 inst/doc/Monty-hall-Example.Rmd  |    6 -
 inst/doc/Monty-hall-Example.html |  179 +++++++++++++--------------------------
 inst/dst.pdf                     |binary
 tests/testthat/test_extmin.R     |   11 ++
 vignettes/Monty-hall-Example.Rmd |    6 -
 14 files changed, 108 insertions(+), 155 deletions(-)

More information about dst at CRAN
Permanent link

Mon, 19 Aug 2019

Package GDINA updated to version 2.7.3 with previous version 2.7.0 dated 2019-08-08

Title: The Generalized DINA Model Framework
Description: A set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> and its extensions, including the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070> for polytomous responses, and the polytomous G-DINA model by Chen and de la Torre <DOI:10.1177/0146621613479818> for polytomous attributes. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided.
Author: Wenchao Ma [aut, cre, cph], Jimmy de la Torre [aut, cph], Miguel Sorrel [ctb], Zhehan Jiang [ctb]
Maintainer: Wenchao Ma <wenchao.ma@ua.edu>

Diff between GDINA versions 2.7.0 dated 2019-08-08 and 2.7.3 dated 2019-08-19

 DESCRIPTION                  |    8 ++---
 MD5                          |   24 ++++++++--------
 NEWS.md                      |    6 ++++
 R/GDI.R                      |    9 +++++-
 R/MultipleGroup_Estimation.R |    2 -
 R/SingleGroup_Estimation.R   |    2 -
 R/print.GDINA.R              |    6 ++--
 R/score.R                    |   13 +++++++-
 R/summary.GDINA.R            |    6 ++--
 README.md                    |    2 -
 inst/doc/GDINA.html          |    4 +-
 inst/shiny/server.R          |   63 ++++++++++---------------------------------
 inst/shiny/ui.R              |    2 -
 13 files changed, 69 insertions(+), 78 deletions(-)

More information about GDINA at CRAN
Permanent link

Package miceFast updated to version 0.5.1 with previous version 0.2.3 dated 2018-05-06

Title: Fast Imputations Using 'Rcpp' and 'Armadillo'
Description: Fast imputations under the object-oriented programming paradigm. There was used quantitative models with a closed-form solution. Thus package is based on linear algebra operations. The biggest improvement in time performance could be achieve for a calculation where a grouping variable have to be used. A single evaluation of a quantitative model for the multiple imputations is another major enhancement. Moreover there are offered a few functions built to work with popular R packages such as 'data.table' or 'dplyr'.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>

Diff between miceFast versions 0.2.3 dated 2018-05-06 and 0.5.1 dated 2019-08-19

 DESCRIPTION                         |   17 
 MD5                                 |   75 ++--
 NAMESPACE                           |   40 ++
 NEWS.md                             |   11 
 R/RcppExports.R                     |  213 ------------
 R/VIF.R                             |only
 R/data.R                            |only
 R/fill_NA.R                         |only
 R/fill_NA_N.R                       |only
 build/vignette.rds                  |binary
 data                                |only
 inst/doc/miceFast-intro.R           |  197 ++++++++++-
 inst/doc/miceFast-intro.Rmd         |  272 +++++++++++----
 inst/doc/miceFast-intro.html        |  638 +++++++++++++++++++++++++++++-------
 inst/extdata/images/g1.png          |binary
 inst/extdata/images/g10.png         |only
 inst/extdata/images/g2.png          |binary
 inst/extdata/images/g3.png          |binary
 inst/extdata/images/g4.png          |binary
 inst/extdata/images/g5.png          |binary
 inst/extdata/images/g6.png          |binary
 inst/extdata/images/g7.png          |binary
 inst/extdata/images/g8.png          |binary
 inst/extdata/images/g9.png          |binary
 inst/extdata/images/g_summary.png   |binary
 inst/extdata/performance_validity.R |  193 ++++++----
 man/VIF.Rd                          |   52 +-
 man/air_miss.Rd                     |only
 man/fill_NA.Rd                      |  223 +++++++++---
 man/fill_NA_N.Rd                    |  226 +++++++++---
 man/miceFast-package.Rd             |    8 
 src/Makevars                        |    2 
 src/Makevars.win                    |    2 
 src/R_funs.cpp                      |  314 ++++-------------
 src/RcppExports.cpp                 |   32 -
 src/corrData.cpp                    |   10 
 src/miceFast.h                      |    2 
 src/miceFast_class.cpp              |    8 
 src/miceFast_quantmodels.cpp        |   25 -
 tests/testthat.R                    |    3 
 tests/testthat/test-imputes_funcs.R |  167 ++++++++-
 vignettes/miceFast-intro.Rmd        |  272 +++++++++++----
 42 files changed, 2005 insertions(+), 997 deletions(-)

More information about miceFast at CRAN
Permanent link

Package sparsevar updated to version 0.0.11 with previous version 0.0.10 dated 2016-11-07

Title: Sparse VAR/VECM Models Estimation
Description: A wrapper for sparse VAR/VECM time series models estimation using penalties like ENET (Elastic Net), SCAD (Smoothly Clipped Absolute Deviation) and MCP (Minimax Concave Penalty). Based on the work of Sumanta Basu and George Michailidis <doi:10.1214/15-AOS1315>.
Author: Simone Vazzoler [aut, cre]
Maintainer: Simone Vazzoler <svazzole@gmail.com>

Diff between sparsevar versions 0.0.10 dated 2016-11-07 and 0.0.11 dated 2019-08-19

 sparsevar-0.0.10/sparsevar/inst/doc/using.pdf             |only
 sparsevar-0.0.11/sparsevar/DESCRIPTION                    |   30 -
 sparsevar-0.0.11/sparsevar/MD5                            |  107 ++-
 sparsevar-0.0.11/sparsevar/NAMESPACE                      |    4 
 sparsevar-0.0.11/sparsevar/NEWS.md                        |    4 
 sparsevar-0.0.11/sparsevar/R/createSparseMatrix.R         |    7 
 sparsevar-0.0.11/sparsevar/R/fitVAR.R                     |  225 ++++++--
 sparsevar-0.0.11/sparsevar/R/fitVARX.R                    |only
 sparsevar-0.0.11/sparsevar/R/fitVECM.R                    |   98 +++
 sparsevar-0.0.11/sparsevar/R/impulseResponse.R            |  376 ++++++++++++--
 sparsevar-0.0.11/sparsevar/R/mcSimulations.R              |    9 
 sparsevar-0.0.11/sparsevar/R/plotIRF.R                    |  121 +++-
 sparsevar-0.0.11/sparsevar/R/plotMatrix.R                 |   67 +-
 sparsevar-0.0.11/sparsevar/R/simulateVAR.R                |   43 -
 sparsevar-0.0.11/sparsevar/R/simulateVARX.R               |only
 sparsevar-0.0.11/sparsevar/R/timeSlice.R                  |   72 +-
 sparsevar-0.0.11/sparsevar/R/twoStepOLS.R                 |only
 sparsevar-0.0.11/sparsevar/R/utils.R                      |    2 
 sparsevar-0.0.11/sparsevar/R/utilsVAR.R                   |   82 ++-
 sparsevar-0.0.11/sparsevar/README.md                      |   29 -
 sparsevar-0.0.11/sparsevar/build/vignette.rds             |binary
 sparsevar-0.0.11/sparsevar/inst/doc/using.R               |    7 
 sparsevar-0.0.11/sparsevar/inst/doc/using.html            |only
 sparsevar-0.0.11/sparsevar/man/accuracy.Rd                |    1 
 sparsevar-0.0.11/sparsevar/man/bootstrappedVAR.Rd         |    1 
 sparsevar-0.0.11/sparsevar/man/checkImpulseZero.Rd        |    1 
 sparsevar-0.0.11/sparsevar/man/checkIsVar.Rd              |    1 
 sparsevar-0.0.11/sparsevar/man/companionVAR.Rd            |    1 
 sparsevar-0.0.11/sparsevar/man/computeForecasts.Rd        |    1 
 sparsevar-0.0.11/sparsevar/man/createSparseMatrix.Rd      |    3 
 sparsevar-0.0.11/sparsevar/man/decomposePi.Rd             |only
 sparsevar-0.0.11/sparsevar/man/errorBandsIRF.Rd           |    8 
 sparsevar-0.0.11/sparsevar/man/fitVAR.Rd                  |   41 -
 sparsevar-0.0.11/sparsevar/man/fitVARX.Rd                 |only
 sparsevar-0.0.11/sparsevar/man/fitVECM.Rd                 |    1 
 sparsevar-0.0.11/sparsevar/man/frobNorm.Rd                |    1 
 sparsevar-0.0.11/sparsevar/man/impulseResponse.Rd         |    1 
 sparsevar-0.0.11/sparsevar/man/informCrit.Rd              |    1 
 sparsevar-0.0.11/sparsevar/man/l1norm.Rd                  |    1 
 sparsevar-0.0.11/sparsevar/man/l2norm.Rd                  |    1 
 sparsevar-0.0.11/sparsevar/man/lInftyNorm.Rd              |    1 
 sparsevar-0.0.11/sparsevar/man/maxNorm.Rd                 |    1 
 sparsevar-0.0.11/sparsevar/man/mcSimulations.Rd           |    6 
 sparsevar-0.0.11/sparsevar/man/multiplot.Rd               |only
 sparsevar-0.0.11/sparsevar/man/plotIRF.Rd                 |    1 
 sparsevar-0.0.11/sparsevar/man/plotIRFGrid.Rd             |    5 
 sparsevar-0.0.11/sparsevar/man/plotMatrix.Rd              |    5 
 sparsevar-0.0.11/sparsevar/man/plotVAR.Rd                 |   10 
 sparsevar-0.0.11/sparsevar/man/plotVECM.Rd                |    1 
 sparsevar-0.0.11/sparsevar/man/simulateVAR.Rd             |    1 
 sparsevar-0.0.11/sparsevar/man/simulateVARX.Rd            |only
 sparsevar-0.0.11/sparsevar/man/spectralNorm.Rd            |    1 
 sparsevar-0.0.11/sparsevar/man/spectralRadius.Rd          |    1 
 sparsevar-0.0.11/sparsevar/man/testGranger.Rd             |    1 
 sparsevar-0.0.11/sparsevar/man/transformData.Rd           |    1 
 sparsevar-0.0.11/sparsevar/man/varENET.Rd                 |    1 
 sparsevar-0.0.11/sparsevar/man/varMCP.Rd                  |    1 
 sparsevar-0.0.11/sparsevar/man/varSCAD.Rd                 |    5 
 sparsevar-0.0.11/sparsevar/tests/testthat/testIsWorking.R |    7 
 59 files changed, 1005 insertions(+), 391 deletions(-)

More information about sparsevar at CRAN
Permanent link

Package rmapzen updated to version 0.4.2 with previous version 0.4.1 dated 2018-10-07

Title: Client for 'Mapzen' and Related Map APIs
Description: Provides an interface to 'Mapzen'-based APIs (including geocode.earth, Nextzen, and NYC GeoSearch) for geographic search and geocoding, isochrone calculation, and vector data to draw map tiles. See <https://mapzen.com/documentation/> for more information. The original Mapzen has gone out of business, but 'rmapzen' can be set up to work with any provider who implements the Mapzen API.
Author: Tarak Shah [aut, cre], Daniel Possenriede [ctb]
Maintainer: Tarak Shah <tarak.shah@gmail.com>

Diff between rmapzen versions 0.4.1 dated 2018-10-07 and 0.4.2 dated 2019-08-19

 DESCRIPTION                        |   10 +++++-----
 MD5                                |   20 ++++++++++----------
 NEWS.md                            |    4 ++++
 R/geocode.R                        |    2 +-
 R/mz-bbox.R                        |    8 ++++----
 R/mz-coordinates.R                 |    2 +-
 R/tidy.R                           |   21 +++++++++++++++------
 R/vector-tiles.R                   |   10 ++++++----
 build/vignette.rds                 |binary
 inst/doc/rmapzen-introduction.html |   36 ++++++++++++++++++------------------
 man/mz_vector_tiles.Rd             |    4 +++-
 11 files changed, 67 insertions(+), 50 deletions(-)

More information about rmapzen at CRAN
Permanent link

Package BNPTSclust updated to version 2.0 with previous version 1.1 dated 2015-04-19

Title: A Bayesian Nonparametric Algorithm for Time Series Clustering
Description: Performs the algorithm for time series clustering described in Nieto-Barajas and Contreras-Cristan (2014).
Author: Martell-Juarez, D.A. & Nieto-Barajas, L.E.
Maintainer: David Alejandro Martell Juarez <alex91599@gmail.com>

Diff between BNPTSclust versions 1.1 dated 2015-04-19 and 2.0 dated 2019-08-19

 BNPTSclust-1.1/BNPTSclust/inst/doc/BNPTSclust1.1.pdf |only
 BNPTSclust-1.1/BNPTSclust/vignettes                  |only
 BNPTSclust-2.0/BNPTSclust/DESCRIPTION                |   10 
 BNPTSclust-2.0/BNPTSclust/MD5                        |   57 +--
 BNPTSclust-2.0/BNPTSclust/NAMESPACE                  |    5 
 BNPTSclust-2.0/BNPTSclust/R/clusterplots.R           |   19 -
 BNPTSclust-2.0/BNPTSclust/R/designmatrices.R         |   56 +--
 BNPTSclust-2.0/BNPTSclust/R/scaleandperiods.R        |   59 ++--
 BNPTSclust-2.0/BNPTSclust/R/tseriesca.R              |  178 ++++++------
 BNPTSclust-2.0/BNPTSclust/R/tseriescm.R              |  152 +++++-----
 BNPTSclust-2.0/BNPTSclust/R/tseriescq.R              |  278 ++++++++++---------
 BNPTSclust-2.0/BNPTSclust/data/gdp.rda               |binary
 BNPTSclust-2.0/BNPTSclust/data/houses.rda            |binary
 BNPTSclust-2.0/BNPTSclust/data/stocks.rda            |binary
 BNPTSclust-2.0/BNPTSclust/data/tseriesca.out.rda     |binary
 BNPTSclust-2.0/BNPTSclust/data/tseriescm.out.rda     |binary
 BNPTSclust-2.0/BNPTSclust/data/tseriescq.out.rda     |binary
 BNPTSclust-2.0/BNPTSclust/inst/doc/BNPTSclust2_0.pdf |only
 BNPTSclust-2.0/BNPTSclust/man/BNPTSclust-package.Rd  |   10 
 BNPTSclust-2.0/BNPTSclust/man/clusterplots.Rd        |    9 
 BNPTSclust-2.0/BNPTSclust/man/designmatrices.Rd      |    2 
 BNPTSclust-2.0/BNPTSclust/man/diagplots.Rd           |    2 
 BNPTSclust-2.0/BNPTSclust/man/gdp.Rd                 |    2 
 BNPTSclust-2.0/BNPTSclust/man/houses.Rd              |    2 
 BNPTSclust-2.0/BNPTSclust/man/scaleandperiods.Rd     |   11 
 BNPTSclust-2.0/BNPTSclust/man/stocks.Rd              |    2 
 BNPTSclust-2.0/BNPTSclust/man/tseriesca.Rd           |   45 ---
 BNPTSclust-2.0/BNPTSclust/man/tseriesca.out.Rd       |    2 
 BNPTSclust-2.0/BNPTSclust/man/tseriescm.Rd           |   33 --
 BNPTSclust-2.0/BNPTSclust/man/tseriescq.Rd           |   29 -
 BNPTSclust-2.0/BNPTSclust/man/tseriescq.out.Rd       |    2 
 31 files changed, 507 insertions(+), 458 deletions(-)

More information about BNPTSclust at CRAN
Permanent link

Package mlflow updated to version 1.2.0 with previous version 1.1.0 dated 2019-07-23

Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for the complete machine learning life cycle, see <https://mlflow.org/>. This package supports installing 'MLflow', tracking experiments, creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre], Javier Luraschi [aut], Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>), RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>

Diff between mlflow versions 1.1.0 dated 2019-07-23 and 1.2.0 dated 2019-08-19

 DESCRIPTION                                |    6 +-
 MD5                                        |   36 ++++++------
 NAMESPACE                                  |    1 
 R/cli.R                                    |    6 +-
 R/install.R                                |   35 +++++++++---
 R/model-serve.R                            |   49 ++++++++++++++++-
 R/model.R                                  |    4 -
 R/project-run.R                            |    4 -
 R/python.R                                 |   17 +++++-
 R/tracking-experiments.R                   |   30 +++++++++-
 man/install_mlflow.Rd                      |   18 +++++-
 man/mlflow_get_experiment.Rd               |    2 
 man/mlflow_load_model.Rd                   |    2 
 man/mlflow_rfunc_serve.Rd                  |    9 ++-
 man/mlflow_run.Rd                          |    4 -
 man/mlflow_set_experiment_tag.Rd           |only
 tests/testthat.R                           |    2 
 tests/testthat/test-bypass-conda.R         |only
 tests/testthat/test-serve.R                |   82 +++++++++++++++++++++++++++++
 tests/testthat/test-tracking-experiments.R |   43 +++++++++++++++
 20 files changed, 300 insertions(+), 50 deletions(-)

More information about mlflow at CRAN
Permanent link

Package MGDrivE updated to version 1.1.0 with previous version 1.0.0 dated 2019-07-12

Title: Mosquito Gene Drive Explorer
Description: Provides a model designed to be a reliable testbed where various gene drive interventions for mosquito-borne diseases control. It is being developed to accommodate the use of various mosquito-specific gene drive systems within a population dynamics framework that allows migration of individuals between patches in landscape. Previous work developing the population dynamics can be found in Deredec et al. (2001) <doi:10.1073/pnas.1110717108> and Hancock & Godfray (2007) <doi:10.1186/1475-2875-6-98>, and extensions to accommodate basic CRISPR homing dynamics in Marshall et al. (2017) <doi:10.1038/s41598-017-02744-7>.
Author: Héctor Manuel Sánchez Castellanos [aut, cre], Jared Bennett [aut], Sean Wu [aut], John M. Marshall [aut]
Maintainer: Héctor Manuel Sánchez Castellanos <sanchez.hmsc@berkeley.edu>

Diff between MGDrivE versions 1.0.0 dated 2019-07-12 and 1.1.0 dated 2019-08-19

 DESCRIPTION                                    |   11 +-
 MD5                                            |  121 ++++++++++++-------------
 NEWS.md                                        |only
 R/Cube-CRISPR2MF.R                             |    2 
 R/Cube-KillerRescue.R                          |    4 
 R/Cube-RIDL.R                                  |    2 
 R/Cube-Wolbachia.R                             |    2 
 R/MGDrivE-Auxiliary.R                          |   26 ++---
 R/MGDrivE-Graphics.R                           |   50 +++++++---
 R/MGDrivE.R                                    |    6 -
 R/Network-Class.R                              |   23 ++--
 R/Network-Parameters.R                         |    6 -
 R/Network-Simulation.R                         |   40 +-------
 R/Patch-Migration.R                            |    4 
 R/Patch-Simulation.R                           |    8 -
 R/RcppExports.R                                |   69 +++++++++++---
 R/zzz.R                                        |    2 
 build/partial.rdb                              |binary
 build/vignette.rds                             |binary
 inst/doc/mgdrive_examples.R                    |   12 ++
 inst/doc/mgdrive_examples.Rmd                  |   48 +++++----
 inst/doc/mgdrive_examples.html                 |   91 +++++++++---------
 inst/doc/mgdrive_math.Rmd                      |    8 -
 inst/doc/mgdrive_math.html                     |    8 -
 inst/doc/mgdrive_run.Rmd                       |   10 +-
 inst/doc/mgdrive_run.html                      |   14 +-
 man/MGDrivE-Model.Rd                           |    2 
 man/MGDrivE.Rd                                 |    4 
 man/Network.Rd                                 |   17 +--
 man/calcAquaticStageSurvivalProbability.Rd     |    2 
 man/calcAquaticStagesSurvivalProbability.Rd    |    2 
 man/calcCos.Rd                                 |    2 
 man/calcDensityDependentDeathRate.Rd           |    2 
 man/calcExpKernel.Rd                           |   10 ++
 man/calcGammaKernel.Rd                         |   11 ++
 man/calcHaversine.Rd                           |    4 
 man/calcHurdleExpKernel.Rd                     |   29 ++++-
 man/calcLognormalKernel.Rd                     |   10 ++
 man/calcQuantiles.Rd                           |   14 +-
 man/calcVinEll.Rd                              |    2 
 man/calcZeroInflation.Rd                       |    2 
 man/cubeHomingDrive.Rd                         |    2 
 man/cubeKillerRescue.Rd                        |    4 
 man/cubeRIDL.Rd                                |    2 
 man/cubeWolbachia.Rd                           |    2 
 man/get_wildType_Network.Rd                    |    2 
 man/oneDay_admSurvival_deterministic_Patch.Rd  |    2 
 man/oneDay_admSurvival_stochastic_Patch.Rd     |    2 
 man/oneDay_af1Survival_deterministic_Patch.Rd  |    2 
 man/oneDay_af1Survival_stochastic_Patch.Rd     |    2 
 man/oneDay_migrationOut_deterministic_Patch.Rd |    2 
 man/oneDay_migrationOut_stochastic_Patch.Rd    |    2 
 man/plotMGDrivEMult.Rd                         |    6 -
 man/rDirichlet.Rd                              |    2 
 man/retrieveOutput.Rd                          |    2 
 src/MGDrivE-Auxilary.cpp                       |    4 
 src/MGDrivE-DistanceFunctions.cpp              |   12 +-
 src/MGDrivE-Kernels.cpp                        |   63 +++++++++++--
 src/RcppExports.cpp                            |    8 -
 vignettes/mgdrive_examples.Rmd                 |   48 +++++----
 vignettes/mgdrive_math.Rmd                     |    8 -
 vignettes/mgdrive_run.Rmd                      |   10 +-
 62 files changed, 521 insertions(+), 346 deletions(-)

More information about MGDrivE at CRAN
Permanent link

Package rnassqs updated to version 0.5.0 with previous version 0.4.0 dated 2019-05-03

Title: Access the NASS 'Quick Stats' API
Description: Interface to access data via the United States Department of Agriculture's National Agricultural Statistical Service (NASS) 'Quick Stats' web API <https://quickstats.nass.usda.gov/api>. Convenience functions facilitate building queries based on available parameters and valid parameter values.
Author: Nicholas Potter [aut, cre], Jonathan Adams [ctb], Joseph Stachelek [ctb], Julia Piaskowski [ctb], Adam Sparks [rev], Neal Richardson [ctb, rev]
Maintainer: Nicholas Potter <potter.nicholas@gmail.com>

Diff between rnassqs versions 0.4.0 dated 2019-05-03 and 0.5.0 dated 2019-08-19

 rnassqs-0.4.0/rnassqs/R/data.R                                |only
 rnassqs-0.4.0/rnassqs/man/expand_list.Rd                      |only
 rnassqs-0.4.0/rnassqs/man/nassqs_area.Rd                      |only
 rnassqs-0.4.0/rnassqs/man/nassqs_yield.Rd                     |only
 rnassqs-0.4.0/rnassqs/man/release_questions.Rd                |only
 rnassqs-0.4.0/rnassqs/tests/testthat/test-local.R             |only
 rnassqs-0.4.0/rnassqs/tests/testthat/test-oncran.R            |only
 rnassqs-0.5.0/rnassqs/DESCRIPTION                             |   27 
 rnassqs-0.5.0/rnassqs/MD5                                     |   71 
 rnassqs-0.5.0/rnassqs/NAMESPACE                               |    6 
 rnassqs-0.5.0/rnassqs/NEWS.md                                 |   21 
 rnassqs-0.5.0/rnassqs/R/auth.R                                |only
 rnassqs-0.5.0/rnassqs/R/helpers.R                             |  113 -
 rnassqs-0.5.0/rnassqs/R/nassqs.R                              |  262 ---
 rnassqs-0.5.0/rnassqs/R/params.R                              |only
 rnassqs-0.5.0/rnassqs/R/request.R                             |only
 rnassqs-0.5.0/rnassqs/R/wrappers.R                            |only
 rnassqs-0.5.0/rnassqs/README.md                               |  345 +++-
 rnassqs-0.5.0/rnassqs/build/vignette.rds                      |binary
 rnassqs-0.5.0/rnassqs/inst/CITATION                           |only
 rnassqs-0.5.0/rnassqs/inst/doc/rnassqs.R                      |    7 
 rnassqs-0.5.0/rnassqs/inst/doc/rnassqs.Rmd                    |  255 ++-
 rnassqs-0.5.0/rnassqs/inst/doc/rnassqs.html                   |  781 +++++-----
 rnassqs-0.5.0/rnassqs/inst/examples/example_parameters.R      |    3 
 rnassqs-0.5.0/rnassqs/inst/figures                            |only
 rnassqs-0.5.0/rnassqs/man/nassqs.Rd                           |   40 
 rnassqs-0.5.0/rnassqs/man/nassqs_GET.Rd                       |   80 -
 rnassqs-0.5.0/rnassqs/man/nassqs_acres.Rd                     |only
 rnassqs-0.5.0/rnassqs/man/nassqs_auth.Rd                      |   39 
 rnassqs-0.5.0/rnassqs/man/nassqs_check.Rd                     |   15 
 rnassqs-0.5.0/rnassqs/man/nassqs_fields.Rd                    |   11 
 rnassqs-0.5.0/rnassqs/man/nassqs_param_values.Rd              |   17 
 rnassqs-0.5.0/rnassqs/man/nassqs_params.Rd                    |   24 
 rnassqs-0.5.0/rnassqs/man/nassqs_parse.Rd                     |   52 
 rnassqs-0.5.0/rnassqs/man/nassqs_record_count.Rd              |   20 
 rnassqs-0.5.0/rnassqs/man/nassqs_yields.Rd                    |only
 rnassqs-0.5.0/rnassqs/man/rnassqs-package.Rd                  |   11 
 rnassqs-0.5.0/rnassqs/tests/testthat/helper.R                 |only
 rnassqs-0.5.0/rnassqs/tests/testthat/quickstats.nass.usda.gov |only
 rnassqs-0.5.0/rnassqs/tests/testthat/test-auth.R              |only
 rnassqs-0.5.0/rnassqs/tests/testthat/test-helpers.R           |only
 rnassqs-0.5.0/rnassqs/tests/testthat/test-params.R            |only
 rnassqs-0.5.0/rnassqs/tests/testthat/test-request.R           |only
 rnassqs-0.5.0/rnassqs/tests/testthat/test-wrappers.R          |only
 rnassqs-0.5.0/rnassqs/tests/testthat/testdata                 |only
 rnassqs-0.5.0/rnassqs/vignettes/rnassqs.Rmd                   |  255 ++-
 46 files changed, 1419 insertions(+), 1036 deletions(-)

More information about rnassqs at CRAN
Permanent link

Package pangaear updated to version 0.8.0 with previous version 0.6.0 dated 2018-01-03

Title: Client for the 'Pangaea' Database
Description: Tools to interact with the 'Pangaea' Database (<https://www.pangaea.de>), including functions for searching for data, fetching 'datasets' by 'dataset' 'ID', and working with the 'Pangaea' 'OAI-PMH' service.
Author: Scott Chamberlain [aut, cre], Kara Woo [aut], Andrew MacDonald [aut], Naupaka Zimmerman [aut], Gavin Simpson [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between pangaear versions 0.6.0 dated 2018-01-03 and 0.8.0 dated 2019-08-19

 DESCRIPTION                         |   20 +-
 LICENSE                             |    2 
 MD5                                 |   78 ++++----
 NAMESPACE                           |    5 
 NEWS.md                             |   18 +
 R/caching.R                         |   52 ++++-
 R/onload.R                          |only
 R/pangaear-package.R                |    9 
 R/pg_cache.R                        |   26 --
 R/pg_data.R                         |   65 +++---
 R/pg_list_identifiers.R             |    4 
 R/pg_search.R                       |    2 
 R/pg_search_es.R                    |    2 
 R/zzz.R                             |   62 ++++++
 README.md                           |  225 ++++++++++++-----------
 build/vignette.rds                  |binary
 inst/doc/pangaear_vignette.Rmd      |  339 +++++++++++++++++++-----------------
 inst/doc/pangaear_vignette.html     |  339 +++++++++++++++++++-----------------
 inst/vign/pangaear_vignette.md      |  339 +++++++++++++++++++-----------------
 man/pangaear-package.Rd             |    7 
 man/pg_cache.Rd                     |only
 man/pg_cache_clear-defunct.Rd       |only
 man/pg_cache_list-defunct.Rd        |only
 man/pg_data.Rd                      |   42 +---
 man/pg_get_record.Rd                |    1 
 man/pg_identify.Rd                  |    1 
 man/pg_list_identifiers.Rd          |    1 
 man/pg_list_metadata_formats.Rd     |    1 
 man/pg_list_records.Rd              |    1 
 man/pg_list_sets.Rd                 |    1 
 man/pg_search_es.Rd                 |    4 
 tests/fixtures                      |only
 tests/testthat/helper-pangaear.R    |only
 tests/testthat/test-oai_functions.R |   45 ++--
 tests/testthat/test-pg_data.R       |   36 +++
 tests/testthat/test-pg_identify.R   |    6 
 tests/testthat/test-pg_search.r     |   26 +-
 tests/testthat/test-pg_search_es.R  |   13 -
 vignettes/pangaear_vignette.Rmd     |  339 +++++++++++++++++++-----------------
 39 files changed, 1197 insertions(+), 914 deletions(-)

More information about pangaear at CRAN
Permanent link

Package HiCglmi updated to version 1.4 with previous version 1.3 dated 2018-04-18

Title: Probing Factor-Dependent Long-Range Contacts using Regression with Higher-Order Interaction Terms
Description: We propose a generalized linear regression with higher-order interaction terms to assess the influences of genomic features such as DNA-binding proteins and functional elements on long-range contacts from Hi-C experiments.
Author: Raphael Mourad
Maintainer: Raphael Mourad <raphael.mourad@ibcg.biotoul.fr>

Diff between HiCglmi versions 1.3 dated 2018-04-18 and 1.4 dated 2019-08-19

 DESCRIPTION            |    8 ++++----
 MD5                    |    8 ++++----
 R/HiCglmiMiscFun.R     |    2 +-
 build/partial.rdb      |binary
 data/dataExample.RData |binary
 5 files changed, 9 insertions(+), 9 deletions(-)

More information about HiCglmi at CRAN
Permanent link

Package ari updated to version 0.3.2 with previous version 0.3.1 dated 2019-07-13

Title: Automated R Instructor
Description: Create videos from 'R Markdown' documents, or images and audio files. These images can come from image files or HTML slides, and the audio files can be provided by the user or computer voice narration can be created using 'Amazon Polly'. The purpose of this package is to allow users to create accessible, translatable, and reproducible lecture videos. See <https://aws.amazon.com/polly/> for more information.
Author: Sean Kross [aut, cre], John Muschelli [ctb]
Maintainer: Sean Kross <sean@seankross.com>

Diff between ari versions 0.3.1 dated 2019-07-13 and 0.3.2 dated 2019-08-19

 DESCRIPTION       |    6 +++---
 MD5               |   12 ++++++------
 NEWS.md           |    6 ++++++
 R/ari_spin.R      |    8 ++++++++
 R/ari_stitch.R    |   51 +++++++++++++++++++++++++++++++++++++++++++--------
 R/ffmpeg_codecs.R |   15 ++++++++++++++-
 man/ari_stitch.Rd |   23 ++++++++++++++++++++---
 7 files changed, 100 insertions(+), 21 deletions(-)

More information about ari at CRAN
Permanent link

Package APfun updated to version 0.1.4 with previous version 0.1.3 dated 2018-04-03

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 0.1.3 dated 2018-04-03 and 0.1.4 dated 2019-08-19

 APfun-0.1.3/APfun/man/APKML2SHP.Rd          |only
 APfun-0.1.4/APfun/DESCRIPTION               |   12 +--
 APfun-0.1.4/APfun/MD5                       |   19 +++--
 APfun-0.1.4/APfun/NAMESPACE                 |    2 
 APfun-0.1.4/APfun/NEWS.md                   |    4 +
 APfun-0.1.4/APfun/R/APSHP.R                 |   90 ++++++++--------------------
 APfun-0.1.4/APfun/R/APcontours.R            |    7 +-
 APfun-0.1.4/APfun/R/APpolygonize.R          |    9 +-
 APfun-0.1.4/APfun/R/APrasterfiles.R         |only
 APfun-0.1.4/APfun/README.md                 |    2 
 APfun-0.1.4/APfun/data/rasterExtensions.rda |only
 APfun-0.1.4/APfun/man/APrasterFiles.Rd      |only
 APfun-0.1.4/APfun/man/rasterExtensions.Rd   |only
 13 files changed, 61 insertions(+), 84 deletions(-)

More information about APfun at CRAN
Permanent link

Package uroot updated to version 2.1-0 with previous version 2.0-11 dated 2019-08-19

Title: Unit Root Tests for Seasonal Time Series
Description: Seasonal unit roots and seasonal stability tests. P-values based on response surface regressions are available for both tests. P-values based on bootstrap are available for seasonal unit root tests.
Author: Javier López-de-Lacalle [aut], Georgi N. Boshnakov [cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

Diff between uroot versions 2.0-11 dated 2019-08-19 and 2.1-0 dated 2019-08-19

 uroot-2.0-11/uroot/R/hegy-test.R.in        |only
 uroot-2.0-11/uroot/cleanup                 |only
 uroot-2.0-11/uroot/cleanup.win             |only
 uroot-2.0-11/uroot/configure               |only
 uroot-2.0-11/uroot/configure.ac            |only
 uroot-2.0-11/uroot/configure.win           |only
 uroot-2.0-11/uroot/src                     |only
 uroot-2.0-11/uroot/tools                   |only
 uroot-2.1-0/uroot/DESCRIPTION              |   13 +++++--------
 uroot-2.1-0/uroot/MD5                      |   23 +++++------------------
 uroot-2.1-0/uroot/NAMESPACE                |    2 --
 uroot-2.1-0/uroot/NEWS                     |    9 ++++++++-
 uroot-2.1-0/uroot/R/hegy-test.R            |only
 uroot-2.1-0/uroot/inst/doc/uroot-intro.pdf |binary
 14 files changed, 18 insertions(+), 29 deletions(-)

More information about uroot at CRAN
Permanent link

Package umap updated to version 0.2.3 with previous version 0.2.2.0 dated 2019-05-13

Title: Uniform Manifold Approximation and Projection
Description: Uniform manifold approximation and projection is a technique for dimension reduction. The algorithm was described by McInnes and Healy (2018) in <arXiv:1802.03426>. This package provides an interface for two implementations. One is written from scratch, including components for nearest-neighbor search and for embedding. The second implementation is a wrapper for 'python' package 'umap-learn' (requires separate installation, see vignette for more details).
Author: Tomasz Konopka [aut, cre]
Maintainer: Tomasz Konopka <tokonopka@gmail.com>

Diff between umap versions 0.2.2.0 dated 2019-05-13 and 0.2.3 dated 2019-08-19

 DESCRIPTION                     |    9 -
 MD5                             |   50 +++---
 NAMESPACE                       |    2 
 R/RcppExports.R                 |   21 ++
 R/coo.R                         |    2 
 R/umap_checks.R                 |   89 ++++++------
 R/umap_naive.R                  |  287 +++++++++++++++++++---------------------
 R/umap_universal.R              |  123 ++++++++++-------
 R/utils.R                       |   36 ++---
 inst/doc/umap.R                 |    6 
 inst/doc/umap.Rmd               |   67 +++++++--
 inst/doc/umap.html              |   87 ++++++++----
 inst/doc/umap_learn.R           |    1 
 inst/doc/umap_learn.Rmd         |   16 +-
 inst/doc/umap_learn.html        |   34 +++-
 man/column.seeds.Rd             |only
 man/naive.optimize.embedding.Rd |    6 
 man/optimize_embedding.Rd       |only
 man/optimize_epoch.Rd           |    7 
 src/RcppExports.cpp             |   18 ++
 src/optimize.cpp                |   64 ++++++++
 tests/testthat/test_methods.R   |   11 -
 tests/testthat/test_naive.R     |  107 ++++++++++----
 tests/testthat/test_synthetic.R |   14 -
 tests/testthat/test_universal.R |   26 +++
 vignettes/umap.Rmd              |   67 +++++++--
 vignettes/umap_learn.Rmd        |   16 +-
 27 files changed, 747 insertions(+), 419 deletions(-)

More information about umap at CRAN
Permanent link

Package tidyLPA updated to version 1.0.4 with previous version 1.0.3 dated 2019-07-30

Title: Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software
Description: An interface to the 'mclust' package to easily carry out latent profile analysis ("LPA"). Provides functionality to estimate commonly-specified models. Follows a tidy approach, in that output is in the form of a data frame that can subsequently be computed on. Also has functions to interface to the commercial 'MPlus' software via the 'MplusAutomation' package.
Author: Joshua M Rosenberg [aut, cre], Caspar van Lissa [aut], Jennifer A Schmidt [ctb], Patrick N Beymer [ctb], Daniel Anderson [ctb], Matthew J. Schell [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>

Diff between tidyLPA versions 1.0.3 dated 2019-07-30 and 1.0.4 dated 2019-08-19

 DESCRIPTION                                 |    6 +-
 MD5                                         |   24 ++++++----
 NEWS.md                                     |    4 +
 R/calc_functions.R                          |   10 ++--
 R/empathy.R                                 |only
 R/estimate-profiles-mclust.R                |   24 +++++++---
 R/estimate-profiles-mplus.R                 |    3 -
 R/id_edu.R                                  |only
 R/plot-profiles.R                           |    1 
 data/empathy.csv                            |only
 data/id_edu.csv                             |only
 inst/doc/Introduction_to_tidyLPA.html       |   66 ++++++++++++++--------------
 inst/doc/benchmarking-mclust-and-mplus.html |    4 -
 inst/doc/introduction-to-major-changes.html |    6 +-
 man/empathy.Rd                              |only
 man/id_edu.Rd                               |only
 16 files changed, 87 insertions(+), 61 deletions(-)

More information about tidyLPA at CRAN
Permanent link

Package smooth updated to version 2.5.3 with previous version 2.5.2 dated 2019-07-25

Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting. The package includes Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>), SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>), Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>), Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>), Vector Exponential Smoothing (de Silva et al., 2010, <doi: 10.1177/1471082X0901000401>) in state space forms, several simulation functions and intermittent demand state space models. It also allows dealing with intermittent demand based on the iETS framework (Svetunkov & Boylan, 2017, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>

Diff between smooth versions 2.5.2 dated 2019-07-25 and 2.5.3 dated 2019-08-19

 DESCRIPTION            |   10 +-
 MD5                    |   44 +++++------
 NAMESPACE              |    1 
 NEWS                   |   20 +++++
 R/cma.R                |    2 
 R/es.R                 |   92 ++++++++++++++++++++++-
 R/methods.R            |    5 +
 R/simes.R              |    2 
 R/ssfunctions.R        |   25 ++++--
 R/vssFunctions.R       |   57 ++++++++++++--
 build/partial.rdb      |binary
 inst/doc/ces.html      |   34 ++++----
 inst/doc/es.html       |  140 ++++++++++++++++++------------------
 inst/doc/gum.html      |   18 ++--
 inst/doc/oes.Rmd       |    4 -
 inst/doc/oes.html      |  189 +++++++++++++++++++++++++------------------------
 inst/doc/simulate.html |   76 +++++++++----------
 inst/doc/sma.html      |    6 -
 inst/doc/smooth.html   |    4 -
 inst/doc/ssarima.html  |   30 +++----
 inst/doc/ves.html      |    6 -
 src/ssGeneral.cpp      |   10 +-
 vignettes/oes.Rmd      |    4 -
 23 files changed, 471 insertions(+), 308 deletions(-)

More information about smooth at CRAN
Permanent link

Package sharpData updated to version 1.2 with previous version 1.1 dated 2019-08-02

Title: Data Sharpening
Description: Functions and data sets inspired by data sharpening - data perturbation to achieve improved performance in nonparametric estimation, as described in Choi, E., Hall, P. and Rousson, V. (2000) <doi:10.1214/aos/1015957396>. Capabilities for enhanced local linear regression function and derivative estimation are included, as well as an asymptotically correct iterated data sharpening estimator for any degree of local polynomial regression estimation. A cross-validation-based bandwidth selector is included which, in concert with the iterated sharpener, will often provide superior performance, according to a median integrated squared error criterion. Sample data sets are provided to illustrate function usage.
Author: W.J. Braun
Maintainer: W.J. Braun <john.braun@ubc.ca>

Diff between sharpData versions 1.1 dated 2019-08-02 and 1.2 dated 2019-08-19

 DESCRIPTION   |   10 +++++-----
 MD5           |   17 +++++++++++++++--
 NAMESPACE     |    6 ++++--
 R/LL.fit.R    |only
 R/LLmat.R     |only
 R/LLmono.R    |only
 R/NW.fit.R    |only
 R/NWmat.R     |only
 R/NWmono.R    |only
 man/LL.fit.Rd |only
 man/LLmat.Rd  |only
 man/LLmono.Rd |only
 man/NW.fit.Rd |only
 man/NWmat.Rd  |only
 man/NWmono.Rd |only
 src           |only
 16 files changed, 24 insertions(+), 9 deletions(-)

More information about sharpData at CRAN
Permanent link

Package RWsearch updated to version 4.6.2 with previous version 4.6 dated 2019-05-29

Title: Lazy Search in R Packages, Task Views, CRAN, the Web. All-in-One Download
Description: Search by keywords in R packages, task views, CRAN, the web and display the results in console, txt, html or pdf pages. Download the whole documentation (html index, pdf manual, vignettes, source code, etc) with a single instruction. Visualize the package dependencies. Several functions for task view maintenance and exploration of CRAN archive. Quick links to more than 70 web search engines. Lazy evaluation of non-standard content is available throughout the package and eases the use of many functions.
Author: Patrice Kiener [aut, cre] (<https://orcid.org/0000-0002-0505-9920>)
Maintainer: Patrice Kiener <fattailsr@inmodelia.com>

Diff between RWsearch versions 4.6 dated 2019-05-29 and 4.6.2 dated 2019-08-19

 DESCRIPTION                                 |    8 
 MD5                                         |   34 +-
 NAMESPACE                                   |    3 
 NEWS                                        |   15 +
 R/archivedb.R                               |    9 
 R/h_R.R                                     |    8 
 R/h_engine.R                                |   27 +-
 build/vignette.rds                          |binary
 data/datalist                               |    4 
 inst/doc/RWsearch-1-Introduction.html       |  258 ++++++++++----------
 inst/doc/RWsearch-2-Print-Download-Doc.html |  212 ++++++++--------
 inst/doc/RWsearch-3-TaskViews.html          |  354 ++++++++++++++--------------
 inst/doc/RWsearch-4-Web-search-engines.Rmd  |    5 
 inst/doc/RWsearch-4-Web-search-engines.html |   78 +++---
 man/archivedb.Rd                            |    3 
 man/h_R.Rd                                  |    3 
 man/h_engine.Rd                             |   11 
 vignettes/RWsearch-4-Web-search-engines.Rmd |    5 
 18 files changed, 560 insertions(+), 477 deletions(-)

More information about RWsearch at CRAN
Permanent link

Package rgl updated to version 0.100.30 with previous version 0.100.26 dated 2019-07-08

Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>

Diff between rgl versions 0.100.26 dated 2019-07-08 and 0.100.30 dated 2019-08-19

 DESCRIPTION               |    6 -
 MD5                       |   32 +++----
 NAMESPACE                 |    2 
 R/ashape3d.R              |    4 
 R/mesh3d.R                |  191 ++++++++++++++++++++++++++++++++++++----------
 build/vignette.rds        |binary
 inst/NEWS                 |   13 +++
 inst/doc/WebGL.html       |    6 -
 inst/doc/legacyWebGL.html |   76 +++++++++---------
 inst/doc/rgl.html         |   10 +-
 man/as.mesh3d.ashape3d.Rd |    6 +
 man/mesh3d.Rd             |   42 +++++-----
 src/Makevars.in           |    1 
 src/gl2ps.c               |    2 
 src/gl2ps.h               |   10 +-
 src/scene.cpp             |    3 
 src/subscene.cpp          |   12 +-
 17 files changed, 281 insertions(+), 135 deletions(-)

More information about rgl at CRAN
Permanent link

Package handlr updated to version 0.2.0 with previous version 0.1.0 dated 2019-02-27

Title: Convert Among Citation Formats
Description: Converts among many citation formats, including 'BibTeX', 'Citeproc', 'Codemeta', 'RDF XML', 'RIS', and 'Schema.org'. A low level 'R6' class is provided, as well as stand-alone functions for each citation format for both read and write.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <sckott@protonmail.com>

Diff between handlr versions 0.1.0 dated 2019-02-27 and 0.2.0 dated 2019-08-19

 DESCRIPTION                                 |    8 +-
 MD5                                         |   39 ++++++------
 NAMESPACE                                   |    2 
 NEWS.md                                     |   13 ++++
 R/client.R                                  |    4 +
 R/handl.R                                   |   52 +++++++++++++++-
 R/handl_to_df.R                             |only
 R/zzz.R                                     |    4 +
 README.md                                   |   86 ++++++++++++++++++++--------
 man/handl.Rd                                |   55 ++++++++++++++++-
 man/handl_to_df.Rd                          |only
 tests/testthat/test-bibtex_reader.R         |    2 
 tests/testthat/test-bibtex_writer.R         |    6 +
 tests/testthat/test-citeproc_reader.R       |    2 
 tests/testthat/test-client.R                |    2 
 tests/testthat/test-client_guesses_format.R |    2 
 tests/testthat/test-codemeta_reader.R       |    4 +
 tests/testthat/test-codemeta_writer.R       |    6 +
 tests/testthat/test-handl-class.R           |    2 
 tests/testthat/test-handl_to_df.R           |only
 tests/testthat/test-ris_reader.R            |    4 +
 tests/testthat/test-ris_writer.R            |    6 +
 22 files changed, 247 insertions(+), 52 deletions(-)

More information about handlr at CRAN
Permanent link

Package eSDM updated to version 0.3.0 with previous version 0.2.1 dated 2019-07-26

Title: Ensemble Tool for Predictions from Species Distribution Models
Description: A tool which allows users to create and evaluate ensembles of species distribution model (SDM) predictions. Functionality is offered through R functions or a GUI (R Shiny app). This tool can assist users in identifying spatial uncertainties and making informed conservation and management decisions. The package is further described in Woodman et al. (in press - contact author for paper).
Author: Sam Woodman [aut, cre]
Maintainer: Sam Woodman <sam.woodman@noaa.gov>

Diff between eSDM versions 0.2.1 dated 2019-07-26 and 0.3.0 dated 2019-08-19

 DESCRIPTION                                                          |   13 
 MD5                                                                  |   57 
 NEWS.md                                                              |only
 build/vignette.rds                                                   |binary
 inst/CITATION                                                        |    6 
 inst/doc/example-analysis.R                                          |   48 
 inst/doc/example-analysis.Rmd                                        |   74 
 inst/doc/example-analysis.html                                       |  990 +++++-----
 inst/eSDM_vignette_helper.R                                          |   24 
 inst/shiny/server.R                                                  |    4 
 inst/shiny/server_2_overlay/server_2_overlay_overlayModels.R         |    2 
 inst/shiny/server_3_createEns/server_3_createEns_create.R            |   12 
 inst/shiny/server_4_evalMetrics/server_4_evalMetrics.R               |   57 
 inst/shiny/server_5_prettyPlot/server_5_prettyPlot_plot.R            |   13 
 inst/shiny/server_5_prettyPlot/server_5_prettyPlot_prep.R            |   39 
 inst/shiny/server_5_prettyPlot/server_5_prettyPlot_renderUI.R        |   10 
 inst/shiny/server_5_prettyPlot/server_5_prettyPlot_update.R          |   94 
 inst/shiny/server_5_prettyPlot/server_5_prettyPlot_update_renderUI.R |   69 
 inst/shiny/server_6_export/server_6_export.R                         |   16 
 inst/shiny/server_other/server_plots.R                               |    4 
 inst/shiny/server_other/server_plots_funcs.R                         |    4 
 inst/shiny/server_other/server_render.R                              |   12 
 inst/shiny/server_other/server_roadmap_download.R                    |   35 
 inst/shiny/server_other/server_tables.R                              |    4 
 inst/shiny/server_other/server_workspace.R                           |    3 
 inst/shiny/ui_files/ui_0_roadmap.R                                   |   52 
 inst/shiny/ui_files/ui_4_evalMetrics.R                               |    4 
 inst/shiny/ui_files/ui_5_prettyPlot.R                                |   63 
 inst/shiny/www/eSDM_manual.pdf                                       |binary
 vignettes/example-analysis.Rmd                                       |   74 
 30 files changed, 889 insertions(+), 894 deletions(-)

More information about eSDM at CRAN
Permanent link

Package envDocument updated to version 2.4.1 with previous version 2.4.0 dated 2017-09-19

Title: Document the R Working Environment
Description: Prints out information about the R working environment (system, R version,loaded and attached packages and versions) from a single function "env_doc()". Optionally adds information on git repository, tags, commits and remotes (if available).
Author: Donald Jackson [aut, cre]
Maintainer: Donald Jackson <donald.jackson@bms.com>

Diff between envDocument versions 2.4.0 dated 2017-09-19 and 2.4.1 dated 2019-08-19

 DESCRIPTION                            |   12 -
 MD5                                    |   60 ++++----
 NAMESPACE                              |   24 +--
 NEWS.md                                |    4 
 R/env_doc.R                            |  182 ++++++++++++-------------
 R/fileStatus.R                         |   11 +
 R/getDominoInfo.R                      |  128 ++++++++---------
 R/getGitInfo.R                         |  177 ++++++++++++++----------
 R/getTag.R                             |   24 +++
 R/infoNotFound.R                       |   10 -
 build/vignette.rds                     |binary
 inst/doc/envDocument-vignette.R        |   26 +--
 inst/doc/envDocument-vignette.Rmd      |   92 ++++++------
 inst/doc/envDocument-vignette.html     |  236 ++++++++++++++++-----------------
 man/collapseInfo.Rd                    |   28 +--
 man/envDocument-package.Rd             |   78 +++++-----
 man/env_doc.Rd                         |  118 ++++++++--------
 man/getDominoInfo.Rd                   |   40 ++---
 man/getGitInfo.Rd                      |   46 +++---
 man/getPackageInfo.Rd                  |   30 ++--
 man/getRepo.Rd                         |   34 ++--
 man/getScriptInfo.Rd                   |   42 ++---
 man/getScriptPath.Rd                   |   46 +++---
 man/getSysInfo.Rd                      |   32 ++--
 man/get_Rversion.Rd                    |   28 +--
 man/infoNotFound.Rd                    |   22 +--
 man/prettyPrintInfo.Rd                 |   30 ++--
 man/remoteInfo.Rd                      |   28 +--
 tests/test_envDocument.html            |only
 tests/testthat/test-gitinfo.R          |only
 tests/testthat/test-return_dataframe.R |   38 ++---
 vignettes/envDocument-vignette.Rmd     |   92 ++++++------
 32 files changed, 890 insertions(+), 828 deletions(-)

More information about envDocument at CRAN
Permanent link

Package cytometree updated to version 2.0.0 with previous version 1.3.0 dated 2019-01-12

Title: Automated Cytometry Gating and Annotation
Description: Given the hypothesis of a bi-modal distribution of cells for each marker, the algorithm constructs a binary tree, the nodes of which are subpopulations of cells. At each node, observed cells and markers are modeled by both a family of normal distributions and a family of bi-modal normal mixture distributions. Splitting is done according to a normalized difference of AIC between the two families.
Author: Chariff Alkhassim, Boris Hejblum, Anthony Devaux, Van Hung Huynh Tran
Maintainer: Boris Hejblum <boris.hejblum@u-bordeaux.fr>

Diff between cytometree versions 1.3.0 dated 2019-01-12 and 2.0.0 dated 2019-08-19

 DESCRIPTION                         |   10 -
 MD5                                 |   38 +++-
 NAMESPACE                           |    2 
 NEWS.md                             |    3 
 R/AsinhTransformation.R             |only
 R/BiexpTransformation.R             |only
 R/CytofEM.R                         |only
 R/CytofTree.R                       |only
 R/Cytof_BinaryTree.R                |only
 R/HIPC.R                            |    3 
 R/IMdata.R                          |only
 R/Log10Transformation.R             |only
 R/cytometree-package.R              |    4 
 build/vignette.rds                  |binary
 data/IMdata.RData                   |only
 data/datalist                       |only
 inst/doc/autogating_cytometree.html |  279 ++++++++++++++++++------------------
 inst/doc/cytoftree.R                |only
 inst/doc/cytoftree.Rmd              |only
 inst/doc/cytoftree.html             |only
 man/AsinhTransformation.Rd          |only
 man/BiexpTransformation.Rd          |only
 man/CytofEM.Rd                      |only
 man/CytofTree.Rd                    |only
 man/Cytof_BinaryTree.Rd             |only
 man/HIPC.Rd                         |    3 
 man/IMdata.Rd                       |only
 man/Log10Transformation.Rd          |only
 man/cytometree-package.Rd           |    4 
 vignettes/cytoftree.Rmd             |only
 30 files changed, 191 insertions(+), 155 deletions(-)

More information about cytometree at CRAN
Permanent link

Package shinybusy updated to version 0.1.3 with previous version 0.1.2 dated 2019-05-07

Title: Busy Indicator for 'Shiny' Applications
Description: Add a global indicator (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), Tobias Ahlin [cph] (spin.css), Chris Antonellis [cph] (freezeframe.js), Jacobo Tabernero [cph] (nanobar.js)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

Diff between shinybusy versions 0.1.2 dated 2019-05-07 and 0.1.3 dated 2019-08-19

 DESCRIPTION                 |    6 +++---
 MD5                         |    8 ++++----
 NEWS.md                     |    5 +++++
 R/busy-spinner.R            |    2 +-
 inst/assets/js/shinybusy.js |   22 ++++++++++++++++++++++
 5 files changed, 35 insertions(+), 8 deletions(-)

More information about shinybusy at CRAN
Permanent link

Package PLmixed updated to version 0.1.4 with previous version 0.1.3 dated 2018-05-02

Title: Estimate (Generalized) Linear Mixed Models with Factor Structures
Description: Utilizes the 'lme4' and 'optimx' packages (previously the optim() function from 'stats') to estimate (generalized) linear mixed models (GLMM) with factor structures using a profile likelihood approach, as outlined in Jeon and Rabe-Hesketh (2012) <doi:10.3102/1076998611417628> and Rockwood and Jeon (2019) <doi:10.1080/00273171.2018.1516541>. Factor analysis and item response models can be extended to allow for an arbitrary number of nested and crossed random effects, making it useful for multilevel and cross-classified models.
Author: Minjeong Jeon [aut], Nicholas Rockwood [aut, cre]
Maintainer: Nicholas Rockwood <nrockwood@llu.edu>

Diff between PLmixed versions 0.1.3 dated 2018-05-02 and 0.1.4 dated 2019-08-19

 DESCRIPTION                 |   23 +-
 MD5                         |   23 +-
 NAMESPACE                   |    1 
 R/PLmixed_add_functions.R   |   58 +++---
 R/PLmixed_main_function.R   |   75 +++++--
 build/vignette.rds          |binary
 inst/CITATION               |only
 inst/doc/PLmixed_intro.Rmd  |    5 
 inst/doc/PLmixed_intro.html |  414 ++++++++++++++++++++++++++++++++++----------
 man/PLmixed-package.Rd      |   12 +
 man/PLmixed.Rd              |   31 ++-
 vignettes/PLmixed_intro.Rmd |    5 
 vignettes/biblio.bib        |   12 +
 13 files changed, 476 insertions(+), 183 deletions(-)

More information about PLmixed at CRAN
Permanent link

Package outliertree updated to version 1.0.1 with previous version 1.0 dated 2019-07-31

Title: Explainable Outlier Detection Through Decision Tree Conditioning
Description: Will try to fit decision trees that try to "predict" values for each column based on the values of each other column. Along the way, each time a split is evaluated, it will take the observations that fall into each branch as a homogeneous cluster in which it will search for outliers in the 1-d distribution of the column being predicted. Outliers are determined according to confidence intervals on this 1-d distribution, and need to have a large gap with respect to the next observation in sorted order to be flagged as outliers. Since outliers are searched for in a decision tree branch, it will know the conditions that make it a rare observation compared to others that meet the same conditions, and the conditions will always be correlated with the target variable (as it's being predicted from them). Loosely based on the 'GritBot' <https://www.rulequest.com/gritbot-info.html> software.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

Diff between outliertree versions 1.0 dated 2019-07-31 and 1.0.1 dated 2019-08-19

 DESCRIPTION        |    8 ++++----
 MD5                |   10 +++++-----
 R/helpers.R        |    6 +++---
 src/clusters.cpp   |    2 +-
 src/fit_model.cpp  |    1 +
 src/outlier_tree.h |    1 -
 6 files changed, 14 insertions(+), 14 deletions(-)

More information about outliertree at CRAN
Permanent link

Package onewaytests updated to version 2.4 with previous version 2.3 dated 2019-05-17

Title: One-Way Tests in Independent Groups Designs
Description: Performs one-way tests in independent groups designs; one-way analysis of variance (ANOVA), Welch's heteroscedastic F test, Welch's heteroscedastic F test with trimmed means and Winsorized variances, Brown-Forsythe test, Alexander-Govern test, James second order test, Kruskal-Wallis test, Scott-Smith test, Box F test and Johansen F test, Generalized tests equivalent to Parametric Bootstrap and Fiducial tests. The package performs pairwise comparisons and graphical approaches. Also, the package includes Student's t test, Welch's t test and Mann-Whitney U test for two samples. Moreover, it assesses variance homogeneity and normality of data in each group via tests and plots (Dag et al., 2018, <https://journal.r-project.org/archive/2018/RJ-2018-022/RJ-2018-022.pdf>).
Author: Osman Dag [aut, cre], Anil Dolgun [aut], N. Meric Konar [aut], Sam Weerahandi [ctb], Malwane Ananda [ctb]
Maintainer: Osman Dag <osman.dag@outlook.com>

Diff between onewaytests versions 2.3 dated 2019-05-17 and 2.4 dated 2019-08-19

 DESCRIPTION        |   12 ++++++------
 MD5                |   14 ++++++++------
 NAMESPACE          |    4 ++--
 R/gp.test.R        |only
 R/paircomp.R       |    3 +++
 R/paircomp.jt.R    |    1 +
 man/box.test.Rd    |    2 +-
 man/gp.test.Rd     |only
 man/onewaytests.Rd |    2 +-
 9 files changed, 22 insertions(+), 16 deletions(-)

More information about onewaytests at CRAN
Permanent link

Package multiDimBio updated to version 1.2.0 with previous version 1.1.1 dated 2016-12-16

Title: Multivariate Analysis and Visualization for Biological Data
Description: Code to support a systems biology research program from inception through publication. The methods focus on dimension reduction approaches to detect patterns in complex, multivariate experimental data and places an emphasis on informative visualizations. The goal for this project is to create a package that will evolve over time, thereby remaining relevant and reflective of current methods and techniques. As a result, we encourage suggested additions to the package, both methodological and graphical.
Author: Samuel V. Scarpino
Maintainer: Samuel V. Scarpino <scarpino@utexas.edu>

Diff between multiDimBio versions 1.1.1 dated 2016-12-16 and 1.2.0 dated 2019-08-19

 DESCRIPTION                |   12 ++++++------
 MD5                        |    6 +++---
 R/h2Estimate.R             |   29 +++++++++++++++++------------
 man/multiDimBio-package.Rd |   11 ++++++-----
 4 files changed, 32 insertions(+), 26 deletions(-)

More information about multiDimBio at CRAN
Permanent link

Package MetricsWeighted updated to version 0.2.0 with previous version 0.1.0 dated 2019-07-28

Title: Weighted Metrics, Scoring Functions and Performance Measures for Machine Learning
Description: Provides weighted versions of several metrics, scoring functions and performance measures used in machine learning, including average unit deviances of the Bernoulli, Tweedie, Poisson, and Gamma distributions, see Jorgensen B. (1997, ISBN: 978-0412997112). The package also contains a weighted version of generalized R-squared, see e.g. Cohen, J. et al. (2002, ISBN: 978-0805822236). Furthermore, 'dplyr' chains are supported.
Author: Michael Mayer [aut, cre, cph], Christian Lorentzen [rev]
Maintainer: Michael Mayer <mayermichael79@gmail.com>

Diff between MetricsWeighted versions 0.1.0 dated 2019-07-28 and 0.2.0 dated 2019-08-19

 DESCRIPTION                   |   40 ++--
 MD5                           |  102 ++++++------
 NAMESPACE                     |    5 
 NEWS.md                       |   10 -
 R/AUC.R                       |   22 +-
 R/accuracy.R                  |   12 -
 R/classification_error.R      |   13 -
 R/deviance_bernoulli.R        |   15 -
 R/deviance_gamma.R            |   35 ++--
 R/deviance_normal.R           |   25 +--
 R/deviance_poisson.R          |   35 ++--
 R/deviance_tweedie.R          |   62 ++++---
 R/f1_score.R                  |   11 -
 R/gini_coefficient.R          |   15 -
 R/logLoss.R                   |   24 +-
 R/mae.R                       |   18 --
 R/mape.R                      |   24 +-
 R/medae.R                     |only
 R/mse.R                       |   20 --
 R/performance.R               |   19 --
 R/precision.R                 |   14 -
 R/r_squared.R                 |   31 +--
 R/recall.R                    |   13 -
 R/rmse.R                      |   19 --
 R/weighted_mean.R             |   22 +-
 R/weighted_median.R           |only
 R/weighted_quantile.R         |only
 README.md                     |    4 
 inst/doc/MetricsWeighted.R    |   28 +++
 inst/doc/MetricsWeighted.Rmd  |   54 ++++--
 inst/doc/MetricsWeighted.html |  341 +++++++++++++++++++++++-------------------
 man/AUC.Rd                    |   11 -
 man/accuracy.Rd               |    6 
 man/classification_error.Rd   |    8 
 man/deviance_bernoulli.Rd     |   12 -
 man/deviance_gamma.Rd         |   24 +-
 man/deviance_normal.Rd        |   19 --
 man/deviance_poisson.Rd       |   24 +-
 man/deviance_tweedie.Rd       |   22 +-
 man/f1_score.Rd               |    8 
 man/gini_coefficient.Rd       |   12 -
 man/logLoss.Rd                |   14 -
 man/mae.Rd                    |   13 -
 man/mape.Rd                   |   19 --
 man/medae.Rd                  |only
 man/mse.Rd                    |   14 -
 man/performance.Rd            |   11 -
 man/precision.Rd              |    6 
 man/r_squared.Rd              |   24 +-
 man/recall.Rd                 |    6 
 man/rmse.Rd                   |   14 -
 man/weighted_mean.Rd          |   13 -
 man/weighted_median.Rd        |only
 man/weighted_quantile.Rd      |only
 vignettes/MetricsWeighted.Rmd |   54 ++++--
 55 files changed, 701 insertions(+), 666 deletions(-)

More information about MetricsWeighted at CRAN
Permanent link

Package MEtest updated to version 1.1 with previous version 1.0 dated 2019-04-25

Title: A Homogeneity Test under the Presence of Measurement Errors
Description: Provides a function me.test() to test equality of distributions when observations are subject to measurement errors.
Author: DongHyuk Lee, Samiran Sinha
Maintainer: DongHyuk Lee <leedhyuk@gmail.com>

Diff between MEtest versions 1.0 dated 2019-04-25 and 1.1 dated 2019-08-19

 DESCRIPTION        |    8 -
 MD5                |   10 -
 NAMESPACE          |    2 
 R/Sources_MEtest.R |   35 +++--
 man/me.test.Rd     |    8 -
 src/TScomp.f90     |  370 ++++++++++++++++++++++++++---------------------------
 6 files changed, 224 insertions(+), 209 deletions(-)

More information about MEtest at CRAN
Permanent link

Package harmonicmeanp updated to version 3.0 with previous version 2.0 dated 2019-07-06

Title: Harmonic Mean p-Values and Model Averaging by Mean Maximum Likelihood
Description: The harmonic mean p-value (HMP) test combines p-values and corrects for multiple testing while controlling the strong-sense family-wise error rate. It is more powerful than common alternatives including Bonferroni and Simes procedures when combining large proportions of all the p-values, at the cost of slightly lower power when combining small proportions of all the p-values. It is more stringent than controlling the false discovery rate, and possesses theoretical robustness to positive correlations between tests and unequal weights. It is a multi-level test in the sense that a superset of one or more significant tests is certain to be significant and conversely when the superset is non-significant, the constituent tests are certain to be non-significant. It is based on MAMML (model averaging by mean maximum likelihood), a frequentist analogue to Bayesian model averaging, and is theoretically grounded in generalized central limit theorem. For detailed examples type vignette("harmonicmeanp") after installation. Version 3.0 addresses errors in versions 1.0 and 2.0 that led function p.hmp to control the familywise error rate only in the weak sense, rather than the strong sense as intended.
Author: Daniel J. Wilson
Maintainer: Daniel Wilson <hmp.R.package@gmail.com>

Diff between harmonicmeanp versions 2.0 dated 2019-07-06 and 3.0 dated 2019-08-19

 DESCRIPTION                 |   10 -
 MD5                         |   24 ++--
 R/hmp.R                     |   18 ++-
 build/vignette.rds          |binary
 inst/doc/harmonicmeanp.R    |   54 ++++++++--
 inst/doc/harmonicmeanp.Rmd  |  105 +++++++++++++-------
 inst/doc/harmonicmeanp.html |  230 +++++++++++++++++++++++++-------------------
 man/harmonicmeanp.Rd        |    6 -
 man/hmp.stat.Rd             |    2 
 man/p.hmp.Rd                |   17 ++-
 man/p.mamml.Rd              |    2 
 man/pharmonicmeanp.Rd       |    2 
 vignettes/harmonicmeanp.Rmd |  105 +++++++++++++-------
 13 files changed, 369 insertions(+), 206 deletions(-)

More information about harmonicmeanp at CRAN
Permanent link

Package fields updated to version 9.8-6 with previous version 9.8-3 dated 2019-05-28

Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis on splines, spatial data, geostatistics, and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development of this package was supported in part by the National Science Foundation Grant 1417857 and the National Center for Atmospheric Research. See the Fields URL for a vignette on using this package and some background on spatial statistics.
Author: Douglas Nychka [aut, cre], Reinhard Furrer [aut], John Paige [aut], Stephan Sain [aut], University Corporation for Atmospheric Research [cph]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>

Diff between fields versions 9.8-3 dated 2019-05-28 and 9.8-6 dated 2019-08-19

 DESCRIPTION        |    8 ++---
 MD5                |   23 ++++++++--------
 R/Krig.family.R    |    2 -
 R/color.scale.R    |   10 +++++--
 R/image.plot.R     |    5 ++-
 R/snow.colors.R    |only
 R/spatialProcess.R |    1 
 R/stationary.cov.R |    5 +++
 R/tim.colors.R     |   20 --------------
 data/datalist      |    3 +-
 man/image.plot.Rd  |   73 +++++++++++++++++++++++++++++++----------------------
 man/mKrigMLE.Rd    |   16 ++++++-----
 man/tim.colors.Rd  |   69 +++++++++++++++++++++++++++++++-------------------
 13 files changed, 133 insertions(+), 102 deletions(-)

More information about fields at CRAN
Permanent link

Package EmbedSOM updated to version 1.9.1 with previous version 1.9 dated 2019-08-19

Title: Fast Embedding Guided by Self-Organizing Map
Description: Provides a smooth mapping of multidimensional points into low-dimensional space defined by a self-organizing map. Designed to work with 'FlowSOM' and flow-cytometry use-cases. See Kratochvil et al. (2019) <doi:10.1101/496869>.
Author: Mirek Kratochvil [aut, cre], Sofie Van Gassen [cph], Britt Callebaut [cph], Yvan Saeys [cph], Ron Wehrens [cph]
Maintainer: Mirek Kratochvil <exa.exa@gmail.com>

Diff between EmbedSOM versions 1.9 dated 2019-08-19 and 1.9.1 dated 2019-08-19

 DESCRIPTION             |    6 +++---
 MD5                     |   16 ++++++++--------
 R/embed.R               |   14 ++++++++++++--
 R/som.R                 |   25 +++++++++++++++++++------
 inst/doc/embedding.html |   34 +++++++++++++++++-----------------
 man/EmbedSOM.Rd         |    2 +-
 man/MapDataToCodes.Rd   |    4 ++--
 src/embed.cpp           |    2 ++
 src/som.cpp             |    2 +-
 9 files changed, 65 insertions(+), 40 deletions(-)

More information about EmbedSOM at CRAN
Permanent link

Package drake updated to version 7.6.1 with previous version 7.5.2 dated 2019-07-21

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>), Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>), Ben Marwick [rev], Peter Slaughter [rev], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

Diff between drake versions 7.5.2 dated 2019-07-21 and 7.6.1 dated 2019-08-19

 drake-7.5.2/drake/R/api-build.R                             |only
 drake-7.5.2/drake/R/api-cache.R                             |only
 drake-7.5.2/drake/R/api-callr.R                             |only
 drake-7.5.2/drake/R/api-clean.R                             |only
 drake-7.5.2/drake/R/api-codetoplan.R                        |only
 drake-7.5.2/drake/R/api-debug.R                             |only
 drake-7.5.2/drake/R/api-diagnose.R                          |only
 drake-7.5.2/drake/R/api-dsl.R                               |only
 drake-7.5.2/drake/R/api-examples.R                          |only
 drake-7.5.2/drake/R/api-exposeimports.R                     |only
 drake-7.5.2/drake/R/api-history.R                           |only
 drake-7.5.2/drake/R/api-make.R                              |only
 drake-7.5.2/drake/R/api-outdated.R                          |only
 drake-7.5.2/drake/R/api-package.R                           |only
 drake-7.5.2/drake/R/api-predict.R                           |only
 drake-7.5.2/drake/R/api-progress.R                          |only
 drake-7.5.2/drake/R/api-read.R                              |only
 drake-7.5.2/drake/R/api-slice.R                             |only
 drake-7.5.2/drake/R/api-source.R                            |only
 drake-7.5.2/drake/R/api-times.R                             |only
 drake-7.5.2/drake/R/api-usedrake.R                          |only
 drake-7.5.2/drake/R/backend-clustermq.R                     |only
 drake-7.5.2/drake/R/backend-future.R                        |only
 drake-7.5.2/drake/R/backend-loop.R                          |only
 drake-7.5.2/drake/R/drake_plan_keywords.R                   |only
 drake-7.5.2/drake/R/exec-backend.R                          |only
 drake-7.5.2/drake/R/exec-build.R                            |only
 drake-7.5.2/drake/R/exec-dependencies.R                     |only
 drake-7.5.2/drake/R/exec-imports.R                          |only
 drake-7.5.2/drake/R/exec-memory.R                           |only
 drake-7.5.2/drake/R/exec-meta.R                             |only
 drake-7.5.2/drake/R/exec-queue.R                            |only
 drake-7.5.2/drake/R/exec-recover.R                          |only
 drake-7.5.2/drake/R/exec-run.R                              |only
 drake-7.5.2/drake/R/exec-session.R                          |only
 drake-7.5.2/drake/R/exec-standardize.R                      |only
 drake-7.5.2/drake/R/exec-store.R                            |only
 drake-7.5.2/drake/R/exec-triggers.R                         |only
 drake-7.5.2/drake/R/preprocess-compatibility.R              |only
 drake-7.5.2/drake/R/preprocess-config.R                     |only
 drake-7.5.2/drake/R/preprocess-graph.R                      |only
 drake-7.5.2/drake/R/preprocess-layout.R                     |only
 drake-7.5.2/drake/R/rstudio-callr.R                         |only
 drake-7.5.2/drake/R/rstudio-loadd.R                         |only
 drake-7.5.2/drake/R/test-dbug.R                             |only
 drake-7.5.2/drake/R/test-scenarios.R                        |only
 drake-7.5.2/drake/R/test-testthat.R                         |only
 drake-7.5.2/drake/R/utils-cache.R                           |only
 drake-7.5.2/drake/R/utils-check.R                           |only
 drake-7.5.2/drake/R/utils-checksums.R                       |only
 drake-7.5.2/drake/R/utils-defunct.R                         |only
 drake-7.5.2/drake/R/utils-deprecate.R                       |only
 drake-7.5.2/drake/R/utils-encoding.R                        |only
 drake-7.5.2/drake/R/utils-graphinfo.R                       |only
 drake-7.5.2/drake/R/utils-handlers.R                        |only
 drake-7.5.2/drake/R/utils-hashtable.R                       |only
 drake-7.5.2/drake/R/utils-hpc.R                             |only
 drake-7.5.2/drake/R/utils-igraph.R                          |only
 drake-7.5.2/drake/R/utils-knitr.R                           |only
 drake-7.5.2/drake/R/utils-parallel.R                        |only
 drake-7.5.2/drake/R/utils-rng.R                             |only
 drake-7.5.2/drake/R/utils-tips.R                            |only
 drake-7.5.2/drake/R/utils-utils.R                           |only
 drake-7.5.2/drake/R/utils-withr.R                           |only
 drake-7.5.2/drake/R/utils-zzz.R                             |only
 drake-7.5.2/drake/R/vis-color.R                             |only
 drake-7.5.2/drake/R/vis-console.R                           |only
 drake-7.5.2/drake/R/vis-ggraph.R                            |only
 drake-7.5.2/drake/R/vis-graphinfo.R                         |only
 drake-7.5.2/drake/R/vis-sankey.R                            |only
 drake-7.5.2/drake/R/vis-shape.R                             |only
 drake-7.5.2/drake/R/vis-txtplot.R                           |only
 drake-7.5.2/drake/R/vis-visnetwork.R                        |only
 drake-7.5.2/drake/man/figures/hist1.png                     |only
 drake-7.5.2/drake/man/figures/hist2.png                     |only
 drake-7.5.2/drake/tests/testthat/test-always-skipped.R      |only
 drake-7.5.2/drake/tests/testthat/test-code-analysis.R       |only
 drake-7.5.2/drake/tests/testthat/test-command-changes.R     |only
 drake-7.5.2/drake/tests/testthat/test-custom-caches.R       |only
 drake-7.5.2/drake/tests/testthat/test-dependencies.R        |only
 drake-7.5.2/drake/tests/testthat/test-edge-cases.R          |only
 drake-7.5.2/drake/tests/testthat/test-expose-imports.R      |only
 drake-7.5.2/drake/tests/testthat/test-full-build.R          |only
 drake-7.5.2/drake/tests/testthat/test-hash-table.R          |only
 drake-7.5.2/drake/tests/testthat/test-hash.R                |only
 drake-7.5.2/drake/tests/testthat/test-import-file.R         |only
 drake-7.5.2/drake/tests/testthat/test-import-object.R       |only
 drake-7.5.2/drake/tests/testthat/test-intermediate-file.R   |only
 drake-7.5.2/drake/tests/testthat/test-knitr.R               |only
 drake-7.5.2/drake/tests/testthat/test-lazy-load.R           |only
 drake-7.5.2/drake/tests/testthat/test-memory-cache.R        |only
 drake-7.5.2/drake/tests/testthat/test-namespaced.R          |only
 drake-7.5.2/drake/tests/testthat/test-other-features.R      |only
 drake-7.5.2/drake/tests/testthat/test-parallel.R            |only
 drake-7.5.2/drake/tests/testthat/test-priority-queue.R      |only
 drake-7.5.2/drake/tests/testthat/test-random.R              |only
 drake-7.5.2/drake/tests/testthat/test-rstudio-loadd.R       |only
 drake-7.5.2/drake/tests/testthat/test-tidy-eval.R           |only
 drake-7.6.1/drake/DESCRIPTION                               |   97 -
 drake-7.6.1/drake/MD5                                       |  595 +++----
 drake-7.6.1/drake/NEWS.md                                   |   35 
 drake-7.6.1/drake/R/analyze_code.R                          |   27 
 drake-7.6.1/drake/R/backend_clustermq.R                     |only
 drake-7.6.1/drake/R/backend_future.R                        |only
 drake-7.6.1/drake/R/backend_loop.R                          |only
 drake-7.6.1/drake/R/build_times.R                           |only
 drake-7.6.1/drake/R/cache.R                                 |only
 drake-7.6.1/drake/R/clean.R                                 |only
 drake-7.6.1/drake/R/create_drake_graph.R                    |only
 drake-7.6.1/drake/R/create_drake_layout.R                   |only
 drake-7.6.1/drake/R/decorate_storr.R                        |only
 drake-7.6.1/drake/R/defunct.R                               |only
 drake-7.6.1/drake/R/deprecated.R                            |only
 drake-7.6.1/drake/R/deps.R                                  |only
 drake-7.6.1/drake/R/drake_build.R                           |only
 drake-7.6.1/drake/R/drake_config.R                          |only
 drake-7.6.1/drake/R/drake_example.R                         |only
 drake-7.6.1/drake/R/drake_ggraph.R                          |only
 drake-7.6.1/drake/R/drake_graph_info.R                      |only
 drake-7.6.1/drake/R/drake_history.R                         |only
 drake-7.6.1/drake/R/drake_meta_.R                           |only
 drake-7.6.1/drake/R/drake_plan.R                            |   94 -
 drake-7.6.1/drake/R/drake_plan_helpers.R                    | 1018 ++++++++++++
 drake-7.6.1/drake/R/encoding.R                              |only
 drake-7.6.1/drake/R/expose_imports.R                        |only
 drake-7.6.1/drake/R/handle_trigger.R                        |only
 drake-7.6.1/drake/R/hash_tables.R                           |only
 drake-7.6.1/drake/R/hpc.R                                   |only
 drake-7.6.1/drake/R/igraph.R                                |only
 drake-7.6.1/drake/R/lifecycle.R                             |only
 drake-7.6.1/drake/R/local_build.R                           |only
 drake-7.6.1/drake/R/log_msg.R                               |only
 drake-7.6.1/drake/R/make.R                                  |only
 drake-7.6.1/drake/R/manage_memory.R                         |only
 drake-7.6.1/drake/R/outdated.R                              |only
 drake-7.6.1/drake/R/package.R                               |only
 drake-7.6.1/drake/R/predict_runtime.R                       |only
 drake-7.6.1/drake/R/priority_queue.R                        |only
 drake-7.6.1/drake/R/process_imports.R                       |only
 drake-7.6.1/drake/R/r_make.R                                |only
 drake-7.6.1/drake/R/rstudio.R                               |only
 drake-7.6.1/drake/R/sankey_drake_graph.R                    |only
 drake-7.6.1/drake/R/store_outputs.R                         |only
 drake-7.6.1/drake/R/text_drake_graph.R                      |only
 drake-7.6.1/drake/R/transform_plan.R                        |only
 drake-7.6.1/drake/R/use_drake.R                             |only
 drake-7.6.1/drake/R/utils.R                                 |only
 drake-7.6.1/drake/R/vis_drake_graph.R                       |only
 drake-7.6.1/drake/R/zzz.R                                   |only
 drake-7.6.1/drake/README.md                                 |  134 +
 drake-7.6.1/drake/build/drake.pdf                           |only
 drake-7.6.1/drake/inst/WORDLIST                             |   14 
 drake-7.6.1/drake/inst/doc/drake.html                       |    4 
 drake-7.6.1/drake/inst/rmarkdown/examples/mtcars/report.Rmd |    6 
 drake-7.6.1/drake/man/Makefile_recipe.Rd                    |    5 
 drake-7.6.1/drake/man/analyses.Rd                           |    4 
 drake-7.6.1/drake/man/analysis_wildcard.Rd                  |    7 
 drake-7.6.1/drake/man/as_drake_filename.Rd                  |    4 
 drake-7.6.1/drake/man/as_file.Rd                            |    4 
 drake-7.6.1/drake/man/available_hash_algos.Rd               |    5 
 drake-7.6.1/drake/man/backend.Rd                            |    4 
 drake-7.6.1/drake/man/bind_plans.Rd                         |    3 
 drake-7.6.1/drake/man/build_drake_graph.Rd                  |    5 
 drake-7.6.1/drake/man/build_graph.Rd                        |    4 
 drake-7.6.1/drake/man/build_times.Rd                        |    5 
 drake-7.6.1/drake/man/built.Rd                              |    5 
 drake-7.6.1/drake/man/cache_namespaces.Rd                   |    5 
 drake-7.6.1/drake/man/cache_path.Rd                         |    7 
 drake-7.6.1/drake/man/cached.Rd                             |    5 
 drake-7.6.1/drake/man/check.Rd                              |    4 
 drake-7.6.1/drake/man/check_plan.Rd                         |    5 
 drake-7.6.1/drake/man/clean.Rd                              |   85 -
 drake-7.6.1/drake/man/clean_main_example.Rd                 |    5 
 drake-7.6.1/drake/man/clean_mtcars_example.Rd               |    5 
 drake-7.6.1/drake/man/cleaned_namespaces.Rd                 |    5 
 drake-7.6.1/drake/man/cmq_build.Rd                          |    5 
 drake-7.6.1/drake/man/code_to_plan.Rd                       |    7 
 drake-7.6.1/drake/man/combine.Rd                            |only
 drake-7.6.1/drake/man/config.Rd                             |    4 
 drake-7.6.1/drake/man/configure_cache.Rd                    |    5 
 drake-7.6.1/drake/man/cross.Rd                              |only
 drake-7.6.1/drake/man/dataframes_graph.Rd                   |    4 
 drake-7.6.1/drake/man/dataset_wildcard.Rd                   |    5 
 drake-7.6.1/drake/man/debug_and_run.Rd                      |    5 
 drake-7.6.1/drake/man/default_Makefile_args.Rd              |    5 
 drake-7.6.1/drake/man/default_Makefile_command.Rd           |    5 
 drake-7.6.1/drake/man/default_graph_title.Rd                |    5 
 drake-7.6.1/drake/man/default_long_hash_algo.Rd             |    5 
 drake-7.6.1/drake/man/default_parallelism.Rd                |    5 
 drake-7.6.1/drake/man/default_recipe_command.Rd             |    5 
 drake-7.6.1/drake/man/default_short_hash_algo.Rd            |    5 
 drake-7.6.1/drake/man/default_system2_args.Rd               |    4 
 drake-7.6.1/drake/man/default_verbose.Rd                    |    5 
 drake-7.6.1/drake/man/dependency_profile.Rd                 |    5 
 drake-7.6.1/drake/man/deprecate_wildcard.Rd                 |    4 
 drake-7.6.1/drake/man/deps.Rd                               |    4 
 drake-7.6.1/drake/man/deps_code.Rd                          |    5 
 drake-7.6.1/drake/man/deps_knitr.Rd                         |    5 
 drake-7.6.1/drake/man/deps_profile.Rd                       |    5 
 drake-7.6.1/drake/man/deps_target.Rd                        |    5 
 drake-7.6.1/drake/man/deps_targets.Rd                       |    7 
 drake-7.6.1/drake/man/diagnose.Rd                           |   19 
 drake-7.6.1/drake/man/do_prework.Rd                         |    5 
 drake-7.6.1/drake/man/doc_of_function_call.Rd               |    4 
 drake-7.6.1/drake/man/drake-package.Rd                      |   15 
 drake-7.6.1/drake/man/drake_batchtools_tmpl_file.Rd         |    5 
 drake-7.6.1/drake/man/drake_build.Rd                        |    5 
 drake-7.6.1/drake/man/drake_cache.Rd                        |   15 
 drake-7.6.1/drake/man/drake_cache_log.Rd                    |    6 
 drake-7.6.1/drake/man/drake_cache_log_file.Rd               |    7 
 drake-7.6.1/drake/man/drake_config.Rd                       |   42 
 drake-7.6.1/drake/man/drake_debug.Rd                        |    5 
 drake-7.6.1/drake/man/drake_envir.Rd                        |   20 
 drake-7.6.1/drake/man/drake_example.Rd                      |    6 
 drake-7.6.1/drake/man/drake_examples.Rd                     |    5 
 drake-7.6.1/drake/man/drake_gc.Rd                           |   17 
 drake-7.6.1/drake/man/drake_get_session_info.Rd             |    6 
 drake-7.6.1/drake/man/drake_ggraph.Rd                       |    6 
 drake-7.6.1/drake/man/drake_graph_info.Rd                   |    6 
 drake-7.6.1/drake/man/drake_history.Rd                      |    5 
 drake-7.6.1/drake/man/drake_hpc_template_file.Rd            |    5 
 drake-7.6.1/drake/man/drake_hpc_template_files.Rd           |    5 
 drake-7.6.1/drake/man/drake_meta.Rd                         |    6 
 drake-7.6.1/drake/man/drake_palette.Rd                      |    5 
 drake-7.6.1/drake/man/drake_plan.Rd                         |   65 
 drake-7.6.1/drake/man/drake_plan_source.Rd                  |    5 
 drake-7.6.1/drake/man/drake_quotes.Rd                       |    5 
 drake-7.6.1/drake/man/drake_session.Rd                      |    6 
 drake-7.6.1/drake/man/drake_slice.Rd                        |    5 
 drake-7.6.1/drake/man/drake_strings.Rd                      |    5 
 drake-7.6.1/drake/man/drake_tip.Rd                          |    5 
 drake-7.6.1/drake/man/drake_unquote.Rd                      |    5 
 drake-7.6.1/drake/man/eager_load_target.Rd                  |    5 
 drake-7.6.1/drake/man/evaluate.Rd                           |    4 
 drake-7.6.1/drake/man/evaluate_plan.Rd                      |    7 
 drake-7.6.1/drake/man/example_drake.Rd                      |    4 
 drake-7.6.1/drake/man/examples_drake.Rd                     |    4 
 drake-7.6.1/drake/man/expand.Rd                             |    4 
 drake-7.6.1/drake/man/expand_plan.Rd                        |    5 
 drake-7.6.1/drake/man/expose_imports.Rd                     |    7 
 drake-7.6.1/drake/man/failed.Rd                             |    4 
 drake-7.6.1/drake/man/figures/hist2-1.png                   |only
 drake-7.6.1/drake/man/figures/histhistory-1.png             |only
 drake-7.6.1/drake/man/figures/readdhist-1.png               |only
 drake-7.6.1/drake/man/figures/recoverhist-1.png             |only
 drake-7.6.1/drake/man/file_in.Rd                            |   36 
 drake-7.6.1/drake/man/file_out.Rd                           |   24 
 drake-7.6.1/drake/man/file_store.Rd                         |    6 
 drake-7.6.1/drake/man/find_cache.Rd                         |    5 
 drake-7.6.1/drake/man/find_knitr_doc.Rd                     |    4 
 drake-7.6.1/drake/man/find_project.Rd                       |    7 
 drake-7.6.1/drake/man/from_plan.Rd                          |    4 
 drake-7.6.1/drake/man/future_build.Rd                       |    5 
 drake-7.6.1/drake/man/gather.Rd                             |    4 
 drake-7.6.1/drake/man/gather_by.Rd                          |    6 
 drake-7.6.1/drake/man/gather_plan.Rd                        |    7 
 drake-7.6.1/drake/man/get_cache.Rd                          |    5 
 drake-7.6.1/drake/man/ignore.Rd                             |   20 
 drake-7.6.1/drake/man/imported.Rd                           |    5 
 drake-7.6.1/drake/man/in_progress.Rd                        |    7 
 drake-7.6.1/drake/man/is_function_call.Rd                   |    4 
 drake-7.6.1/drake/man/isolate_example.Rd                    |    7 
 drake-7.6.1/drake/man/knitr_deps.Rd                         |    5 
 drake-7.6.1/drake/man/knitr_in.Rd                           |   20 
 drake-7.6.1/drake/man/legend_nodes.Rd                       |    5 
 drake-7.6.1/drake/man/load_basic_example.Rd                 |    4 
 drake-7.6.1/drake/man/load_main_example.Rd                  |    5 
 drake-7.6.1/drake/man/load_mtcars_example.Rd                |    5 
 drake-7.6.1/drake/man/long_hash.Rd                          |    5 
 drake-7.6.1/drake/man/macros                                |only
 drake-7.6.1/drake/man/make.Rd                               |   42 
 drake-7.6.1/drake/man/make_imports.Rd                       |    5 
 drake-7.6.1/drake/man/make_targets.Rd                       |    5 
 drake-7.6.1/drake/man/make_with_config.Rd                   |    5 
 drake-7.6.1/drake/man/manage_memory.Rd                      |    5 
 drake-7.6.1/drake/man/map.Rd                                |only
 drake-7.6.1/drake/man/map_plan.Rd                           |    6 
 drake-7.6.1/drake/man/max_useful_jobs.Rd                    |    4 
 drake-7.6.1/drake/man/migrate_drake_project.Rd              |    4 
 drake-7.6.1/drake/man/missed.Rd                             |    5 
 drake-7.6.1/drake/man/new_cache.Rd                          |   11 
 drake-7.6.1/drake/man/no_deps.Rd                            |   20 
 drake-7.6.1/drake/man/outdated.Rd                           |    5 
 drake-7.6.1/drake/man/parallel_stages.Rd                    |    4 
 drake-7.6.1/drake/man/parallelism_choices.Rd                |    5 
 drake-7.6.1/drake/man/plan.Rd                               |    4 
 drake-7.6.1/drake/man/plan_analyses.Rd                      |    5 
 drake-7.6.1/drake/man/plan_drake.Rd                         |    4 
 drake-7.6.1/drake/man/plan_summaries.Rd                     |    5 
 drake-7.6.1/drake/man/plan_to_code.Rd                       |    6 
 drake-7.6.1/drake/man/plan_to_notebook.Rd                   |    6 
 drake-7.6.1/drake/man/plot_graph.Rd                         |    4 
 drake-7.6.1/drake/man/predict_load_balancing.Rd             |    5 
 drake-7.6.1/drake/man/predict_runtime.Rd                    |    5 
 drake-7.6.1/drake/man/predict_workers.Rd                    |    5 
 drake-7.6.1/drake/man/process_import.Rd                     |    7 
 drake-7.6.1/drake/man/progress.Rd                           |   12 
 drake-7.6.1/drake/man/prune_drake_graph.Rd                  |    5 
 drake-7.6.1/drake/man/r_make.Rd                             |   16 
 drake-7.6.1/drake/man/r_recipe_wildcard.Rd                  |    5 
 drake-7.6.1/drake/man/rate_limiting_times.Rd                |    4 
 drake-7.6.1/drake/man/read_config.Rd                        |    4 
 drake-7.6.1/drake/man/read_drake_config.Rd                  |    5 
 drake-7.6.1/drake/man/read_drake_graph.Rd                   |    5 
 drake-7.6.1/drake/man/read_drake_meta.Rd                    |    4 
 drake-7.6.1/drake/man/read_drake_plan.Rd                    |    5 
 drake-7.6.1/drake/man/read_drake_seed.Rd                    |    5 
 drake-7.6.1/drake/man/read_graph.Rd                         |    4 
 drake-7.6.1/drake/man/read_plan.Rd                          |    4 
 drake-7.6.1/drake/man/readd.Rd                              |    5 
 drake-7.6.1/drake/man/recover_cache.Rd                      |   12 
 drake-7.6.1/drake/man/recoverable.Rd                        |    8 
 drake-7.6.1/drake/man/reduce_by.Rd                          |    5 
 drake-7.6.1/drake/man/reduce_plan.Rd                        |    6 
 drake-7.6.1/drake/man/render_drake_ggraph.Rd                |    7 
 drake-7.6.1/drake/man/render_drake_graph.Rd                 |    5 
 drake-7.6.1/drake/man/render_graph.Rd                       |    4 
 drake-7.6.1/drake/man/render_sankey_drake_graph.Rd          |    7 
 drake-7.6.1/drake/man/render_static_drake_graph.Rd          |    5 
 drake-7.6.1/drake/man/render_text_drake_graph.Rd            |    7 
 drake-7.6.1/drake/man/rescue_cache.Rd                       |    5 
 drake-7.6.1/drake/man/rs_addin_loadd.Rd                     |   18 
 drake-7.6.1/drake/man/rs_addin_r_make.Rd                    |    8 
 drake-7.6.1/drake/man/rs_addin_r_outdated.Rd                |    8 
 drake-7.6.1/drake/man/rs_addin_r_vis_drake_graph.Rd         |    8 
 drake-7.6.1/drake/man/running.Rd                            |    5 
 drake-7.6.1/drake/man/sankey_drake_graph.Rd                 |    7 
 drake-7.6.1/drake/man/session.Rd                            |    4 
 drake-7.6.1/drake/man/shell_file.Rd                         |    5 
 drake-7.6.1/drake/man/short_hash.Rd                         |    5 
 drake-7.6.1/drake/man/show_source.Rd                        |    5 
 drake-7.6.1/drake/man/split.Rd                              |only
 drake-7.6.1/drake/man/static_drake_graph.Rd                 |    5 
 drake-7.6.1/drake/man/summaries.Rd                          |    4 
 drake-7.6.1/drake/man/target.Rd                             |  106 +
 drake-7.6.1/drake/man/target_namespaces.Rd                  |    6 
 drake-7.6.1/drake/man/text_drake_graph.Rd                   |    6 
 drake-7.6.1/drake/man/this_cache.Rd                         |    5 
 drake-7.6.1/drake/man/tracked.Rd                            |    5 
 drake-7.6.1/drake/man/transform_plan.Rd                     |   61 
 drake-7.6.1/drake/man/trigger.Rd                            |    5 
 drake-7.6.1/drake/man/triggers.Rd                           |    5 
 drake-7.6.1/drake/man/type_sum.expr_list.Rd                 |    3 
 drake-7.6.1/drake/man/use_drake.Rd                          |    5 
 drake-7.6.1/drake/man/vis_drake_graph.Rd                    |    5 
 drake-7.6.1/drake/man/workflow.Rd                           |    4 
 drake-7.6.1/drake/man/workplan.Rd                           |    4 
 drake-7.6.1/drake/tests/scenarios/tests-all.R               |    2 
 drake-7.6.1/drake/tests/testthat/helper-checkers.R          |only
 drake-7.6.1/drake/tests/testthat/helper-dbug.R              |only
 drake-7.6.1/drake/tests/testthat/helper-operators.R         |only
 drake-7.6.1/drake/tests/testthat/helper-scenarios.R         |only
 drake-7.6.1/drake/tests/testthat/helper-testrun.R           |only
 drake-7.6.1/drake/tests/testthat/helper-testthat.R          |only
 drake-7.6.1/drake/tests/testthat/test-analysis.R            |only
 drake-7.6.1/drake/tests/testthat/test-build.R               |only
 drake-7.6.1/drake/tests/testthat/test-cache.R               |  365 +++-
 drake-7.6.1/drake/tests/testthat/test-checks.R              |only
 drake-7.6.1/drake/tests/testthat/test-commands.R            |only
 drake-7.6.1/drake/tests/testthat/test-decorated-storr.R     |only
 drake-7.6.1/drake/tests/testthat/test-deprecate.R           |   18 
 drake-7.6.1/drake/tests/testthat/test-dsl.R                 |  354 ++++
 drake-7.6.1/drake/tests/testthat/test-encoding.R            |only
 drake-7.6.1/drake/tests/testthat/test-examples.R            |   10 
 drake-7.6.1/drake/tests/testthat/test-files.R               |only
 drake-7.6.1/drake/tests/testthat/test-flow.R                |only
 drake-7.6.1/drake/tests/testthat/test-future.R              |    2 
 drake-7.6.1/drake/tests/testthat/test-graph.R               |   22 
 drake-7.6.1/drake/tests/testthat/test-hash-tables.R         |only
 drake-7.6.1/drake/tests/testthat/test-history.R             |   26 
 drake-7.6.1/drake/tests/testthat/test-hpc.R                 |only
 drake-7.6.1/drake/tests/testthat/test-imports.R             |only
 drake-7.6.1/drake/tests/testthat/test-interactive.R         |only
 drake-7.6.1/drake/tests/testthat/test-lazy.R                |only
 drake-7.6.1/drake/tests/testthat/test-lock.R                |only
 drake-7.6.1/drake/tests/testthat/test-memory.R              |   10 
 drake-7.6.1/drake/tests/testthat/test-meta.R                |only
 drake-7.6.1/drake/tests/testthat/test-missed.R              |only
 drake-7.6.1/drake/tests/testthat/test-plans.R               |  132 +
 drake-7.6.1/drake/tests/testthat/test-prework.R             |only
 drake-7.6.1/drake/tests/testthat/test-queue.R               |only
 drake-7.6.1/drake/tests/testthat/test-rng.R                 |only
 drake-7.6.1/drake/tests/testthat/test-rstudio.R             |only
 drake-7.6.1/drake/tests/testthat/test-testing.R             |   13 
 drake-7.6.1/drake/tests/testthat/test-time.R                |    1 
 drake-7.6.1/drake/tests/testthat/test-utils.R               |  317 ---
 drake-7.6.1/drake/tests/testthat/test-visuals.R             |   33 
 drake-7.6.1/drake/tests/testthat/test-zzz-callr.R           |   28 
 388 files changed, 3549 insertions(+), 1316 deletions(-)

More information about drake at CRAN
Permanent link

Package CAISEr updated to version 1.0.15 with previous version 1.0.14 dated 2019-08-02

Title: Comparison of Algorithms with Iterative Sample Size Estimation
Description: Functions for performing experimental comparisons of algorithms using adequate sample sizes for power and accuracy. Implements the methodology originally presented in Campelo and Takahashi (2019) <doi:10.1007/s10732-018-9396-7> for the comparison of two algorithms, and later generalised in Campelo and Wanner (Submitted, 2019) <arxiv:1908.01720>.
Author: Felipe Campelo [aut, cre], Fernanda Takahashi [ctb], Elizabeth Wanner [ctb]
Maintainer: Felipe Campelo <f.campelo@aston.ac.uk>

Diff between CAISEr versions 1.0.14 dated 2019-08-02 and 1.0.15 dated 2019-08-19

 DESCRIPTION                                 |   19 +++--
 MD5                                         |   18 ++--
 NEWS.md                                     |    5 +
 R/onAttach.R                                |    6 -
 R/plot_caiser.R                             |    2 
 inst/doc/Adapting_Algorithm_for_CAISEr.R    |    3 
 inst/doc/Adapting_Algorithm_for_CAISEr.Rmd  |   13 ++-
 inst/doc/Adapting_Algorithm_for_CAISEr.html |  101 ++++++++++++++--------------
 man/plot.CAISEr.Rd                          |    2 
 vignettes/Adapting_Algorithm_for_CAISEr.Rmd |   13 ++-
 10 files changed, 103 insertions(+), 79 deletions(-)

More information about CAISEr at CRAN
Permanent link

Package biclique updated to version 1.0.3 with previous version 1.0.2 dated 2019-04-07

Title: Maximal Biclique Enumeration in Bipartite Graphs
Description: A tool for enumerating maximal complete bipartite graphs. The input should be a edge list file or a binary matrix file. The output are maximal complete bipartite graphs. Algorithms used can be found in this paper Y Zhang et al. BMC Bioinformatics 2014 15:110 <doi:10.1186/1471-2105-15-110>.
Author: Yuping Lu [aut, cre, cph], Charles Phillips [aut], Michael Langston [aut], Department of Computer Science, University of Tennessee, Knoxville [cph]
Maintainer: Yuping Lu <yupinglu89@gmail.com>

Diff between biclique versions 1.0.2 dated 2019-04-07 and 1.0.3 dated 2019-08-19

 DESCRIPTION             |    6 +++---
 MD5                     |   10 +++++-----
 NEWS.md                 |    4 ++++
 README.md               |    4 ++++
 src/R_biclique_driver.c |    4 ++--
 src/biclique.c          |    6 +++---
 6 files changed, 21 insertions(+), 13 deletions(-)

More information about biclique at CRAN
Permanent link

Package transport updated to version 0.12-1 with previous version 0.12-0 dated 2019-08-06

Title: Computation of Optimal Transport Plans and Wasserstein Distances
Description: Solve optimal transport problems. Compute Wasserstein distances (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p distances), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, (weighted) point patterns, and mass vectors.
Author: Dominic Schuhmacher [aut, cre], Björn Bähre [aut] (aha and power diagrams), Nicolas Bonneel [aut] (networkflow), Carsten Gottschlich [aut] (simplex and shortlist), Valentin Hartmann [aut] (semidiscrete1), Florian Heinemann [aut] (transport_track and networkflow integration), Bernhard Schmitzer [aut] (shielding), Jörn Schrieber [aut] (subsampling), Timo Wilm [ctb] (wpp)
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>

Diff between transport versions 0.12-0 dated 2019-08-06 and 0.12-1 dated 2019-08-19

 transport-0.12-0/transport/cleanup                  |only
 transport-0.12-0/transport/configure                |only
 transport-0.12-0/transport/configure.ac             |only
 transport-0.12-0/transport/src/Makevars.in          |only
 transport-0.12-0/transport/src/Makevars.win         |only
 transport-0.12-1/transport/DESCRIPTION              |    8 ++++----
 transport-0.12-1/transport/MD5                      |   14 +++++---------
 transport-0.12-1/transport/NEWS                     |   14 ++++++++++++++
 transport-0.12-1/transport/R/fundament.R            |   16 +++++++---------
 transport-0.12-1/transport/man/transport-package.Rd |    4 ++--
 transport-0.12-1/transport/src/Makevars             |only
 11 files changed, 32 insertions(+), 24 deletions(-)

More information about transport at CRAN
Permanent link

Package StratifiedMedicine updated to version 0.1.2 with previous version 0.1.1 dated 2019-07-22

Title: Stratified Medicine
Description: A toolkit for stratified medicine, subgroup identification, and precision medicine. Current tools include (1) filtering models (reduce covariate space), (2) patient-level estimate models (counterfactual patient-level quantities, for example the individual treatment effect), (3) subgroup identification models (find subsets of patients with similar treatment effects), and (4) parameter estimation and inference (for the overall population and discovered subgroups). These tools can directly feed into stratified medicine algorithms including PRISM (patient response identifiers for stratified medicine; Jemielita and Mehrotra 2019 (in progress)). PRISM is a flexible and general framework which accepts user-created models/functions. This package is in beta and will be continually updated.
Author: Thomas Jemielita [aut, cre]
Maintainer: Thomas Jemielita <thomasjemielita@gmail.com>

Diff between StratifiedMedicine versions 0.1.1 dated 2019-07-22 and 0.1.2 dated 2019-08-19

 DESCRIPTION                      |    6 
 MD5                              |   58 ++++---
 NAMESPACE                        |    4 
 R/PRISM.R                        |  295 ++++++---------------------------------
 R/PRISM_resamp.R                 |only
 R/PRISM_train.R                  |only
 R/filter_glmnet.R                |    1 
 R/filter_ranger.R                |    3 
 R/param_cox.R                    |   17 +-
 R/param_dr.R                     |   26 ++-
 R/param_lm.R                     |   39 +++--
 R/param_ple.R                    |   25 ++-
 R/param_rmst.R                   |   13 +
 R/ple_bart.R                     |    1 
 R/ple_causal_forest.R            |    5 
 R/ple_glmnet.R                   |    1 
 R/ple_ranger.R                   |   13 -
 R/plot.R                         |   37 +++-
 README.md                        |   40 ++++-
 inst/doc/SM_PRISM.R              |   33 +---
 inst/doc/SM_PRISM.Rmd            |   41 +----
 inst/doc/SM_PRISM.html           |  140 +++++++++---------
 man/PRISM.Rd                     |   27 +--
 man/PRISM_resamp.Rd              |only
 man/PRISM_train.Rd               |only
 man/figures/README-example-1.png |binary
 man/figures/README-example-2.png |binary
 man/figures/README-example-4.png |binary
 man/ple_ranger.Rd                |    6 
 man/plot.PRISM.Rd                |    7 
 man/predict.ple_ranger.Rd        |    2 
 vignettes/SM_PRISM.Rmd           |   41 +----
 32 files changed, 377 insertions(+), 504 deletions(-)

More information about StratifiedMedicine at CRAN
Permanent link

Package spiderbar updated to version 0.2.2 with previous version 0.2.1 dated 2017-11-17

Title: Parse and Test Robots Exclusion Protocol Files and Rules
Description: The 'Robots Exclusion Protocol' <https://www.robotstxt.org/orig.html> documents a set of standards for allowing or excluding robot/spider crawling of different areas of site content. Tools are provided which wrap The 'rep-cpp' <https://github.com/seomoz/rep-cpp> C++ library for processing these 'robots.txt' files.
Author: Bob Rudis (bob@rud.is) [aut, cre], SEOmoz, Inc [aut]
Maintainer: Bob Rudis <bob@rud.is>

Diff between spiderbar versions 0.2.1 dated 2017-11-17 and 0.2.2 dated 2019-08-19

 spiderbar-0.2.1/spiderbar/README.md             |only
 spiderbar-0.2.2/spiderbar/DESCRIPTION           |   17 ++--
 spiderbar-0.2.2/spiderbar/MD5                   |    9 +-
 spiderbar-0.2.2/spiderbar/R/spiderbar-package.R |    2 
 spiderbar-0.2.2/spiderbar/man/spiderbar.Rd      |    2 
 spiderbar-0.2.2/spiderbar/src/robots.cpp        |   85 +++++++++++++-----------
 6 files changed, 62 insertions(+), 53 deletions(-)

More information about spiderbar at CRAN
Permanent link

Package securitytxt updated to version 0.1.1 with previous version 0.1.0 dated 2017-10-21

Title: Identify and Parse Web Security Policies Files
Description: When security risks in web services are discovered by independent security researchers who understand the severity of the risk, they often lack the channels to properly disclose them. As a result, security issues may be left unreported. The 'security.txt' 'Web Security Policies' specification defines an 'IETF' draft standard <https://tools.ietf.org/html/draft-foudil-securitytxt-00> to help organizations define the process for security researchers to securely disclose security vulnerabilities. Tools are provided to help identify and parse 'security.txt' files to enable analysis of the usage and adoption of these policies.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>), SEOmoz Inc [aut, cph] (url-cpp library, <https://github.com/seomoz/url-cpp>)
Maintainer: Bob Rudis <bob@rud.is>

Diff between securitytxt versions 0.1.0 dated 2017-10-21 and 0.1.1 dated 2019-08-19

 securitytxt-0.1.0/securitytxt/README.md        |only
 securitytxt-0.1.1/securitytxt/DESCRIPTION      |   17 +--
 securitytxt-0.1.1/securitytxt/MD5              |    5 -
 securitytxt-0.1.1/securitytxt/src/security.cpp |  117 ++++++++++++++-----------
 4 files changed, 77 insertions(+), 62 deletions(-)

More information about securitytxt at CRAN
Permanent link

Package MSPRT updated to version 2.1 with previous version 2.0 dated 2019-02-17

Title: A Modified Sequential Probability Ratio Test (MSPRT)
Description: A modified SPRT (MSPRT) can be designed and implemented with the help of this package. In a MSPRT design, (i) the maximum sample size of an experiment is fixed prior to the start of an experiment; (ii) the alternative hypothesis used to define the rejection region of the test is derived from the size of the test (Type I error), the maximum available sample size (N), and (iii) the targeted Type 2 error (equals to 1 minus the power) is also prespecified. Given these values, the MSPRT is defined in a manner very similar to Wald's initial proposal. This test can reduce the average sample size required to perform statistical hypothesis tests at the specified level of significance and power. This package implements one-sample proportion tests, one-sample Z-tests, one-sample T-tests, two-sample Z-tests and two-sample T-tests. A user guidance for this package is provided here. One can also refer to the supplemental information for the same.
Author: Sandipan Pramanik [aut, cre], Valen E. Johnson [aut], Anirban Bhattacharya [aut]
Maintainer: Sandipan Pramanik <sandy@stat.tamu.edu>

Diff between MSPRT versions 2.0 dated 2019-02-17 and 2.1 dated 2019-08-19

 DESCRIPTION            |   10 
 MD5                    |   12 
 R/MSPRT.R              |13156 +++++++++++++++++++++++++------------------------
 build/partial.rdb      |binary
 man/OC.MSPRT.Rd        |  389 -
 man/design.MSPRT.Rd    |   46 
 man/implement.MSPRT.Rd |   60 
 7 files changed, 7148 insertions(+), 6525 deletions(-)

More information about MSPRT at CRAN
Permanent link

Package khroma updated to version 1.2.0 with previous version 1.1.3 dated 2019-06-05

Title: Colour Schemes for Scientific Data Visualization
Description: An implementation of Paul Tol's colour schemes for use with 'graphics' or 'ggplot2'. These schemes are ready for each type of data (qualitative, diverging or sequential), with colours that are distinct for all people, including colour-blind readers. This package provides tools to simulate colour-blindness and to test how well the colours of any palette are identifiable. Several scientific thematic schemes (geologic timescale, land cover, FAO soils, etc.) are also implemented.
Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>), Brice Lebrun [ctb] (<https://orcid.org/0000-0001-7503-8685>)
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>

Diff between khroma versions 1.1.3 dated 2019-06-05 and 1.2.0 dated 2019-08-19

 khroma-1.1.3/khroma/man/figures/README-tol-diverging-1.png     |only
 khroma-1.1.3/khroma/man/figures/README-tol-qualitative-1.png   |only
 khroma-1.1.3/khroma/man/figures/README-tol-sequential-1.png    |only
 khroma-1.2.0/khroma/DESCRIPTION                                |   31 +-
 khroma-1.2.0/khroma/MD5                                        |   87 +++---
 khroma-1.2.0/khroma/NAMESPACE                                  |    3 
 khroma-1.2.0/khroma/R/anomalize.R                              |only
 khroma-1.2.0/khroma/R/colour.R                                 |   45 ++-
 khroma-1.2.0/khroma/R/ggplot2-science.R                        |   14 -
 khroma-1.2.0/khroma/R/ggplot2-tol.R                            |   35 +-
 khroma-1.2.0/khroma/R/ggplot2.R                                |    8 
 khroma-1.2.0/khroma/R/khroma-package.R                         |   13 
 khroma-1.2.0/khroma/R/plot.R                                   |only
 khroma-1.2.0/khroma/R/sysdata.rda                              |binary
 khroma-1.2.0/khroma/README.md                                  |  140 ++++++++--
 khroma-1.2.0/khroma/build                                      |only
 khroma-1.2.0/khroma/inst/CITATION                              |   19 +
 khroma-1.2.0/khroma/inst/doc                                   |only
 khroma-1.2.0/khroma/inst/examples/ex-anomalize.R               |only
 khroma-1.2.0/khroma/inst/examples/ex-palettes.R                |   38 +-
 khroma-1.2.0/khroma/inst/examples/ex-plot.R                    |only
 khroma-1.2.0/khroma/inst/examples/ex-science-land.R            |   10 
 khroma-1.2.0/khroma/inst/examples/ex-science-soil.R            |   10 
 khroma-1.2.0/khroma/inst/examples/ex-science-stratigraphy.R    |   12 
 khroma-1.2.0/khroma/inst/examples/ex-tol-discrete.R            |   54 +--
 khroma-1.2.0/khroma/inst/examples/ex-tol-diverging.R           |   19 -
 khroma-1.2.0/khroma/inst/examples/ex-tol-sequential.R          |   17 -
 khroma-1.2.0/khroma/man/colour.Rd                              |   72 +++--
 khroma-1.2.0/khroma/man/convert.Rd                             |only
 khroma-1.2.0/khroma/man/figures/README-usage-1.png             |only
 khroma-1.2.0/khroma/man/figures/README-usage-colourblind-1.png |only
 khroma-1.2.0/khroma/man/figures/README-usage-colourblind-2.png |only
 khroma-1.2.0/khroma/man/figures/README-usage-colourblind-3.png |only
 khroma-1.2.0/khroma/man/figures/README-usage-colourblind-4.png |only
 khroma-1.2.0/khroma/man/figures/README-usage-colourblind-5.png |only
 khroma-1.2.0/khroma/man/figures/README-usage-ggplot2-1.png     |only
 khroma-1.2.0/khroma/man/figures/logo.png                       |binary
 khroma-1.2.0/khroma/man/figures/logo.svg                       |   14 -
 khroma-1.2.0/khroma/man/khroma-package.Rd                      |   21 -
 khroma-1.2.0/khroma/man/plot.Rd                                |only
 khroma-1.2.0/khroma/man/scale.Rd                               |   10 
 khroma-1.2.0/khroma/man/scale_land.Rd                          |   20 -
 khroma-1.2.0/khroma/man/scale_soil.Rd                          |   15 -
 khroma-1.2.0/khroma/man/scale_stratigraphy.Rd                  |   17 -
 khroma-1.2.0/khroma/man/scale_tol_discrete.Rd                  |   64 ++--
 khroma-1.2.0/khroma/man/scale_tol_diverging.Rd                 |   37 +-
 khroma-1.2.0/khroma/man/scale_tol_sequential.Rd                |   35 +-
 khroma-1.2.0/khroma/tests/figs                                 |only
 khroma-1.2.0/khroma/tests/testthat/test-colour.R               |   46 ++-
 khroma-1.2.0/khroma/tests/testthat/test-plot.R                 |only
 khroma-1.2.0/khroma/vignettes                                  |only
 51 files changed, 572 insertions(+), 334 deletions(-)

More information about khroma at CRAN
Permanent link

Package googledrive updated to version 1.0.0 with previous version 0.1.3 dated 2019-01-24

Title: An Interface to Google Drive
Description: Manage Google Drive files from R.
Author: Lucy D'Agostino McGowan [aut], Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>), RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>

Diff between googledrive versions 0.1.3 dated 2019-01-24 and 1.0.0 dated 2019-08-19

 googledrive-0.1.3/googledrive/R/generate_request.R                                                   |only
 googledrive-0.1.3/googledrive/R/make_request.R                                                       |only
 googledrive-0.1.3/googledrive/R/process_response.R                                                   |only
 googledrive-0.1.3/googledrive/man/drive_api_key.Rd                                                   |only
 googledrive-0.1.3/googledrive/man/drive_auth_config.Rd                                               |only
 googledrive-0.1.3/googledrive/man/generate_request.Rd                                                |only
 googledrive-0.1.3/googledrive/man/is_legit_token.Rd                                                  |only
 googledrive-0.1.3/googledrive/man/make_request.Rd                                                    |only
 googledrive-0.1.3/googledrive/man/process_response.Rd                                                |only
 googledrive-0.1.3/googledrive/man/token_available.Rd                                                 |only
 googledrive-0.1.3/googledrive/tests/testthat/clean.html                                              |only
 googledrive-0.1.3/googledrive/tests/testthat/test-drive_mkdir.R                                      |only
 googledrive-0.1.3/googledrive/tests/testthat/test-files/right-content.rds                            |only
 googledrive-0.1.3/googledrive/tests/testthat/test-files/wrong-content.rds                            |only
 googledrive-0.1.3/googledrive/tests/testthat/test-process_response.R                                 |only
 googledrive-0.1.3/googledrive/vignettes/articles                                                     |only
 googledrive-1.0.0/googledrive/DESCRIPTION                                                            |   18 
 googledrive-1.0.0/googledrive/LICENSE                                                                |    4 
 googledrive-1.0.0/googledrive/MD5                                                                    |  187 ++-
 googledrive-1.0.0/googledrive/NAMESPACE                                                              |   16 
 googledrive-1.0.0/googledrive/NEWS.md                                                                |  159 +++
 googledrive-1.0.0/googledrive/R/aaa.R                                                                |   39 
 googledrive-1.0.0/googledrive/R/as_dribble.R                                                         |   13 
 googledrive-1.0.0/googledrive/R/as_id.R                                                              |   16 
 googledrive-1.0.0/googledrive/R/deprecated.R                                                         |only
 googledrive-1.0.0/googledrive/R/dribble.R                                                            |    3 
 googledrive-1.0.0/googledrive/R/drive_about.R                                                        |    6 
 googledrive-1.0.0/googledrive/R/drive_auth.R                                                         |  470 +++-------
 googledrive-1.0.0/googledrive/R/drive_cp.R                                                           |   51 -
 googledrive-1.0.0/googledrive/R/drive_create.R                                                       |only
 googledrive-1.0.0/googledrive/R/drive_download.R                                                     |   12 
 googledrive-1.0.0/googledrive/R/drive_endpoints.R                                                    |   47 -
 googledrive-1.0.0/googledrive/R/drive_fields.R                                                       |    6 
 googledrive-1.0.0/googledrive/R/drive_find.R                                                         |   63 -
 googledrive-1.0.0/googledrive/R/drive_get.R                                                          |   58 -
 googledrive-1.0.0/googledrive/R/drive_ls.R                                                           |    4 
 googledrive-1.0.0/googledrive/R/drive_mkdir.R                                                        |   76 -
 googledrive-1.0.0/googledrive/R/drive_mv.R                                                           |   60 -
 googledrive-1.0.0/googledrive/R/drive_publish.R                                                      |   14 
 googledrive-1.0.0/googledrive/R/drive_put.R                                                          |only
 googledrive-1.0.0/googledrive/R/drive_rename.R                                                       |   24 
 googledrive-1.0.0/googledrive/R/drive_reveal.R                                                       |   12 
 googledrive-1.0.0/googledrive/R/drive_reveal_path.R                                                  |    7 
 googledrive-1.0.0/googledrive/R/drive_rm.R                                                           |   13 
 googledrive-1.0.0/googledrive/R/drive_share.R                                                        |   14 
 googledrive-1.0.0/googledrive/R/drive_trash.R                                                        |   22 
 googledrive-1.0.0/googledrive/R/drive_update.R                                                       |   25 
 googledrive-1.0.0/googledrive/R/drive_upload.R                                                       |   65 -
 googledrive-1.0.0/googledrive/R/drive_user.R                                                         |    4 
 googledrive-1.0.0/googledrive/R/googledrive-package.R                                                |   13 
 googledrive-1.0.0/googledrive/R/request_generate.R                                                   |only
 googledrive-1.0.0/googledrive/R/request_make.R                                                       |only
 googledrive-1.0.0/googledrive/R/sysdata.rda                                                          |binary
 googledrive-1.0.0/googledrive/R/team_drive_create.R                                                  |    6 
 googledrive-1.0.0/googledrive/R/team_drive_find.R                                                    |    4 
 googledrive-1.0.0/googledrive/R/team_drive_get.R                                                     |    6 
 googledrive-1.0.0/googledrive/R/team_drive_rm.R                                                      |    6 
 googledrive-1.0.0/googledrive/R/team_drive_update.R                                                  |    8 
 googledrive-1.0.0/googledrive/R/utils-paths.R                                                        |   93 +
 googledrive-1.0.0/googledrive/R/utils-pipe.R                                                         |only
 googledrive-1.0.0/googledrive/R/utils.R                                                              |   32 
 googledrive-1.0.0/googledrive/README.md                                                              |   73 -
 googledrive-1.0.0/googledrive/build/vignette.rds                                                     |binary
 googledrive-1.0.0/googledrive/inst/doc/googledrive.html                                              |    7 
 googledrive-1.0.0/googledrive/inst/extdata/files_fields.csv                                          |   44 
 googledrive-1.0.0/googledrive/inst/extdata/mime_tbl.csv                                              |    7 
 googledrive-1.0.0/googledrive/inst/extdata/translate_mime_types.csv                                  |  142 +--
 googledrive-1.0.0/googledrive/inst/secret                                                            |only
 googledrive-1.0.0/googledrive/man/as_dribble.Rd                                                      |   10 
 googledrive-1.0.0/googledrive/man/drive_auth.Rd                                                      |  147 +--
 googledrive-1.0.0/googledrive/man/drive_auth_configure.Rd                                            |only
 googledrive-1.0.0/googledrive/man/drive_cp.Rd                                                        |   37 
 googledrive-1.0.0/googledrive/man/drive_create.Rd                                                    |only
 googledrive-1.0.0/googledrive/man/drive_deauth.Rd                                                    |   27 
 googledrive-1.0.0/googledrive/man/drive_download.Rd                                                  |    6 
 googledrive-1.0.0/googledrive/man/drive_endpoints.Rd                                                 |   39 
 googledrive-1.0.0/googledrive/man/drive_find.Rd                                                      |   55 -
 googledrive-1.0.0/googledrive/man/drive_get.Rd                                                       |   12 
 googledrive-1.0.0/googledrive/man/drive_has_token.Rd                                                 |only
 googledrive-1.0.0/googledrive/man/drive_mkdir.Rd                                                     |   47 -
 googledrive-1.0.0/googledrive/man/drive_mv.Rd                                                        |   29 
 googledrive-1.0.0/googledrive/man/drive_put.Rd                                                       |only
 googledrive-1.0.0/googledrive/man/drive_rename.Rd                                                    |   39 
 googledrive-1.0.0/googledrive/man/drive_reveal.Rd                                                    |    4 
 googledrive-1.0.0/googledrive/man/drive_token.Rd                                                     |   31 
 googledrive-1.0.0/googledrive/man/drive_update.Rd                                                    |   12 
 googledrive-1.0.0/googledrive/man/drive_upload.Rd                                                    |   51 -
 googledrive-1.0.0/googledrive/man/figures                                                            |only
 googledrive-1.0.0/googledrive/man/googledrive-deprecated.Rd                                          |only
 googledrive-1.0.0/googledrive/man/pipe.Rd                                                            |    4 
 googledrive-1.0.0/googledrive/man/request_generate.Rd                                                |only
 googledrive-1.0.0/googledrive/man/request_make.Rd                                                    |only
 googledrive-1.0.0/googledrive/tests/testthat/all-test-clean.R                                        |only
 googledrive-1.0.0/googledrive/tests/testthat/all-test-setup.R                                        |only
 googledrive-1.0.0/googledrive/tests/testthat/all-test-setup.html                                     |only
 googledrive-1.0.0/googledrive/tests/testthat/driver.R                                                |   10 
 googledrive-1.0.0/googledrive/tests/testthat/helper.R                                                |   67 -
 googledrive-1.0.0/googledrive/tests/testthat/setup-testing.R                                         |only
 googledrive-1.0.0/googledrive/tests/testthat/test-as_id.R                                            |   10 
 googledrive-1.0.0/googledrive/tests/testthat/test-dplyr-compatibility.R                              |   10 
 googledrive-1.0.0/googledrive/tests/testthat/test-drive_auth.R                                       |only
 googledrive-1.0.0/googledrive/tests/testthat/test-drive_create.R                                     |only
 googledrive-1.0.0/googledrive/tests/testthat/test-drive_endpoints.R                                  |only
 googledrive-1.0.0/googledrive/tests/testthat/test-drive_get.R                                        |   13 
 googledrive-1.0.0/googledrive/tests/testthat/test-drive_link.R                                       |   13 
 googledrive-1.0.0/googledrive/tests/testthat/test-drive_ls.R                                         |    2 
 googledrive-1.0.0/googledrive/tests/testthat/test-drive_put.R                                        |only
 googledrive-1.0.0/googledrive/tests/testthat/test-drive_update.R                                     |   26 
 googledrive-1.0.0/googledrive/tests/testthat/test-drive_upload.R                                     |   44 
 googledrive-1.0.0/googledrive/tests/testthat/test-files/client_secret_123.googleusercontent.com.json |only
 googledrive-1.0.0/googledrive/tests/testthat/test-generate_request.R                                 |   57 -
 googledrive-1.0.0/googledrive/tests/testthat/test-path-utils.R                                       |  131 ++
 googledrive-1.0.0/googledrive/tests/testthat/test-utils.R                                            |    8 
 113 files changed, 1672 insertions(+), 1218 deletions(-)

More information about googledrive at CRAN
Permanent link

Package rqdatatable updated to version 1.2.0 with previous version 1.1.9 dated 2019-07-04

Title: 'rquery' for 'data.table'
Description: Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows for a high-speed in memory implementation of Codd-style data manipulation tools.
Author: John Mount [aut, cre], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

Diff between rqdatatable versions 1.1.9 dated 2019-07-04 and 1.2.0 dated 2019-08-19

 DESCRIPTION                   |   14 +++++++-------
 MD5                           |   18 +++++++++---------
 NEWS.md                       |    5 +++++
 R/relop_non_sql.R             |    4 ++--
 R/rq_ufn.R                    |    4 ++--
 inst/doc/GroupedSampling.html |   10 +++++++---
 inst/doc/R_mapping.html       |   10 +++++++---
 inst/doc/logisticexample.html |   10 +++++++---
 man/rq_df_funciton_node.Rd    |    2 +-
 man/rq_ufn.Rd                 |    2 +-
 10 files changed, 48 insertions(+), 31 deletions(-)

More information about rqdatatable at CRAN
Permanent link

Package kiwisR updated to version 0.1.7 with previous version 0.1.6 dated 2019-05-28

Title: A Wrapper for Querying KISTERS 'WISKI' Databases via the 'KiWIS' API
Description: A wrapper for querying 'WISKI' databases via the 'KiWIS' 'REST' API. 'WISKI' is an 'SQL' relational database used for the collection and storage of water data developed by KISTERS and 'KiWIS' is a 'REST' service that provides access to 'WISKI' databases via HTTP requests (<https://water.kisters.de/en/technology-trends/kisters-and-open-data/>). Contains a list of default databases (called 'hubs') and also allows users to provide their own 'KiWIS' URL. Supports the entire query process- from metadata to specific time series values. All data is returned as tidy tibbles.
Author: Ryan Whaley [aut, cre], Sam Albers [ctb]
Maintainer: Ryan Whaley <rdgwhaley@gmail.com>

Diff between kiwisR versions 0.1.6 dated 2019-05-28 and 0.1.7 dated 2019-08-19

 DESCRIPTION                                |    6 
 MD5                                        |   30 ++--
 NEWS.md                                    |    9 +
 R/ki_group_list.R                          |    2 
 R/ki_station_list.R                        |   12 +
 R/ki_timeseries_list.R                     |    3 
 R/ki_timeseries_values.R                   |    2 
 R/utils.R                                  |    6 
 README.md                                  |  187 ++++++++++++++---------------
 man/ki_group_list.Rd                       |    2 
 man/ki_station_list.Rd                     |    2 
 man/ki_timeseries_list.Rd                  |    5 
 man/ki_timeseries_values.Rd                |    2 
 tests/testthat/test_ki_group_list.R        |    2 
 tests/testthat/test_ki_timeseries_list.R   |   13 +-
 tests/testthat/test_ki_timeseries_values.R |    6 
 16 files changed, 163 insertions(+), 126 deletions(-)

More information about kiwisR at CRAN
Permanent link

Package dlookr updated to version 0.3.11 with previous version 0.3.9 dated 2019-03-16

Title: Tools for Data Diagnosis, Exploration, Transformation
Description: A collection of tools that support data diagnosis, exploration, and transformation. Data diagnostics provides information and visualization of missing values and outliers and unique and negative values to help you understand the distribution and quality of your data. Data exploration provides information and visualization of the descriptive statistics of univariate variables, normality tests and outliers, correlation of two variables, and relationship between target variable and predictor. Data transformation supports binning for categorizing continuous variables, imputates missing values and outliers, resolving skewness. And it creates automated reports that support these three tasks.
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>

Diff between dlookr versions 0.3.9 dated 2019-03-16 and 0.3.11 dated 2019-08-19

 DESCRIPTION                              |   10 -
 MD5                                      |   30 ++---
 NAMESPACE                                |    1 
 NEWS                                     |   34 +++++
 R/binning.R                              |    5 
 R/diagnose.R                             |   26 +++-
 R/discribe.R                             |   57 ++++++---
 R/imputation.R                           |   80 +++++++++++--
 R/transform.R                            |    4 
 inst/doc/EDA.html                        |   12 +-
 inst/doc/transformation.html             |  184 ++++++++++---------------------
 inst/report/03_Transformation.Rnw        |   21 +++
 inst/report/03_Transformation_KR.Rnw     |   21 +++
 inst/report/Transformation_Report.Rmd    |   20 +++
 inst/report/Transformation_Report_KR.Rmd |   21 +++
 man/imputate_na.Rd                       |    2 
 16 files changed, 339 insertions(+), 189 deletions(-)

More information about dlookr at CRAN
Permanent link

Package BRISC updated to version 0.2.0 with previous version 0.1.0 dated 2018-07-22

Title: Fast Inference for Large Spatial Datasets using BRISC
Description: Fits Bootstrap with univariate spatial regression models using Bootstrap for Rapid Inference on Spatial Covariances (BRISC) for large datasets using Nearest Neighbor Gaussian Processes detailed in Saha and Datta (2018) <doi:10.1002/sta4.184>.
Author: Arkajyoti Saha [aut, cre], Abhirup Datta [aut], Jorge Nocedal [ctb], Naoaki Okazaki [ctb]
Maintainer: Arkajyoti Saha <arkajyotisaha93@gmail.com>

Diff between BRISC versions 0.1.0 dated 2018-07-22 and 0.2.0 dated 2019-08-19

 DESCRIPTION               |   10 ++---
 MD5                       |   22 ++++++------
 NAMESPACE                 |    2 +
 R/Brisc_Variogram.CI.R    |only
 R/bootstrap.R             |   17 ++++-----
 R/bootstrap_brisc.R       |    4 +-
 R/estimation.R            |    9 +++-
 R/prediction.R            |   20 +++++++++--
 man/BRISC_bootstrap.Rd    |    4 +-
 man/BRISC_estimation.Rd   |    8 ++--
 man/BRISC_prediction.Rd   |    8 ++--
 man/BRISC_variogram.ci.Rd |only
 src/BRISC.cpp             |   83 +++++++++++++++++++++++-----------------------
 13 files changed, 110 insertions(+), 77 deletions(-)

More information about BRISC at CRAN
Permanent link

Package TLMoments updated to version 0.7.4.4 with previous version 0.7.4.3 dated 2019-04-30

Title: Calculate TL-Moments and Convert Them to Distribution Parameters
Description: Calculates empirical TL-moments (trimmed L-moments) of arbitrary order and trimming, and converts them to distribution parameters.
Author: Jona Lilienthal
Maintainer: Jona Lilienthal <lilienthal@statistik.tu-dortmund.de>

Diff between TLMoments versions 0.7.4.3 dated 2019-04-30 and 0.7.4.4 dated 2019-08-19

 DESCRIPTION                                  |    8 
 MD5                                          |   30 -
 R/summary.PWMs.R                             |    2 
 R/summary.TLMoments.R                        |    4 
 R/summary.parameters.R                       |    2 
 R/summary.quantiles.R                        |    2 
 build/vignette.rds                           |binary
 inst/doc/comparison_of_computation_time.Rmd  |   28 -
 inst/doc/comparison_of_computation_time.html |  606 ++++++++++++++--------
 inst/doc/short_introduction.R                |   87 +--
 inst/doc/short_introduction.Rmd              |  150 +++--
 inst/doc/short_introduction.html             |  740 ++++++++++++++++++---------
 src/PWM.cpp                                  |    5 
 src/TLMoments.cpp                            |   10 
 vignettes/comparison_of_computation_time.Rmd |   28 -
 vignettes/short_introduction.Rmd             |  150 +++--
 16 files changed, 1198 insertions(+), 654 deletions(-)

More information about TLMoments at CRAN
Permanent link

Package spiritR updated to version 0.1.1 with previous version 0.1.0 dated 2019-08-10

Title: Template for Clinical Trial Protocol
Description: Contains an R Markdown template for a clinical trial protocol adhering to the SPIRIT statement. The SPIRIT (Standard Protocol Items for Interventional Trials) statement outlines recommendations for a minimum set of elements to be addressed in a clinical trial protocol. Also contains functions to create a xml document from the template and upload it to clinicaltrials.gov<https://www.clinicaltrials.gov/> for trial registration.
Author: Aaron Conway [aut, cre] (<https://orcid.org/0000-0002-9583-8636>)
Maintainer: Aaron Conway <aaron.conway@utoronto.ca>

Diff between spiritR versions 0.1.0 dated 2019-08-10 and 0.1.1 dated 2019-08-19

 DESCRIPTION            |   12 +++++++-----
 MD5                    |   12 ++++++------
 NEWS.md                |    8 ++++++++
 README.md              |    7 ++++---
 inst/doc/spiritR.html  |    4 ++--
 man/spiritR-package.Rd |    8 ++++++++
 tests/testthat/tests.R |    6 ++++++
 7 files changed, 41 insertions(+), 16 deletions(-)

More information about spiritR at CRAN
Permanent link

Package RTransferEntropy updated to version 0.2.12 with previous version 0.2.8 dated 2019-03-12

Title: Measuring Information Flow Between Time Series with Shannon and Renyi Transfer Entropy
Description: Measuring information flow between time series with Shannon and Rényi transfer entropy. See also Dimpfl and Peter (2013) <doi:10.1515/snde-2012-0044> and Dimpfl and Peter (2014) <doi:10.1016/j.intfin.2014.03.004> for theory and applications to financial time series. Additional references can be found in the theory part of the vignette.
Author: Simon Behrendt [aut, cre], David Zimmermann [aut], Thomas Dimpfl [aut], Franziska Peter [aut]
Maintainer: Simon Behrendt <simon.behrendt@zu.de>

Diff between RTransferEntropy versions 0.2.8 dated 2019-03-12 and 0.2.12 dated 2019-08-19

 DESCRIPTION                            |    6 -
 MD5                                    |   33 +++----
 R/calc_ete.R                           |    6 -
 R/calc_te.R                            |    6 -
 R/te_class.R                           |  151 ++++++++++++++++++++++++++-------
 R/transfer_entropy.R                   |   16 ++-
 R/zzz.R                                |   31 ++++++
 README.md                              |   47 ++++++----
 build/vignette.rds                     |binary
 inst/CITATION                          |only
 inst/doc/transfer-entropy.html         |   59 ++++++------
 man/calc_ete.Rd                        |    6 +
 man/calc_te.Rd                         |    6 +
 man/figures/README-contemp_plot-1.png  |binary
 man/print.transfer_entropy.Rd          |   23 ++++-
 man/transfer_entropy.Rd                |    5 -
 tests/testthat.R                       |    3 
 tests/testthat/test.transfer_entropy.R |   22 +++-
 18 files changed, 308 insertions(+), 112 deletions(-)

More information about RTransferEntropy at CRAN
Permanent link

Package rjags updated to version 4-9 with previous version 4-8 dated 2018-10-19

Title: Bayesian Graphical Models using MCMC
Description: Interface to the JAGS MCMC library.
Author: Martyn Plummer [aut, cre], Alexey Stukalov [ctb], Matt Denwood [ctb]
Maintainer: Martyn Plummer <martyn.plummer@gmail.com>

Diff between rjags versions 4-8 dated 2018-10-19 and 4-9 dated 2019-08-19

 DESCRIPTION      |    8 ++++----
 MD5              |    4 ++--
 src/Makevars.win |    2 ++
 3 files changed, 8 insertions(+), 6 deletions(-)

More information about rjags at CRAN
Permanent link

Package JADE updated to version 2.0-2 with previous version 2.0-1 dated 2018-03-02

Title: Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria
Description: Cardoso's JADE algorithm as well as his functions for joint diagonalization are ported to R. Also several other blind source separation (BSS) methods, like AMUSE and SOBI, and some criteria for performance evaluation of BSS algorithms, are given. The package is described in Miettinen, Nordhausen and Taskinen (2017) <doi:10.18637/jss.v076.i02>.
Author: Klaus Nordhausen, Jean-Francois Cardoso, Jari Miettinen, Hannu Oja, Esa Ollila, Sara Taskinen
Maintainer: Klaus Nordhausen <klaus.nordhausen@tuwien.ac.at>

Diff between JADE versions 2.0-1 dated 2018-03-02 and 2.0-2 dated 2019-08-19

 JADE-2.0-1/JADE/data/datalist              |only
 JADE-2.0-2/JADE/DESCRIPTION                |    8 -
 JADE-2.0-2/JADE/MD5                        |   23 +--
 JADE-2.0-2/JADE/NAMESPACE                  |    2 
 JADE-2.0-2/JADE/R/frjd.R                   |  108 +++++++++++-------
 JADE-2.0-2/JADE/build/partial.rdb          |binary
 JADE-2.0-2/JADE/build/vignette.rds         |binary
 JADE-2.0-2/JADE/inst/ChangeLog             |    4 
 JADE-2.0-2/JADE/inst/doc/JADE-BSSasymp.pdf |binary
 JADE-2.0-2/JADE/man/CPPdata.Rd             |    4 
 JADE-2.0-2/JADE/man/JADE-package.Rd        |    4 
 JADE-2.0-2/JADE/man/SOBI.Rd                |    4 
 JADE-2.0-2/JADE/man/rjd.Rd                 |  171 +++++++++++++++--------------
 13 files changed, 181 insertions(+), 147 deletions(-)

More information about JADE at CRAN
Permanent link

Package Infusion updated to version 1.4.1 with previous version 1.3.0 dated 2018-09-24

Title: Inference Using Simulation
Description: Implements functions for simulation-based inference. In particular, implements functions to perform likelihood inference from data summaries whose distributions are simulated (Rousset et al. 2017 <doi:10.1111/1755-0998.12627>).
Author: François Rousset [aut, cre, cph] (<https://orcid.org/0000-0003-4670-0371>)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>

Diff between Infusion versions 1.3.0 dated 2018-09-24 and 1.4.1 dated 2019-08-19

 DESCRIPTION                    |   10 
 MD5                            |   66 +++--
 NAMESPACE                      |    2 
 R/MSL.R                        |   10 
 R/Rmixmod.R                    |  186 ++++++++++------
 R/SLik.R                       |   10 
 R/SLikSQuant.R                 |  472 +++++++++++++++++++++++------------------
 R/add_simulation.R             |   57 ++--
 R/calc_all_slices.R            |    3 
 R/confintLR.SLik.R             |    2 
 R/coresWrapper.R               |   20 +
 R/generate_data.R              |    4 
 R/infer_logLs.R                |   18 +
 R/infer_surface.R              |    9 
 R/jointDens.R                  |  396 ++++++++++++++++++++++++++--------
 R/keras.R                      |only
 R/mclust.R                     |   36 +--
 R/minImIze.R                   |only
 R/plot.SLik.R                  |    8 
 R/plot.SLik_j.R                |   11 
 R/plotProfiles.R               |   29 +-
 R/profile.R                    |   20 +
 R/project.R                    |  320 +++++++++++++++++++--------
 inst/NEWS.Rd                   |   27 ++
 man/Infusion.Rd                |   46 ---
 man/MSL.Rd                     |   11 
 man/add.simulation.Rd          |   19 +
 man/dMixmod.Rd                 |only
 man/example_raw.Rd             |only
 man/example_reftable.Rd        |only
 man/infer_jointDens.Rd         |   19 -
 man/options.Rd                 |   10 
 man/project.Rd                 |   46 +--
 man/refine.SLik.Rd             |   19 +
 tests/test-all.R               |    1 
 tests/testthat/test-3par.R     |    2 
 tests/testthat/test-reftable.R |only
 37 files changed, 1214 insertions(+), 675 deletions(-)

More information about Infusion at CRAN
Permanent link

Package ggstance updated to version 0.3.3 with previous version 0.3.2 dated 2019-06-24

Title: Horizontal 'ggplot2' Components
Description: A 'ggplot2' extension that provides flipped components: horizontal versions of 'Stats' and 'Geoms', and vertical versions of 'Positions'.
Author: Lionel Henry [aut, cre], Hadley Wickham [aut], Winston Chang [aut], RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>

Diff between ggstance versions 0.3.2 dated 2019-06-24 and 0.3.3 dated 2019-08-19

 DESCRIPTION                                                             |    6 
 MD5                                                                     |   21 
 NEWS.md                                                                 |    8 
 R/position-dodge2v.R                                                    |    4 
 R/position-stackv.R                                                     |    2 
 man/position-vertical.Rd                                                |    2 
 tests/figs/geoms/geom-boxploth-facet-wrap-with-fill.svg                 |  402 +++++-----
 tests/figs/geoms/geom-boxploth-with-fill.svg                            |  122 +--
 tests/figs/positions/boxplot-with-legend-order-aligned-to-bar-order.svg |only
 tests/figs/positions/position-stackv-with-hjust-argument.svg            |    4 
 tests/testthat/test-geoms.R                                             |    1 
 tests/testthat/test-positions.R                                         |    9 
 12 files changed, 300 insertions(+), 281 deletions(-)

More information about ggstance at CRAN
Permanent link

Package broomExtra updated to version 0.0.5 with previous version 0.0.4 dated 2019-06-25

Title: Enhancements for 'broom' Package Family
Description: Collection of functions to assist 'broom' and 'broom.mixed' package-related data analysis workflows. In particular, the generic functions tidy(), glance(), and augment() choose appropriate S3 methods from these two packages depending on which package exports the needed method. Additionally, 'grouped_' and 'boot_' variants of the generics provides a convenient way to execute functions across a combination of grouping variable(s) in a dataframe or bootstrap them.
Author: Indrajeet Patil [aut, cre, ctb] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>

Diff between broomExtra versions 0.0.4 dated 2019-06-25 and 0.0.5 dated 2019-08-19

 broomExtra-0.0.4/broomExtra/tests/testthat/test_boot_generics.R    |only
 broomExtra-0.0.4/broomExtra/tests/testthat/test_generics.R         |only
 broomExtra-0.0.4/broomExtra/tests/testthat/test_grouped_generics.R |only
 broomExtra-0.0.5/broomExtra/DESCRIPTION                            |   12 
 broomExtra-0.0.5/broomExtra/MD5                                    |   62 ++---
 broomExtra-0.0.5/broomExtra/NAMESPACE                              |   10 
 broomExtra-0.0.5/broomExtra/NEWS.md                                |   23 +
 broomExtra-0.0.5/broomExtra/R/boot_generics.R                      |   89 +++----
 broomExtra-0.0.5/broomExtra/R/generics.R                           |   67 +++--
 broomExtra-0.0.5/broomExtra/R/global_vars.R                        |    3 
 broomExtra-0.0.5/broomExtra/R/grouped_generics.R                   |   30 +-
 broomExtra-0.0.5/broomExtra/R/reexports.R                          |   18 +
 broomExtra-0.0.5/broomExtra/README.md                              |  124 ++++------
 broomExtra-0.0.5/broomExtra/build/broomExtra.pdf                   |binary
 broomExtra-0.0.5/broomExtra/build/vignette.rds                     |binary
 broomExtra-0.0.5/broomExtra/inst/WORDLIST                          |    1 
 broomExtra-0.0.5/broomExtra/inst/doc/available_methods.html        |   98 +++++--
 broomExtra-0.0.5/broomExtra/inst/doc/tests_and_coverage.Rmd        |   50 ++--
 broomExtra-0.0.5/broomExtra/inst/doc/tests_and_coverage.html       |   70 ++---
 broomExtra-0.0.5/broomExtra/man/augment.Rd                         |    9 
 broomExtra-0.0.5/broomExtra/man/boot_augment.Rd                    |   21 +
 broomExtra-0.0.5/broomExtra/man/boot_glance.Rd                     |   21 +
 broomExtra-0.0.5/broomExtra/man/boot_tidy.Rd                       |   21 +
 broomExtra-0.0.5/broomExtra/man/glance.Rd                          |    9 
 broomExtra-0.0.5/broomExtra/man/grouped_augment.Rd                 |    9 
 broomExtra-0.0.5/broomExtra/man/grouped_glance.Rd                  |    9 
 broomExtra-0.0.5/broomExtra/man/grouped_tidy.Rd                    |    9 
 broomExtra-0.0.5/broomExtra/man/reexports.Rd                       |   10 
 broomExtra-0.0.5/broomExtra/man/tidy.Rd                            |   15 +
 broomExtra-0.0.5/broomExtra/tests/README.md                        |   52 ++--
 broomExtra-0.0.5/broomExtra/tests/spelling.R                       |    3 
 broomExtra-0.0.5/broomExtra/tests/testthat/test-boot_generics.R    |only
 broomExtra-0.0.5/broomExtra/tests/testthat/test-generics.R         |only
 broomExtra-0.0.5/broomExtra/tests/testthat/test-grouped_generics.R |only
 broomExtra-0.0.5/broomExtra/vignettes/tests_and_coverage.Rmd       |   50 ++--
 35 files changed, 536 insertions(+), 359 deletions(-)

More information about broomExtra at CRAN
Permanent link

Package benchmarkme updated to version 1.0.2 with previous version 1.0.0 dated 2019-01-28

Title: Crowd Sourced System Benchmarks
Description: Benchmark your CPU and compare against other CPUs. Also provides functions for obtaining system specifications, such as RAM, CPU type, and R version.
Author: Colin Gillespie [aut, cre] (<https://orcid.org/0000-0003-1787-0275>)
Maintainer: Colin Gillespie <csgillespie@gmail.com>

Diff between benchmarkme versions 1.0.0 dated 2019-01-28 and 1.0.2 dated 2019-08-19

 DESCRIPTION                  |   35 ++++++++++++++++++++---------------
 MD5                          |   18 +++++++++---------
 NEWS.md                      |    6 ++++++
 R/get_byte_compiler.R        |    2 +-
 README.md                    |    5 +++++
 build/vignette.rds           |binary
 inst/doc/a_introduction.R    |    2 +-
 inst/doc/a_introduction.Rmd  |   10 +++++++++-
 inst/doc/a_introduction.html |   14 +++++++++++---
 vignettes/a_introduction.Rmd |   10 +++++++++-
 10 files changed, 71 insertions(+), 31 deletions(-)

More information about benchmarkme at CRAN
Permanent link

Package ryandexdirect updated to version 3.2.1 with previous version 3.2.0 dated 2019-07-01

Title: Load Data From 'Yandex Direct'
Description: Load data from 'Yandex Direct' API V5 <https://tech.yandex.ru/direct/doc/dg/concepts/about-docpage/> into R. Provide function for load lists of campaings, ads, keywords and other objects from 'Yandex Direct' account. Also you can load statistic from API 'Reports Service' <https://tech.yandex.ru/direct/doc/reports/reports-docpage/>. And allows keyword bids management.
Author: Alexey Seleznev [aut, cre]
Maintainer: Alexey Seleznev <selesnow@gmail.com>

Diff between ryandexdirect versions 3.2.0 dated 2019-07-01 and 3.2.1 dated 2019-08-19

 DESCRIPTION                               |    8 +-
 MD5                                       |   22 +++----
 NEWS.md                                   |    4 +
 R/yadirGetKeyWordsBids.R                  |    8 ++
 R/yadirSetAutoKeyWordsBids.R              |   92 ++++++++++++++++--------------
 R/yadirSetKeyWordsBids.R                  |   78 ++++++++++++++-----------
 README.md                                 |   15 ++++
 build/partial.rdb                         |binary
 build/vignette.rds                        |binary
 inst/doc/yandex-direct-auth.html          |    4 -
 inst/doc/yandex-direct-get-statistic.html |    4 -
 inst/doc/yandex-direct-keyword-bids.html  |    4 -
 12 files changed, 143 insertions(+), 96 deletions(-)

More information about ryandexdirect at CRAN
Permanent link

Package RcppQuantuccia updated to version 0.0.3 with previous version 0.0.2 dated 2017-11-06

Title: R Bindings to the 'Quantuccia' Header-Only Essentials of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' and the header-only 'Quantuccia' variant (put together by Peter Caspers) offering an essential subset of 'QuantLib'. See the included file 'AUTHORS' for a full list of contributors to both 'QuantLib' and 'Quantuccia'.
Author: Dirk Eddelbuettel; the authors and contributors of QuantLib
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppQuantuccia versions 0.0.2 dated 2017-11-06 and 0.0.3 dated 2019-08-19

 RcppQuantuccia-0.0.2/RcppQuantuccia/inst/include/ql/math/randomnumbers/sobolrsg.hpp           |only
 RcppQuantuccia-0.0.2/RcppQuantuccia/inst/include/ql/models                                    |only
 RcppQuantuccia-0.0.3/RcppQuantuccia/ChangeLog                                                 |   45 ++
 RcppQuantuccia-0.0.3/RcppQuantuccia/DESCRIPTION                                               |    8 
 RcppQuantuccia-0.0.3/RcppQuantuccia/MD5                                                       |   50 +--
 RcppQuantuccia-0.0.3/RcppQuantuccia/README.md                                                 |   12 
 RcppQuantuccia-0.0.3/RcppQuantuccia/build/partial.rdb                                         |binary
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/NEWS.Rd                                              |   11 
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/array.hpp                            |   38 +-
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/distributions/normaldistribution.hpp |   16 
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/functional.hpp                       |  161 +++++++++-
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/generallinearleastsquares.hpp        |    3 
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/matrix.hpp                           |   44 +-
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/optimization/levenbergmarquardt.hpp  |   14 
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/randomnumbers/all.hpp                |    5 
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/randomnumbers/rngtraits.hpp          |    8 
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/statistics/incrementalstatistics.hpp |   16 
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/quantlib.hpp                              |    2 
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/time/calendars/unitedstates.hpp           |    6 
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/time/date.hpp                             |   18 -
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/time/imm.hpp                              |   14 
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/timegrid.hpp                              |    4 
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/utilities/dataparsers.hpp                 |   16 
 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/utilities/null.hpp                        |   14 
 RcppQuantuccia-0.0.3/RcppQuantuccia/src/Makevars                                              |    2 
 25 files changed, 348 insertions(+), 159 deletions(-)

More information about RcppQuantuccia at CRAN
Permanent link

Package MVar.pt updated to version 2.0.8 with previous version 2.0.7 dated 2019-07-30

Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, tendo funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise discriminante linear (LDA) e quadratica (QDA), analise de cluster hierarquico e nao hierarquico, regressao linear simples e multipla, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos, projection pursuit (PP), grant tour e outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com> Marcelo Angelo Cirillo <macufla@des.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

Diff between MVar.pt versions 2.0.7 dated 2019-07-30 and 2.0.8 dated 2019-08-19

 DESCRIPTION            |    8 ++---
 MD5                    |   24 ++++++++--------
 R/Biplot.R             |    6 ++--
 R/GrandTour.R          |   72 ++++++++++++++++++++++++-------------------------
 R/MDS.R                |   14 ++++-----
 R/Plot.CA.R            |   22 +++++++-------
 R/Plot.CCA.R           |   21 +++++++-------
 R/Plot.FA.R            |   24 ++++++++--------
 R/Plot.MFA.R           |   27 +++++++++---------
 R/Plot.PCA.R           |   17 ++++++-----
 R/Plot.PP.R            |   30 ++++++++++----------
 R/Plot.Regr.R          |   12 ++++----
 man/MVar.pt-package.Rd |    4 +-
 13 files changed, 142 insertions(+), 139 deletions(-)

More information about MVar.pt at CRAN
Permanent link

Package MVar updated to version 2.0.8 with previous version 2.0.7 dated 2019-07-30

Title: Multivariate Analysis
Description: Package for multivariate analysis, having functions that perform simple correspondence analysis (CA) and multiple correspondence analysis (MCA), principal components analysis (PCA), canonical correlation analysis (CCA), factorial analysis (FA), multidimensional scaling (MDS), linear (LDA) and quadratic discriminant analysis (QDA), hierarchical and non-hierarchical cluster analysis, simple and multiple linear regression, multiple factor analysis (MFA) for quantitative, qualitative, frequency (MFACT) and mixed data, projection pursuit (PP), grant tour method and other useful functions for the multivariate analysis.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com> Marcelo Angelo Cirillo <macufla@des.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

Diff between MVar versions 2.0.7 dated 2019-07-30 and 2.0.8 dated 2019-08-19

 DESCRIPTION           |    8 +++----
 MD5                   |   24 ++++++++++-----------
 R/Biplot_English.R    |    6 ++---
 R/GrandTour_English.R |   56 +++++++++++++++++++++++++-------------------------
 R/MDS_English.R       |   20 ++++++++---------
 R/Plot.CA_English.R   |   38 ++++++++++++++++-----------------
 R/Plot.CCA_English.R  |   39 +++++++++++++++++-----------------
 R/Plot.FA_English.R   |   32 ++++++++++++++--------------
 R/Plot.MFA_English.R  |   45 ++++++++++++++++++++--------------------
 R/Plot.PCA_English.R  |   27 ++++++++++++------------
 R/Plot.PP_English.R   |   38 ++++++++++++++++-----------------
 R/Plot.Regr_English.R |   22 +++++++++----------
 man/MVar-package.Rd   |    4 +--
 13 files changed, 181 insertions(+), 178 deletions(-)

More information about MVar at CRAN
Permanent link

Package MatchIt.mice updated to version 2.1.5 with previous version 2.0.2 dated 2019-07-02

Title: Matching Multiply Imputed Datasets
Description: Simplifies the process of matching control and treatment groups of multiply imputed datasets; selects matched samples from the control and treatment groups, enables complete data analysis, and pools the obtained results on each imputed dataset according to Rubin’s rules. Please see the package repository <https://github.com/FarhadPishgar/MatchIt.mice> for details.
Author: Farhad Pishgar
Maintainer: Farhad Pishgar <Farhad.Pishgar@Gmail.com>

Diff between MatchIt.mice versions 2.0.2 dated 2019-07-02 and 2.1.5 dated 2019-08-19

 DESCRIPTION              |    6 +-
 MD5                      |   77 +++++++++++++++++++------------------
 NAMESPACE                |    6 ++
 NEWS.md                  |   12 +++--
 R/as2.mids.R             |only
 R/binditmice.R           |   96 +++++++++++++++++++++++++++++++++++++++++------
 R/handoa.R               |    1 
 R/is.R                   |    6 ++
 R/matchitmice.R          |   10 ++--
 R/matchitmice.data.R     |   12 +++--
 R/mergeitmice.R          |only
 R/plot.mimids.R          |    4 +
 R/plot.wimids.R          |    4 +
 R/pool.R                 |   15 +++++--
 R/print.mimids.R         |    4 +
 R/print.wimids.R         |    6 ++
 R/summary.mimids.R       |    4 +
 R/summary.wimids.R       |    7 +--
 R/weightitmice.R         |   13 ++----
 R/weightitmice.data.R    |   13 ++++--
 R/with.mimids.R          |    4 +
 R/with.wimids.R          |    4 +
 README.md                |   16 +++----
 man/binditmice.Rd        |   11 +++--
 man/handoa.Rd            |    1 
 man/is.mimids.Rd         |    1 
 man/is.wimids.Rd         |    3 -
 man/matchitmice.Rd       |    7 ---
 man/matchitmice.data.Rd  |    5 +-
 man/mergeitmice.Rd       |only
 man/plot.mimids.Rd       |    3 -
 man/plot.wimids.Rd       |    3 -
 man/pool.Rd              |    5 +-
 man/print.mimids.Rd      |    3 -
 man/print.wimids.Rd      |    3 -
 man/summary.mimids.Rd    |    3 -
 man/summary.wimids.Rd    |    6 --
 man/weightitmice.Rd      |   10 ----
 man/weightitmice.data.Rd |    5 +-
 man/with.mimids.Rd       |    3 -
 man/with.wimids.Rd       |    3 -
 41 files changed, 258 insertions(+), 137 deletions(-)

More information about MatchIt.mice at CRAN
Permanent link

Package GSED updated to version 2.4 with previous version 2.3 dated 2019-07-10

Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>

Diff between GSED versions 2.3 dated 2019-07-10 and 2.4 dated 2019-08-19

 DESCRIPTION         |    8 ++++----
 MD5                 |    6 +++---
 R/GSED.R            |    2 +-
 man/GSED-package.Rd |    4 ++--
 4 files changed, 10 insertions(+), 10 deletions(-)

More information about GSED at CRAN
Permanent link

Package CalibratR updated to version 0.1.2 with previous version 0.1.1 dated 2018-08-27

Title: Mapping ML Scores to Calibrated Predictions
Description: Transforms your uncalibrated Machine Learning scores to well-calibrated prediction estimates that can be interpreted as probability estimates. The implemented BBQ (Bayes Binning in Quantiles) model is taken from Naeini (2015, ISBN:0-262-51129-0). Please cite this paper: Schwarz J and Heider D, Bioinformatics 2019, 35(14):2458-2465.
Author: Johanna Schwarz, Dominik Heider
Maintainer: Dominik Heider <heiderd@mathematik.uni-marburg.de>

Diff between CalibratR versions 0.1.1 dated 2018-08-27 and 0.1.2 dated 2019-08-19

 DESCRIPTION       |   11 +++++------
 MD5               |   13 +++++++------
 NAMESPACE         |    8 ++++++--
 R/build_GUESS.R   |    3 ++-
 R/getECE.R        |    5 +++--
 R/getMCE.R        |    3 ++-
 R/predict_GUESS.R |    3 ++-
 inst              |only
 8 files changed, 27 insertions(+), 19 deletions(-)

More information about CalibratR at CRAN
Permanent link

Package asnipe updated to version 1.1.12 with previous version 1.1.11 dated 2018-11-22

Title: Animal Social Network Inference and Permutations for Ecologists
Description: Implements several tools that are used in animal social network analysis. 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 1.1.11 dated 2018-11-22 and 1.1.12 dated 2019-08-19

 DESCRIPTION                |   12 ++++-----
 MD5                        |   14 +++++-----
 R/get_network.R            |   59 +++++++++++++++++++++++++++++++--------------
 R/get_sampling_periods.R   |    2 -
 R/network_permutation.R    |   34 ++++++++++++++++++++++---
 man/asnipe-package.Rd      |    6 ++--
 man/get_network.Rd         |   11 +++++++-
 man/network_permutation.Rd |   12 ++++++++-
 8 files changed, 109 insertions(+), 41 deletions(-)

More information about asnipe at CRAN
Permanent link

Package txtq updated to version 0.1.5 with previous version 0.1.4 dated 2019-07-19

Title: A Small Message Queue for Parallel Processes
Description: This queue is a data structure that lets parallel processes send and receive messages, and it can help coordinate the work of complicated parallel tasks. Processes can push new messages to the queue, pop old messages, and obtain a log of all the messages ever pushed. File locking preserves the integrity of the data even when multiple processes access the queue simultaneously.
Author: William Michael Landau [aut, cre] (<https://orcid.org/0000-0003-1878-3253>), Ian E. Fellows [ctb], Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

Diff between txtq versions 0.1.4 dated 2019-07-19 and 0.1.5 dated 2019-08-19

 DESCRIPTION                |    8 ++++----
 MD5                        |    8 ++++----
 NEWS.md                    |    4 ++++
 R/utils.R                  |    2 +-
 tests/testthat/test-txtq.R |    7 +++++++
 5 files changed, 20 insertions(+), 9 deletions(-)

More information about txtq at CRAN
Permanent link

Package svd updated to version 0.5 with previous version 0.4.3 dated 2019-04-05

Title: Interfaces to Various State-of-Art SVD and Eigensolvers
Description: R bindings to SVD and eigensolvers (PROPACK, nuTRLan).
Author: Anton Korobeynikov [aut, cre], Rasmus Munk Larsen [ctb, cph], Lawrence Berkeley National Laboratory [ctb, cph]
Maintainer: Anton Korobeynikov <anton@korobeynikov.info>

Diff between svd versions 0.4.3 dated 2019-04-05 and 0.5 dated 2019-08-19

 svd-0.4.3/svd/src/propack/printstat.f |only
 svd-0.5/svd/DESCRIPTION               |    6 +++---
 svd-0.5/svd/MD5                       |   24 ++++++++++++------------
 svd-0.5/svd/src/Makevars              |    2 +-
 svd-0.5/svd/src/propack/printstat.f90 |only
 svd-0.5/svd/src/propack/propack_svd.c |   31 ++++++++++++-------------------
 svd-0.5/svd/src/propack/stat.h        |   33 ++++++++++++++++-----------------
 svd-0.5/svd/src/trlan/dstqrb.c        |   30 +++++++++++++++++-------------
 svd-0.5/svd/src/trlan/trlan.c         |   14 +++++++++-----
 svd-0.5/svd/src/trlan/trlan_R.c       |   10 +++++++---
 svd-0.5/svd/src/trlan/trlaux.c        |    9 +++++----
 svd-0.5/svd/src/trlan/trlcore.c       |   10 +++++++---
 svd-0.5/svd/src/trlan/trlmap.c        |   12 ++++++++----
 svd-0.5/svd/src/trlan/ztrlan_R.c      |   10 +++++++---
 14 files changed, 104 insertions(+), 87 deletions(-)

More information about svd at CRAN
Permanent link

Package opalr updated to version 1.2.0 with previous version 1.1.0 dated 2019-06-26

Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is the core database application for biobanks. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. 'Opal' is such a central repository. It can import, process, validate, query, analyze, report, and export data. 'Opal' is typically used in a research center to analyze the data acquired at assessment centres. Its ultimate purpose is to achieve seamless data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal' web services and to perform operations on the R server side. 'DataSHIELD' administration tools are also provided.
Author: Yannick Marcon [aut, cre] (<https://orcid.org/0000-0003-0138-2023>), Amadou Gaye [ctb] (<https://orcid.org/0000-0002-1180-2792>), OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>

Diff between opalr versions 1.1.0 dated 2019-06-26 and 1.2.0 dated 2019-08-19

 opalr-1.1.0/opalr/man/dot-authToken.Rd                   |only
 opalr-1.2.0/opalr/DESCRIPTION                            |    6 -
 opalr-1.2.0/opalr/MD5                                    |   38 +++----
 opalr-1.2.0/opalr/R/opal.admin.r                         |    2 
 opalr-1.2.0/opalr/R/opal.r                               |   79 +++++++++------
 opalr-1.2.0/opalr/build/vignette.rds                     |binary
 opalr-1.2.0/opalr/inst/doc/opal-files.html               |   10 +
 opalr-1.2.0/opalr/inst/doc/opal-projects.html            |   10 +
 opalr-1.2.0/opalr/inst/doc/opal-rsession.html            |   10 +
 opalr-1.2.0/opalr/inst/examples/opal-login-certificate.R |only
 opalr-1.2.0/opalr/inst/examples/opal-login-token.R       |only
 opalr-1.2.0/opalr/inst/reports/basic/opal.Rmd            |    6 -
 opalr-1.2.0/opalr/inst/reports/report-exec.R             |    6 -
 opalr-1.2.0/opalr/inst/reports/table/opal-table.Rmd      |   14 +-
 opalr-1.2.0/opalr/inst/reports/tutorial/opal-dev.Rmd     |    6 -
 opalr-1.2.0/opalr/inst/reports/tutorial/opal-exec.R      |    2 
 opalr-1.2.0/opalr/inst/reports/tutorial/opal-prod.Rmd    |    6 -
 opalr-1.2.0/opalr/inst/reports/tutorial/opal-prod.html   |only
 opalr-1.2.0/opalr/inst/reports/tutorial/opal.R           |    4 
 opalr-1.2.0/opalr/man/dot-authorizationHeader.Rd         |only
 opalr-1.2.0/opalr/man/dot-opal.login.Rd                  |    3 
 opalr-1.2.0/opalr/man/dot-tokenHeader.Rd                 |only
 opalr-1.2.0/opalr/man/opal.login.Rd                      |   20 +++
 23 files changed, 140 insertions(+), 82 deletions(-)

More information about opalr at CRAN
Permanent link

Package MAINT.Data updated to version 2.3.0 with previous version 2.2.0 dated 2019-05-08

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 2.2.0 dated 2019-05-08 and 2.3.0 dated 2019-08-19

 MAINT.Data-2.2.0/MAINT.Data/R/Idtoutl_methods.R           |only
 MAINT.Data-2.3.0/MAINT.Data/CHANGELOG                     |    2 
 MAINT.Data-2.3.0/MAINT.Data/DESCRIPTION                   |   10 
 MAINT.Data-2.3.0/MAINT.Data/MD5                           |   83 ++--
 MAINT.Data-2.3.0/MAINT.Data/NAMESPACE                     |    8 
 MAINT.Data-2.3.0/MAINT.Data/R/CEMGauss.R                  |only
 MAINT.Data-2.3.0/MAINT.Data/R/CPMaxLik.R                  |    3 
 MAINT.Data-2.3.0/MAINT.Data/R/ClasGenMetDef.R             |   13 
 MAINT.Data-2.3.0/MAINT.Data/R/DACrossVal.R                |  206 +++++------
 MAINT.Data-2.3.0/MAINT.Data/R/IData.R                     |   60 +--
 MAINT.Data-2.3.0/MAINT.Data/R/IdtMaxLikSN.R               |    5 
 MAINT.Data-2.3.0/MAINT.Data/R/IdtMclust_methods.R         |  155 ++++++--
 MAINT.Data-2.3.0/MAINT.Data/R/IdtOutl_methods.R           |only
 MAINT.Data-2.3.0/MAINT.Data/R/Idtmclust.R                 |  252 +++++++-------
 MAINT.Data-2.3.0/MAINT.Data/R/RepEMGauss.R                |only
 MAINT.Data-2.3.0/MAINT.Data/R/RepLOptim.R                 |   18 -
 MAINT.Data-2.3.0/MAINT.Data/R/RestCPMaxLik.R              |    2 
 MAINT.Data-2.3.0/MAINT.Data/R/RobMxtDEst.R                |    1 
 MAINT.Data-2.3.0/MAINT.Data/R/Robldaqda.R                 |    2 
 MAINT.Data-2.3.0/MAINT.Data/R/fasttle.R                   |    1 
 MAINT.Data-2.3.0/MAINT.Data/R/fulltle.R                   |    1 
 MAINT.Data-2.3.0/MAINT.Data/R/lqda.R                      |   13 
 MAINT.Data-2.3.0/MAINT.Data/R/mle.R                       |   78 +++-
 MAINT.Data-2.3.0/MAINT.Data/R/mleVCOV.R                   |    2 
 MAINT.Data-2.3.0/MAINT.Data/R/q1Config.R                  |only
 MAINT.Data-2.3.0/MAINT.Data/R/sknda.R                     |    5 
 MAINT.Data-2.3.0/MAINT.Data/man/ConfTests-class.Rd        |    6 
 MAINT.Data-2.3.0/MAINT.Data/man/IData-class.Rd            |  152 ++++----
 MAINT.Data-2.3.0/MAINT.Data/man/IDtOutl-class.Rd          |  130 +++----
 MAINT.Data-2.3.0/MAINT.Data/man/IdtMANOVA-class.Rd        |    6 
 MAINT.Data-2.3.0/MAINT.Data/man/IdtOutl-methods.Rd        |    6 
 MAINT.Data-2.3.0/MAINT.Data/man/LRTest-class.Rd           |    6 
 MAINT.Data-2.3.0/MAINT.Data/man/MAINT.Data-package.Rd     |    4 
 MAINT.Data-2.3.0/MAINT.Data/man/MANOVAPermTest.Rd         |only
 MAINT.Data-2.3.0/MAINT.Data/man/RobEstControl-class.Rd    |    4 
 MAINT.Data-2.3.0/MAINT.Data/man/RobEstControl.Rd          |    4 
 MAINT.Data-2.3.0/MAINT.Data/man/fasttle-methods.Rd        |    4 
 MAINT.Data-2.3.0/MAINT.Data/man/fulltle-methods.Rd        |    4 
 MAINT.Data-2.3.0/MAINT.Data/man/getIdtOutl.Rd             |    2 
 MAINT.Data-2.3.0/MAINT.Data/man/pcoordplot-methos.Rd      |only
 MAINT.Data-2.3.0/MAINT.Data/man/plot-methods.Rd           |   80 ++--
 MAINT.Data-2.3.0/MAINT.Data/src/AuxTmplFoo.cpp            |   32 -
 MAINT.Data-2.3.0/MAINT.Data/src/CEMGauss.cpp              |only
 MAINT.Data-2.3.0/MAINT.Data/src/CEMGauss.h                |only
 MAINT.Data-2.3.0/MAINT.Data/src/EigenTmplFoo.cpp          |   88 ++++
 MAINT.Data-2.3.0/MAINT.Data/src/MDataGaussLogLik.cpp      |only
 MAINT.Data-2.3.0/MAINT.Data/src/MDataGaussLogLik.h        |only
 MAINT.Data-2.3.0/MAINT.Data/src/registerDynamicSimbol.cpp |    4 
 48 files changed, 858 insertions(+), 594 deletions(-)

More information about MAINT.Data at CRAN
Permanent link

Package gtsummary updated to version 1.2.0 with previous version 0.1.0 dated 2019-05-10

Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers. The package is enhanced when the 'gt' package is installed. Use this code to install: 'remotes::install_github("rstudio/gt")'.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>), Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>), Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>), Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>), Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>), Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>), Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

Diff between gtsummary versions 0.1.0 dated 2019-05-10 and 1.2.0 dated 2019-08-19

 gtsummary-0.1.0/gtsummary/R/add_comparison.R                                 |only
 gtsummary-0.1.0/gtsummary/R/add_global.R                                     |only
 gtsummary-0.1.0/gtsummary/R/as_tibble.R                                      |only
 gtsummary-0.1.0/gtsummary/R/bold_labels.R                                    |only
 gtsummary-0.1.0/gtsummary/R/bold_levels.R                                    |only
 gtsummary-0.1.0/gtsummary/R/fmt_beta.R                                       |only
 gtsummary-0.1.0/gtsummary/R/fmt_percent.R                                    |only
 gtsummary-0.1.0/gtsummary/R/fmt_pvalue.R                                     |only
 gtsummary-0.1.0/gtsummary/R/fmt_regression.R                                 |only
 gtsummary-0.1.0/gtsummary/R/fmt_table1.R                                     |only
 gtsummary-0.1.0/gtsummary/R/fmt_uni_regression.R                             |only
 gtsummary-0.1.0/gtsummary/R/indent_key.R                                     |only
 gtsummary-0.1.0/gtsummary/R/italicize_labels.R                               |only
 gtsummary-0.1.0/gtsummary/R/italicize_levels.R                               |only
 gtsummary-0.1.0/gtsummary/R/knit_print.R                                     |only
 gtsummary-0.1.0/gtsummary/R/row_to_name.R                                    |only
 gtsummary-0.1.0/gtsummary/R/utils-assign_class.R                             |only
 gtsummary-0.1.0/gtsummary/R/utils-assign_dichotomous_value.R                 |only
 gtsummary-0.1.0/gtsummary/R/utils-assign_stat_display.R                      |only
 gtsummary-0.1.0/gtsummary/R/utils-assign_summary_type.R                      |only
 gtsummary-0.1.0/gtsummary/R/utils-assign_test.R                              |only
 gtsummary-0.1.0/gtsummary/R/utils-assign_var_label.R                         |only
 gtsummary-0.1.0/gtsummary/R/utils-calculate_pvalue.R                         |only
 gtsummary-0.1.0/gtsummary/R/utils-calculate_summary_stat.R                   |only
 gtsummary-0.1.0/gtsummary/R/utils-continuous_digits_guess.R                  |only
 gtsummary-0.1.0/gtsummary/R/utils-create_header.R                            |only
 gtsummary-0.1.0/gtsummary/R/utils-fill_blanks.R                              |only
 gtsummary-0.1.0/gtsummary/R/utils-get_by_info.R                              |only
 gtsummary-0.1.0/gtsummary/R/utils-null-default.R                             |only
 gtsummary-0.1.0/gtsummary/R/utils-parse_terms.R                              |only
 gtsummary-0.1.0/gtsummary/R/utils-pipe.R                                     |only
 gtsummary-0.1.0/gtsummary/R/utils-summarize_categorical.R                    |only
 gtsummary-0.1.0/gtsummary/R/utils-summarize_continuous.R                     |only
 gtsummary-0.1.0/gtsummary/R/utils-table1_header.R                            |only
 gtsummary-0.1.0/gtsummary/R/utils-table1_input_checks.R                      |only
 gtsummary-0.1.0/gtsummary/R/utils-tee.R                                      |only
 gtsummary-0.1.0/gtsummary/R/utils-tidy_wrap.R                                |only
 gtsummary-0.1.0/gtsummary/inst/doc/fmt_regression.R                          |only
 gtsummary-0.1.0/gtsummary/inst/doc/fmt_regression.Rmd                        |only
 gtsummary-0.1.0/gtsummary/inst/doc/fmt_regression.html                       |only
 gtsummary-0.1.0/gtsummary/inst/doc/fmt_table1.R                              |only
 gtsummary-0.1.0/gtsummary/inst/doc/fmt_table1.Rmd                            |only
 gtsummary-0.1.0/gtsummary/inst/doc/fmt_table1.html                           |only
 gtsummary-0.1.0/gtsummary/man/add_comparison.Rd                              |only
 gtsummary-0.1.0/gtsummary/man/add_global.Rd                                  |only
 gtsummary-0.1.0/gtsummary/man/add_global.fmt_regression.Rd                   |only
 gtsummary-0.1.0/gtsummary/man/add_global.fmt_uni_regression.Rd               |only
 gtsummary-0.1.0/gtsummary/man/add_q.fmt_table1.Rd                            |only
 gtsummary-0.1.0/gtsummary/man/add_q.fmt_uni_regression.Rd                    |only
 gtsummary-0.1.0/gtsummary/man/as_data_frame.Rd                               |only
 gtsummary-0.1.0/gtsummary/man/as_tibble.Rd                                   |only
 gtsummary-0.1.0/gtsummary/man/as_tibble.fmt_regression.Rd                    |only
 gtsummary-0.1.0/gtsummary/man/as_tibble.fmt_table1.Rd                        |only
 gtsummary-0.1.0/gtsummary/man/as_tibble.fmt_uni_regression.Rd                |only
 gtsummary-0.1.0/gtsummary/man/assign_class.Rd                                |only
 gtsummary-0.1.0/gtsummary/man/assign_dichotomous_value.Rd                    |only
 gtsummary-0.1.0/gtsummary/man/assign_stat_display.Rd                         |only
 gtsummary-0.1.0/gtsummary/man/assign_summary_type.Rd                         |only
 gtsummary-0.1.0/gtsummary/man/assign_test.Rd                                 |only
 gtsummary-0.1.0/gtsummary/man/bold_labels.Rd                                 |only
 gtsummary-0.1.0/gtsummary/man/bold_labels.fmt_regression.Rd                  |only
 gtsummary-0.1.0/gtsummary/man/bold_labels.fmt_table1.Rd                      |only
 gtsummary-0.1.0/gtsummary/man/bold_labels.fmt_uni_regression.Rd              |only
 gtsummary-0.1.0/gtsummary/man/bold_levels.Rd                                 |only
 gtsummary-0.1.0/gtsummary/man/bold_levels.fmt_regression.Rd                  |only
 gtsummary-0.1.0/gtsummary/man/bold_levels.fmt_table1.Rd                      |only
 gtsummary-0.1.0/gtsummary/man/bold_levels.fmt_uni_regression.Rd              |only
 gtsummary-0.1.0/gtsummary/man/bold_p.fmt_regression.Rd                       |only
 gtsummary-0.1.0/gtsummary/man/bold_p.fmt_table1.Rd                           |only
 gtsummary-0.1.0/gtsummary/man/bold_p.fmt_uni_regression.Rd                   |only
 gtsummary-0.1.0/gtsummary/man/calculate_pvalue.Rd                            |only
 gtsummary-0.1.0/gtsummary/man/calculate_summary_stat.Rd                      |only
 gtsummary-0.1.0/gtsummary/man/continuous_digits_guess.Rd                     |only
 gtsummary-0.1.0/gtsummary/man/create_header.Rd                               |only
 gtsummary-0.1.0/gtsummary/man/fmt_beta.Rd                                    |only
 gtsummary-0.1.0/gtsummary/man/fmt_percent.Rd                                 |only
 gtsummary-0.1.0/gtsummary/man/fmt_pvalue.Rd                                  |only
 gtsummary-0.1.0/gtsummary/man/fmt_regression.Rd                              |only
 gtsummary-0.1.0/gtsummary/man/fmt_table1.Rd                                  |only
 gtsummary-0.1.0/gtsummary/man/fmt_table1_header.Rd                           |only
 gtsummary-0.1.0/gtsummary/man/fmt_uni_regression.Rd                          |only
 gtsummary-0.1.0/gtsummary/man/get_by_info.Rd                                 |only
 gtsummary-0.1.0/gtsummary/man/grapes-T-greater-than-grapes.Rd                |only
 gtsummary-0.1.0/gtsummary/man/indent_key.Rd                                  |only
 gtsummary-0.1.0/gtsummary/man/indent_key.fmt_regression.Rd                   |only
 gtsummary-0.1.0/gtsummary/man/indent_key.fmt_table1.Rd                       |only
 gtsummary-0.1.0/gtsummary/man/indent_key.fmt_uni_regression.Rd               |only
 gtsummary-0.1.0/gtsummary/man/inline_text.fmt_regression.Rd                  |only
 gtsummary-0.1.0/gtsummary/man/inline_text.fmt_table1.Rd                      |only
 gtsummary-0.1.0/gtsummary/man/italicize_labels.Rd                            |only
 gtsummary-0.1.0/gtsummary/man/italicize_labels.fmt_regression.Rd             |only
 gtsummary-0.1.0/gtsummary/man/italicize_labels.fmt_table1.Rd                 |only
 gtsummary-0.1.0/gtsummary/man/italicize_labels.fmt_uni_regression.Rd         |only
 gtsummary-0.1.0/gtsummary/man/italicize_levels.Rd                            |only
 gtsummary-0.1.0/gtsummary/man/italicize_levels.fmt_regression.Rd             |only
 gtsummary-0.1.0/gtsummary/man/italicize_levels.fmt_table1.Rd                 |only
 gtsummary-0.1.0/gtsummary/man/italicize_levels.fmt_uni_regression.Rd         |only
 gtsummary-0.1.0/gtsummary/man/knit_print.Rd                                  |only
 gtsummary-0.1.0/gtsummary/man/knit_print.fmt_regression.Rd                   |only
 gtsummary-0.1.0/gtsummary/man/knit_print.fmt_table1.Rd                       |only
 gtsummary-0.1.0/gtsummary/man/knit_print.fmt_uni_regression.Rd               |only
 gtsummary-0.1.0/gtsummary/man/modify_header.fmt_regression.Rd                |only
 gtsummary-0.1.0/gtsummary/man/modify_header.fmt_table1.Rd                    |only
 gtsummary-0.1.0/gtsummary/man/modify_header.fmt_uni_regression.Rd            |only
 gtsummary-0.1.0/gtsummary/man/null-default.Rd                                |only
 gtsummary-0.1.0/gtsummary/man/parse_terms.Rd                                 |only
 gtsummary-0.1.0/gtsummary/man/pipe.Rd                                        |only
 gtsummary-0.1.0/gtsummary/man/print.fmt_regression.Rd                        |only
 gtsummary-0.1.0/gtsummary/man/print.fmt_table1.Rd                            |only
 gtsummary-0.1.0/gtsummary/man/print.fmt_uni_regression.Rd                    |only
 gtsummary-0.1.0/gtsummary/man/row_to_name.Rd                                 |only
 gtsummary-0.1.0/gtsummary/man/summarize_categorical.Rd                       |only
 gtsummary-0.1.0/gtsummary/man/summarize_continuous.Rd                        |only
 gtsummary-0.1.0/gtsummary/man/tidy_wrap.Rd                                   |only
 gtsummary-0.1.0/gtsummary/tests/testthat/test-add_global.R                   |only
 gtsummary-0.1.0/gtsummary/tests/testthat/test-as_tibble.R                    |only
 gtsummary-0.1.0/gtsummary/tests/testthat/test-fmt_percent.R                  |only
 gtsummary-0.1.0/gtsummary/tests/testthat/test-fmt_pvalue.R                   |only
 gtsummary-0.1.0/gtsummary/tests/testthat/test-fmt_regression.R               |only
 gtsummary-0.1.0/gtsummary/tests/testthat/test-fmt_uni_regression.R           |only
 gtsummary-0.1.0/gtsummary/tests/testthat/test-indent_key.R                   |only
 gtsummary-0.1.0/gtsummary/tests/testthat/test-inline_text.table1.R           |only
 gtsummary-0.1.0/gtsummary/tests/testthat/test-table1.R                       |only
 gtsummary-0.1.0/gtsummary/vignettes/fmt_regression.Rmd                       |only
 gtsummary-0.1.0/gtsummary/vignettes/fmt_table1.Rmd                           |only
 gtsummary-1.2.0/gtsummary/DESCRIPTION                                        |   81 -
 gtsummary-1.2.0/gtsummary/MD5                                                |  334 +++--
 gtsummary-1.2.0/gtsummary/NAMESPACE                                          |  196 ++-
 gtsummary-1.2.0/gtsummary/NEWS.md                                            |   93 +
 gtsummary-1.2.0/gtsummary/R/add_global_p.R                                   |only
 gtsummary-1.2.0/gtsummary/R/add_n.R                                          |  143 +-
 gtsummary-1.2.0/gtsummary/R/add_nevent.R                                     |only
 gtsummary-1.2.0/gtsummary/R/add_overall.R                                    |  101 -
 gtsummary-1.2.0/gtsummary/R/add_p.R                                          |only
 gtsummary-1.2.0/gtsummary/R/add_q.R                                          |  251 +++-
 gtsummary-1.2.0/gtsummary/R/add_stat_label.R                                 |  121 --
 gtsummary-1.2.0/gtsummary/R/as_gt.R                                          |only
 gtsummary-1.2.0/gtsummary/R/as_kable.R                                       |only
 gtsummary-1.2.0/gtsummary/R/bold_italicise_labels_levels.R                   |only
 gtsummary-1.2.0/gtsummary/R/bold_p.R                                         |  263 ++--
 gtsummary-1.2.0/gtsummary/R/compat-lifecycle.R                               |only
 gtsummary-1.2.0/gtsummary/R/data.R                                           |    2 
 gtsummary-1.2.0/gtsummary/R/deprecated.R                                     |only
 gtsummary-1.2.0/gtsummary/R/gtsummary-package.R                              |   19 
 gtsummary-1.2.0/gtsummary/R/gtsummary_logo.R                                 |only
 gtsummary-1.2.0/gtsummary/R/inline_text.R                                    |  585 ++++++----
 gtsummary-1.2.0/gtsummary/R/modify_header.R                                  |  517 ++------
 gtsummary-1.2.0/gtsummary/R/print.R                                          |  180 ++-
 gtsummary-1.2.0/gtsummary/R/reexport.R                                       |only
 gtsummary-1.2.0/gtsummary/R/select_helpers.R                                 |only
 gtsummary-1.2.0/gtsummary/R/sort_p.R                                         |only
 gtsummary-1.2.0/gtsummary/R/style_percent.R                                  |only
 gtsummary-1.2.0/gtsummary/R/style_pvalue.R                                   |only
 gtsummary-1.2.0/gtsummary/R/style_ratio.R                                    |only
 gtsummary-1.2.0/gtsummary/R/style_sigfig.R                                   |only
 gtsummary-1.2.0/gtsummary/R/tbl_merge.R                                      |only
 gtsummary-1.2.0/gtsummary/R/tbl_regression.R                                 |only
 gtsummary-1.2.0/gtsummary/R/tbl_stack.R                                      |only
 gtsummary-1.2.0/gtsummary/R/tbl_summary.R                                    |only
 gtsummary-1.2.0/gtsummary/R/tbl_survival.R                                   |only
 gtsummary-1.2.0/gtsummary/R/tbl_uvregression.R                               |only
 gtsummary-1.2.0/gtsummary/R/tidyselect_to_list.R                             |only
 gtsummary-1.2.0/gtsummary/R/utils-add_p.R                                    |only
 gtsummary-1.2.0/gtsummary/R/utils-table_headers.R                            |only
 gtsummary-1.2.0/gtsummary/R/utils-tbl_regression.R                           |only
 gtsummary-1.2.0/gtsummary/R/utils-tbl_summary.R                              |only
 gtsummary-1.2.0/gtsummary/README.md                                          |  178 ++-
 gtsummary-1.2.0/gtsummary/build/vignette.rds                                 |binary
 gtsummary-1.2.0/gtsummary/data/trial.rda                                     |binary
 gtsummary-1.2.0/gtsummary/inst/WORDLIST                                      |only
 gtsummary-1.2.0/gtsummary/inst/doc/tbl_regression.R                          |only
 gtsummary-1.2.0/gtsummary/inst/doc/tbl_regression.Rmd                        |only
 gtsummary-1.2.0/gtsummary/inst/doc/tbl_regression.html                       |only
 gtsummary-1.2.0/gtsummary/inst/doc/tbl_summary.R                             |only
 gtsummary-1.2.0/gtsummary/inst/doc/tbl_summary.Rmd                           |only
 gtsummary-1.2.0/gtsummary/inst/doc/tbl_summary.html                          |only
 gtsummary-1.2.0/gtsummary/man/add_global_p.Rd                                |only
 gtsummary-1.2.0/gtsummary/man/add_global_p.tbl_regression.Rd                 |only
 gtsummary-1.2.0/gtsummary/man/add_global_p.tbl_uvregression.Rd               |only
 gtsummary-1.2.0/gtsummary/man/add_n.Rd                                       |   42 
 gtsummary-1.2.0/gtsummary/man/add_nevent.Rd                                  |only
 gtsummary-1.2.0/gtsummary/man/add_nevent.tbl_regression.Rd                   |only
 gtsummary-1.2.0/gtsummary/man/add_nevent.tbl_uvregression.Rd                 |only
 gtsummary-1.2.0/gtsummary/man/add_overall.Rd                                 |   41 
 gtsummary-1.2.0/gtsummary/man/add_p.Rd                                       |only
 gtsummary-1.2.0/gtsummary/man/add_q.Rd                                       |   15 
 gtsummary-1.2.0/gtsummary/man/add_q.tbl_summary.Rd                           |only
 gtsummary-1.2.0/gtsummary/man/add_q.tbl_uvregression.Rd                      |only
 gtsummary-1.2.0/gtsummary/man/add_stat_label.Rd                              |   43 
 gtsummary-1.2.0/gtsummary/man/as_gt.Rd                                       |only
 gtsummary-1.2.0/gtsummary/man/as_kable.Rd                                    |only
 gtsummary-1.2.0/gtsummary/man/assign_var_label.Rd                            |    5 
 gtsummary-1.2.0/gtsummary/man/bold_italicize_labels_levels.Rd                |only
 gtsummary-1.2.0/gtsummary/man/bold_p.Rd                                      |   17 
 gtsummary-1.2.0/gtsummary/man/bold_p.tbl_regression.Rd                       |only
 gtsummary-1.2.0/gtsummary/man/bold_p.tbl_stack.Rd                            |only
 gtsummary-1.2.0/gtsummary/man/bold_p.tbl_summary.Rd                          |only
 gtsummary-1.2.0/gtsummary/man/bold_p.tbl_uvregression.Rd                     |only
 gtsummary-1.2.0/gtsummary/man/deprecated.Rd                                  |only
 gtsummary-1.2.0/gtsummary/man/figures                                        |only
 gtsummary-1.2.0/gtsummary/man/gtsummary-package.Rd                           |   45 
 gtsummary-1.2.0/gtsummary/man/gtsummary_logo.Rd                              |only
 gtsummary-1.2.0/gtsummary/man/inline_text.Rd                                 |   17 
 gtsummary-1.2.0/gtsummary/man/inline_text.tbl_regression.Rd                  |only
 gtsummary-1.2.0/gtsummary/man/inline_text.tbl_summary.Rd                     |only
 gtsummary-1.2.0/gtsummary/man/inline_text.tbl_survival.Rd                    |only
 gtsummary-1.2.0/gtsummary/man/inline_text.tbl_uvregression.Rd                |only
 gtsummary-1.2.0/gtsummary/man/modify_header.Rd                               |  108 +
 gtsummary-1.2.0/gtsummary/man/print_gtsummary.Rd                             |only
 gtsummary-1.2.0/gtsummary/man/reexports.Rd                                   |only
 gtsummary-1.2.0/gtsummary/man/select_helpers.Rd                              |only
 gtsummary-1.2.0/gtsummary/man/sort_p.Rd                                      |only
 gtsummary-1.2.0/gtsummary/man/sort_p.tbl_regression.Rd                       |only
 gtsummary-1.2.0/gtsummary/man/sort_p.tbl_summary.Rd                          |only
 gtsummary-1.2.0/gtsummary/man/sort_p.tbl_uvregression.Rd                     |only
 gtsummary-1.2.0/gtsummary/man/style_percent.Rd                               |only
 gtsummary-1.2.0/gtsummary/man/style_pvalue.Rd                                |only
 gtsummary-1.2.0/gtsummary/man/style_ratio.Rd                                 |only
 gtsummary-1.2.0/gtsummary/man/style_sigfig.Rd                                |only
 gtsummary-1.2.0/gtsummary/man/tbl_merge.Rd                                   |only
 gtsummary-1.2.0/gtsummary/man/tbl_regression.Rd                              |only
 gtsummary-1.2.0/gtsummary/man/tbl_stack.Rd                                   |only
 gtsummary-1.2.0/gtsummary/man/tbl_summary.Rd                                 |only
 gtsummary-1.2.0/gtsummary/man/tbl_survival.Rd                                |only
 gtsummary-1.2.0/gtsummary/man/tbl_survival.survfit.Rd                        |only
 gtsummary-1.2.0/gtsummary/man/tbl_uvregression.Rd                            |only
 gtsummary-1.2.0/gtsummary/man/trial.Rd                                       |    2 
 gtsummary-1.2.0/gtsummary/tests/testthat/test-add_global_p.R                 |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-add_n.R                        |    9 
 gtsummary-1.2.0/gtsummary/tests/testthat/test-add_nevent.R                   |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-add_overall.R                  |   18 
 gtsummary-1.2.0/gtsummary/tests/testthat/test-add_p.R                        |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-add_p_test_safe.R              |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-add_q.R                        |   45 
 gtsummary-1.2.0/gtsummary/tests/testthat/test-add_stat_label.R               |   12 
 gtsummary-1.2.0/gtsummary/tests/testthat/test-as_gt.R                        |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-as_kable.R                     |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-assign_dichotomous_value-.R    |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-assign_dichotomous_value.R     |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-assign_summary_type.R          |    2 
 gtsummary-1.2.0/gtsummary/tests/testthat/test-bold_italicize_labels_levels.R |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-bold_p.R                       |   52 
 gtsummary-1.2.0/gtsummary/tests/testthat/test-continuous_digits_guess.R      |    2 
 gtsummary-1.2.0/gtsummary/tests/testthat/test-gtsummary_logo.R               |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-inline_text.R                  |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-modify_header.R                |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-select_helpers.R               |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-sort_p.R                       |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-style_percent.R                |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-style_pvalue.R                 |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-tbl_merge.R                    |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-tbl_regression.R               |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-tbl_stack.R                    |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-tbl_summary.R                  |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-tbl_summary_input_checks.R     |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-tbl_survival.R                 |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-tbl_uvregression.R             |only
 gtsummary-1.2.0/gtsummary/tests/testthat/test-utils-calculate_summary_stat.R |only
 gtsummary-1.2.0/gtsummary/vignettes/tbl_regression.Rmd                       |only
 gtsummary-1.2.0/gtsummary/vignettes/tbl_summary.Rmd                          |only
 260 files changed, 2097 insertions(+), 1442 deletions(-)

More information about gtsummary at CRAN
Permanent link

Package scam updated to version 1.2-5 with previous version 1.2-4 dated 2019-06-14

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 1.2-4 dated 2019-06-14 and 1.2-5 dated 2019-08-19

 ChangeLog           |    9 ++
 DESCRIPTION         |    8 +-
 MD5                 |   20 ++---
 R/bfgs.R            |  133 +------------------------------------
 R/estimate.scam.R   |  183 ++++++++++++++++++++++++++++++++++++++++++++++++++--
 R/print.scam.R      |    2 
 R/scam.check.R      |   12 ++-
 R/scam.r            |   15 +++-
 build/partial.rdb   |binary
 man/scam.Rd         |   13 +++
 man/scam.control.Rd |   10 ++
 11 files changed, 245 insertions(+), 160 deletions(-)

More information about scam at CRAN
Permanent link

Package jsmodule updated to version 1.0.0 with previous version 0.9.9 dated 2019-07-14

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 0.9.9 dated 2019-07-14 and 1.0.0 dated 2019-08-19

 DESCRIPTION                                                      |   11 
 MD5                                                              |   42 -
 NAMESPACE                                                        |    2 
 NEWS.md                                                          |   26 
 R/FilePsInput.R                                                  |  277 ++++++----
 R/FileRepeatedInput.R                                            |  155 ++++-
 R/FileSurveyInput.R                                              |  209 +++++--
 R/coxph.R                                                        |   86 +--
 R/csvFileInput.R                                                 |  166 ++++-
 R/gee.R                                                          |  112 ++--
 R/jsBasicGadget.R                                                |  181 ++++--
 R/jsPropensityGadget.R                                           |  257 ++++++---
 R/jsRepeatedGadget.R                                             |  189 +++++-
 R/jsSurveyGadget.R                                               |  245 ++++++--
 R/kaplan.R                                                       |  124 ++--
 R/regress.R                                                      |  165 +++--
 R/roc.R                                                          |  176 ++++--
 R/tb1.R                                                          |   26 
 R/timeroc.R                                                      |  133 +++-
 inst/doc/jsmodule.html                                           |   10 
 tests/testthat/shinytest/basic/app.R                             |    8 
 tests/testthat/shinytest/basic/tests/basicTest-expected/001.json |    1 
 22 files changed, 1808 insertions(+), 793 deletions(-)

More information about jsmodule at CRAN
Permanent link

Package ispd updated to version 0.2 with previous version 0.1 dated 2019-07-18

Title: Incomplete Split-Plot Designs
Description: A collection of several functions related to construction and analysis of incomplete split-plot designs. The package contains functions to obtain and analyze incomplete split-plot designs for three kinds of situations namely (i) when blocks are complete with respect to main plot treatments and main plots are incomplete with respect to subplot treatments, (ii) when blocks are incomplete with respect to main plot treatments and main plots are complete with respect to subplot treatments and (iii) when blocks are incomplete with respect to main plot treatments and main plots are incomplete with respect to subplot treatments.
Author: Baidya Nath Mandal [aut, cre], Sukanta Dash [aut], Rajender Parsad [aut]
Maintainer: Baidya Nath Mandal <mandal.stat@gmail.com>

Diff between ispd versions 0.1 dated 2019-07-18 and 0.2 dated 2019-08-19

 DESCRIPTION |    8 ++++----
 MD5         |    4 ++--
 R/ispd.R    |   30 +++++++++++++++---------------
 3 files changed, 21 insertions(+), 21 deletions(-)

More information about ispd at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.