Title: Download DBnomics Data
Description: R access to hundreds of millions data series from DBnomics API
(<https://db.nomics.world/>).
Author: Sebastien Galais [cre, ctb],
Thomas Brand [aut]
Maintainer: Sebastien Galais <s915.stem@gmail.com>
Diff between rdbnomics versions 0.4.7 dated 2019-03-19 and 0.5.0 dated 2019-09-23
DESCRIPTION | 18 MD5 | 43 - NEWS.md | 8 R/rdb.R | 64 ++ R/rdb_by_api_link.R | 330 +++++++++++++ R/rdb_last_updates.R | 18 R/rdb_providers.R | 18 R/rdbnomics.R | 5 R/sysdata.rda |binary R/utils.R | 233 +++++++++ R/zzz.R | 7 README.md | 227 ++++++++- build/vignette.rds |binary inst/doc/rdbnomics.R | 99 +++- inst/doc/rdbnomics.Rmd | 166 +++++-- inst/doc/rdbnomics.html | 802 ++++++++++++++++++++-------------- man/rdb.Rd | 42 + man/rdb_by_api_link.Rd | 51 +- man/rdb_last_updates.Rd | 18 man/rdb_providers.Rd | 18 tests/testthat/test-rdb_by_api_link.R | 9 vignettes/dbnomics005.png |only vignettes/rdbnomics.Rmd | 166 +++++-- 23 files changed, 1779 insertions(+), 563 deletions(-)
Title: Tools to Visualize, Manipulate, and Summarize MCMC Output
Description: Performs key functions for MCMC analysis using minimal code - visualizes, manipulates, and summarizes MCMC output. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and 'publication-ready' output. MCMC output may be derived from Bayesian model output fit with JAGS, Stan, or other MCMC samplers.
Author: Casey Youngflesh [aut, cre] (<https://orcid.org/0000-0001-6343-3311>),
Christian Che-Castaldo [aut] (<https://orcid.org/0000-0002-7670-2178>),
Tyler Hardy [ctb]
Maintainer: Casey Youngflesh <caseyyoungflesh@gmail.com>
Diff between MCMCvis versions 0.12.2 dated 2019-02-24 and 0.13.0 dated 2019-09-23
MCMCvis-0.12.2/MCMCvis/R/data.R |only MCMCvis-0.13.0/MCMCvis/DESCRIPTION | 10 MCMCvis-0.13.0/MCMCvis/MD5 | 44 MCMCvis-0.13.0/MCMCvis/NEWS.md | 32 MCMCvis-0.13.0/MCMCvis/R/MCMC_data.R |only MCMCvis-0.13.0/MCMCvis/R/MCMC_data2.R |only MCMCvis-0.13.0/MCMCvis/R/MCMCchains.R | 65 - MCMCvis-0.13.0/MCMCvis/R/MCMCplot.R | 1120 +++++++++++------- MCMCvis-0.13.0/MCMCvis/R/MCMCpstr.R | 16 MCMCvis-0.13.0/MCMCvis/R/MCMCsummary.R | 755 ++++++------ MCMCvis-0.13.0/MCMCvis/R/MCMCtrace.R | 1220 ++++++++++---------- MCMCvis-0.13.0/MCMCvis/build/vignette.rds |binary MCMCvis-0.13.0/MCMCvis/data/MCMC_data2.rda |only MCMCvis-0.13.0/MCMCvis/data/datalist |only MCMCvis-0.13.0/MCMCvis/inst/doc/MCMCvis.R | 112 + MCMCvis-0.13.0/MCMCvis/inst/doc/MCMCvis.Rmd | 190 ++- MCMCvis-0.13.0/MCMCvis/inst/doc/MCMCvis.html | 509 ++++---- MCMCvis-0.13.0/MCMCvis/man/MCMC_data.Rd | 7 MCMCvis-0.13.0/MCMCvis/man/MCMC_data2.Rd |only MCMCvis-0.13.0/MCMCvis/man/MCMCchains.Rd | 4 MCMCvis-0.13.0/MCMCvis/man/MCMCplot.Rd | 46 MCMCvis-0.13.0/MCMCvis/man/MCMCpstr.Rd | 2 MCMCvis-0.13.0/MCMCvis/man/MCMCsummary.Rd | 21 MCMCvis-0.13.0/MCMCvis/man/MCMCtrace.Rd | 26 MCMCvis-0.13.0/MCMCvis/tests/testthat/test_master.R | 168 ++ MCMCvis-0.13.0/MCMCvis/vignettes/MCMCvis.Rmd | 190 ++- 26 files changed, 2689 insertions(+), 1848 deletions(-)
Title: Programmatic Analysis of Sediment Cores Using Computed
Tomography Imaging
Description: Computed tomography (CT) imaging is a powerful tool for understanding the composition of sediment cores. This package streamlines and accelerates the analysis of CT data generated in the context of environmental science. Included are tools for processing raw DICOM images to characterize sediment composition (sand, peat, etc.). Root analyses are also enabled, including measures of external surface area and volumes for user-defined root size classes. For a detailed description of the application of computed tomography imaging for sediment characterization, see: Davey, E., C. Wigand, R. Johnson, K. Sundberg, J. Morris, and C. Roman. (2011) <DOI: 10.1890/10-2037.1>.
Author: Troy D. Hill [aut, cre] (<https://orcid.org/0000-0003-2980-4099>),
Earl Davey [ctb]
Maintainer: Troy D. Hill <Hill.Troy@gmail.com>
Diff between coreCT versions 1.2.3 dated 2018-06-24 and 1.3.0 dated 2019-09-23
DESCRIPTION | 23 +- MD5 | 40 ++-- NAMESPACE | 1 NEWS | 18 ++ R/conv.R | 68 +++++--- R/convDir.R | 34 +--- R/coreHist.R | 57 ++++-- R/getSurface.R | 8 R/rootSize.R | 60 +++++-- R/rootSizeDir.R | 31 +-- R/voxDims.R | 2 README.md | 40 ++-- build/vignette.rds |binary inst/doc/Using_coreCT.html | 367 +++++++++++---------------------------------- man/conv.Rd | 28 --- man/convDir.Rd | 22 -- man/coreHist.Rd | 23 -- man/getSurface.Rd | 3 man/rootSize.Rd | 17 -- man/rootSizeDir.Rd | 18 -- tests |only 21 files changed, 368 insertions(+), 492 deletions(-)
More information about Phase12Compare at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-09-07 0.1.0
Title: A Graph-Based Test for Comparing Multivariate Distributions in
the Multi Sample Framework
Description: We introduce a nonparametric, graphical test based on optimal matching for assessing whether multiple unknown multivariate probability distributions are equal. This method is consistent, and does not make any distributional assumptions on the data. Our procedure combines data that belong to different classes or groups to create a graph on the pooled data, and then utilizes the number of edges connecting data points from different classes to examine equality of distributions among the classes. The functions available through this package implement the work described here: <arXiv:1906.04776>.
Author: Somabha Mukherjee <somabha@wharton.upenn.edu>
Divyansh Agarwal <divyansh.agarwal@pennmedicine.upenn.edu>
Bhaswar Bhattacharya <bhaswar@wharton.upenn.edu>
Nancy R. Zhang <nzh@wharton.upenn.edu>
Maintainer: Divyansh Agarwal <divyansh.agarwal@pennmedicine.upenn.edu>
Diff between multicross versions 1.0.0 dated 2019-06-03 and 2.0.0 dated 2019-09-23
DESCRIPTION | 16 +++--- MD5 | 14 +++-- NAMESPACE | 10 ++++ R/multicross.R | 127 ++++++++++++++++++++++++++++++++++++++++++++++++++-- man/matchpar.Rd |only man/mhcccreate.Rd | 4 - man/multigene.Rd |only man/scPath.Rd |only man/select_class.Rd | 4 - man/split_mat.Rd |only 10 files changed, 156 insertions(+), 19 deletions(-)
Title: Computations over Distributed Data without Aggregation
Description: Implementing algorithms and fitting models when sites (possibly remote) share
computation summaries rather than actual data over HTTP with a master R process (using
'opencpu', for example). A stratified Cox model and a singular value decomposition are
provided. The former makes direct use of code from the R 'survival' package. (That is,
the underlying Cox model code is derived from that in the R 'survival' package.)
Sites may provide data via several means: CSV files, Redcap API, etc. An extensible
design allows for new methods to be added in the future and includes facilities
for local prototyping and testing. Web applications are provided (via 'shiny') for
the implemented methods to help in designing and deploying the computations.
Author: Balasubramanian Narasimhan [aut, cre],
Marina Bendersky [aut],
Sam Gross [aut],
Terry M. Therneau [ctb],
Thomas Lumley [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between distcomp versions 1.0-1 dated 2017-05-16 and 1.1 dated 2019-09-23
distcomp-1.0-1/distcomp/inst/ex/Rprofile |only distcomp-1.1/distcomp/DESCRIPTION | 18 distcomp-1.1/distcomp/MD5 | 38 distcomp-1.1/distcomp/R/coxstuff.R | 469 +++++---- distcomp-1.1/distcomp/R/distcomp.R | 53 - distcomp-1.1/distcomp/R/svdstuff.R | 486 +++++----- distcomp-1.1/distcomp/README.md | 91 - distcomp-1.1/distcomp/build |only distcomp-1.1/distcomp/inst/doc/prototyping.R |only distcomp-1.1/distcomp/inst/doc/prototyping.Rmd |only distcomp-1.1/distcomp/inst/doc/prototyping.html |only distcomp-1.1/distcomp/inst/extdata |only distcomp-1.1/distcomp/inst/stuff |only distcomp-1.1/distcomp/inst/webApps/dataschema |only distcomp-1.1/distcomp/inst/webApps/definitionApp/defineNewCoxModel/server.R | 314 +++--- distcomp-1.1/distcomp/inst/webApps/definitionApp/defineNewSVDModel/server.R | 326 +++--- distcomp-1.1/distcomp/inst/webApps/setupWorkerApp/setupCoxWorker/server.R | 257 ++--- distcomp-1.1/distcomp/man/CoxMaster.Rd | 10 distcomp-1.1/distcomp/man/CoxWorker.Rd | 2 distcomp-1.1/distcomp/man/SVDMaster.Rd | 10 distcomp-1.1/distcomp/man/SVDWorker.Rd | 3 distcomp-1.1/distcomp/man/distcompSetup.Rd | 27 distcomp-1.1/distcomp/vignettes |only 23 files changed, 1097 insertions(+), 1007 deletions(-)
Title: eBird Data Extraction and Processing in R
Description: Extract and process bird sightings records from
eBird (<http://ebird.org>), an online tool for recording bird
observations. Public access to the full eBird database is via the
eBird Basic Dataset (EBD; see <http://ebird.org/ebird/data/download>
for access), a downloadable text file. This package is an interface to
AWK for extracting data from the EBD based on taxonomic, spatial, or
temporal filters, to produce a manageable file size that can be
imported into R.
Author: Matthew Strimas-Mackey [aut, cre]
(<https://orcid.org/0000-0001-8929-7776>),
Eliot Miller [aut],
Wesley Hochachka [aut],
Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between auk versions 0.3.3 dated 2019-06-23 and 0.4.0 dated 2019-09-23
DESCRIPTION | 6 ++-- MD5 | 62 +++++++++++++++++++++--------------------- NAMESPACE | 3 ++ NEWS.md | 6 ++++ R/auk-date.r | 2 - R/auk-ebd.r | 10 ++++-- R/auk-filter.r | 46 ++++++++++++++++++++++++------- R/auk-observer.R |only R/auk-sampling.r | 9 ++++-- R/auk-version.r | 6 ++-- R/auk-zerofill.r | 7 ++-- build/vignette.rds |binary data/ebird_taxonomy.rda |binary inst/doc/auk.html | 18 +++++++----- inst/doc/development.html | 6 +++- man/auk_bbox.Rd | 3 +- man/auk_bcr.Rd | 3 +- man/auk_breeding.Rd | 3 +- man/auk_complete.Rd | 3 +- man/auk_country.Rd | 3 +- man/auk_date.Rd | 5 ++- man/auk_distance.Rd | 3 +- man/auk_duration.Rd | 3 +- man/auk_extent.Rd | 3 +- man/auk_filter.Rd | 3 +- man/auk_last_edited.Rd | 7 ++-- man/auk_observer.Rd |only man/auk_project.Rd | 5 ++- man/auk_protocol.Rd | 5 ++- man/auk_species.Rd | 5 ++- man/auk_state.Rd | 5 ++- man/auk_time.Rd | 5 ++- tests/testthat/test_filters.r | 15 ++++++++++ 33 files changed, 171 insertions(+), 89 deletions(-)
Title: Robust Model-Based Clustering
Description: Performs robust cluster analysis allowing for outliers and noise that cannot be fitted by any cluster. The data are modelled by a mixture of Gaussian distributions and a noise component, which is an improper uniform distribution covering the whole Euclidean space. Parameters are estimated by (pseudo) maximum likelihood. This is fitted by a EM-type algorithm. See Coretto and Hennig (2016) <doi:10.1080/01621459.2015.1100996>, and Coretto and Hennig (2017) <http://jmlr.org/papers/v18/16-382.html>.
Author: Pietro Coretto [aut, cre],
Christian Hennig [aut]
Maintainer: Pietro Coretto <pcoretto@unisa.it>
Diff between otrimle versions 1.0 dated 2017-06-27 and 1.2 dated 2019-09-23
ChangeLog | 11 +++++++---- DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- NAMESPACE | 4 +++- R/otrimle.R | 1 + inst/CITATION | 21 +++++++++++---------- 6 files changed, 34 insertions(+), 26 deletions(-)
Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between NAM versions 1.7.2 dated 2019-04-12 and 1.7.3 dated 2019-09-23
DESCRIPTION | 13 MD5 | 40 - NAMESPACE | 1 R/RcppExports.R | 302 +++++---- R/gmm.R | 95 --- R/reml.R | 11 R/snp.R | 63 -- build/vignette.rds |binary inst/add/wgrMIXED.R | 107 +-- inst/doc/gwa_description.pdf |binary inst/doc/vignette1.Rmd | 10 inst/doc/vignette1.html | 1301 ++++++++++++++++++++++++++----------------- inst/doc/vignette2.R | 38 - inst/doc/vignette2.html | 463 +++++++++------ man/Internals.Rd | 8 man/NAM-package.Rd | 4 man/gmm.Rd | 8 man/snpQC.Rd | 7 src/Functions.cpp | 396 ++++++++++++- src/RcppExports.cpp | 55 + vignettes/vignette1.Rmd | 10 21 files changed, 1829 insertions(+), 1103 deletions(-)
Title: Miscellaneous Functions for the USGS INL Project Office
Description: A collection of functions for creating high-level graphics,
performing raster-based analysis, processing MODFLOW-based models,
selecting subsets using a genetic algorithm, creating interactive web maps,
accessing color palettes, etc. Used to support packages and scripts written
by researchers at the United States Geological Survey (USGS)
Idaho National Laboratory (INL) Project Office.
Author: Jason C. Fisher [aut, cre] (<https://orcid.org/0000-0001-9032-8912>)
Maintainer: Jason C. Fisher <jfisher@usgs.gov>
Diff between inlmisc versions 0.4.7 dated 2019-08-06 and 0.4.8 dated 2019-09-23
inlmisc-0.4.7/inlmisc/R/PrintHelpPages.R |only inlmisc-0.4.7/inlmisc/man/PrintHelpPages.Rd |only inlmisc-0.4.8/inlmisc/DESCRIPTION | 12 inlmisc-0.4.8/inlmisc/LICENSE.note | 5 inlmisc-0.4.8/inlmisc/MD5 | 198 ++--- inlmisc-0.4.8/inlmisc/NAMESPACE | 2 inlmisc-0.4.8/inlmisc/NEWS.md | 35 inlmisc-0.4.8/inlmisc/R/AddColorKey.R | 14 inlmisc-0.4.8/inlmisc/R/AddGradientLegend.R | 10 inlmisc-0.4.8/inlmisc/R/AddInsetMap.R | 16 inlmisc-0.4.8/inlmisc/R/AddIntervals.R | 2 inlmisc-0.4.8/inlmisc/R/AddNorthArrow.R | 5 inlmisc-0.4.8/inlmisc/R/AddPoints.R | 21 inlmisc-0.4.8/inlmisc/R/AddScaleBar.R | 13 inlmisc-0.4.8/inlmisc/R/AddWebMapElements.R | 21 inlmisc-0.4.8/inlmisc/R/BuildVignettes.R | 20 inlmisc-0.4.8/inlmisc/R/BumpDisconnectCells.R | 2 inlmisc-0.4.8/inlmisc/R/BumpRiverStage.R | 2 inlmisc-0.4.8/inlmisc/R/CreateWebMap.R | 11 inlmisc-0.4.8/inlmisc/R/Deprecated.R | 9 inlmisc-0.4.8/inlmisc/R/ExportRasterStack.R | 14 inlmisc-0.4.8/inlmisc/R/ExtractAlongTransect.R | 27 inlmisc-0.4.8/inlmisc/R/FindOptimalSubset.R | 31 inlmisc-0.4.8/inlmisc/R/FormatPval.R | 4 inlmisc-0.4.8/inlmisc/R/GetColors.R | 93 +- inlmisc-0.4.8/inlmisc/R/GetDaysInMonth.R | 2 inlmisc-0.4.8/inlmisc/R/GetInsetLocation.R | 2 inlmisc-0.4.8/inlmisc/R/GetRegionOfInterest.R | 8 inlmisc-0.4.8/inlmisc/R/Grid2Polygons.R | 108 +- inlmisc-0.4.8/inlmisc/R/POSIXct2Character.R | 10 inlmisc-0.4.8/inlmisc/R/PlotCrossSection.R | 56 - inlmisc-0.4.8/inlmisc/R/PlotGraph.R | 24 inlmisc-0.4.8/inlmisc/R/PlotMap.R | 36 inlmisc-0.4.8/inlmisc/R/PrintFigure.R | 19 inlmisc-0.4.8/inlmisc/R/PrintPackageHelp.R |only inlmisc-0.4.8/inlmisc/R/PrintTable.R | 52 - inlmisc-0.4.8/inlmisc/R/ReadCodeChunks.R | 15 inlmisc-0.4.8/inlmisc/R/ReadModflowBinary.R | 4 inlmisc-0.4.8/inlmisc/R/RecreateLibrary.R | 36 inlmisc-0.4.8/inlmisc/R/ReplaceInTemplate.R | 2 inlmisc-0.4.8/inlmisc/R/RmSmallCellChunks.R | 4 inlmisc-0.4.8/inlmisc/R/SetHinge.R | 55 - inlmisc-0.4.8/inlmisc/R/SetPolygons.R | 60 - inlmisc-0.4.8/inlmisc/R/SummariseBudget.R | 2 inlmisc-0.4.8/inlmisc/R/sysdata.rda |binary inlmisc-0.4.8/inlmisc/R/usgs_article.R | 24 inlmisc-0.4.8/inlmisc/README.md | 6 inlmisc-0.4.8/inlmisc/inst/misc/latex-packages.txt |only inlmisc-0.4.8/inlmisc/inst/misc/preamble.tex | 8 inlmisc-0.4.8/inlmisc/inst/raw/LICENSE-2.0.txt |only inlmisc-0.4.8/inlmisc/inst/raw/build-datasets.R | 387 ++++++++-- inlmisc-0.4.8/inlmisc/inst/raw/render-tables.R | 17 inlmisc-0.4.8/inlmisc/inst/rmarkdown/templates/usgs_article/skeleton/usgs.sty | 4 inlmisc-0.4.8/inlmisc/man/AddColorKey.Rd | 14 inlmisc-0.4.8/inlmisc/man/AddGradientLegend.Rd | 10 inlmisc-0.4.8/inlmisc/man/AddInsetMap.Rd | 16 inlmisc-0.4.8/inlmisc/man/AddIntervals.Rd | 2 inlmisc-0.4.8/inlmisc/man/AddNorthArrow.Rd | 5 inlmisc-0.4.8/inlmisc/man/AddPoints.Rd | 22 inlmisc-0.4.8/inlmisc/man/AddScaleBar.Rd | 13 inlmisc-0.4.8/inlmisc/man/AddWebMapElements.Rd | 21 inlmisc-0.4.8/inlmisc/man/BuildVignettes.Rd | 14 inlmisc-0.4.8/inlmisc/man/BumpDisconnectCells.Rd | 2 inlmisc-0.4.8/inlmisc/man/BumpRiverStage.Rd | 2 inlmisc-0.4.8/inlmisc/man/CreateWebMap.Rd | 11 inlmisc-0.4.8/inlmisc/man/Deprecated.Rd | 3 inlmisc-0.4.8/inlmisc/man/ExportRasterStack.Rd | 15 inlmisc-0.4.8/inlmisc/man/ExtractAlongTransect.Rd | 27 inlmisc-0.4.8/inlmisc/man/FindOptimalSubset.Rd | 27 inlmisc-0.4.8/inlmisc/man/FindPolyNodes.Rd | 2 inlmisc-0.4.8/inlmisc/man/FormatPval.Rd | 4 inlmisc-0.4.8/inlmisc/man/GetColors.Rd | 39 - inlmisc-0.4.8/inlmisc/man/GetDaysInMonth.Rd | 2 inlmisc-0.4.8/inlmisc/man/GetInsetLocation.Rd | 2 inlmisc-0.4.8/inlmisc/man/GetRegionOfInterest.Rd | 8 inlmisc-0.4.8/inlmisc/man/Grid2Polygons.Rd | 12 inlmisc-0.4.8/inlmisc/man/IsColor.Rd | 2 inlmisc-0.4.8/inlmisc/man/IsPackageInstalled.Rd | 2 inlmisc-0.4.8/inlmisc/man/POSIXct2Character.Rd | 11 inlmisc-0.4.8/inlmisc/man/PlotCrossSection.Rd | 51 - inlmisc-0.4.8/inlmisc/man/PlotGraph.Rd | 24 inlmisc-0.4.8/inlmisc/man/PlotMap.Rd | 36 inlmisc-0.4.8/inlmisc/man/PrintFigure.Rd | 19 inlmisc-0.4.8/inlmisc/man/PrintPackageHelp.Rd |only inlmisc-0.4.8/inlmisc/man/PrintTable.Rd | 53 - inlmisc-0.4.8/inlmisc/man/ReadCodeChunks.Rd | 16 inlmisc-0.4.8/inlmisc/man/ReadModflowBinary.Rd | 4 inlmisc-0.4.8/inlmisc/man/RecreateLibrary.Rd | 35 inlmisc-0.4.8/inlmisc/man/ReplaceInTemplate.Rd | 2 inlmisc-0.4.8/inlmisc/man/RmSmallCellChunks.Rd | 5 inlmisc-0.4.8/inlmisc/man/SetHinge.Rd | 39 - inlmisc-0.4.8/inlmisc/man/SetPolygons.Rd | 39 - inlmisc-0.4.8/inlmisc/man/SummariseBudget.Rd | 2 inlmisc-0.4.8/inlmisc/man/figures/table01.pdf |binary inlmisc-0.4.8/inlmisc/man/figures/table01.svg | 2 inlmisc-0.4.8/inlmisc/man/figures/table02.pdf |binary inlmisc-0.4.8/inlmisc/man/figures/table02.svg | 2 inlmisc-0.4.8/inlmisc/man/figures/table03.pdf |binary inlmisc-0.4.8/inlmisc/man/figures/table03.svg | 2 inlmisc-0.4.8/inlmisc/man/figures/table04.pdf |binary inlmisc-0.4.8/inlmisc/man/figures/table04.svg | 2 inlmisc-0.4.8/inlmisc/man/figures/table05.pdf |only inlmisc-0.4.8/inlmisc/man/figures/table05.svg |only inlmisc-0.4.8/inlmisc/man/usgs_article.Rd | 14 104 files changed, 1358 insertions(+), 785 deletions(-)
Title: Propensity to Cycle Tool
Description: Functions and example data to teach and
increase the reproducibility of the methods and code underlying
the Propensity to Cycle Tool (PCT), a research project and web application
hosted at <https://www.pct.bike/>.
For an academic paper on the methods,
see Lovelace et al (2017) <doi:10.5198/jtlu.2016.862>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between pct versions 0.2.5 dated 2019-08-29 and 0.2.6 dated 2019-09-23
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/get_pct.R | 16 ++++++++++------ inst/doc/pct-international.html | 26 +++++++++++++------------- inst/doc/pct.html | 22 +++++++++++----------- inst/doc/pct_training.html | 16 ++++++++-------- man/get_pct.Rd | 6 ++++-- man/get_pct_rnet.Rd | 4 ++-- 8 files changed, 58 insertions(+), 52 deletions(-)
Title: Fitting Linear Quantile Regression Mixed Models
Description: Fit a quantile regression mixed model using a sparse implementation of the
Frisch-Newton interior-point algorithm as described in
Portnoy and Koenker (1977, Statistical Science) <https://www.jstor.org/stable/2246217>.
Author: Sayyed Reza Alavian, Majid Sarmad, Mehdi Jabbari Nooghabi.(Ferdowsi University Of Mashhad)
Maintainer: Sayyed Reza Alavian <s.rezaalavian@mail.um.ac.ir>
Diff between LRQMM versions 1.1.1 dated 2019-09-17 and 1.1.10 dated 2019-09-23
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Cartography for Statistical Analysis
Description: Creating maps for statistical analysis such as proportional circles, chroropleth, typology and flows. Some functions use 'shiny' or 'leaflet' technologies for dynamism and interactivity.
The great features are :
- Create maps in a web environment where the parameters are modifiable on the fly ('shiny' and 'leaflet' technology).
- Create interactive maps through zoom and pop-up ('leaflet' technology).
- Create frozen maps with the possibility to add labels.
Author: Sébastien CALVET - PSAR-AT - DR Provence-Alpes-Cote d'Azur - INSEE [cre, aut],
Sophie AUDRIC - PSAR-AT - DR Provence-Alpes-Cote d'Azur - INSEE [aut],
SED - DR Hauts-de-France - INSEE [ctb],
PSAR-SL - DR Auvergne-Rhone-Alpes - INSEE [ctb],
PSAR-EEP - DR Occitanie - INSEE [ctb],
SED - DR Pays-de-la-Loire - INSEE [ctb]
Maintainer: Sébastien CALVET <sebastien.calvet@insee.fr>
Diff between oceanis versions 1.0.1 dated 2019-08-28 and 1.0.4 dated 2019-09-23
DESCRIPTION | 10 ++-- MD5 | 66 +++++++++++++-------------- NEWS | 21 ++++++++ R/add_fond_osm.R | 25 ++++++++-- R/extract_fond_leaflet_classes.R | 33 ++----------- R/extract_fond_leaflet_classes_ronds.R | 78 +++++++++++++-------------------- R/extract_fond_leaflet_joignantes.R | 39 +--------------- R/extract_fond_leaflet_oursins.R | 38 +--------------- R/extract_fond_leaflet_ronds.R | 22 +-------- R/extract_fond_leaflet_ronds_classes.R | 62 ++++++++++---------------- R/extract_fond_leaflet_saphirs.R | 38 +--------------- R/extract_fond_leaflet_typo.R | 31 ------------- R/leafletVerifParamClassesRonds.R | 2 R/leaflet_classes.R | 23 +++++++-- R/leaflet_classes_ronds.R | 23 +++++++-- R/leaflet_joignantes.R | 25 ++++++++-- R/leaflet_oursins.R | 25 ++++++++-- R/leaflet_ronds.R | 23 +++++++-- R/leaflet_ronds_classes.R | 28 ++++++++--- R/leaflet_saphirs.R | 25 ++++++++-- R/leaflet_typo.R | 23 +++++++-- R/sf_reg02.R | 2 build/partial.rdb |binary inst/doc/integration_shiny.Rmd | 12 +++++ inst/doc/integration_shiny.html | 12 +++++ inst/doc/oceanis.R | 4 - inst/doc/oceanis.Rmd | 4 - inst/doc/oceanis.html | 4 - man/add_fond_osm.Rd | 15 +++++- man/add_legende.Rd | 1 man/leaflet.Rd | 21 +++++--- man/oceanis-package.Rd | 10 ++-- vignettes/integration_shiny.Rmd | 12 +++++ vignettes/oceanis.Rmd | 4 - 34 files changed, 382 insertions(+), 379 deletions(-)
Title: Procedures for Ecological Assessment of Surface Waters
Description: Functions for evaluating and visualizing
ecological assessment procedures for surface waters
containing physical, chemical and biological assessments
in the form of value functions.
Author: Nele Schuwirth <nele.schuwirth@eawag.ch> and Peter Reichert <peter.reichert@eawag.ch>
with contributions by Simone Langhans and Christian Michel
Maintainer: Nele Schuwirth <nele.schuwirth@eawag.ch>
Diff between ecoval versions 1.2.4 dated 2019-05-14 and 1.2.5 dated 2019-09-23
DESCRIPTION | 8 ++-- MD5 | 20 +++++----- R/msk.macrophytes.2017.plaus.crit.R | 8 ++-- R/msk.macrophytes.2017.prepare.data.R | 66 ++++++++++++++++++++++++++++++++-- data/ecoval_data.RData |binary inst/NEWS | 8 ++++ inst/ecoval.dictionaries.default.dat | 5 ++ man/ecoval-package.Rd | 4 +- man/figures/lakemorphol2016.pdf |binary man/figures/lakemorphol2016French.pdf |binary man/figures/lakemorphol2016German.pdf |binary 11 files changed, 95 insertions(+), 24 deletions(-)
Title: Visible Vowels: Visualization of Vowel Variation
Description: Visualizes vowel variation in f0, F1, F2, F3 and duration.
Author: Wilbert Heeringa, Hans Van de Velde
Maintainer: Wilbert Heeringa <wjheeringa@gmail.com>
Diff between visvow versions 0.7.0 dated 2019-08-06 and 0.8.0 dated 2019-09-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/visvow.R | 46 +++++++++++++++++++++++++++++++++++----------- build/partial.rdb |binary 4 files changed, 41 insertions(+), 17 deletions(-)
Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest
Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the 'Rcpp' package,
exposing the same interface as the original Python wrapper to 'Annoy'. See
<https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released
under Version 2.0 of the Apache License. Also included is a small Windows
port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAnnoy versions 0.0.12 dated 2019-05-12 and 0.0.13 dated 2019-09-23
ChangeLog | 40 ++++ DESCRIPTION | 9 - MD5 | 27 +-- R/annoy.R | 10 - README.md | 20 +- build/vignette.rds |binary inst/NEWS.Rd | 16 + inst/doc/UsingAnnoyInCcppWrapper.pdf |binary inst/include/annoylib.h | 299 ++++++++++++++++++++++++++++------- inst/include/mman.h | 90 ++++++---- inst/tinytest/testIndex.R | 51 ++--- inst/tinytest/testOnDiskBuild.R |only inst/tinytest/testSeeds.R | 58 +++--- man/AnnoyIndex.Rd | 7 src/annoy.cpp | 31 +++ 15 files changed, 476 insertions(+), 182 deletions(-)
Title: Grades Setting and Exam Maker
Description: Programs to determine student grades and create
examinations from Question banks. Programs will create numerous
multiple choice exams, randomly shuffled, for different versions of same question list.
Author: Jonathan M. Lees [aut, cre]
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between ProfessR versions 2.3-5 dated 2017-03-13 and 2.4-1 dated 2019-09-23
DESCRIPTION | 12 +++++++----- MD5 | 25 ++++++++++++++++--------- R/GetStudentNames.R |only R/deblank.R |only R/getgroup.R |only build/vignette.rds |binary data/datalist |only inst/doc/ExamMaker.pdf |binary inst/doc/Grader.R | 9 +++------ inst/doc/Grader.pdf |binary man/DUMPbank.Rd | 4 ++++ man/Get.testbank.Rd | 2 -- man/GetStudentNames.Rd |only man/ProfessR-package.Rd | 3 ++- man/deblank.Rd |only man/getgroup.Rd |only man/prep.solution.Rd | 2 ++ 17 files changed, 34 insertions(+), 23 deletions(-)
Title: Graphical User Interface (GUI) for Interactive R Analysis
Sessions
Description: Really Poor Man's Graphical User Interface, used to create interactive R analysis sessions with simple R commands.
Author: Jonathan M. Lees [aut, cre],
Jake Anderson [ctb]
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between RPMG versions 2.2-2 dated 2018-01-18 and 2.2-3 dated 2019-09-23
DESCRIPTION | 10 ++++----- MD5 | 16 +++++++------- R/HOZscale.R | 57 ++++++++++++++++++++++++++++++++++++++++++++++------- R/circle.R | 7 +++--- man/HOZscale.Rd | 21 ++++++++++++++++++- man/circle.Rd | 3 +- man/jpng.Rd | 10 +++++---- man/jpostscript.Rd | 3 +- man/pickcolors.Rd | 19 +++++++++++++++++ 9 files changed, 116 insertions(+), 30 deletions(-)
Title: The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reduction
Description: An implementation of the Uniform Manifold Approximation and
Projection dimensionality reduction by McInnes et al. (2018)
<arXiv:1802.03426>. It also provides means to transform new data and to
carry out supervised dimensionality reduction. An implementation of the
related LargeVis method of Tang et al. (2016) <arXiv:1602.00370> is also
provided. This is a complete re-implementation in R (and C++, via the 'Rcpp'
package): no Python installation is required. See the uwot website
(<https://github.com/jlmelville/uwot>) for more documentation and examples.
Author: James Melville [aut, cre]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between uwot versions 0.1.3 dated 2019-04-07 and 0.1.4 dated 2019-09-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 10 ++++++++++ R/uwot.R | 5 +++-- src/optimize.cpp | 1 + 5 files changed, 21 insertions(+), 9 deletions(-)
Title: Technical Trading Rules
Description: Functions and data to construct technical trading rules with R.
Author: Joshua Ulrich
Maintainer: Joshua Ulrich <josh.m.ulrich@gmail.com>
Diff between TTR versions 0.23-4 dated 2018-09-20 and 0.23-5 dated 2019-09-23
TTR-0.23-4/TTR/src/movingAverages.f |only TTR-0.23-4/TTR/src/runFun.f |only TTR-0.23-5/TTR/DESCRIPTION | 6 TTR-0.23-5/TTR/MD5 | 113 ++++---- TTR-0.23-5/TTR/R/ADX.R | 6 TTR-0.23-5/TTR/R/ATR.R | 6 TTR-0.23-5/TTR/R/CCI.R | 1 TTR-0.23-5/TTR/R/CLV.R | 1 TTR-0.23-5/TTR/R/CMF.R | 1 TTR-0.23-5/TTR/R/CMO.R | 1 TTR-0.23-5/TTR/R/DPO.R | 7 TTR-0.23-5/TTR/R/DVI.R | 1 TTR-0.23-5/TTR/R/DonchianChannel.R | 1 TTR-0.23-5/TTR/R/EMV.R | 1 TTR-0.23-5/TTR/R/GMMA.R | 1 TTR-0.23-5/TTR/R/KST.R | 1 TTR-0.23-5/TTR/R/MACD.R | 1 TTR-0.23-5/TTR/R/MFI.R | 1 TTR-0.23-5/TTR/R/MovingAverages.R | 58 ---- TTR-0.23-5/TTR/R/OBV.R | 3 TTR-0.23-5/TTR/R/RSI.R | 6 TTR-0.23-5/TTR/R/SAR.R | 1 TTR-0.23-5/TTR/R/SNR.R | 1 TTR-0.23-5/TTR/R/TDI.R | 1 TTR-0.23-5/TTR/R/TRIX.R | 1 TTR-0.23-5/TTR/R/TTR-package.R | 5 TTR-0.23-5/TTR/R/TTRtools.R | 3 TTR-0.23-5/TTR/R/VHF.R | 1 TTR-0.23-5/TTR/R/WPR.R | 1 TTR-0.23-5/TTR/R/WebData.R | 4 TTR-0.23-5/TTR/R/ZigZag.R | 4 TTR-0.23-5/TTR/R/adjRatios.R | 1 TTR-0.23-5/TTR/R/aroon.R | 1 TTR-0.23-5/TTR/R/bollingerBands.R | 1 TTR-0.23-5/TTR/R/chaikinAD.R | 1 TTR-0.23-5/TTR/R/chaikinVolatility.R | 1 TTR-0.23-5/TTR/R/changes.R | 2 TTR-0.23-5/TTR/R/percentRank.R | 1 TTR-0.23-5/TTR/R/priceBands.R | 1 TTR-0.23-5/TTR/R/rollFun.R | 1 TTR-0.23-5/TTR/R/runFun.R | 242 ++++-------------- TTR-0.23-5/TTR/R/stochastics.R | 2 TTR-0.23-5/TTR/R/ultimateOscillator.R | 1 TTR-0.23-5/TTR/R/volatility.R | 1 TTR-0.23-5/TTR/R/williamsAD.R | 1 TTR-0.23-5/TTR/inst/unitTests/runit.TTR.Oscillators.R | 6 TTR-0.23-5/TTR/inst/unitTests/runit.TTR.Trend.R | 12 TTR-0.23-5/TTR/inst/unitTests/runit.TTR.runFun.R | 83 ++++++ TTR-0.23-5/TTR/man/DPO.Rd | 9 TTR-0.23-5/TTR/man/MovingAverages.Rd | 7 TTR-0.23-5/TTR/man/OBV.Rd | 2 TTR-0.23-5/TTR/man/TTRtools.Rd | 1 TTR-0.23-5/TTR/man/WebData.Rd | 1 TTR-0.23-5/TTR/man/ZigZag.Rd | 6 TTR-0.23-5/TTR/man/changes.Rd | 1 TTR-0.23-5/TTR/man/runFun.Rd | 10 TTR-0.23-5/TTR/src/init.c | 41 +-- TTR-0.23-5/TTR/src/moving_averages.c | 116 ++++++++ TTR-0.23-5/TTR/src/runfun.c |only 59 files changed, 401 insertions(+), 389 deletions(-)
Title: Density Estimation by Life Time Distributions
Description: It plots densities by using asymmetrical kernels which belong to
life time distributions and calculate its related MSE. For details see Chen (2000),
Jin and Kawczak (2003) and Salha et al. (2014) <doi:10.12988/pms.2014.4616>.
Author: Javaria Ahmad Khan, Atif Akbar.
Maintainer: Javaria Ahmad Khan <jakhan0@yahoo.com>
Diff between DELTD versions 0.1.0 dated 2019-07-11 and 1.2.1 dated 2019-09-23
DESCRIPTION | 6 +- MD5 | 16 +++--- NAMESPACE | 1 R/DELTD.R | 139 ++++++++++++++++++++++++++++++++++++++++++++++++++++---- man/dencomb.Rd |only man/mseBS.Rd | 2 man/mseEr.Rd | 2 man/mseGamma.Rd | 2 man/mseLN.Rd | 2 man/suicide.Rd |only 10 files changed, 148 insertions(+), 22 deletions(-)
Title: Linguistic Phonetic Fieldwork Tools
Description: There are a lot of different typical tasks that should be solved during phonetic research and experiments, such as creation of presentation that will contain all stimuli, rename and concatenate multiple sound files recorded during phonetic session, automatically annotate 'Praat' TextGrids (this is one of the sound annotation standards provided by 'Praat' software, see Paul Boersma, David Weenink 2018 <http://www.fon.hum.uva.nl/praat/>), create an html that includes annotation and spectrogram tables, convert multiple formats ('Praat' TextGrid, 'EXMARaLDA' and 'ELAN') into each other. All those tasks could be solved by mixture of different tools (some programs in any programming language for automatic renaming, some Praat scripts for the file concatenation and renaming, etc). This package provides functionality that will make it easier to solve those tasks independently of any of tools. You could also compare the functionality with other packages: 'rPraat' <https://CRAN.R-project.org/package=rPraat>, 'textgRid' <https://CRAN.R-project.org/package=textgRid>.
Author: George Moroz
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between phonfieldwork versions 0.0.1 dated 2019-08-24 and 0.0.2 dated 2019-09-23
phonfieldwork-0.0.1/phonfieldwork/README.md |only phonfieldwork-0.0.2/phonfieldwork/DESCRIPTION | 8 +- phonfieldwork-0.0.2/phonfieldwork/MD5 | 40 ++++++---- phonfieldwork-0.0.2/phonfieldwork/NAMESPACE | 14 +++ phonfieldwork-0.0.2/phonfieldwork/NEWS | 7 + phonfieldwork-0.0.2/phonfieldwork/R/add_leading_symbols.R |only phonfieldwork-0.0.2/phonfieldwork/R/concatenate_soundfiles.R | 10 +- phonfieldwork-0.0.2/phonfieldwork/R/create_presentation.R | 7 + phonfieldwork-0.0.2/phonfieldwork/R/create_viewer.R |only phonfieldwork-0.0.2/phonfieldwork/R/df_to_tier.R | 4 - phonfieldwork-0.0.2/phonfieldwork/R/draw_sound.R |only phonfieldwork-0.0.2/phonfieldwork/R/extract_intervals.R | 19 ++-- phonfieldwork-0.0.2/phonfieldwork/R/get_textgrid_names.R |only phonfieldwork-0.0.2/phonfieldwork/R/rename_soundfiles.R | 9 +- phonfieldwork-0.0.2/phonfieldwork/R/set_textgrid_names.R |only phonfieldwork-0.0.2/phonfieldwork/R/tier_to_df.R | 2 phonfieldwork-0.0.2/phonfieldwork/inst/CITATION |only phonfieldwork-0.0.2/phonfieldwork/inst/rmarkdown |only phonfieldwork-0.0.2/phonfieldwork/man/add_leading_symbols.Rd |only phonfieldwork-0.0.2/phonfieldwork/man/concatenate_soundfiles.Rd | 6 - phonfieldwork-0.0.2/phonfieldwork/man/create_presentation.Rd | 2 phonfieldwork-0.0.2/phonfieldwork/man/create_viewer.Rd |only phonfieldwork-0.0.2/phonfieldwork/man/draw_sound.Rd |only phonfieldwork-0.0.2/phonfieldwork/man/extract_intervals.Rd | 8 +- phonfieldwork-0.0.2/phonfieldwork/man/get_textgrid_names.Rd |only phonfieldwork-0.0.2/phonfieldwork/man/set_textgrid_names.Rd |only phonfieldwork-0.0.2/phonfieldwork/man/tier_to_df.Rd | 2 27 files changed, 83 insertions(+), 55 deletions(-)
Title: A Statistically Sound 'data.frame' Processor/Conditioner
Description: A 'data.frame' processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner.
'vtreat' prepares variables so that data has fewer exceptional cases, making
it easier to safely use models in production. Common problems 'vtreat' defends
against: 'Inf', 'NA', too many categorical levels, rare categorical levels, and new
categorical levels (levels seen during application, but not during training). Reference:
"'vtreat': a data.frame Processor for Predictive Modeling", Zumel, Mount, 2016, <DOI:10.5281/zenodo.1173313>.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 1.4.5 dated 2019-09-11 and 1.4.6 dated 2019-09-23
DESCRIPTION | 8 +++---- MD5 | 30 +++++++++++++-------------- README.md | 24 ++++++++++----------- inst/doc/MultiClassVtreat.html | 4 +-- inst/doc/SavingTreamentPlans.html | 4 +-- inst/doc/VariableImportance.html | 10 ++++----- inst/doc/vtreat.html | 6 ++--- inst/doc/vtreatCrossFrames.html | 38 +++++++++++++++++----------------- inst/doc/vtreatGrouping.html | 4 +-- inst/doc/vtreatOverfit.html | 38 +++++++++++++++++----------------- inst/doc/vtreatRareLevels.html | 4 +-- inst/doc/vtreatScaleMode.html | 16 +++++++------- inst/doc/vtreatSignificance.html | 18 ++++++++-------- inst/doc/vtreatSplitting.html | 4 +-- inst/doc/vtreatVariableTypes.html | 42 +++++++++++++++++++------------------- inst/doc/vtreat_article.pdf |binary 16 files changed, 125 insertions(+), 125 deletions(-)
Title: Download 'Qualtrics' Survey Data
Description: Provides functions to access survey results directly into R using
the 'Qualtrics' API. 'Qualtrics' <https://www.qualtrics.com/about/> is an
online survey and data collection software platform. See
<https://api.qualtrics.com/> for more information about the 'Qualtrics' API.
This package is community-maintained and is not officially supported by
'Qualtrics'.
Author: Jasper Ginn [aut],
Samuel Kaminsky [ctb],
Eric Knudsen [ctb],
Julia Silge [aut, cre] (<https://orcid.org/0000-0002-3671-836X>),
Phoebe Wong [ctb]
Maintainer: Julia Silge <julia.silge@gmail.com>
Diff between qualtRics versions 3.1.0 dated 2019-04-12 and 3.1.1 dated 2019-09-23
DESCRIPTION | 10 +- MD5 | 41 ++++++----- NAMESPACE | 5 - R/assertions.R | 52 ++++++++------ R/column_map.R |only R/deprecated.R | 6 - R/fetch_survey.R | 40 +---------- R/globals.R |only R/metadata.R | 18 ++--- R/read_survey.R | 39 ++++++++-- R/survey_questions.R | 49 +++++-------- R/utils.R | 132 +++++++++++++++++-------------------- R/zzz.R | 29 -------- inst/doc/qualtRics.html | 10 +- man/column_map.Rd |only man/download_qualtrics_export.Rd | 2 man/fetch_survey.Rd | 7 + man/getSurveyQuestions.Rd | 5 - man/metadata.Rd | 4 - man/read_survey.Rd | 13 ++- man/survey_questions.Rd | 2 man/wrapper_mc.Rd | 6 - tests/testthat/test-fetch-survey.R | 7 + 23 files changed, 229 insertions(+), 248 deletions(-)
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 0.2.2 dated 2019-08-21 and 0.2.3 dated 2019-09-23
ggimage-0.2.2/ggimage/README.md |only ggimage-0.2.3/ggimage/DESCRIPTION | 6 +++--- ggimage-0.2.3/ggimage/MD5 | 13 ++++++------- ggimage-0.2.3/ggimage/NEWS.md | 4 ++++ ggimage-0.2.3/ggimage/R/geom_icon.R | 3 ++- ggimage-0.2.3/ggimage/inst/doc/ggimage.Rmd | 4 ++++ ggimage-0.2.3/ggimage/inst/doc/ggimage.html | 5 +++-- ggimage-0.2.3/ggimage/vignettes/ggimage.Rmd | 4 ++++ 8 files changed, 26 insertions(+), 13 deletions(-)
Title: Assigns Colours to Values
Description: Maps one of the viridis colour palettes, or a user-specified palette to values.
Viridis colour maps are created by Stéfan van der Walt and Nathaniel Smith.
They were set as the default palette for the 'Python' 'Matplotlib' library,
introduced at SciPy 2015 conference <http://scipy2015.scipy.org/ehome/index.php?eventid=115969&>.
Other palettes available in this library have been derived from
'RColorBrewer' <https://CRAN.R-project.org/package=RColorBrewer> and
'colorspace' <https://CRAN.R-project.org/package=colorspace> packages.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between colourvalues versions 0.2.2 dated 2019-01-17 and 0.3.0 dated 2019-09-23
colourvalues-0.2.2/colourvalues/src/ColourValues_HEX.cpp |only colourvalues-0.2.2/colourvalues/src/ColourValues_RGB.cpp |only colourvalues-0.3.0/colourvalues/DESCRIPTION | 10 colourvalues-0.3.0/colourvalues/MD5 | 104 +-- colourvalues-0.3.0/colourvalues/NAMESPACE | 9 colourvalues-0.3.0/colourvalues/NEWS.md | 8 colourvalues-0.3.0/colourvalues/R/RcppExports.R | 76 -- colourvalues-0.3.0/colourvalues/R/colour_values_hex.R | 205 +++--- colourvalues-0.3.0/colourvalues/R/colour_values_rgb.R | 204 +++--- colourvalues-0.3.0/colourvalues/R/palettes.R | 26 colourvalues-0.3.0/colourvalues/R/scratch.R |only colourvalues-0.3.0/colourvalues/README.md | 130 ++-- colourvalues-0.3.0/colourvalues/inst/include/colourvalues/alpha/alpha.hpp | 13 colourvalues-0.3.0/colourvalues/inst/include/colourvalues/api |only colourvalues-0.3.0/colourvalues/inst/include/colourvalues/colours/colours_hex.hpp | 306 ++++++---- colourvalues-0.3.0/colourvalues/inst/include/colourvalues/colours/colours_rgb.hpp | 271 +++++--- colourvalues-0.3.0/colourvalues/inst/include/colourvalues/colours/generate_colours.hpp |only colourvalues-0.3.0/colourvalues/inst/include/colourvalues/convert/convert_colours.hpp | 4 colourvalues-0.3.0/colourvalues/inst/include/colourvalues/format/format.hpp | 38 + colourvalues-0.3.0/colourvalues/inst/include/colourvalues/list |only colourvalues-0.3.0/colourvalues/inst/include/colourvalues/output |only colourvalues-0.3.0/colourvalues/inst/include/colourvalues/palette_utils/palette_utils.hpp | 6 colourvalues-0.3.0/colourvalues/inst/include/colourvalues/scale/scale.hpp | 2 colourvalues-0.3.0/colourvalues/inst/include/colourvalues/utils/utils.hpp | 47 + colourvalues-0.3.0/colourvalues/man/colour_values.Rd | 41 - colourvalues-0.3.0/colourvalues/man/colour_values_rgb.Rd | 41 - colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-1-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-10-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-11-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-12-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-13-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-18-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-19-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-20-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-21-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-22-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-4-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-5-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-6-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-7-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-8-1.png |binary colourvalues-0.3.0/colourvalues/man/figures/README-unnamed-chunk-9-1.png |binary colourvalues-0.3.0/colourvalues/man/get_palette.Rd |only colourvalues-0.3.0/colourvalues/src/ColourValues.cpp |only colourvalues-0.3.0/colourvalues/src/ConvertColours.cpp | 4 colourvalues-0.3.0/colourvalues/src/Makevars | 2 colourvalues-0.3.0/colourvalues/src/Makevars.win | 2 colourvalues-0.3.0/colourvalues/src/RcppExports.cpp | 302 ++------- colourvalues-0.3.0/colourvalues/src/format.cpp |only colourvalues-0.3.0/colourvalues/src/list.cpp |only colourvalues-0.3.0/colourvalues/src/palette_utils.cpp |only colourvalues-0.3.0/colourvalues/src/palettes.cpp | 16 colourvalues-0.3.0/colourvalues/tests/testthat/test-alpha.R | 33 - colourvalues-0.3.0/colourvalues/tests/testthat/test-colour_values_hex.R | 4 colourvalues-0.3.0/colourvalues/tests/testthat/test-convert_colours.R | 2 colourvalues-0.3.0/colourvalues/tests/testthat/test-factors.R |only colourvalues-0.3.0/colourvalues/tests/testthat/test-format.R |only colourvalues-0.3.0/colourvalues/tests/testthat/test-lists.R |only colourvalues-0.3.0/colourvalues/tests/testthat/test-palette_utils.R |only colourvalues-0.3.0/colourvalues/tests/testthat/test-palettes.R | 11 60 files changed, 1071 insertions(+), 846 deletions(-)
Title: Interaction Between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap
API. REDCap (Research Electronic Data CAPture) is a web application for
building and managing online surveys and databases developed at Vanderbilt
University. The Application Programming Interface (API) offers an avenue
to access and modify data programmatically, improving the capacity for
literate and reproducible programming.
Author: Will Beasley [aut, cre] (<https://orcid.org/0000-0002-5613-5006>),
David Bard [ctb],
Thomas Wilson [ctb],
John J Aponte [ctb],
Rollie Parrish [ctb],
Benjamin Nutter [ctb],
Andrew Peters [ctb],
Hao Zhu [ctb] (<https://orcid.org/0000-0002-3386-6076>)
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between REDCapR versions 0.9.8 dated 2017-05-18 and 0.10.2 dated 2019-09-23
REDCapR-0.10.2/REDCapR/DESCRIPTION | 46 REDCapR-0.10.2/REDCapR/MD5 | 200 - REDCapR-0.10.2/REDCapR/NAMESPACE | 9 REDCapR-0.10.2/REDCapR/NEWS.md |only REDCapR-0.10.2/REDCapR/R/REDCapR-package.R | 3 REDCapR-0.10.2/REDCapR/R/constant.R |only REDCapR-0.10.2/REDCapR/R/create-batch-glossary.R | 22 REDCapR-0.10.2/REDCapR/R/kernel-api.R |only REDCapR-0.10.2/REDCapR/R/metadata-utilities.R | 42 REDCapR-0.10.2/REDCapR/R/project-simple.R | 30 REDCapR-0.10.2/REDCapR/R/redcap-column-sanitize.R | 24 REDCapR-0.10.2/REDCapR/R/redcap-download-file-oneshot.R | 114 REDCapR-0.10.2/REDCapR/R/redcap-metadata-read.R | 92 REDCapR-0.10.2/REDCapR/R/redcap-next-free-record-name.R |only REDCapR-0.10.2/REDCapR/R/redcap-project.R | 86 REDCapR-0.10.2/REDCapR/R/redcap-read-oneshot-eav.R | 273 - REDCapR-0.10.2/REDCapR/R/redcap-read-oneshot.R | 197 - REDCapR-0.10.2/REDCapR/R/redcap-read.R | 179 REDCapR-0.10.2/REDCapR/R/redcap-upload-file-oneshot.R | 121 REDCapR-0.10.2/REDCapR/R/redcap-users-export.R |only REDCapR-0.10.2/REDCapR/R/redcap-variables.R | 105 REDCapR-0.10.2/REDCapR/R/redcap-version.R | 68 REDCapR-0.10.2/REDCapR/R/redcap-write-oneshot.R | 96 REDCapR-0.10.2/REDCapR/R/redcap-write.R | 41 REDCapR-0.10.2/REDCapR/R/retrieve-credential.R | 79 REDCapR-0.10.2/REDCapR/R/sanitize-token.R | 13 REDCapR-0.10.2/REDCapR/R/utilities.R | 65 REDCapR-0.10.2/REDCapR/R/validate.R | 26 REDCapR-0.10.2/REDCapR/README.md | 105 REDCapR-0.10.2/REDCapR/build/vignette.rds |binary REDCapR-0.10.2/REDCapR/inst/doc/BasicREDCapROperations.R | 7 REDCapR-0.10.2/REDCapR/inst/doc/BasicREDCapROperations.Rmd | 9 REDCapR-0.10.2/REDCapR/inst/doc/BasicREDCapROperations.html | 1797 ++-------- REDCapR-0.10.2/REDCapR/inst/doc/SecurityDatabase.Rmd | 253 - REDCapR-0.10.2/REDCapR/inst/doc/SecurityDatabase.html | 878 +++- REDCapR-0.10.2/REDCapR/inst/doc/TroubleshootingApiCalls.Rmd | 113 REDCapR-0.10.2/REDCapR/inst/doc/TroubleshootingApiCalls.html | 548 ++- REDCapR-0.10.2/REDCapR/inst/doc/advanced-redcapr-operations.R | 44 REDCapR-0.10.2/REDCapR/inst/doc/advanced-redcapr-operations.Rmd | 58 REDCapR-0.10.2/REDCapR/inst/doc/advanced-redcapr-operations.html | 1480 ++------ REDCapR-0.10.2/REDCapR/inst/misc/example.credentials | 10 REDCapR-0.10.2/REDCapR/inst/test-data/project-clinical-trial |only REDCapR-0.10.2/REDCapR/inst/test-data/project-dag |only REDCapR-0.10.2/REDCapR/inst/test-data/project-longitudinal/expected/default.rds |binary REDCapR-0.10.2/REDCapR/inst/test-data/project-longitudinal/expected/filter-bmi.rds |binary REDCapR-0.10.2/REDCapR/inst/test-data/project-longitudinal/expected/filter-email.rds |binary REDCapR-0.10.2/REDCapR/inst/test-data/project-simple/simple-data-dictionary.csv | 34 REDCapR-0.10.2/REDCapR/inst/test-data/project-simple/simple-metadata.csv | 34 REDCapR-0.10.2/REDCapR/inst/test-data/project-survey |only REDCapR-0.10.2/REDCapR/inst/test-data/super-wide |only REDCapR-0.10.2/REDCapR/man/REDCapR-package.Rd | 4 REDCapR-0.10.2/REDCapR/man/collapse_vector.Rd |only REDCapR-0.10.2/REDCapR/man/constant.Rd |only REDCapR-0.10.2/REDCapR/man/create_batch_glossary.Rd | 11 REDCapR-0.10.2/REDCapR/man/figures |only REDCapR-0.10.2/REDCapR/man/kernel_api.Rd |only REDCapR-0.10.2/REDCapR/man/metadata_utilities.Rd | 21 REDCapR-0.10.2/REDCapR/man/redcap_column_sanitize.Rd | 4 REDCapR-0.10.2/REDCapR/man/redcap_download_file_oneshot.Rd | 26 REDCapR-0.10.2/REDCapR/man/redcap_metadata_read.Rd | 18 REDCapR-0.10.2/REDCapR/man/redcap_next_free_record_name.Rd |only REDCapR-0.10.2/REDCapR/man/redcap_project.Rd | 21 REDCapR-0.10.2/REDCapR/man/redcap_read.Rd | 39 REDCapR-0.10.2/REDCapR/man/redcap_read_oneshot.Rd | 43 REDCapR-0.10.2/REDCapR/man/redcap_read_oneshot_eav.Rd | 35 REDCapR-0.10.2/REDCapR/man/redcap_upload_file_oneshot.Rd | 39 REDCapR-0.10.2/REDCapR/man/redcap_users_export.Rd |only REDCapR-0.10.2/REDCapR/man/redcap_variables.Rd | 20 REDCapR-0.10.2/REDCapR/man/redcap_version.Rd | 12 REDCapR-0.10.2/REDCapR/man/redcap_write.Rd | 10 REDCapR-0.10.2/REDCapR/man/redcap_write_oneshot.Rd | 11 REDCapR-0.10.2/REDCapR/man/replace_nas_with_explicit.Rd | 11 REDCapR-0.10.2/REDCapR/man/retrieve_credential.Rd | 11 REDCapR-0.10.2/REDCapR/man/sanitize_token.Rd | 9 REDCapR-0.10.2/REDCapR/man/validate.Rd | 9 REDCapR-0.10.2/REDCapR/tests/manual/test-stress-test-serial.R | 65 REDCapR-0.10.2/REDCapR/tests/test-all.R | 2 REDCapR-0.10.2/REDCapR/tests/testthat/test-constant.R |only REDCapR-0.10.2/REDCapR/tests/testthat/test-create-batch-glossary.R | 82 REDCapR-0.10.2/REDCapR/tests/testthat/test-file-oneshot.R | 60 REDCapR-0.10.2/REDCapR/tests/testthat/test-metadata-read.R | 326 - REDCapR-0.10.2/REDCapR/tests/testthat/test-metadata-utilities.R | 20 REDCapR-0.10.2/REDCapR/tests/testthat/test-next-free-record-name.R |only REDCapR-0.10.2/REDCapR/tests/testthat/test-project.R | 54 REDCapR-0.10.2/REDCapR/tests/testthat/test-read-batch-longitudinal.R | 92 REDCapR-0.10.2/REDCapR/tests/testthat/test-read-batch-simple.R | 711 ++- REDCapR-0.10.2/REDCapR/tests/testthat/test-read-batch-survey.R |only REDCapR-0.10.2/REDCapR/tests/testthat/test-read-clinical-trial.R |only REDCapR-0.10.2/REDCapR/tests/testthat/test-read-errors.R | 58 REDCapR-0.10.2/REDCapR/tests/testthat/test-read-oneshot-eav.R | 700 ++- REDCapR-0.10.2/REDCapR/tests/testthat/test-read-oneshot.R | 946 ++++- REDCapR-0.10.2/REDCapR/tests/testthat/test-read-russian.R | 2 REDCapR-0.10.2/REDCapR/tests/testthat/test-read-superwide.R |only REDCapR-0.10.2/REDCapR/tests/testthat/test-retrieve-credential-local.R | 34 REDCapR-0.10.2/REDCapR/tests/testthat/test-retrieve-credential-mssql.R | 41 REDCapR-0.10.2/REDCapR/tests/testthat/test-users-export.R |only REDCapR-0.10.2/REDCapR/tests/testthat/test-utilities-collapse_vector.R |only REDCapR-0.10.2/REDCapR/tests/testthat/test-utilities-replace_nas_with_explicit.R |only REDCapR-0.10.2/REDCapR/tests/testthat/test-variables.R | 44 REDCapR-0.10.2/REDCapR/tests/testthat/test-version.R | 8 REDCapR-0.10.2/REDCapR/tests/testthat/test-write-batch.R | 287 + REDCapR-0.10.2/REDCapR/tests/testthat/test-write-oneshot.R | 258 - REDCapR-0.10.2/REDCapR/vignettes/BasicREDCapROperations.Rmd | 9 REDCapR-0.10.2/REDCapR/vignettes/SecurityDatabase.Rmd | 253 - REDCapR-0.10.2/REDCapR/vignettes/TroubleshootingApiCalls.Rmd | 113 REDCapR-0.10.2/REDCapR/vignettes/advanced-redcapr-operations.Rmd | 58 REDCapR-0.9.8/REDCapR/NEWS |only REDCapR-0.9.8/REDCapR/R/retrieve-token.R |only REDCapR-0.9.8/REDCapR/man/retrieve_token.Rd |only REDCapR-0.9.8/REDCapR/tests/testthat/test-retrieve-token.R |only REDCapR-0.9.8/REDCapR/tests/testthat/test-utilities.R |only REDCapR-0.9.8/REDCapR/vignettes/styles.css |only 112 files changed, 6200 insertions(+), 5678 deletions(-)
Title: A Shiny Application for Automatic Measurements of Tree-Ring
Widths on Digital Images
Description: Use morphological image processing and edge detection algorithms to automatically measure tree ring widths on digital images. Users can also manually mark tree rings on species with complex anatomical structures. The arcs of inner-rings and angles of successive inclined ring boundaries are used to correct ring-width series. The package provides a Shiny-based application, allowing R beginners to easily analyze tree ring images and export ring-width series in standard file formats.
Author: Jingning Shi [aut, cre],
Wei Xiang [aut]
Maintainer: Jingning Shi <snow940220@bjfu.edu.cn>
Diff between MtreeRing versions 1.3.1 dated 2019-05-29 and 1.4.1 dated 2019-09-23
DESCRIPTION | 6 MD5 | 24 NEWS.md | 9 R/pith_measure.R | 4 R/ring_app_launch.R | 7 R/ring_modify.R | 4 R/ring_read.R | 11 README.md | 14 inst/mtr_app/app.R | 2057 ++++++++++++++++++++++++++----------------------- man/pith_measure.Rd | 4 man/ring_app_launch.Rd | 7 man/ring_modify.Rd | 4 man/ring_read.Rd | 11 13 files changed, 1172 insertions(+), 990 deletions(-)
Title: Processing various types of data on GEO and TCGA
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA)
provide us with a wealth of data, such as RNA-seq, DNA Methylation,
and Copy number variation data. It's easy to download data from TCGA using the
gdc tool, but processing these data into a format suitable for bioinformatics
analysis requires more work. This R package was developed to handle these data.
Author: Erqiang Hu [aut, cre]
Maintainer: Erqiang Hu <13766876214@163.com>
Diff between GeoTcgaData versions 0.1.0 dated 2019-09-16 and 0.2.0 dated 2019-09-23
DESCRIPTION | 8 MD5 | 34 ++- NAMESPACE | 7 R/Proce_cli.R | 1 R/ann_merge.r |only R/fpkm_count_conversion.r |only R/id_conversion_all.r |only R/prepareChi.r |only R/sysdata.rda |binary README.md | 255 ++++++++++++++++++++++++++++- inst/doc/GeoTcgaData.R | 104 +++++++++++ inst/doc/GeoTcgaData.Rmd | 114 ++++++++++++ inst/doc/GeoTcgaData.html | 100 ++++++++++- inst/extdata/cnv |only inst/extdata/metadata.cart.2018-11-09.json |only man/ann_merge.Rd |only man/countToFpkm_matrix.Rd |only man/countToTpm_matrix.Rd |only man/differential_cnv.Rd |only man/fpkmToTpm_matrix.Rd |only man/id_conversion_vector.Rd |only man/prepare_chi.Rd |only vignettes/GeoTcgaData.Rmd | 114 ++++++++++++ 23 files changed, 715 insertions(+), 22 deletions(-)