Title: Parallel Model-Based Clustering using
Expectation-Gathering-Maximization Algorithm for Finite Mixture
Gaussian Model
Description: Aims to utilize model-based clustering (unsupervised)
for high dimensional and ultra large data, especially in a distributed
manner. The code employs 'pbdMPI' to perform a
expectation-gathering-maximization algorithm
for finite mixture Gaussian
models. The unstructured dispersion matrices are assumed in the
Gaussian models. The implementation is default in the single program
multiple data programming model. The code can be executed
through 'pbdMPI' and MPI' implementations such as 'OpenMPI'
and 'MPICH'.
See the High Performance Statistical Computing website
<https://snoweye.github.io/hpsc/>
for more information, documents and examples.
Author: Wei-Chen Chen [aut, cre],
George Ostrouchov [aut]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pmclust versions 0.1-9 dated 2016-12-19 and 0.2-0 dated 2018-02-01
ChangeLog | 3 +++ DESCRIPTION | 21 +++++++++++---------- MD5 | 25 +++++++++++++++---------- NAMESPACE | 1 + R/00_pmclust_reduceK.r |only R/00_pmclust_reduceK_dmat.r |only R/dmat_em_base.r | 34 ++++++++++++++++++++++++++-------- R/pm_aecm_base.r | 33 +++++++++++++++++++++++++-------- R/pm_apecm_base.r | 6 +++++- R/pm_apecma_base.r | 33 +++++++++++++++++++++++++-------- R/pm_em_base.r | 33 +++++++++++++++++++++++++-------- data/control.r | 3 ++- man/13_d.control.Rd | 1 + man/zz-internal.Rd |only src/zzz.c |only src/zzz.h |only 16 files changed, 139 insertions(+), 54 deletions(-)
Title: Programming with Big Data -- Remote Procedure Call
Description: A very light implementation yet secure for remote procedure calls
with unified interface via ssh (OpenSSH) or plink/plink.exe (PuTTY).
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdRPC versions 0.1-1 dated 2017-01-01 and 0.2-0 dated 2018-02-01
ChangeLog | 17 ++ DESCRIPTION | 19 +- MD5 | 79 ++++++----- NAMESPACE | 10 + R/111_control.r | 25 ++- R/machine.r |only R/pbdRPC-package.r | 4 R/rpc.r | 111 ++------------- R/rpc_cs_example.r | 96 ++++--------- R/rpc_options.r | 4 R/rpc_pid.r |only R/rpc_rr_example.r | 141 +++++++++++--------- R/srpc.r |only R/ssh_plink.r | 9 + R/tunnel.r |only R/utils.r |only README.md | 49 +++++- TODO | 2 inst/CITATION | 10 - inst/doc/pbdRPC-guide.Rnw | 1 inst/doc/pbdRPC-guide.pdf |binary man/a0_b_control.Rd | 9 - man/a0_c_options.Rd | 9 - man/find_plink.Rd | 1 man/machine.Rd |only man/pbdRPC-package.Rd | 7 man/print-machine.Rd |only man/rpc.Rd | 52 ------- man/rpc_cs_example.Rd | 61 ++------ man/rpc_options.Rd | 7 man/rpc_pid.Rd |only man/rpc_rr_example.Rd | 68 ++++----- man/srpc.Rd |only man/ssh_plink.Rd | 7 man/tunnel.Rd |only man/zz_rpc_control.Rd | 26 ++- vignettes/pbdRPC-guide.Rnw | 1 vignettes/pbdRPC-include/02-introduction.tex | 31 ++-- vignettes/pbdRPC-include/03-login_information.tex | 14 - vignettes/pbdRPC-include/04-application_rr.tex | 17 +- vignettes/pbdRPC-include/05-application_cs.tex | 17 +- vignettes/pbdRPC-include/06-port_forwarding.tex | 99 ++++++++++++-- vignettes/pbdRPC-include/07-advance_pbdmpi.tex | 14 - vignettes/pbdRPC-include/08-machine_information.tex |only vignettes/pbdRPC-include/99-faq.tex | 13 - vignettes/pbdRPC-include/pbdRPC.bib | 2 46 files changed, 525 insertions(+), 507 deletions(-)
Title: Internet Memes for Data Analysts
Description: Generates internet memes that optionally include a superimposed inset plot and other atypical features,
combining the visual impact of an attention-grabbing meme with graphic results of data analysis.
The package differs from related packages that focus on imitating and reproducing standard memes.
Some packages do this by interfacing with online meme generators whereas others achieve this natively.
This package takes the latter approach. It does not interface with online meme generators or require any authentication with external websites.
It reads images directly from local files or via URL and meme generation is done by the package.
While this is similar to the 'meme' package available on CRAN, it differs in that the focus is on
allowing for non-standard meme layouts and hybrids of memes mixed with graphs.
While this package can be used to make basic memes like an online meme generator would produce,
it caters primarily to hybrid graph-meme plots where the meme presentation can be seen as a backdrop highlighting
foreground graphs of data analysis results.
The package also provides support for an arbitrary number of meme text labels with arbitrary size, position and other attributes
rather than restricting to the standard top and/or bottom text placement.
This is useful for proper aesthetic interleaving of plots of data between meme image backgrounds and overlain text labels.
The package offers a selection of templates for graph placement and appearance with respect to the underlying meme.
Graph templates also permit additional template-specific customization.
Animated gif support is provided but this is optional and functional only if the 'magick' package is installed.
'magick' is not required unless gif functionality is desired.
Author: Matthew Leonawicz [aut, cre]
Maintainer: Matthew Leonawicz <mfleonawicz@alaska.edu>
Diff between memery versions 0.3.1 dated 2017-11-14 and 0.4.0 dated 2018-02-01
DESCRIPTION | 12 ++--- MD5 | 33 +++++++------ NAMESPACE | 2 NEWS.md | 14 +++++ R/inset.R | 6 -- R/meme.R | 108 ++++++++++++++++++++++++++++++++++++++++----- R/memery.R | 36 +++++++++++++++ build/vignette.rds |binary inst/doc/memery.R | 20 +++++++- inst/doc/memery.Rmd | 61 +++++++++++++++++++++---- inst/doc/memery.html | 46 +++++++++++++++---- inst/shiny |only man/inset.Rd | 8 ++- man/meme.Rd | 60 ++++++++++++++++++++++--- man/memeApp.Rd |only man/memery.Rd | 2 tests/testthat/test-meme.R | 24 ++++++++++ vignettes/memery.Rmd | 61 +++++++++++++++++++++---- 18 files changed, 417 insertions(+), 76 deletions(-)
Title: Feature Selection Algorithms for Computer Aided Diagnosis
Description: Contains a set of utilities for building and testing formula-based models (linear, logistic or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization.
Author: Jose Gerardo Tamez-Pena, Antonio Martinez-Torteya and Israel Alanis
Maintainer: Jose Gerardo Tamez-Pena <jose.tamezpena@itesm.mx>
Diff between FRESA.CAD versions 3.0.0 dated 2018-02-01 and 3.0.1 dated 2018-02-01
FRESA.CAD-3.0.0/FRESA.CAD/src/outcheck.txt |only FRESA.CAD-3.0.1/FRESA.CAD/DESCRIPTION | 8 ++++---- FRESA.CAD-3.0.1/FRESA.CAD/MD5 | 11 +++++------ FRESA.CAD-3.0.1/FRESA.CAD/NAMESPACE | 2 +- FRESA.CAD-3.0.1/FRESA.CAD/NEWS | 4 ++++ FRESA.CAD-3.0.1/FRESA.CAD/man/FRESA.CAD-package.Rd | 4 ++-- FRESA.CAD-3.0.1/FRESA.CAD/src/FRESACAD_init.cpp | 5 +++++ 7 files changed, 21 insertions(+), 13 deletions(-)
Title: Toolbox for Connectivity Informatics Technology Initiative
('CIFTI') Files
Description: Functions for the input/output and visualization of
medical imaging data in the form of 'CIFTI' files
<https://www.nitrc.org/projects/cifti/>.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between cifti versions 0.4.2 dated 2017-05-05 and 0.4.5 dated 2018-02-01
DESCRIPTION | 16 ++++++++++------ MD5 | 30 ++++++++++++++++++++---------- NAMESPACE | 3 +++ NEWS.md |only R/aaa_utils.R |only R/get_cifti_type.R | 24 ++++++++++++++++++++++++ R/nifti_2_hdr.R | 3 ++- R/parse_parcel.R | 7 +++++-- R/read_cifti.R | 17 +++++++++++++---- README.md | 18 +++++++++++++++++- build |only inst |only man/get_cifti_type.Rd | 4 ++++ man/nifti_2_hdr.Rd | 3 ++- man/read_cifti.Rd | 5 +++-- vignettes |only 16 files changed, 103 insertions(+), 27 deletions(-)
Title: Default Color Maps from 'matplotlib' (Lite Version)
Description: Implementation of the 'viridis' - the default -, 'magma', 'plasma',
'inferno', and 'cividis' color maps for 'R'. 'viridis', 'magma', 'plasma',
and 'inferno' are ported from 'matplotlib' <http://matplotlib.org/>, a
popular plotting library for 'python'. 'cividis', was developed by Jamie R.
Nuñez and Sean M. Colby. These color maps are designed in such a way that
they will analytically be perfectly perceptually-uniform, both in regular
form and also when converted to black-and-white. They are also designed to
be perceived by readers with the most common form of color blindness (all
color maps in this package) and color vision deficiency ('cividis' only).
This is the 'lite' version of the more complete 'viridis' package that can
be found at <https://cran.r-project.org/package=viridis>.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph],
Bob Rudis [ctb, cph],
Marco Sciaini [ctb, cph],
Cédric Scherer [ctb, cph]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridisLite versions 0.2.0 dated 2017-03-24 and 0.3.0 dated 2018-02-01
viridisLite-0.2.0/viridisLite/README.md |only viridisLite-0.3.0/viridisLite/DESCRIPTION | 33 +++++--- viridisLite-0.3.0/viridisLite/MD5 | 17 ++-- viridisLite-0.3.0/viridisLite/NAMESPACE | 1 viridisLite-0.3.0/viridisLite/R/viridis.R | 41 ++++++++--- viridisLite-0.3.0/viridisLite/data/viridis.map.rda |binary viridisLite-0.3.0/viridisLite/man/figures/viridis-scales.png |binary viridisLite-0.3.0/viridisLite/man/viridis.Rd | 23 ++++-- viridisLite-0.3.0/viridisLite/man/viridis.map.Rd | 12 ++- viridisLite-0.3.0/viridisLite/tests/testthat/test-palettes.R | 13 ++- 10 files changed, 96 insertions(+), 44 deletions(-)
Title: Implementation of the Hydrological Model TOPMODEL in R
Description: Set of hydrological functions including an R
implementation of the hydrological model TOPMODEL, which is
based on the 1995 FORTRAN version by Keith Beven. From version
0.7.0, the package is put into maintenance mode.
Author: Wouter Buytaert
Maintainer: Wouter Buytaert <w.buytaert@imperial.ac.uk>
Diff between topmodel versions 0.7.2-2 dated 2011-01-11 and 0.7.3 dated 2018-02-01
topmodel-0.7.2-2/topmodel/doc |only topmodel-0.7.2-2/topmodel/src/flowlength.c |only topmodel-0.7.2-2/topmodel/src/infiltration.c |only topmodel-0.7.2-2/topmodel/src/sinkfill.c |only topmodel-0.7.2-2/topmodel/src/streamorder.c |only topmodel-0.7.2-2/topmodel/src/subcatch.c |only topmodel-0.7.2-2/topmodel/src/topidx.c |only topmodel-0.7.2-2/topmodel/src/topmodel.c |only topmodel-0.7.3/topmodel/DESCRIPTION | 20 +++++++++----------- topmodel-0.7.3/topmodel/MD5 |only topmodel-0.7.3/topmodel/NAMESPACE | 4 +++- topmodel-0.7.3/topmodel/R/flowlength.R | 2 +- topmodel-0.7.3/topmodel/R/infiltration.R | 2 +- topmodel-0.7.3/topmodel/R/sinkfill.R | 2 +- topmodel-0.7.3/topmodel/R/streamorder.R | 2 +- topmodel-0.7.3/topmodel/R/subcatch.R | 2 +- topmodel-0.7.3/topmodel/R/topidx.R | 2 +- topmodel-0.7.3/topmodel/R/topmodel.R | 6 +++--- topmodel-0.7.3/topmodel/data/huagrahuma.RData |binary topmodel-0.7.3/topmodel/man/flowlength.Rd | 2 +- topmodel-0.7.3/topmodel/man/huagrahuma.Rd | 4 ++-- topmodel-0.7.3/topmodel/man/infiltration.Rd | 2 +- topmodel-0.7.3/topmodel/man/outlet.Rd | 2 +- topmodel-0.7.3/topmodel/man/river.Rd | 2 +- topmodel-0.7.3/topmodel/man/sinkfill.Rd | 2 +- topmodel-0.7.3/topmodel/man/subcatch.Rd | 2 +- topmodel-0.7.3/topmodel/man/topidx.Rd | 2 +- topmodel-0.7.3/topmodel/man/topmodel.Rd | 12 ++++++------ topmodel-0.7.3/topmodel/src/c_flowlength.c |only topmodel-0.7.3/topmodel/src/c_infiltration.c |only topmodel-0.7.3/topmodel/src/c_sinkfill.c |only topmodel-0.7.3/topmodel/src/c_streamorder.c |only topmodel-0.7.3/topmodel/src/c_subcatch.c |only topmodel-0.7.3/topmodel/src/c_topidx.c |only topmodel-0.7.3/topmodel/src/c_topmodel.c |only topmodel-0.7.3/topmodel/src/core_topmodel.c | 6 +++--- topmodel-0.7.3/topmodel/src/river.c | 4 ++-- topmodel-0.7.3/topmodel/src/topmodel_init.c |only 38 files changed, 41 insertions(+), 41 deletions(-)
Title: Additional Tools for Developing Spatially Explicit Discrete
Event Simulation (SpaDES) Models
Description: Provides GIS and map utilities, plus additional modeling tools for
developing cellular automata, dynamic raster models,
and agent based models in 'SpaDES'.
Included are various methods for spatial spreading, spatial agents, GIS
operations, random map generation, and others.
See '?SpaDES.tools' for an categorized overview of these additional tools.
Author: Alex M Chubaty [aut, cre],
Eliot J B McIntire [aut],
Yong Luo [ctb],
Steve Cumming [ctb],
Jean Marchal [ctb],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alexander.chubaty@canada.ca>
Diff between SpaDES.tools versions 0.1.0 dated 2017-08-12 and 0.1.1 dated 2018-02-01
.aspell/defaults.R | 12 DESCRIPTION | 45 MD5 | 153 - NAMESPACE | 269 +- NEWS.md | 18 R/RcppExports.R | 140 - R/SELES.R | 590 +++--- R/distanceFromEachPoint.R | 820 ++++---- R/downloadInputs.R |only R/environment.R | 14 R/gis.R |only R/heading.R | 174 - R/initialize.R | 763 ++++--- R/mapReduce.R | 148 - R/mergeRaster.R | 134 - R/movement.R | 252 +- R/neighbourhood.R | 2140 +++++++++++----------- R/numerical-comparisons.R | 74 R/resample.R | 72 R/rings.R | 186 - R/spades-tools-package.R | 218 +- R/splitRaster.R | 232 +- R/spread.R | 2324 +++++++++++------------ R/spread2.R | 2102 +++++++++++---------- R/zzz.R | 42 README.md | 97 - inst/examples/example_cir.R | 174 - inst/examples/example_distanceFromEachPoint.R | 100 - inst/examples/example_mapReduce.R | 44 inst/examples/example_rings.R | 76 inst/examples/example_splitRaster.R | 118 - inst/examples/example_spokes.R | 74 inst/examples/example_spread.R | 552 ++--- inst/examples/example_spread2.R | 254 +- man/SELESagentLocation.Rd | 54 man/SELESnumAgents.Rd | 56 man/SELESprobInit.Rd | 86 man/SELEStransitions.Rd | 58 man/SpaDES.tools-package.Rd | 269 +- man/adj.Rd | 248 +- man/cir.Rd | 404 +--- man/cirSpecialQuick.Rd |only man/crw.Rd | 162 - man/directions.Rd | 178 - man/distances.Rd | 390 ++-- man/duplicated.Rd | 36 man/extractFromArchive.Rd |only man/fastCrop.Rd |only man/fastMask.Rd |only man/findFactors.Rd | 38 man/gaussmap.Rd | 98 - man/heading.Rd | 126 - man/inRange.Rd | 62 man/initiateAgents.Rd | 174 - man/match.Rd | 36 man/matchedPointDirection.Rd | 26 man/patchSize.Rd | 28 man/pkgEnv.Rd | 28 man/prepInputs.Rd |only man/randomPolygons.Rd | 124 - man/rasterizeReduce.Rd | 128 - man/rcpp-extras.Rd | 34 man/resample.Rd | 64 man/rings.Rd | 234 +- man/sampleV.Rd | 60 man/specnumperpatch-probs.Rd | 130 - man/splitRaster.Rd | 284 +- man/spokes.Rd | 260 +- man/spread.Rd | 1262 ++++++------- man/spread2-internals.Rd | 96 man/spread2.Rd | 891 ++++----- man/wrap.Rd | 186 - tests/test-all.R | 4 tests/testthat/test-adj.R | 322 +-- tests/testthat/test-examples.R | 22 tests/testthat/test-gis.R |only tests/testthat/test-inRange.R | 48 tests/testthat/test-mapReduce.R | 206 +- tests/testthat/test-randomPolygon.R |only tests/testthat/test-spelling.R | 58 tests/testthat/test-splitRaster.R | 536 ++--- tests/testthat/test-spread.R | 2519 +++++++++++++------------- tests/testthat/test-spread2.R | 1769 +++++++++--------- 83 files changed, 12208 insertions(+), 11997 deletions(-)
Title: The Official SolveBio API Client
Description: R language bindings for SolveBio's API.
SolveBio is a biomedical knowledge hub that enables life science
organizations to collect and harmonize the complex, disparate
"multi-omic" data essential for today's R&D and BI needs.
For more information, visit <https://www.solvebio.com>.
Author: David Caplan
Maintainer: David Caplan <dcaplan@solvebio.com>
Diff between solvebio versions 2.3.0 dated 2018-01-08 and 2.3.1 dated 2018-02-01
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/dataset.R | 37 ++++++++++++------------------------- R/object.R | 11 ----------- R/utils.R | 43 +++++++++++++++++++++++++------------------ R/vault.R | 35 +++++++++++++++-------------------- 7 files changed, 68 insertions(+), 84 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that
the user is probably willing to make: 'import()' and 'export()' determine
the data structure from the file extension, reasonable defaults are used for
data import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is
natively supported (including from SSL/HTTPS), compressed files can be read
directly without explicit decompression, and fast import packages are used where
appropriate. An additional convenience function, 'convert()', provides a simple
method for converting between file types.
Author: Jason Becker [ctb],
Chung-hong Chan [aut],
Geoffrey CH Chan [ctb],
Thomas J. Leeper [aut, cre] (<https://orcid.org/0000-0003-4097-6326>),
Christopher Gandrud [ctb],
Andrew MacDonald [ctb],
Ista Zahn [ctb],
Stanislaus Stadlmann [ctb],
Ruaridh Williamson [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between rio versions 0.5.5 dated 2017-06-18 and 0.5.9 dated 2018-02-01
rio |only 1 file changed
Title: 'Neuroconductor' Base Package with Helper Functions for 'nifti'
Objects
Description: Base package for 'Neuroconductor', which includes many helper
functions that interact with objects of class 'nifti', implemented by
package 'oro.nifti', for reading/writing and also other manipulation
functions.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between neurobase versions 1.13.2 dated 2017-03-03 and 1.26.1 dated 2018-02-01
neurobase-1.13.2/neurobase/man/applyEmptyImageDimensions.Rd |only neurobase-1.13.2/neurobase/man/maskEmptyImageDimensions.Rd |only neurobase-1.13.2/neurobase/vignettes/nifti_basics_cache |only neurobase-1.13.2/neurobase/vignettes/nifti_basics_files |only neurobase-1.26.1/neurobase/DESCRIPTION | 33 neurobase-1.26.1/neurobase/MD5 | 164 +- neurobase-1.26.1/neurobase/NAMESPACE | 52 neurobase-1.26.1/neurobase/R/applyEmptyImageDimensions.R | 152 + neurobase-1.26.1/neurobase/R/breaker.R | 2 neurobase-1.26.1/neurobase/R/check_nifti.R | 161 +- neurobase-1.26.1/neurobase/R/check_nifti_header.R |only neurobase-1.26.1/neurobase/R/checkimg.R | 2 neurobase-1.26.1/neurobase/R/cog.R | 2 neurobase-1.26.1/neurobase/R/cut.R |only neurobase-1.26.1/neurobase/R/dicer.R |only neurobase-1.26.1/neurobase/R/dropEmptyImageDimensions.R | 77 neurobase-1.26.1/neurobase/R/emptyImageDimensionsMask.R |only neurobase-1.26.1/neurobase/R/ensure_array.R |only neurobase-1.26.1/neurobase/R/finite_img.R | 2 neurobase-1.26.1/neurobase/R/flip_img.R |only neurobase-1.26.1/neurobase/R/getEmptyImageDimensions.R | 7 neurobase-1.26.1/neurobase/R/img_color_df.R |only neurobase-1.26.1/neurobase/R/img_indices.R | 2 neurobase-1.26.1/neurobase/R/img_ts_to_list.R |only neurobase-1.26.1/neurobase/R/maskEmptyImageDimensions.R | 203 ++ neurobase-1.26.1/neurobase/R/mask_img.R | 52 neurobase-1.26.1/neurobase/R/mask_vals.R | 2 neurobase-1.26.1/neurobase/R/minmax_img.R |only neurobase-1.26.1/neurobase/R/nii.stub.R | 4 neurobase-1.26.1/neurobase/R/ortho2.R | 83 - neurobase-1.26.1/neurobase/R/overlay2.R | 19 neurobase-1.26.1/neurobase/R/parse_img_ext.R | 12 neurobase-1.26.1/neurobase/R/quantile.nifti.R | 2 neurobase-1.26.1/neurobase/R/quantile_img.R | 2 neurobase-1.26.1/neurobase/R/readNIfTI2.R | 17 neurobase-1.26.1/neurobase/R/remap_filename.R | 14 neurobase-1.26.1/neurobase/R/replace_dropped_dimensions.R | 2 neurobase-1.26.1/neurobase/R/rescale_img.R | 158 -- neurobase-1.26.1/neurobase/R/separate_img.R |only neurobase-1.26.1/neurobase/R/slice_colour_df.R |only neurobase-1.26.1/neurobase/R/subset_dti.R |only neurobase-1.26.1/neurobase/R/window_img.R | 117 + neurobase-1.26.1/neurobase/R/write_nifti.R |only neurobase-1.26.1/neurobase/R/writenii.R | 14 neurobase-1.26.1/neurobase/R/zlimmer.R | 12 neurobase-1.26.1/neurobase/R/zscore_img.R |only neurobase-1.26.1/neurobase/build/vignette.rds |binary neurobase-1.26.1/neurobase/inst/doc/neurobase.html | 654 +++++--- neurobase-1.26.1/neurobase/inst/doc/nifti_basics.R | 7 neurobase-1.26.1/neurobase/inst/doc/nifti_basics.Rmd | 2 neurobase-1.26.1/neurobase/inst/doc/nifti_basics.html | 779 ++++++---- neurobase-1.26.1/neurobase/man/applyEmptyImageDimensions-methods.Rd |only neurobase-1.26.1/neurobase/man/breaker.Rd | 2 neurobase-1.26.1/neurobase/man/check_nifti-methods.Rd | 21 neurobase-1.26.1/neurobase/man/check_nifti_header-methods.Rd |only neurobase-1.26.1/neurobase/man/colorbar.Rd | 2 neurobase-1.26.1/neurobase/man/cut.nifti.Rd |only neurobase-1.26.1/neurobase/man/dicer.Rd |only neurobase-1.26.1/neurobase/man/emptyImageDimensionsMask.Rd |only neurobase-1.26.1/neurobase/man/ensure_array.Rd |only neurobase-1.26.1/neurobase/man/flip_img.Rd |only neurobase-1.26.1/neurobase/man/img_colour_df.Rd |only neurobase-1.26.1/neurobase/man/img_indices.Rd | 2 neurobase-1.26.1/neurobase/man/img_list_to_ts.Rd |only neurobase-1.26.1/neurobase/man/img_ts_to_df.Rd |only neurobase-1.26.1/neurobase/man/img_ts_to_list.Rd |only neurobase-1.26.1/neurobase/man/img_ts_to_matrix.Rd |only neurobase-1.26.1/neurobase/man/maskEmptyImageDimensions-methods.Rd |only neurobase-1.26.1/neurobase/man/mask_img.Rd | 4 neurobase-1.26.1/neurobase/man/mask_vals-methods.Rd | 2 neurobase-1.26.1/neurobase/man/minmax_img-methods.Rd |only neurobase-1.26.1/neurobase/man/multi_overlay.Rd | 8 neurobase-1.26.1/neurobase/man/nii.stub.Rd | 5 neurobase-1.26.1/neurobase/man/ortho2.Rd | 23 neurobase-1.26.1/neurobase/man/quantile.nifti.Rd | 2 neurobase-1.26.1/neurobase/man/quantile_img.Rd | 2 neurobase-1.26.1/neurobase/man/readNIfTI2.Rd | 7 neurobase-1.26.1/neurobase/man/remap_filename.Rd | 8 neurobase-1.26.1/neurobase/man/replace_dropped_dimensions.Rd | 2 neurobase-1.26.1/neurobase/man/separate_img-methods.Rd |only neurobase-1.26.1/neurobase/man/slice_colour_df.Rd |only neurobase-1.26.1/neurobase/man/subset_dti-methods.Rd |only neurobase-1.26.1/neurobase/man/window_img.Rd | 23 neurobase-1.26.1/neurobase/man/writeNIfTI2.Rd | 9 neurobase-1.26.1/neurobase/man/write_nifti.Rd |only neurobase-1.26.1/neurobase/man/xyz.Rd | 2 neurobase-1.26.1/neurobase/man/zlimmer.Rd | 5 neurobase-1.26.1/neurobase/man/zscore_img.Rd | 24 neurobase-1.26.1/neurobase/vignettes/nifti_basics.Rmd | 2 89 files changed, 1883 insertions(+), 1083 deletions(-)
Title: An Interface for MATLAB using System Calls
Description: Provides users to call MATLAB from using the "system" command.
Allows users to submit lines of code or MATLAB m files.
This is in comparison to 'R.matlab', which creates a MATLAB server.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between matlabr versions 1.4.3 dated 2017-10-11 and 1.5.0 dated 2018-02-01
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/matlab_script.R | 16 +++++++++++++--- man/get_matlab.Rd | 5 ++++- man/run_matlab_script.Rd | 5 ++++- 6 files changed, 34 insertions(+), 14 deletions(-)
Title: Example T1 Structural Data from the Multi-Modal MRI
'Reproducibility' Resource
Description: Structural T1 magnetic resonance imaging ('MRI') data from the
'Kirby21' 'reproducibility' study
<doi:10.1016/j.neuroimage.2010.11.047>.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between kirby21.t1 versions 1.5.1 dated 2017-03-02 and 1.6.0 dated 2018-02-01
DESCRIPTION | 17 +++++++++-------- MD5 | 7 ++++--- NEWS.md |only R/get_t1_filenames.R | 2 +- man/get_t1_filenames.Rd | 2 +- 5 files changed, 15 insertions(+), 13 deletions(-)
Title: Interactive Cluster Heat Maps Using 'plotly'
Description: Create interactive cluster 'heatmaps' that can be saved as a stand-
alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and
available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to
show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical
method for visualizing high-dimensional data, in which a table of numbers
are encoded as a grid of colored cells. The rows and columns of the matrix
are ordered to highlight patterns and are often accompanied by 'dendrograms'.
'Heatmaps' are used in many fields for visualizing observations, correlations,
missing values patterns, and more. Interactive 'heatmaps' allow the inspection
of specific value by hovering the mouse over a cell, as well as zooming into
a region of the 'heatmap' by dragging a rectangle around the relevant area.
This work is based on the 'ggplot2' and 'plotly.js' engine. It produces
similar 'heatmaps' as 'heatmap.2' or 'd3heatmap', with the advantage of speed
('plotly.js' is able to handle larger size matrix), the ability to zoom from
the 'dendrogram' panes, and the placing of factor variables in the sides of the
'heatmap'.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Jonathan Sidi [ctb] (https://github.com/yonicd),
Alan O'Callaghan [ctb] (https://github.com/Alanocallaghan),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between heatmaply versions 0.14.0 dated 2018-01-20 and 0.14.1 dated 2018-02-01
ChangeLog | 36 ++++++++++++++++++++++-- DESCRIPTION | 8 ++--- MD5 | 20 ++++++------- NEWS | 10 ++++++ NEWS.md | 10 ++++++ R/heatmaply.R | 6 ---- R/heatmapr.R | 10 +++++- R/plots.R | 17 +++++------ inst/doc/heatmaply.html | 70 ++++++++++++++++++++++++------------------------ man/heatmaply.Rd | 2 - man/heatmapr.Rd | 5 ++- 11 files changed, 123 insertions(+), 71 deletions(-)
Title: Accesses Google Maps APIs to Retrieve Data and Plot Maps
Description: Provides a mechanism to plot a Google Map from R and overlay
it with shapes and markers. Also provides access to Google Maps APIs,
including places, directions, roads, distances, geocoding, elevation and
timezone.
Author: David Cooley [aut, cre],
Paulo Barcelos [ctb] (Author of c++ decode_pl),
Rstudio [ctb] (Functions written for the Leaflet pacakge)
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between googleway versions 2.2.0 dated 2017-06-25 and 2.4.0 dated 2018-02-01
googleway-2.2.0/googleway/R/get_route.R |only googleway-2.2.0/googleway/R/methods_polyline.R |only googleway-2.2.0/googleway/man/get_route.Rd |only googleway-2.2.0/googleway/src/googleway_init.c |only googleway-2.2.0/googleway/src/polyline_encode.cpp |only googleway-2.2.0/googleway/tests/testthat/test-get_route.R |only googleway-2.2.0/googleway/vignettes/img/melbourne_polygons.png |only googleway-2.2.0/googleway/vignettes/img/melbourne_to_sydney.png |only googleway-2.2.0/googleway/vignettes/img/nearest_roads.png |only googleway-2.2.0/googleway/vignettes/img/snap_to_roads.png |only googleway-2.4.0/googleway/DESCRIPTION | 15 googleway-2.4.0/googleway/MD5 | 290 - googleway-2.4.0/googleway/NAMESPACE | 112 googleway-2.4.0/googleway/R/RcppExports.R | 6 googleway-2.4.0/googleway/R/colours.R |only googleway-2.4.0/googleway/R/data.R | 9 googleway-2.4.0/googleway/R/google_directions.R | 105 googleway-2.4.0/googleway/R/google_distance.R | 63 googleway-2.4.0/googleway/R/google_elevation.R | 16 googleway-2.4.0/googleway/R/google_geocode.R | 57 googleway-2.4.0/googleway/R/google_keys.R |only googleway-2.4.0/googleway/R/google_map.R | 154 googleway-2.4.0/googleway/R/google_map_layer_circle.R |only googleway-2.4.0/googleway/R/google_map_layer_drawing.R |only googleway-2.4.0/googleway/R/google_map_layer_fusion.R |only googleway-2.4.0/googleway/R/google_map_layer_geojson.R |only googleway-2.4.0/googleway/R/google_map_layer_heatmap.R |only googleway-2.4.0/googleway/R/google_map_layer_kml.R |only googleway-2.4.0/googleway/R/google_map_layer_marker.R |only googleway-2.4.0/googleway/R/google_map_layer_methods.R |only googleway-2.4.0/googleway/R/google_map_layer_overlay.R |only googleway-2.4.0/googleway/R/google_map_layer_parameters.R |only googleway-2.4.0/googleway/R/google_map_layer_polygon.R |only googleway-2.4.0/googleway/R/google_map_layer_polyline.R |only googleway-2.4.0/googleway/R/google_map_layer_rectangle.R |only googleway-2.4.0/googleway/R/google_map_layer_sf.R |only googleway-2.4.0/googleway/R/google_map_layers.R | 1817 --------- googleway-2.4.0/googleway/R/google_map_shape_constructors.R |only googleway-2.4.0/googleway/R/google_map_urls.R |only googleway-2.4.0/googleway/R/google_place_autocomplete.R | 55 googleway-2.4.0/googleway/R/google_place_details.R | 20 googleway-2.4.0/googleway/R/google_places.R | 142 googleway-2.4.0/googleway/R/google_reverse_geocode.R | 58 googleway-2.4.0/googleway/R/google_roads.R | 36 googleway-2.4.0/googleway/R/google_streetview.R | 39 googleway-2.4.0/googleway/R/google_timezone.R | 27 googleway-2.4.0/googleway/R/google_utilities.R | 212 - googleway-2.4.0/googleway/R/googleway-package.R | 176 googleway-2.4.0/googleway/R/legend.R |only googleway-2.4.0/googleway/R/onLoad.R |only googleway-2.4.0/googleway/R/parameter_checks.R | 553 ++ googleway-2.4.0/googleway/R/polyline.R | 4 googleway-2.4.0/googleway/R/polyline_constructors.R |only googleway-2.4.0/googleway/R/results_access.R |only googleway-2.4.0/googleway/R/results_directions.R |only googleway-2.4.0/googleway/R/results_distance.R |only googleway-2.4.0/googleway/R/results_elevation.R |only googleway-2.4.0/googleway/R/results_geocode.R |only googleway-2.4.0/googleway/R/results_places.R |only googleway-2.4.0/googleway/R/results_roads.R |only googleway-2.4.0/googleway/R/scratch.R | 7 googleway-2.4.0/googleway/build/vignette.rds |binary googleway-2.4.0/googleway/data/geo_melbourne.rda |only googleway-2.4.0/googleway/data/melbourne.rda |binary googleway-2.4.0/googleway/inst/doc/googleway-vignette.R | 19 googleway-2.4.0/googleway/inst/doc/googleway-vignette.Rmd | 717 +++ googleway-2.4.0/googleway/inst/doc/googleway-vignette.html | 734 +++ googleway-2.4.0/googleway/inst/htmlwidgets/google_map.js | 1885 +--------- googleway-2.4.0/googleway/inst/htmlwidgets/google_map.yaml | 58 googleway-2.4.0/googleway/inst/htmlwidgets/lib/circles.js |only googleway-2.4.0/googleway/inst/htmlwidgets/lib/drawing.js |only googleway-2.4.0/googleway/inst/htmlwidgets/lib/fusion.js |only googleway-2.4.0/googleway/inst/htmlwidgets/lib/geojson.js |only googleway-2.4.0/googleway/inst/htmlwidgets/lib/heatmap.js |only googleway-2.4.0/googleway/inst/htmlwidgets/lib/kml.js |only googleway-2.4.0/googleway/inst/htmlwidgets/lib/legend.js |only googleway-2.4.0/googleway/inst/htmlwidgets/lib/map_events.js |only googleway-2.4.0/googleway/inst/htmlwidgets/lib/map_layer_methods.js |only googleway-2.4.0/googleway/inst/htmlwidgets/lib/map_layers.js |only googleway-2.4.0/googleway/inst/htmlwidgets/lib/map_style.css | 69 googleway-2.4.0/googleway/inst/htmlwidgets/lib/markers.js |only googleway-2.4.0/googleway/inst/htmlwidgets/lib/overlay.js |only googleway-2.4.0/googleway/inst/htmlwidgets/lib/polygons.js |only googleway-2.4.0/googleway/inst/htmlwidgets/lib/polylines.js |only googleway-2.4.0/googleway/inst/htmlwidgets/lib/rectangles.js |only googleway-2.4.0/googleway/man/access_result.Rd |only 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googleway-2.4.0/googleway/man/geo_melbourne.Rd |only googleway-2.4.0/googleway/man/google_directions.Rd | 55 googleway-2.4.0/googleway/man/google_dispatch.Rd | 6 googleway-2.4.0/googleway/man/google_distance.Rd | 27 googleway-2.4.0/googleway/man/google_elevation.Rd | 7 googleway-2.4.0/googleway/man/google_geocode.Rd | 8 googleway-2.4.0/googleway/man/google_keys.Rd |only googleway-2.4.0/googleway/man/google_map-shiny.Rd | 1 googleway-2.4.0/googleway/man/google_map.Rd | 47 googleway-2.4.0/googleway/man/google_map_directions.Rd |only googleway-2.4.0/googleway/man/google_map_panorama.Rd |only googleway-2.4.0/googleway/man/google_map_search.Rd |only googleway-2.4.0/googleway/man/google_map_update.Rd | 1 googleway-2.4.0/googleway/man/google_map_url.Rd |only googleway-2.4.0/googleway/man/google_nearestRoads.Rd | 8 googleway-2.4.0/googleway/man/google_place_autocomplete.Rd | 9 googleway-2.4.0/googleway/man/google_place_details.Rd | 9 googleway-2.4.0/googleway/man/google_places.Rd | 18 googleway-2.4.0/googleway/man/google_reverse_geocode.Rd | 9 googleway-2.4.0/googleway/man/google_snapToRoads.Rd | 8 googleway-2.4.0/googleway/man/google_speedLimits.Rd | 9 googleway-2.4.0/googleway/man/google_streetview.Rd | 6 googleway-2.4.0/googleway/man/google_timezone.Rd | 8 googleway-2.4.0/googleway/man/map_styles.Rd | 3 googleway-2.4.0/googleway/man/melbourne.Rd | 1 googleway-2.4.0/googleway/man/pipe.Rd | 1 googleway-2.4.0/googleway/man/set_key.Rd |only googleway-2.4.0/googleway/man/tram_route.Rd | 1 googleway-2.4.0/googleway/man/tram_stops.Rd | 1 googleway-2.4.0/googleway/man/update_circles.Rd | 63 googleway-2.4.0/googleway/man/update_geojson.Rd |only googleway-2.4.0/googleway/man/update_heatmap.Rd | 67 googleway-2.4.0/googleway/man/update_polygons.Rd | 63 googleway-2.4.0/googleway/man/update_polylines.Rd | 55 googleway-2.4.0/googleway/man/update_rectangles.Rd | 56 googleway-2.4.0/googleway/man/update_style.Rd | 3 googleway-2.4.0/googleway/src/RcppExports.cpp | 23 googleway-2.4.0/googleway/tests/manual_tests.R |only googleway-2.4.0/googleway/tests/testthat/test-colours.R |only googleway-2.4.0/googleway/tests/testthat/test-decode_pl.R | 13 googleway-2.4.0/googleway/tests/testthat/test-google_directions.R | 55 googleway-2.4.0/googleway/tests/testthat/test-google_distances.R | 20 googleway-2.4.0/googleway/tests/testthat/test-google_elevation.R | 44 googleway-2.4.0/googleway/tests/testthat/test-google_geocode.R | 4 googleway-2.4.0/googleway/tests/testthat/test-google_keys.R |only googleway-2.4.0/googleway/tests/testthat/test-google_map.R | 41 googleway-2.4.0/googleway/tests/testthat/test-google_map_layer_circles.R |only googleway-2.4.0/googleway/tests/testthat/test-google_map_layer_fusion.R |only googleway-2.4.0/googleway/tests/testthat/test-google_map_layer_geojson.R |only googleway-2.4.0/googleway/tests/testthat/test-google_map_layer_kml.R |only googleway-2.4.0/googleway/tests/testthat/test-google_map_layer_methods.R |only googleway-2.4.0/googleway/tests/testthat/test-google_map_layer_parameters.R |only googleway-2.4.0/googleway/tests/testthat/test-google_map_layer_polygons.R |only googleway-2.4.0/googleway/tests/testthat/test-google_map_layer_polyline.R |only googleway-2.4.0/googleway/tests/testthat/test-google_map_layer_rectangles.R |only googleway-2.4.0/googleway/tests/testthat/test-google_map_layer_sf.R |only googleway-2.4.0/googleway/tests/testthat/test-google_map_layers.R | 211 - googleway-2.4.0/googleway/tests/testthat/test-google_map_shape_constructors.R |only googleway-2.4.0/googleway/tests/testthat/test-google_map_urls.R |only googleway-2.4.0/googleway/tests/testthat/test-google_place_autocomplete.R | 38 googleway-2.4.0/googleway/tests/testthat/test-google_place_details.R | 2 googleway-2.4.0/googleway/tests/testthat/test-google_places.R | 8 googleway-2.4.0/googleway/tests/testthat/test-google_reverse_geocode.R | 2 googleway-2.4.0/googleway/tests/testthat/test-google_streetview.R | 7 googleway-2.4.0/googleway/tests/testthat/test-google_timezone.R | 4 googleway-2.4.0/googleway/tests/testthat/test-google_utilities.R | 37 googleway-2.4.0/googleway/tests/testthat/test-legend.R |only googleway-2.4.0/googleway/tests/testthat/test-parameter_checks.R | 270 + googleway-2.4.0/googleway/tests/testthat/test-results_access.R |only googleway-2.4.0/googleway/tests/testthat/test-results_access_api.R |only googleway-2.4.0/googleway/vignettes/googleway-vignette.Rmd | 717 +++ googleway-2.4.0/googleway/vignettes/img/fusion_layer.png |only googleway-2.4.0/googleway/vignettes/img/fusion_layer_style.png |only googleway-2.4.0/googleway/vignettes/img/geojson.png |only googleway-2.4.0/googleway/vignettes/img/google_map.png |binary googleway-2.4.0/googleway/vignettes/img/heatmap.png |binary googleway-2.4.0/googleway/vignettes/img/heatmap_colour.png |binary googleway-2.4.0/googleway/vignettes/img/kml.png |only googleway-2.4.0/googleway/vignettes/img/marker_info.png |binary googleway-2.4.0/googleway/vignettes/img/melbourne_to_sydney_add_polylines.png |binary googleway-2.4.0/googleway/vignettes/img/overlay.png |only googleway-2.4.0/googleway/vignettes/img/polygon_custom_legend.png |only googleway-2.4.0/googleway/vignettes/img/polygon_legend.png |only googleway-2.4.0/googleway/vignettes/img/polygon_multiple_colours.png |only googleway-2.4.0/googleway/vignettes/img/polygon_palette.png |only googleway-2.4.0/googleway/vignettes/img/polygon_single_colour.png |only googleway-2.4.0/googleway/vignettes/img/polygons.png |only googleway-2.4.0/googleway/vignettes/img/sf_marker_lines.png |only googleway-2.4.0/googleway/vignettes/img/sf_north_carolina.png |only 195 files changed, 5086 insertions(+), 5081 deletions(-)
Title: Reads in 'Neuroimaging' 'GIFTI' Files with Geometry Information
Description: Functions to read in the geometry format under the
'Neuroimaging' 'Informatics' Technology Initiative ('NIfTI'), called
'GIFTI' <https://www.nitrc.org/projects/gifti/>.
These files contain surfaces of brain imaging data.
Author: John Muschelli
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between gifti versions 0.7.4 dated 2017-07-26 and 0.7.5 dated 2018-02-01
DESCRIPTION | 6 MD5 | 20 +- NEWS.md | 9 R/create_data_matrix.R | 3 R/surf_triangles.R | 2 build/vignette.rds |binary inst/doc/Reading_GIFTI_Files.Rmd | 6 inst/doc/Reading_GIFTI_Files.html | 362 ++++++++++++++++++++++++++++++-------- man/create_data_matrix.Rd | 4 man/surf_triangles.Rd | 2 vignettes/Reading_GIFTI_Files.Rmd | 6 11 files changed, 319 insertions(+), 101 deletions(-)
Title: Analyzing Data with Cellwise Outliers
Description: Tools for detecting cellwise outliers and robust methods to analyze data which may contain them.
Author: Jakob Raymaekers [aut, cre],
Peter Rousseeuw [aut],
Wannes Van den Bossche [aut]
Maintainer: Jakob Raymaekers <jakob.raymaekers@kuleuven.be>
Diff between cellWise versions 1.0.0 dated 2016-12-06 and 2.0.7 dated 2018-02-01
cellWise-1.0.0/cellWise/R/DDC_code.R |only cellWise-2.0.7/cellWise/DESCRIPTION | 21 cellWise-2.0.7/cellWise/MD5 | 68 +- cellWise-2.0.7/cellWise/NAMESPACE | 9 cellWise-2.0.7/cellWise/R/DDC.R |only cellWise-2.0.7/cellWise/R/RcppExports.R |only cellWise-2.0.7/cellWise/R/Wrap.R |only cellWise-2.0.7/cellWise/R/cellMap.R |only cellWise-2.0.7/cellWise/R/checkDataSet.R |only cellWise-2.0.7/cellWise/R/estLocScale.R |only cellWise-2.0.7/cellWise/build/vignette.rds |binary cellWise-2.0.7/cellWise/data/datalist |only cellWise-2.0.7/cellWise/data/dog_walker.rdata |only cellWise-2.0.7/cellWise/inst/doc/DDC_examples.R | 41 - cellWise-2.0.7/cellWise/inst/doc/DDC_examples.Rmd | 41 - cellWise-2.0.7/cellWise/inst/doc/DDC_examples.html | 655 ++++++++++++-------- cellWise-2.0.7/cellWise/inst/doc/Wrap_examples.R |only cellWise-2.0.7/cellWise/inst/doc/Wrap_examples.Rmd |only cellWise-2.0.7/cellWise/inst/doc/Wrap_examples.html |only cellWise-2.0.7/cellWise/man/DetectDeviatingCells.Rd | 20 cellWise-2.0.7/cellWise/man/cellMap.Rd | 12 cellWise-2.0.7/cellWise/man/checkDataSet.Rd | 8 cellWise-2.0.7/cellWise/man/dog_walker.Rd |only cellWise-2.0.7/cellWise/man/estLocScale.Rd |only cellWise-2.0.7/cellWise/man/wrap.Rd |only cellWise-2.0.7/cellWise/src |only cellWise-2.0.7/cellWise/vignettes/DDC_examples.Rmd | 41 - cellWise-2.0.7/cellWise/vignettes/Wrap_examples.Rmd |only 28 files changed, 614 insertions(+), 302 deletions(-)
Title: Multidimensional Scaling of Asymmetric Data
Description: Multidimensional scaling models and methods for the visualization for asymmetric data. A matrix is asymmetric if the number of rows equals the number of columns, and these rows and columns refer to the same set of objects. An example is a student migration table, where the rows correspond to the countries of origin of the students and the columns to the destination countries. This package provides the slide-vector model, a scaling model with unique dimensions and the asymscal model for asymmetric multidimensional scaling. Furthermore, a heat map for skew-symmetric data, and the decomposition of asymmetry are provided for the analysis of asymmetric tables.
Author: Berrie Zielman
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>
Diff between asymmetry versions 1.2.4 dated 2017-10-27 and 1.2.5 dated 2018-02-01
DESCRIPTION | 12 ++++++------ MD5 | 35 ++++++++++++++++++++--------------- NAMESPACE | 1 + R/mdsunique.R | 10 ++++++++-- R/plot.skewsymmetry.R | 8 +++++++- R/print.mdsunique.R | 2 +- R/skewsymmetry.R | 2 ++ R/summary.mdsunique.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/asymmetricmds.R |only inst/doc/asymmetricmds.Rmd |only inst/doc/asymmetricmds.html |only inst/doc/asymmetry.Rmd | 2 +- inst/doc/asymmetry.html | 8 ++++---- man/asymscal.Rd | 5 ++--- man/mdsunique.Rd | 6 ++++-- man/slidevector.Rd | 11 +++++------ man/summary.mdsunique.Rd |only man/summary.slidevector.Rd | 2 +- vignettes/asymmetry.Rmd | 2 +- 21 files changed, 63 insertions(+), 43 deletions(-)
Title: Generate XMR Control Chart Data from Time-Series Data
Description: XMRs combine X-Bar control charts and Moving Range control charts. These functions also will recalculate the reference lines when significant change has occurred.
Author: Alex Zanidean [aut, cre]
Maintainer: Alex Zanidean <AZanidean@mhc.ab.ca>
Diff between xmrr versions 1.0.0 dated 2017-12-15 and 1.0.1 dated 2018-02-01
DESCRIPTION | 13 LICENSE | 825 ++++------------------ MD5 | 27 R/xmR.R | 99 +- R/xmR_chart.R | 14 README.md |only build |only inst |only man/xmr.Rd | 4 man/xmr_chart.Rd | 6 tests/testthat/test-xmr_recalc_lowerlongrun.R | 6 tests/testthat/test-xmr_recalc_shortruns.R | 8 tests/testthat/test-xmr_recalc_shortruns_4.R | 5 tests/testthat/test-xmr_recalc_upperlongrun.R | 5 tests/testthat/test-xmr_single_longrunrunvector.R |only vignettes |only 16 files changed, 284 insertions(+), 728 deletions(-)
Title: Human 'Connectome' Project Interface
Description: Downloads and reads data from Human 'Connectome' Project
<https://db.humanconnectome.org> using Amazon Web Services ('AWS')
'S3' buckets.
Author: John Muschelli [aut, cre],
Adi Gherman [ctb]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between neurohcp versions 0.6 dated 2017-05-14 and 0.7.3 dated 2018-02-01
DESCRIPTION | 31 ++- MD5 | 53 +++-- NAMESPACE | 8 NEWS.md |only R/download_hcp_dir.R | 17 + R/download_hcp_file.R | 9 + R/get_hcp_file.R | 18 ++ R/hcp_ids.R | 5 R/hcp_list_files.R | 86 +++++++++ R/hcp_scanning_info.R | 7 R/make_aws_call.R | 2 R/set_aws_api_key.R | 2 README.md | 1 build/vignette.rds |binary data/hcp_1200_scanning_info.rda |only data/hcp_900_scanning_info.rda |binary data/hcp_scanning_info.rda |binary inst/doc/hcp.R | 4 inst/doc/hcp.Rmd | 4 inst/doc/hcp.html | 359 +++++++++++++++++++++++++++++++--------- man/download_hcp_dir.Rd | 7 man/download_hcp_file.Rd | 3 man/get_hcp_file.Rd | 6 man/hcp_1200_scanning_info.Rd |only man/hcp_ids.Rd | 2 man/hcp_list_files.Rd | 26 ++ man/make_aws_call.Rd | 2 man/set_aws_api_key.Rd | 2 vignettes/hcp.Rmd | 4 29 files changed, 525 insertions(+), 133 deletions(-)
Title: Constrained Inference for Linear Mixed Effects Models
Description: Estimation and inference for linear models where some or all of the
fixed-effects coefficients are subject to order restrictions. This package uses
the robust residual bootstrap methodology for inference, and can handle some
structure in the residual variance matrix.
Author: Casey M. Jelsema, Shyamal D. Peddada
Maintainer: Casey M. Jelsema <jelsema.casey@gmail.com>
Diff between CLME versions 2.0-8 dated 2017-12-08 and 2.0-9 dated 2018-02-01
DESCRIPTION | 10 ++--- MD5 | 14 +++---- NAMESPACE | 6 --- NEWS | 4 +- R/00Package.r | 4 +- R/summary_clme.r | 96 +++++++++++++++++++++++++++--------------------------- R/utilities.r | 17 ++++++--- man/sigma.clme.Rd | 1 8 files changed, 78 insertions(+), 74 deletions(-)
Title: Calculating Childhood Mortality Rates
Description: Calculates childhood (neonatal, postneonatal, infant, child, and under-five) mortality rates using Demographic and Health Survey (DHS) microdata.
The 'childhoodmortality' package was developed in accordance to the methodology outlined in the "DHS Guide to Statistics" (Rutstein 2006,
<http://dhsprogram.com/pubs/pdf/DHSG1/Guide_to_DHS_Statistics_29Oct2012_DHSG1.pdf>) Specifically, the package uses a synthetic cohort
life table approach, combining mortality probabilities for age segments with actual cohort mortality experience into more common age
segments. Standard errors for mortality estimates are computed using the jackknife repeated replication method outlined in the "Estimates of Sampling Errors"
appendix of DHS Final Reports (DHS 2004, <http://dhsprogram.com/pubs/pdf/FR175/19AppendixB.pdf>). This methodology controls for sample design.
Author: Casey Breen
Maintainer: Casey Breen <cbreen@umn.edu>
Diff between childhoodmortality versions 0.1.0 dated 2017-12-14 and 0.2.0 dated 2018-02-01
DESCRIPTION | 8 +-- MD5 | 15 +++-- R/childhoodmortality.R | 22 ++++---- R/utilities.R | 20 +++---- README.md | 122 +++++++++++++++++++++++++++++++++++++++++++++- build |only inst |only man/childhoodmortality.Rd | 2 vignettes |only 9 files changed, 160 insertions(+), 29 deletions(-)
More information about childhoodmortality at CRAN
Permanent link
Title: Example Functional Imaging Data from the Multi-Modal MRI
'Reproducibility' Resource
Description: Functional magnetic resonance imaging ('fMRI') data from the
'Kirby21' 'reproducibility' study
<doi:10.1016/j.neuroimage.2010.11.047>.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between kirby21.fmri versions 1.5.1 dated 2017-03-02 and 1.6.0 dated 2018-02-01
DESCRIPTION | 20 +++++++++++--------- MD5 | 7 ++++--- NEWS.md |only R/get_fmri_filenames.R | 2 +- man/get_fmri_filenames.Rd | 2 +- 5 files changed, 17 insertions(+), 14 deletions(-)
Title: Targeted Maximum Likelihood Estimation
Description: Targeted maximum likelihood estimation of point treatment effects (Targeted Maximum Likelihood Learning, The International Journal of biostatistics, 2(1), 2006. This version automatically estimates the additive treatment effect among the treated (ATT) and among the controls (ATC). The tmle() function calculates the adjusted marginal difference in mean outcome associated with a binary point treatment, for continuous or binary outcomes. Relative risk and odds ratio estimates are also reported for binary outcomes. Missingness in the outcome is allowed, but not in treatment assignment or baseline covariate values. The population mean is calculated when there is missingness, and no variation in the treatment assignment. The tmleMSM() function estimates the parameters of a marginal structural model for a binary point treatment effect. Effect estimation stratified by a binary mediating variable is also available. An ID argument can be used to identify repeated measures. Default settings call 'SuperLearner' to estimate the Q and g portions of the likelihood, unless values or a user-supplied regression function are passed in as arguments.
Author: Susan Gruber [aut, cre],
Mark van der Laan [aut]
Maintainer: Susan Gruber <sgruber@cal.berkeley.edu>
Diff between tmle versions 1.2.0-5 dated 2017-01-07 and 1.3.0 dated 2018-02-01
DESCRIPTION | 12 ++-- MD5 | 29 +++++------ NEWS | 4 + R/tmle.R | 125 +++++++++++++++++++++++++++++++++++++++++++++++-- R/zzz.R | 2 man/calcParameters.Rd | 8 +-- man/calcSigma.Rd | 2 man/estimateG.Rd | 2 man/estimateQ.Rd | 2 man/oneStepATT.Rd |only man/summary.tmle.Rd | 2 man/summary.tmleMSM.Rd | 2 man/tmle-package.Rd | 12 ++-- man/tmle.Rd | 6 +- man/tmleMSM.Rd | 2 man/tmleNews.Rd | 4 - 16 files changed, 169 insertions(+), 45 deletions(-)
Title: Develop and Run Spatially Explicit Discrete Event Simulation
Models
Description: Metapackage for implementing a variety of event-based models, with
a focus on spatially explicit models. These include raster-based,
event-based, and agent-based models. The core simulation components
(provided by 'SpaDES.core') are built upon a discrete event simulation (DES;
see Matloff (2011) ch 7.8.3 <https://nostarch.com/artofr.htm>)
framework that facilitates modularity, and easily enables the user to
include additional functionality by running user-built simulation modules
(see also 'SpaDES.tools'). Included are numerous tools to visualize rasters
and other maps (via 'quickPlot'), and caching methods for reproducible
simulations (via 'reproducible'). Additional functionality is provided by
the 'SpaDES.addins' and 'SpaDES.shiny' packages.
Author: Alex M Chubaty [aut, cre],
Eliot J B McIntire [aut],
Yong Luo [ctb],
Steve Cumming [ctb],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alexander.chubaty@canada.ca>
Diff between SpaDES versions 2.0.0 dated 2017-09-05 and 2.0.1 dated 2018-02-01
DESCRIPTION | 18 - MD5 | 18 - NAMESPACE | 5 NEWS.md | 5 R/spades-package.R | 10 R/zzz.R | 1 README.md | 26 +- build/vignette.rds |binary inst/doc/iii-cache.html | 513 +++++++++++++++++++++++++++++++++--------------- man/SpaDES-package.Rd | 3 10 files changed, 417 insertions(+), 182 deletions(-)
Title: Sensory and Consumer Data Mapping
Description: External preference mapping technique is commonly used in sensory analysis
field to connect consumer rating data that contains liking scores to sensory data
that incorporates sensory attributes' evaluations of the perceived products
Danzart(1998) (<doi:10.1006/fstl.1998.0373>). SensMap package provides the
mapping visualization from several features : options in dimension reduction methods
and prediction models ranging from linear to non linear regressions. A smoothed
version of the map performed using LOESS algorithm is available. A selection process
of map stability is provided. A 'shiny' application is included. It presents an easy
GUI for the implemented functions as well as a comparative tool of fit models
using several criteria. Basic analysis such as characterization of products,
panelists and sessions likewise consumer segmentation are also made available.
Author: Ibtihel Rebhi [aut, cre], Rihab Boubakri [ctb], Dhafer Malouche [ctb]
Maintainer: Ibtihel Rebhi <ibtihel.rebhi@enit.utm.tn>
Diff between SensMap versions 0.5 dated 2018-01-29 and 0.6 dated 2018-02-01
DESCRIPTION | 12 MD5 | 4 inst/SensMapUI/ui.R | 691 +++++++++++++++++++++++++--------------------------- 3 files changed, 353 insertions(+), 354 deletions(-)
Title: R Interface to the Vowpal Wabbit
Description: The 'Vowpal Wabbit' project is a fast out-of-core learning
system sponsored by Microsoft Research (having started at Yahoo! Research)
and written by John Langford along with a number of contributors. This R
package does not include the distributed computing implementation of the
cluster/ directory of the upstream sources. Use of the software as a network
service is also not directly supported as the aim is a simpler direct call
from R for validation and comparison. Note that this package contains an
embedded older version of 'Vowpal Wabbit'. The package 'rvw' at the GitHub
repo <https://github.com/eddelbuettel/rvw> can provide an alternative using
an external 'Vowpal Wabbit' library installation.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RVowpalWabbit versions 0.0.11 dated 2018-01-28 and 0.0.12 dated 2018-02-01
ChangeLog | 17 ++++++++++++++++- DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- demo/vw.R | 10 +++++----- man/vw.Rd | 2 +- src/active_interactor.cc | 8 ++++---- src/bfgs.cc | 10 +++++----- tests/test1.r | 2 +- tests/test5.r | 2 +- tests/test7.r | 2 +- 10 files changed, 47 insertions(+), 32 deletions(-)
Title: Likelihood Based Optimal Partitioning and Indicator Species
Analysis
Description: Likelihood based optimal partitioning and indicator
species analysis. Finding the best binary partition for each species
based on model selection, with the possibility to take into account
modifying/confounding variables as described
in Kemencei et al. (2014) <doi:10.1556/ComEc.15.2014.2.6>.
The package implements binary and multi-level response models,
various measures of uncertainty, Lorenz-curve based thresholding,
with native support for parallel computations.
Author: Peter Solymos [cre, aut], Ermias T. Azeria [ctb]
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between opticut versions 0.1-1 dated 2018-01-31 and 0.1-2 dated 2018-02-01
DESCRIPTION | 8 ++++---- MD5 | 21 +++++++++++---------- R/opticut1dot.R | 6 +++++- R/zzz.R | 3 ++- build/partial.rdb |binary inst |only man/birdrec.Rd | 2 +- man/multicut.Rd | 3 +++ man/occolors.Rd | 2 +- man/ocoptions.Rd | 11 +++++++++++ man/opticut.Rd | 3 +++ man/optilevels.Rd | 3 +++ 12 files changed, 44 insertions(+), 18 deletions(-)
Title: Calculating Marginal Effects and Levels with Errors
Description: Calculate predicted levels and marginal effects,
using the delta method to calculate standard errors. This is an R-based
version of the 'margins' command from Stata.
Author: Alex Gold [aut],
Nat Olin [aut],
Annie Wang [aut, cre]
Maintainer: Annie Wang <anniejw6@gmail.com>
Diff between modmarg versions 0.9.0 dated 2017-10-29 and 0.9.2 dated 2018-02-01
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/glm_marg.R | 2 +- R/marg.R | 14 +++++++++----- README.md | 2 +- inst/doc/delta-method.html | 4 ++-- inst/doc/usage.html | 4 ++-- tests/testthat/test_glm.R | 11 ++++++++++- 9 files changed, 40 insertions(+), 23 deletions(-)
Title: Multilevel Model for Multivariate Responses with Missing Values
Description: To conduct Bayesian inference regression for responses with
multilevel explanatory variables and missing values; It uses function from
'Stan', a software to implement posterior sampling using Hamiltonian MC and
its variation Non-U-Turn algorithms. It implements the posterior sampling of
regression coefficients from the multilevel regression models. The package has
two main functions to handle not-missing-at-random missing responses and left-
censored with not-missing-at random responses. The purpose is to provide a
similar format as the other R regression functions but using 'Stan' models.
Author: Irene SL Zeng [aut, cre],
Thomas Lumley [ctb]
Maintainer: Irene SL Zeng <i.zeng@auckland.ac.nz>
Diff between mlmm versions 1.0 dated 2017-11-02 and 1.5.0 dated 2018-02-01
mlmm-1.0/mlmm/inst/chunks/mlmc_i32.rds |only mlmm-1.0/mlmm/inst/chunks/mlmc_i64.rds |only mlmm-1.5.0/mlmm/DESCRIPTION | 24 mlmm-1.5.0/mlmm/MD5 | 32 mlmm-1.5.0/mlmm/NAMESPACE | 21 mlmm-1.5.0/mlmm/R/mlmc.R | 29 mlmm-1.5.0/mlmm/R/mlmm-internal.R | 252 +- mlmm-1.5.0/mlmm/R/mlmm.R | 17 mlmm-1.5.0/mlmm/R/readstancode.R | 550 +++--- mlmm-1.5.0/mlmm/R/setinitialvalues.R | 50 mlmm-1.5.0/mlmm/R/stanmodels.R | 80 mlmm-1.5.0/mlmm/R/zzz.R | 8 mlmm-1.5.0/mlmm/exec/mlmc_code.stan | 270 +-- mlmm-1.5.0/mlmm/exec/mmlm_code.stan | 258 +-- mlmm-1.5.0/mlmm/man/mlmc.Rd | 20 mlmm-1.5.0/mlmm/man/mlmm.Rd | 12 mlmm-1.5.0/mlmm/src/include/models.hpp | 2802 +++++++++++++++++---------------- mlmm-1.5.0/mlmm/tools/make_cpp.R | 98 - 18 files changed, 2344 insertions(+), 2179 deletions(-)
Title: Robust Linear Quantile Regression
Description: It fits a robust linear quantile regression model using a new
family of zero-quantile distributions for the error term as in Galarza et.al.(2017) <doi:10.1002/sta4.140>. This family of
distribution includes skewed versions of the Normal, Student's t, Laplace, Slash
and Contaminated Normal distribution. It also performs logistic quantile regression for bounded responses
as shown in Bottai et.al.(2009) <doi:10.1002/sim.3781>. It provides estimates and full inference.
It also provides envelopes plots for assessing the fit and confidences bands
when several quantiles are provided simultaneously.
Author: Christian E. Galarza, Luis Benites, Victor H. Lachos
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>
Diff between lqr versions 1.5 dated 2016-05-19 and 1.7 dated 2018-02-01
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- R/EMonly.R | 13 +++++++------ R/bestlqr.R | 20 +++++++++++++------- man/SKD.Rd | 2 +- man/best.lqr.Rd | 3 +-- man/dist.Truncated.Rd | 3 +-- man/logbestlqr.Rd | 13 ++++++------- man/loglqr.Rd | 14 +++++++------- man/lqr-package.Rd | 4 ++-- man/resistence.Rd | 3 +-- 11 files changed, 54 insertions(+), 51 deletions(-)
Title: Fast Probabilistic Record Linkage with Missing Data
Description: Implements a Fellegi-Sunter probabilistic record linkage model that allows for missing data
and the inclusion of auxiliary information. This includes functionalities to conduct a merge of two datasets under the Fellegi-Sunter model
using the Expectation-Maximization algorithm. In addition, tools for preparing, adjusting, and summarizing
data merges are included. The package implements methods described in Enamorado, Fifield,
and Imai (2017) ''Using a Probabilistic Model to Assist Merging of Large-scale Administrative
Records'', available at <http://imai.princeton.edu/research/linkage.html>.
Author: Ted Enamorado [aut, cre],
Ben Fifield [aut],
Kosuke Imai [aut]
Maintainer: Ted Enamorado <fastlinkr@gmail.com>
Diff between fastLink versions 0.3.0 dated 2018-01-26 and 0.3.1 dated 2018-02-01
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/confusion.R | 4 ++-- R/fastLink.R | 12 ++++++++++-- data/countyname_to_fips.RData |binary data/cps_statemovers.RData |binary data/irs_countymigration.RData |binary data/irs_statemigration.RData |binary data/samplematch.RData |binary data/statecode_to_fips.RData |binary 10 files changed, 25 insertions(+), 17 deletions(-)
Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework
in R. CanvasXpress is a standalone JavaScript library for reproducible research
with complete tracking of data and end-user modifications stored in a single
PNG image that can be played back. See <http://canvasxpress.org> for more
information.
Author: Isaac Neuhaus [aut, cre],
Connie Brett [ctb]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress versions 1.18.2 dated 2018-01-18 and 1.18.3 dated 2018-02-01
DESCRIPTION | 6 MD5 | 28 - NEWS.md | 2 README.md | 4 inst/doc/additional_examples.html | 4 inst/doc/getting_started.html | 4 inst/extdata/cX-networkbasic-edges.txt | 14 inst/extdata/cX-networkbasic-nodes.txt | 12 inst/extdata/cX-wpapoptosis-edges.txt | 134 ++++----- inst/extdata/cX-wpapoptosis-nodes.txt | 32 +- inst/htmlwidgets/canvasXpress.js | 4 inst/htmlwidgets/lib/canvasXpress/canvasXpress.css | 256 ++---------------- inst/htmlwidgets/lib/canvasXpress/canvasXpress.min.js | 6 tests/cX-function.R | 17 - tests/cX-test-setup.R | 3 15 files changed, 176 insertions(+), 350 deletions(-)
Title: Class and Methods Definitions for Packages 'aws', 'adimpro',
'fmri', 'dwi'
Description: Defines the method extract and provides 'openMP' support as needed in several packages.
Author: Joerg Polzehl [aut, cre],
Felix Anker [ctb]
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Diff between awsMethods versions 1.0-4 dated 2016-09-14 and 1.1-0 dated 2018-02-01
awsMethods-1.0-4/awsMethods/configure |only awsMethods-1.0-4/awsMethods/src/Makevars.in |only awsMethods-1.0-4/awsMethods/src/cleanup |only awsMethods-1.1-0/awsMethods/DESCRIPTION | 12 ++++++------ awsMethods-1.1-0/awsMethods/MD5 | 13 +++++++------ awsMethods-1.1-0/awsMethods/NAMESPACE | 2 +- awsMethods-1.1-0/awsMethods/R/onAttach.r |only awsMethods-1.1-0/awsMethods/R/utilities.r | 6 +++--- awsMethods-1.1-0/awsMethods/cleanup |only awsMethods-1.1-0/awsMethods/src/Makevars |only awsMethods-1.1-0/awsMethods/src/init.c |only 11 files changed, 17 insertions(+), 16 deletions(-)
Title: The Asymmetric Laplace Distribution
Description: It provides the density, distribution function, quantile function,
random number generator, likelihood function, moments and Maximum Likelihood estimators for a given sample, all this for
the three parameter Asymmetric Laplace Distribution defined
in Koenker and Machado (1999). This is a special case of the skewed family of distributions
available in Galarza et.al. (2017) <doi:10.1002/sta4.140> useful for quantile regression.
Author: Christian E. Galarza <cgalarza88@gmail.com> and Victor H. Lachos <hlachos@ime.unicamp.br>
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>
Diff between ald versions 1.1 dated 2016-06-06 and 1.2 dated 2018-02-01
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- man/ALD.Rd | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: TraMineR Extension
Description: Collection of ancillary functions and utilities to be used in conjunction with the 'TraMineR' package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of 'TraMineR'.
Author: Gilbert Ritschard [aut, cre, ths, cph],
Matthias Studer [aut],
Reto Buergin [aut],
Alexis Gabadinho [ctb],
Pierre-Alexandre Fonta [ctb],
Nicolas Muller [ctb],
Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineRextras versions 0.4.1 dated 2017-08-16 and 0.4.2 dated 2018-02-01
DESCRIPTION | 12 +++++---- MD5 | 51 +++++++++++++++++++++++++----------------- NAMESPACE | 12 +++++++++ R/dissvar-grp.R | 2 - R/eventLatex-gr.R | 12 ++++----- R/pamward.R | 18 +++++++++----- R/plot.stslist.surv.R |only R/seqplot-tentrop.R | 3 ++ R/seqprecarity.R |only R/seqprecorr.R |only R/seqprecstart.R |only R/seqrep-grp.R | 25 ++++++++++++++++---- R/seqsplot.R |only R/seqsurv.R |only R/seqtabstocc.R | 9 ++++--- inst/CITATION | 26 ++++++++++++++++++--- inst/NEWS | 30 ++++++++++++++++++++++++ inst/NEWS.Rd | 49 ++++++++++++++++++++++++++++++++++++++++ man/TraMineRextras-package.Rd | 2 - man/pamward.Rd | 10 ++++---- man/plot.emlt.Rd | 42 ++++++++++++++++++---------------- man/plot.stslist.surv.Rd |only man/seqedplot.Rd | 4 +-- man/seqemlt.Rd | 23 +++++++++--------- man/seqentrans.Rd | 2 - man/seqeordplot.Rd | 5 ++-- man/seqprecarity.Rd |only man/seqprecstart.Rd |only man/seqrep-grp.Rd | 13 ++++++---- man/seqsplot.Rd |only man/seqsurv.Rd |only man/seqtabstocc.Rd | 4 ++- 32 files changed, 257 insertions(+), 97 deletions(-)
More information about TraMineRextras at CRAN
Permanent link
Title: Interactive Heat Maps Using 'htmlwidgets' and 'D3.js'
Description: Create interactive heat maps that are usable from the R console, in
the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover
the mouse pointer over a cell to show details, drag a rectangle to zoom, and
click row/column labels to highlight.
Author: Joe Cheng [aut, cre],
Tal Galili [aut],
RStudio, Inc. [cph],
Michael Bostock [ctb, cph] (D3.js library),
Justin Palmer [ctb, cph] (d3.tip library)
Maintainer: ORPHANED
Diff between d3heatmap versions 0.6.1.1 dated 2016-02-23 and 0.6.1.2 dated 2018-02-01
d3heatmap-0.6.1.1/d3heatmap/tests/smoketest.R |only d3heatmap-0.6.1.2/d3heatmap/DESCRIPTION | 15 +++++++++------ d3heatmap-0.6.1.2/d3heatmap/MD5 | 5 +++-- d3heatmap-0.6.1.2/d3heatmap/tests/Note |only d3heatmap-0.6.1.2/d3heatmap/tests/smoketest.R.duff |only 5 files changed, 12 insertions(+), 8 deletions(-)
Title: Gaussian Graphs Models Selection
Description: Graph estimation in Gaussian Graphical Models. The main functions return the adjacency matrix of an undirected graph estimated from a data matrix.
Author: Annie Bouvier, Christophe Giraud, Sylvie Huet, Verzelen N.
Maintainer: ORPHANED
Diff between GGMselect versions 0.1-12 dated 2017-04-19 and 0.1-12.1 dated 2018-02-01
DESCRIPTION | 11 +++++++---- MD5 | 30 +++++++++++++++--------------- src/Makevars | 2 +- tests/bsch.Rout.save | 10 +++++----- tests/penInf.Rout.save | 16 +++++++++------- tests/sh9.2012.Rout.save | 10 +++++----- tests/shPUR.Rout.save | 10 +++++----- tests/test1Fast.Rout.save | 10 +++++----- tests/test1QE.Rout.save | 10 +++++----- tests/test2Fast.Rout.save | 10 +++++----- tests/test2QE.Rout.save | 10 +++++----- tests/test3Fast.Rout.save | 10 +++++----- tests/test3QE.Rout.save | 10 +++++----- tests/test5Fast.Rout.save | 10 +++++----- tests/test7Fast.Rout.save | 10 +++++----- tests/testMyFam.Rout.save | 10 +++++----- 16 files changed, 92 insertions(+), 87 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-05-24 0.2.1
2016-05-12 0.2
2016-01-28 0.1.1
Title: Computing Weighted Topological Overlaps (wTO) & Consensus wTO
Network
Description: Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks (Nowick et al. (2009) <doi:10.1073/pnas.0911376106>) given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks.
Author: Deisy Morselli Gysi, Andre Voigt, Tiago Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy@bioinf.uni-leipzig.de>
Diff between wTO versions 1.4.1 dated 2017-11-22 and 1.4.2 dated 2018-02-01
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- R/wTO.Complete2.R | 2 +- R/wTO.Consensus.R | 2 +- inst |only man/wTO.Complete.Rd | 2 +- man/wTO.Consensus.Rd | 2 +- 7 files changed, 13 insertions(+), 12 deletions(-)
Title: Feature Selection Algorithms for Computer Aided Diagnosis
Description: Contains a set of utilities for building and testing formula-based models (linear, logistic or COX) for Computer Aided Diagnosis/Prognosis applications. Utilities include data adjustment, univariate analysis, model building, model-validation, longitudinal analysis, reporting and visualization.
Author: Jose Gerardo Tamez-Pena, Antonio Martinez-Torteya and Israel Alanis
Maintainer: Jose Gerardo Tamez-Pena <jose.tamezpena@itesm.mx>
Diff between FRESA.CAD versions 2.2.1 dated 2016-09-10 and 3.0.0 dated 2018-02-01
FRESA.CAD-2.2.1/FRESA.CAD/R/medianPredict.R |only FRESA.CAD-2.2.1/FRESA.CAD/man/medianPredict.Rd |only FRESA.CAD-3.0.0/FRESA.CAD/DESCRIPTION | 11 FRESA.CAD-3.0.0/FRESA.CAD/MD5 | 162 - FRESA.CAD-3.0.0/FRESA.CAD/NAMESPACE | 53 FRESA.CAD-3.0.0/FRESA.CAD/NEWS | 37 FRESA.CAD-3.0.0/FRESA.CAD/R/BSWiMS.r |only FRESA.CAD-3.0.0/FRESA.CAD/R/EmpiricalSurvDiff.r |only FRESA.CAD-3.0.0/FRESA.CAD/R/FRESA.Model.R | 320 +- FRESA.CAD-3.0.0/FRESA.CAD/R/ForwardSelection.Model.Bin.R | 371 +- FRESA.CAD-3.0.0/FRESA.CAD/R/ForwardSelection.Model.Res.R | 165 - FRESA.CAD-3.0.0/FRESA.CAD/R/backVarElimination.Bin.R | 73 FRESA.CAD-3.0.0/FRESA.CAD/R/backVarElimination.Res.R | 64 FRESA.CAD-3.0.0/FRESA.CAD/R/baggedModel.R | 775 +++-- FRESA.CAD-3.0.0/FRESA.CAD/R/bootstrapValidation.Bin.R | 90 FRESA.CAD-3.0.0/FRESA.CAD/R/bootstrapValidation.Res.R | 97 FRESA.CAD-3.0.0/FRESA.CAD/R/bootstrapVarElimination.Bin.R | 308 +- FRESA.CAD-3.0.0/FRESA.CAD/R/bootstrapVarElimination.Res.R | 331 +- FRESA.CAD-3.0.0/FRESA.CAD/R/crossValidationFeatureSelection.Bin.R | 464 +-- FRESA.CAD-3.0.0/FRESA.CAD/R/crossValidationFeatureSelection.Res.R | 444 +-- FRESA.CAD-3.0.0/FRESA.CAD/R/ensemblePredict.R |only FRESA.CAD-3.0.0/FRESA.CAD/R/getKNNpredictionFromFormula.R | 34 FRESA.CAD-3.0.0/FRESA.CAD/R/getSignature.r |only FRESA.CAD-3.0.0/FRESA.CAD/R/getVar.Bin.R | 228 + FRESA.CAD-3.0.0/FRESA.CAD/R/getVar.Res.R | 154 - FRESA.CAD-3.0.0/FRESA.CAD/R/heatMaps.R | 631 ++-- FRESA.CAD-3.0.0/FRESA.CAD/R/modelFitting.R | 177 - FRESA.CAD-3.0.0/FRESA.CAD/R/nearestneighborimpute.R |only FRESA.CAD-3.0.0/FRESA.CAD/R/plot.bootstrapValidation.Bin.R | 87 FRESA.CAD-3.0.0/FRESA.CAD/R/plot.bootstrapValidation.Res.R | 17 FRESA.CAD-3.0.0/FRESA.CAD/R/plotModels.ROC.R | 178 - FRESA.CAD-3.0.0/FRESA.CAD/R/predictForFresa.R | 134 FRESA.CAD-3.0.0/FRESA.CAD/R/rankInverseNormalDataFrame.R | 13 FRESA.CAD-3.0.0/FRESA.CAD/R/reportEquivalentVariables.R | 234 + FRESA.CAD-3.0.0/FRESA.CAD/R/residualtForFRESA.R | 21 FRESA.CAD-3.0.0/FRESA.CAD/R/signatureDistance.r |only FRESA.CAD-3.0.0/FRESA.CAD/R/summary.bootstrapValidation.R | 98 FRESA.CAD-3.0.0/FRESA.CAD/R/summary.fitFRESA.R |only FRESA.CAD-3.0.0/FRESA.CAD/R/timeSerieAnalysis.R | 47 FRESA.CAD-3.0.0/FRESA.CAD/R/uniRankVar.R | 1432 +++++----- FRESA.CAD-3.0.0/FRESA.CAD/R/univariateRankVariables.R | 4 FRESA.CAD-3.0.0/FRESA.CAD/R/update.uniRankVar.R | 2 FRESA.CAD-3.0.0/FRESA.CAD/R/updateModel.Bin.R | 314 -- FRESA.CAD-3.0.0/FRESA.CAD/R/updateModel.Res.R | 309 -- FRESA.CAD-3.0.0/FRESA.CAD/man/BSWiMS.Rd |only FRESA.CAD-3.0.0/FRESA.CAD/man/EmpiricalSurvDiff.Rd |only FRESA.CAD-3.0.0/FRESA.CAD/man/FRESA.CAD-package.Rd | 425 +- FRESA.CAD-3.0.0/FRESA.CAD/man/FRESA.Model.Rd | 83 FRESA.CAD-3.0.0/FRESA.CAD/man/ForwardModel.Bin.Rd | 57 FRESA.CAD-3.0.0/FRESA.CAD/man/ForwardModel.Res.Rd | 66 FRESA.CAD-3.0.0/FRESA.CAD/man/backVarElimination.Bin.Rd | 58 FRESA.CAD-3.0.0/FRESA.CAD/man/backVarElimination.Res.Rd | 58 FRESA.CAD-3.0.0/FRESA.CAD/man/baggedModel.Rd | 54 FRESA.CAD-3.0.0/FRESA.CAD/man/bootstrapValidation.Bin.Rd | 52 FRESA.CAD-3.0.0/FRESA.CAD/man/bootstrapValidation.Res.Rd | 60 FRESA.CAD-3.0.0/FRESA.CAD/man/bootstrapVarElimination.Bin.Rd | 78 FRESA.CAD-3.0.0/FRESA.CAD/man/bootstrapVarElimination.Res.Rd | 79 FRESA.CAD-3.0.0/FRESA.CAD/man/crossValidationFeatureSelection.Bin.Rd | 103 FRESA.CAD-3.0.0/FRESA.CAD/man/crossValidationFeatureSelection.Res.Rd | 93 FRESA.CAD-3.0.0/FRESA.CAD/man/ensemblePredict.Rd |only FRESA.CAD-3.0.0/FRESA.CAD/man/featureAdjustment.Rd | 34 FRESA.CAD-3.0.0/FRESA.CAD/man/getKNNpredictionFromFormula.Rd | 51 FRESA.CAD-3.0.0/FRESA.CAD/man/getSignature.Rd |only FRESA.CAD-3.0.0/FRESA.CAD/man/getVar.Bin.Rd | 54 FRESA.CAD-3.0.0/FRESA.CAD/man/getVar.Res.Rd | 54 FRESA.CAD-3.0.0/FRESA.CAD/man/heatMaps.Rd | 88 FRESA.CAD-3.0.0/FRESA.CAD/man/improvedResiduals.Rd | 55 FRESA.CAD-3.0.0/FRESA.CAD/man/modelFitting.Rd | 54 FRESA.CAD-3.0.0/FRESA.CAD/man/nearestneighborimpute.Rd |only FRESA.CAD-3.0.0/FRESA.CAD/man/plot.bootstrapValidation.Bin.Rd | 56 FRESA.CAD-3.0.0/FRESA.CAD/man/plot.bootstrapValidation.Res.Rd | 45 FRESA.CAD-3.0.0/FRESA.CAD/man/plotModels.ROC.Rd | 72 FRESA.CAD-3.0.0/FRESA.CAD/man/predictForFresa.Rd | 67 FRESA.CAD-3.0.0/FRESA.CAD/man/reportEquivalentVariables.Rd | 84 FRESA.CAD-3.0.0/FRESA.CAD/man/residualForFRESA.Rd | 51 FRESA.CAD-3.0.0/FRESA.CAD/man/signatureDistance.Rd |only FRESA.CAD-3.0.0/FRESA.CAD/man/summary.bootstrapValidation.Rd | 49 FRESA.CAD-3.0.0/FRESA.CAD/man/summary.fitFRESA.Rd |only FRESA.CAD-3.0.0/FRESA.CAD/man/summaryReport.Rd | 68 FRESA.CAD-3.0.0/FRESA.CAD/man/uniRankVar.Rd | 53 FRESA.CAD-3.0.0/FRESA.CAD/man/univariateRankVariables.Rd | 56 FRESA.CAD-3.0.0/FRESA.CAD/man/update.uniRankVar.Rd | 2 FRESA.CAD-3.0.0/FRESA.CAD/man/updateModel.Bin.Rd | 66 FRESA.CAD-3.0.0/FRESA.CAD/man/updateModel.Res.Rd | 75 FRESA.CAD-3.0.0/FRESA.CAD/src/FRESACAD_init.cpp |only FRESA.CAD-3.0.0/FRESA.CAD/src/FRESAcommons.cpp | 866 +++--- FRESA.CAD-3.0.0/FRESA.CAD/src/FRESAcommons.h | 37 FRESA.CAD-3.0.0/FRESA.CAD/src/binaryFeatureSelectionCpp.cpp | 411 +- FRESA.CAD-3.0.0/FRESA.CAD/src/outcheck.txt |only FRESA.CAD-3.0.0/FRESA.CAD/src/rankInverseNormalCpp.cpp | 4 FRESA.CAD-3.0.0/FRESA.CAD/src/regresionFeatureSelectionCpp.cpp | 320 +- 91 files changed, 5984 insertions(+), 5933 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-26 1.0-41
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-04 1.4.1
2016-06-13 1.4.0
2016-01-22 1.3.9
2015-10-19 1.3.8
2015-08-13 1.3.7
2015-07-27 1.3.6
2015-07-15 1.3.5
2015-02-14 1.02.12
2014-11-21 0.11.21
2014-05-27 0.05.21
2014-03-20 0.03.21
2013-08-27 0.3.8.27
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-01-20 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-18 1.1.0
2017-06-19 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-31 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-05-04 0.3.1
2017-04-18 0.3.0
2017-02-23 0.2.2
2016-07-09 0.2.1
2016-02-15 0.2.0
2016-02-10 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-02 1.3.2
2017-06-15 1.3.0
2017-03-27 1.2.2
2017-03-12 1.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-12 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-09 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-12 0.1.0
Title: Roll Call Analysis Software
Description: Estimates Poole and Rosenthal W-NOMINATE scores from roll
call votes supplied though a 'rollcall' object from package
'pscl'.
Author: Keith Poole <ktpoole@uga.edu>, Jeffrey Lewis
<jblewis@ucla.edu>, James Lo <lojames@usc.edu> and Royce
Carroll <rcarroll@rice.edu>
Maintainer: ORPHANED
Diff between wnominate versions 1.2 dated 2016-07-30 and 1.2.1 dated 2018-02-01
wnominate-1.2.1/wnominate/DESCRIPTION | 10 ++++++---- wnominate-1.2.1/wnominate/MD5 | 10 +++++----- wnominate-1.2.1/wnominate/build/vignette.rds |binary wnominate-1.2.1/wnominate/inst/doc/wnominate.pdf |binary wnominate-1.2.1/wnominate/src/init.c |only wnominate-1.2.1/wnominate/src/wnominate.f90 | 14 +++++++------- wnominate-1.2/wnominate/src/Makevars |only 7 files changed, 18 insertions(+), 16 deletions(-)
Title: Bayes Screening and Model Discrimination
Description: Bayes screening and model discrimination follow-up designs.
Author: Ernesto Barrios based on Daniel Meyer's code.
Maintainer: ORPHANED
Diff between BsMD versions 2013.0718 dated 2013-07-19 and 2013.0718-1 dated 2018-02-01
DESCRIPTION | 13 ++++++++----- MD5 | 7 ++++--- NAMESPACE | 1 + src/bsmd.f | 4 ++-- src/init.c |only 5 files changed, 15 insertions(+), 10 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-18 3.1-0
2012-06-05 2.1-0
2012-05-07 2.0-0
2011-10-20 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-07 0.98
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-06 1.0.2
2015-08-08 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-25 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-02-17 2.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-05-23 0.1-3
2012-05-09 0.1-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-07 1.1-1
2013-11-15 1.1
2013-07-22 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-22 0.6-8
2017-11-15 0.6-7
2017-07-28 0.6-6
2017-06-06 0.6-5
2017-04-25 0.6-4
2016-12-14 0.6-3
2016-11-23 0.6-2
2016-10-11 0.6-1
2016-09-02 0.6
Title: Recurrent Event Regression
Description: A collection of regression models for recurrent event process and failure time.
Available methods include these from Xu et al. (2017) <doi:10.1080/01621459.2016.1173557>,
Lin et al. (2000) <doi:10.1111/1467-9868.00259>,
Wang et al. (2001) <doi:10.1198/016214501753209031>,
Ghosh and Lin (2003) <doi:10.1111/j.0006-341X.2003.00102.x>, and
Huang and Wang (2004) <doi:10.1198/016214504000001033>.
Author: Sy Han (Steven) Chiou
Maintainer: Sy Han (Steven) Chiou <schiou@utdallas.edu>
Diff between reReg versions 1.1-0 dated 2017-12-22 and 1.1-1 dated 2018-02-01
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/plot.reReg.Rd | 2 +- man/plotHaz.Rd | 2 +- man/plotRate.Rd | 2 +- man/reReg.Rd | 4 ++-- 6 files changed, 14 insertions(+), 14 deletions(-)
Title: Visual Regression Testing and Graphical Diffing
Description: An extension to the 'testthat' package that makes it easy
to add graphical unit tests. It provides a Shiny application to
manage the test cases.
Author: Lionel Henry [cre, aut],
RStudio [cph],
Carl Sutherland [aut] (jg-imagediff library),
Humble Software [cph] (jg-imagediff library),
David Hong [aut] (TwoFace library),
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/htmlwidgets/lib/jquery-authors.txt)
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between vdiffr versions 0.2.1 dated 2017-10-09 and 0.2.2 dated 2018-02-01
DESCRIPTION | 6 - MD5 | 10 +- NEWS.md | 11 +++ R/testthat-ui.R | 35 ++++++---- tests/testthat/mock-pkg-skip-newer/tests/testthat/test-skip-newer.R | 4 - tests/testthat/mock-pkg-skip-older/tests/testthat/test-skip-newer.R | 4 - 6 files changed, 46 insertions(+), 24 deletions(-)
Title: Orthogonalizing EM
Description: Solves penalized least squares problems for big tall data
using the orthogonalizing EM algorithm of Xiong et al. (2016) <doi:
10.1080/00401706.2015.1054436>. The main fitting function is oem() and the
functions cv.oem() and xval.oem() are for cross validation, the latter being an
accelerated cross validation function for linear models. The big.oem() function
allows for out of memory fitting.
Author: Bin Dai [aut],
Jared Huling [aut, cre],
Yixuan Qiu [ctb],
Gael Guennebaud [cph],
Jitse Niesen [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between oem versions 2.0.6 dated 2017-07-08 and 2.0.7 dated 2018-02-01
DESCRIPTION | 15 +- MD5 | 36 +++--- R/big_oem.R | 71 +++++++++--- R/cv_oem.R | 2 R/methods.R | 2 R/oem_xtx.R | 2 R/oem_xval.R | 2 R/utils.R | 47 ++++---- README.md | 151 +++++++++++++-------------- build/vignette.rds |binary inst/doc/oem_vignette.Rmd | 6 - inst/doc/oem_vignette.html | 232 +++++++++++++----------------------------- man/big.oem.Rd | 4 man/cv.oem.Rd | 4 man/oem.xtx.Rd | 4 man/xval.oem.Rd | 4 src/oem_fb_big.cpp |only vignettes/The_oem_Package.pdf |only vignettes/mult-1.png |binary vignettes/oem_vignette.Rmd | 6 - 20 files changed, 273 insertions(+), 315 deletions(-)