Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Josh O'Brien [ctb],
Joseph O'Rourke [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 1.3-1 dated 2018-06-05 and 1.3-2 dated 2019-11-07
DESCRIPTION | 6 +- MD5 | 28 ++++++------- NAMESPACE | 2 R/CRS-methods.R | 4 + R/SpatialPointsDataFrame-methods.R | 2 R/SpatialPolygonsDataFrame-methods.R | 2 build/vignette.rds |binary inst/NEWS.Rd | 6 ++ inst/doc/csdacm.pdf |binary inst/doc/intro_sp.pdf |binary inst/doc/over.pdf |binary inst/include/sp.h | 2 src/sp.h | 2 tests/pass1.Rout.save | 74 +++++++++++++++++------------------ tests/zerodist.Rout.save | 10 ++-- 15 files changed, 75 insertions(+), 63 deletions(-)
Title: Utility Functions for Parametric Multi-State Models
Description: Provides functions for working with multi-state modelling,
such as efficient simulation routines for estimating transition probabilities and length of stay.
It is designed as an extension to multi-state modelling capabilities provided with the 'flexsurv'
package (see Jackson (2016) <doi:10.18637/jss.v070.i08>).
Author: Stuart Lacy
Maintainer: Stuart Lacy <stuart.lacy@gmail.com>
Diff between multistateutils versions 1.2.2 dated 2019-02-04 and 1.2.3 dated 2019-11-07
DESCRIPTION | 10 MD5 | 16 NEWS.md | 4 R/msprep2.R | 7 build/vignette.rds |binary inst/doc/Examples.html | 1260 ++++++++++++++++++++++++------------------------- man/msprep2.Rd | 4 src/Makevars | 4 src/simulation.h | 2 9 files changed, 666 insertions(+), 641 deletions(-)
More information about multistateutils at CRAN
Permanent link
Title: Continuous Time Structural Equation Modelling
Description: Hierarchical continuous time state space modelling, for linear
and nonlinear systems measured by continuous variables, with limited support for
binary data. The subject specific dynamic system is modelled as a stochastic
differential equation (SDE), measurement models are typically multivariate normal factor models.
Using the original ctsem formulation based on OpenMx, described in the JSS paper
"Continuous Time Structural Equation Modeling with R Package ctsem", with updated version
as CRAN vignette <https://cran.r-project.org/web/packages/ctsem/vignettes/ctsem.pdf> ,
linear mixed effects SDE's estimated via maximum likelihood and optimization are possible.
Using the Stan based formulation, described in <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf> ,
nonlinearity (state dependent parameters) and random effects on all parameters
are possible, using either optimization (with optional importance sampling) or
Stan's Hamiltonian Monte Carlo sampling. Priors may be used. For the conceptual
overview of the hierarchical Bayesian linear SDE approach, see <https://www.researchgate.net/publication/324093594_Hierarchical_Bayesian_Continuous_Time_Dynamic_Modeling>.
Exogenous inputs may also be included, for an overview of such possibilities see <https://www.researchgate.net/publication/328221807_Understanding_the_Time_Course_of_Interventions_with_Continuous_Time_Dynamic_Models> .
Stan based functions are not available on 32 bit Windows systems at present.
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph],
Trustees of Columbia University [cph]
Maintainer: Charles Driver <driver@mpib-berlin.mpg.de>
Diff between ctsem versions 3.0.4 dated 2019-09-12 and 3.0.8 dated 2019-11-07
DESCRIPTION | 12 MD5 | 101 ++--- NAMESPACE | 2 NEWS | 9 R/ctDiscretePars.R | 172 +++++---- R/ctFit.R | 43 +- R/ctGuessPriors.R |only R/ctJacobian.R | 5 R/ctKalman.R | 514 +++++++++++++++------------- R/ctModel.R | 40 +- R/ctModelLatex.R | 47 +- R/ctPlotArray.R | 245 +++++++------ R/ctPostPredict.R | 2 R/ctStanContinuousPars.R | 10 R/ctStanFit.R | 323 ++++++++---------- R/ctStanGenerateFromFit.R | 6 R/ctStanKalman.R | 112 +++--- R/ctStanModel.R | 104 ++++- R/ctStanModelWriter.R | 322 ++++++++++-------- R/ctStanParMatrices.R | 4 R/ctStanPlotPost.R | 234 +++++-------- R/ctStanPostPredict.R | 232 +++++++++---- R/ctStanTIpredMarginal.R | 111 ++++-- R/ctStanTIpredeffects.R | 27 - R/ctsem.R | 1 R/ctsemUtils.R | 132 +++++-- R/plot.ctStanModel.R | 147 +++++--- R/plothelpers.R |only R/stanWplot.R | 11 R/stanoptimis.R | 54 ++- R/summary.ctStanFit.R | 22 + R/summary.ctsemFit.R | 7 README.md | 72 ++-- inst/doc/ctsem.pdf |binary man/ctFit.Rd | 2 man/ctModel.Rd | 37 +- man/ctModelLatex.Rd | 5 man/ctPostPredict.Rd | 2 man/ctStanDiscretePars.Rd | 7 man/ctStanDiscreteParsPlot.Rd | 26 + man/ctStanModel.Rd | 5 man/ctStanPlotPost.Rd | 17 man/ctStanPostPredict.Rd | 27 - man/ctStanTIpredMarginal.Rd | 12 man/ctStanTIpredeffects.Rd | 6 man/plot.ctKalman.Rd | 18 - man/plot.ctKalmanDF.Rd |only man/plot.ctStanModel.Rd | 4 src/stan_files/ctsm.stan | 86 ++-- src/stan_files/ctsmgen.stan | 86 ++-- tests/testthat/test-fixedvalsunspot.R | 92 ++--- tests/testthat/test-knownFits.R | 1 vignettes/hierarchicalrefs.bib | 606 +++++++++++++++++----------------- 53 files changed, 2367 insertions(+), 1795 deletions(-)
Title: Polynomial Spline Routines
Description: Routines for the polynomial spline fitting routines
hazard regression, hazard estimation with flexible tails, logspline,
lspec, polyclass, and polymars, by C. Kooperberg and co-authors.
Author: Charles Kooperberg [aut, cre],
Cleve Moler [ctb] (LINPACK routines in src),
Jack Dongarra [ctb] (LINPACK routines in src)
Maintainer: Charles Kooperberg <clk@fredhutch.org>
Diff between polspline versions 1.1.16 dated 2019-10-04 and 1.1.17 dated 2019-11-07
DESCRIPTION | 20 ++++++++++++++------ MD5 | 2 +- 2 files changed, 15 insertions(+), 7 deletions(-)
Title: Client for the Open Citations Corpus
Description: Client for the Open Citations Corpus (<http://opencitations.net/>).
Includes a set of functions for getting one identifier type from another,
as well as getting references and citations for a given identifier.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between citecorp versions 0.1.0 dated 2019-08-24 and 0.2.0 dated 2019-11-07
DESCRIPTION | 11 +- MD5 | 29 ++++-- NEWS.md | 14 +++ R/citecorp-package.R | 30 ++++++ R/oc_lookup.R | 40 +++++---- R/sparql_strings.R | 124 +++++++++++++++------------- README.md | 124 ++++++++++++++++------------ data |only man/oc_dois.Rd |only man/oc_lookup.Rd | 24 ++++- man/oc_pmcids.Rd |only man/oc_pmids.Rd |only tests/fixtures/oc_doi2ids.yml | 23 +++-- tests/fixtures/oc_doi2ids_fewer_columns.yml |only tests/fixtures/oc_pmcid2ids.yml | 23 +++-- tests/fixtures/oc_pmid2ids.yml | 23 +++-- tests/testthat/test-oc_lookup.R | 38 +++++--- 17 files changed, 320 insertions(+), 183 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 2.6.1 dated 2018-10-25 and 2.7.0 dated 2019-11-07
DESCRIPTION | 10 ++++----- MD5 | 18 ++++++++--------- NEWS.md | 6 +++++ R/shiny.R | 31 ++++++++++++------------------ R/solvebio.R | 2 - man/Annotator.annotate.Rd | 4 +-- man/Dataset.get_or_create_by_full_path.Rd | 3 -- man/Vault.create_folder.Rd | 4 +-- man/Vault.get_or_create_by_full_path.Rd | 3 -- man/createEnv.Rd | 3 -- 10 files changed, 41 insertions(+), 43 deletions(-)
Title: Linking R with the Open-Source 'SAGA-GIS' Software
Description: Provides an R scripting interface to the open-source 'SAGA-GIS' (System for Automated Geoscientific Analyses Geographical Information System) software. 'Rsagacmd' dynamically generates R functions for every 'SAGA-GIS' geoprocessing tool based on the user's currently installed 'SAGA-GIS' version. These functions are contained within an S3 object and are accessed as a named list of libraries and tools. This structure facilitates an easier scripting experience by organizing the large number of 'SAGA-GIS' geoprocessing tools (>700) by their respective library. Interactive scripting can fully take advantage of code autocompletion tools (e.g. in 'Rstudio'), allowing for each tools syntax to be quickly recognized. Furthermore, the most common types of spatial data (via the 'raster', 'sp', and 'sf' packages) along with non-spatial data are automatically passed from R to the 'SAGA-GIS' command line tool for geoprocessing operations, and the results are loaded as the appropriate R object. Outputs from individual 'SAGA-GIS' tools can also be chained using pipes from the 'magrittr' and 'dplyr' packages to combine complex geoprocessing operations together in a single statement. 'SAGA-GIS' is available under a GPLv2 / LGPLv2 licence from <https://sourceforge.net/projects/saga-gis/> including Windows x86/x84 binaries. SAGA-GIS is also included in Debian/Ubuntu default software repositories and is available for macOS using homebrew (<https://brew.sh/>) from the osgeo/osgeo4mac (<https://github.com/OSGeo/homebrew-osgeo4mac>) formula tap. Rsagacmd has currently been tested on 'SAGA-GIS' versions from 2.3.1 to 7.4.0 on Windows, Linux and macOS.
Author: Steven Pawley [aut, cre]
Maintainer: Steven Pawley <dr.stevenpawley@gmail.com>
Diff between Rsagacmd versions 0.0.1 dated 2019-07-23 and 0.0.2 dated 2019-11-07
Rsagacmd-0.0.1/Rsagacmd/R/functions.R |only Rsagacmd-0.0.2/Rsagacmd/DESCRIPTION | 12 Rsagacmd-0.0.2/Rsagacmd/MD5 | 51 +- Rsagacmd-0.0.2/Rsagacmd/NAMESPACE | 2 Rsagacmd-0.0.2/Rsagacmd/R/Rsagacmd.R | 143 ++++--- Rsagacmd-0.0.2/Rsagacmd/R/create_function.R |only Rsagacmd-0.0.2/Rsagacmd/R/create_tool.R |only Rsagacmd-0.0.2/Rsagacmd/R/saga.R |only Rsagacmd-0.0.2/Rsagacmd/R/saga_execute.R |only Rsagacmd-0.0.2/Rsagacmd/R/saga_search.R |only Rsagacmd-0.0.2/Rsagacmd/R/saga_version.R |only Rsagacmd-0.0.2/Rsagacmd/R/tempfiles.R |only Rsagacmd-0.0.2/Rsagacmd/R/utils.R | 82 +++- Rsagacmd-0.0.2/Rsagacmd/README.md | 22 + Rsagacmd-0.0.2/Rsagacmd/man/Rsagacmd.Rd | 139 ++++--- Rsagacmd-0.0.2/Rsagacmd/man/create_tool.Rd |only Rsagacmd-0.0.2/Rsagacmd/man/mrvbf_threshold.Rd | 10 Rsagacmd-0.0.2/Rsagacmd/man/print.saga_tool.Rd | 6 Rsagacmd-0.0.2/Rsagacmd/man/saga_configure.Rd | 27 - Rsagacmd-0.0.2/Rsagacmd/man/saga_env.Rd | 20 - Rsagacmd-0.0.2/Rsagacmd/man/saga_execute.Rd | 26 - Rsagacmd-0.0.2/Rsagacmd/man/saga_gis.Rd | 48 +- Rsagacmd-0.0.2/Rsagacmd/man/saga_remove_tmpfiles.Rd | 21 - Rsagacmd-0.0.2/Rsagacmd/man/saga_search.Rd | 15 Rsagacmd-0.0.2/Rsagacmd/man/saga_show_tmpfiles.Rd | 24 - Rsagacmd-0.0.2/Rsagacmd/man/saga_version.Rd | 11 Rsagacmd-0.0.2/Rsagacmd/man/search_tools.Rd | 8 Rsagacmd-0.0.2/Rsagacmd/man/tile_geoprocessor.Rd | 18 Rsagacmd-0.0.2/Rsagacmd/tests/testthat/test-saga_environment.R | 31 + Rsagacmd-0.0.2/Rsagacmd/tests/testthat/test-sagatools.R | 59 +-- Rsagacmd-0.0.2/Rsagacmd/tests/testthat/test-supported-saga-versions.R | 182 ++++++++-- 31 files changed, 600 insertions(+), 357 deletions(-)
Title: 'NOAA' Weather Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC' climate
'API' at <https://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for
each of the 'API' 'endpoints': data, data categories, data sets, data types,
locations, location categories, and stations. In addition, we have an interface
for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical
Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS',
tornado data via the 'NOAA' storm prediction center, and more.
Author: Scott Chamberlain [aut, cre],
Brooke Anderson [ctb],
Maëlle Salmon [ctb],
Adam Erickson [ctb],
Nicholas Potter [ctb],
Joseph Stachelek [ctb],
Alex Simmons [ctb],
Karthik Ram [ctb],
Hart Edmund [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rnoaa versions 0.9.2 dated 2019-10-23 and 0.9.4 dated 2019-11-07
DESCRIPTION | 6 +- MD5 | 34 +++++++------- NAMESPACE | 2 NEWS.md | 16 ++++++ R/argo.R | 8 +++ R/gefs.R | 97 +++++++++++++++++++++++++++++------------- inst/doc/buoy_vignette.html | 4 - inst/doc/homr_vignette.html | 4 - inst/doc/ncdc_attributes.html | 4 - inst/doc/ncdc_vignette.html | 4 - inst/doc/ncdc_workflow.html | 4 - inst/doc/rnoaa_ropenaq.html | 4 - inst/doc/seaice_vignette.html | 4 - inst/doc/storms_vignette.html | 4 - inst/doc/swdi_vignette.html | 4 - man/argo.Rd | 92 +++++++++++++++++++++++++-------------- man/gefs.Rd | 26 ++++++----- tests/testthat/test-gefs.R | 81 +++++++++++++++++++++++++---------- 18 files changed, 266 insertions(+), 132 deletions(-)
Title: Generalized Mortality Estimator
Description: Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Author: Daniel Dalthorp [aut, cre],
Juniper Simonis [aut],
Lisa Madsen [aut],
Manuela Huso [aut],
Paul Rabie [aut],
Jeffrey Mintz [aut],
Robert Wolpert [aut],
Jared Studyvin [aut],
Franzi Korner-Nievergelt [aut]
Maintainer: Daniel Dalthorp <ddalthorp@usgs.gov>
Diff between GenEst versions 1.3.2 dated 2019-09-14 and 1.4.0 dated 2019-11-07
GenEst-1.3.2/GenEst/man/GenEstInlineCSS.Rd |only GenEst-1.3.2/GenEst/man/GenEstServer.Rd |only GenEst-1.3.2/GenEst/man/GenEstShinyJS.Rd |only GenEst-1.3.2/GenEst/man/GenEstUI.Rd |only GenEst-1.3.2/GenEst/man/aboutContent.Rd |only GenEst-1.3.2/GenEst/man/cButtonStyle.Rd |only GenEst-1.3.2/GenEst/man/classText.Rd |only GenEst-1.3.2/GenEst/man/clearNotifications.Rd |only GenEst-1.3.2/GenEst/man/createvtext.Rd |only GenEst-1.3.2/GenEst/man/dataDownloadWidget.Rd |only GenEst-1.3.2/GenEst/man/dataInputWidget.Rd |only GenEst-1.3.2/GenEst/man/dataTabPanel.Rd |only GenEst-1.3.2/GenEst/man/disclaimersContent.Rd |only GenEst-1.3.2/GenEst/man/downloadCPFig.Rd |only GenEst-1.3.2/GenEst/man/downloadCPmod.Rd |only GenEst-1.3.2/GenEst/man/downloadData.Rd |only GenEst-1.3.2/GenEst/man/downloadMFig.Rd |only GenEst-1.3.2/GenEst/man/downloadMres.Rd |only GenEst-1.3.2/GenEst/man/downloadSEFig.Rd |only GenEst-1.3.2/GenEst/man/downloadSEmod.Rd |only GenEst-1.3.2/GenEst/man/downloadTable.Rd |only GenEst-1.3.2/GenEst/man/downloadgFig.Rd |only GenEst-1.3.2/GenEst/man/estText.Rd |only GenEst-1.3.2/GenEst/man/gettingStartedContent.Rd |only GenEst-1.3.2/GenEst/man/initialOutput.Rd |only GenEst-1.3.2/GenEst/man/initialReactiveValues.Rd |only GenEst-1.3.2/GenEst/man/kFixedWidget.Rd |only GenEst-1.3.2/GenEst/man/matchCells.Rd |only GenEst-1.3.2/GenEst/man/modNamePaste.Rd |only GenEst-1.3.2/GenEst/man/modNameSplit.Rd |only GenEst-1.3.2/GenEst/man/modelInputWidget.Rd |only GenEst-1.3.2/GenEst/man/modelOutputPanel.Rd |only GenEst-1.3.2/GenEst/man/modelOutputWidget.Rd |only GenEst-1.3.2/GenEst/man/modelRunWidget.Rd |only GenEst-1.3.2/GenEst/man/modelSelectionWidget.Rd |only GenEst-1.3.2/GenEst/man/modelSetCells.Rd |only GenEst-1.3.2/GenEst/man/modelSetModelCells.Rd |only GenEst-1.3.2/GenEst/man/modelSetModelPredictors.Rd |only GenEst-1.3.2/GenEst/man/modelSetPredictors.Rd |only GenEst-1.3.2/GenEst/man/msgFracNote.Rd |only GenEst-1.3.2/GenEst/man/msgList.Rd |only GenEst-1.3.2/GenEst/man/msgModDone.Rd |only GenEst-1.3.2/GenEst/man/msgModFail.Rd |only GenEst-1.3.2/GenEst/man/msgModPartialFail.Rd |only GenEst-1.3.2/GenEst/man/msgModRun.Rd |only GenEst-1.3.2/GenEst/man/msgModSENobs.Rd |only GenEst-1.3.2/GenEst/man/msgModWarning.Rd |only GenEst-1.3.2/GenEst/man/msgSSavgFail.Rd |only GenEst-1.3.2/GenEst/man/msgSSinputFail.Rd |only GenEst-1.3.2/GenEst/man/msgSampleSize.Rd |only GenEst-1.3.2/GenEst/man/msgSplitFail.Rd |only GenEst-1.3.2/GenEst/man/navbar.Rd |only GenEst-1.3.2/GenEst/man/pickSizeclass.Rd |only GenEst-1.3.2/GenEst/man/plotNA.Rd |only GenEst-1.3.2/GenEst/man/prepSizeclassText.Rd |only GenEst-1.3.2/GenEst/man/reNULL.Rd |only GenEst-1.3.2/GenEst/man/reVal.Rd |only GenEst-1.3.2/GenEst/man/selectData.Rd |only GenEst-1.3.2/GenEst/man/selectedDataPanel.Rd |only GenEst-1.3.2/GenEst/man/setFigW.Rd |only GenEst-1.3.2/GenEst/man/setNotSuspending.Rd |only GenEst-1.3.2/GenEst/man/setkNeed.Rd |only GenEst-1.3.2/GenEst/man/style.Rd |only GenEst-1.3.2/GenEst/man/updateColNames_size.Rd |only GenEst-1.3.2/GenEst/man/updateSizeclasses.Rd |only GenEst-1.3.2/GenEst/man/updatesizeCol.Rd |only GenEst-1.3.2/GenEst/man/widgetMaker.Rd |only GenEst-1.4.0/GenEst/DESCRIPTION | 14 GenEst-1.4.0/GenEst/MD5 | 230 -- GenEst-1.4.0/GenEst/NAMESPACE | 125 - 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Title: Harrell Miscellaneous
Description: Contains many functions useful for data
analysis, high-level graphics, utility operations, functions for
computing sample size and power, importing and annotating datasets,
imputing missing values, advanced table making, variable clustering,
character string manipulation, conversion of R objects to LaTeX and html code,
and recoding variables.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>, with
contributions from Charles Dupont and many others.
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Diff between Hmisc versions 4.2-0 dated 2019-01-26 and 4.3-0 dated 2019-11-07
DESCRIPTION | 8 ++--- MD5 | 43 +++++++++++++++--------------- NAMESPACE | 2 - NEWS | 15 ++++++++++ R/Misc.s | 50 ++++++++++++++++++++++++++++++++++++ R/describe.s | 46 ++++++++++++++++++++++----------- R/dotchart3.s | 68 +++++++++++++++++++++++++++++++++++++++++++++++++ R/dotchartpl.s | 5 ++- R/fit.mult.impute.s | 6 ++++ R/ggfreqScatter.r | 27 +++++++++++++++++-- R/html.s | 46 ++++++++++++++++----------------- R/plot.describe.s | 10 ++++--- R/upData.s | 60 +++++++++++++++++++++++++++++++------------ inst/tests/describe2.r |only man/Hmisc-internal.Rd | 1 man/aregImpute.Rd | 8 ++--- man/describe.Rd | 2 - man/dotchart3.Rd | 35 ++++++++++++++++++++++--- man/dotchartpl.Rd | 6 ++-- man/ggfreqScatter.Rd | 25 ++++++++++++++++-- man/mdb.get.Rd | 2 - man/mtitle.Rd | 1 man/upData.Rd | 26 ++++++++++++++++++ 23 files changed, 387 insertions(+), 105 deletions(-)
Title: Create Interactive Web Graphics via 'plotly.js'
Description: Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.
Author: Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>),
Chris Parmer [aut],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut] (<https://orcid.org/0000-0002-1994-3581>),
Pedro Despouy [aut],
Plotly Technologies Inc. [cph]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 4.9.0 dated 2019-04-10 and 4.9.1 dated 2019-11-07
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Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
Siem Heisterkamp [ctb] (Author fixed sigma),
Bert Van Willigen [ctb] (Programmer fixed sigma),
R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>
Diff between nlme versions 3.1-141 dated 2019-08-01 and 3.1-142 dated 2019-11-07
ChangeLog | 8 ++++ DESCRIPTION | 8 ++-- INDEX |only MD5 | 93 +++++++++++++++++++++++------------------------ data/Alfalfa.rda |binary data/Assay.rda |binary data/BodyWeight.rda |binary data/Cefamandole.rda |binary data/Dialyzer.rda |binary data/Earthquake.rda |binary data/Fatigue.rda |binary data/Gasoline.rda |binary data/Glucose.rda |binary data/Glucose2.rda |binary data/Gun.rda |binary data/IGF.rda |binary data/Machines.rda |binary data/MathAchSchool.rda |binary data/MathAchieve.rda |binary data/Meat.rda |binary data/Milk.rda |binary data/Muscle.rda |binary data/Nitrendipene.rda |binary data/Oats.rda |binary data/Orthodont.rda |binary data/Ovary.rda |binary data/Oxboys.rda |binary data/Oxide.rda |binary data/PBG.rda |binary data/Phenobarb.rda |binary data/Pixel.rda |binary data/Quinidine.rda |binary data/Rail.rda |binary data/RatPupWeight.rda |binary data/Relaxin.rda |binary data/Remifentanil.rda |binary data/Soybean.rda |binary data/Spruce.rda |binary data/Tetracycline1.rda |binary data/Tetracycline2.rda |binary data/Wafer.rda |binary data/Wheat.rda |binary data/Wheat2.rda |binary data/bdf.rda |binary data/ergoStool.rda |binary man/pairs.compareFits.Rd | 2 - src/nlmefit.c | 2 - tests/nlme.R | 3 + 48 files changed, 63 insertions(+), 53 deletions(-)
Title: Estimation and Validation Methods for Subgroup Identification
and Personalized Medicine
Description: Provides functions for fitting and validation of models for subgroup
identification and personalized medicine / precision medicine under the general subgroup
identification framework of Chen et al. (2017) <doi:10.1111/biom.12676>.
This package is intended for use for both randomized controlled trials and
observational studies.
Author: Jared Huling [aut, cre] (<https://orcid.org/0000-0003-0670-4845>),
Aaron Potvien [ctb],
Alexandros Karatzoglou [cph],
Alex Smola [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between personalized versions 0.2.4 dated 2019-05-22 and 0.2.5 dated 2019-11-07
DESCRIPTION | 8 +-- MD5 | 32 +++++++++----- NAMESPACE | 3 + R/augmentation_utils.R |only build/vignette.rds |binary inst/NEWS.Rd |only inst/doc/efficiency_augmentation_personalized.R |only inst/doc/efficiency_augmentation_personalized.Rmd |only inst/doc/efficiency_augmentation_personalized.html |only inst/doc/multicategory_treatments_with_personalized.R |only inst/doc/multicategory_treatments_with_personalized.Rmd |only inst/doc/multicategory_treatments_with_personalized.html |only inst/doc/usage_of_the_personalized_package.html | 34 ++++++++------- man/create.augmentation.function.Rd |only man/create.propensity.function.Rd |only man/figures/sticker.png |binary tests/testthat/test-fitsubgroup.R | 17 ++++--- tests/testthat/test-validatesubgroup.R | 24 +++++----- tests/testthat/test-wksvm.R | 23 ++++++---- vignettes/efficiency_augmentation_personalized.Rmd |only vignettes/multicategory_treatments_with_personalized.Rmd |only vignettes/usage_overview-1.png |binary vignettes/vis_val-1.png |binary 23 files changed, 85 insertions(+), 56 deletions(-)
Title: Derive Polygenic Risk Score Based on Emprical Bayes Theory
Description: EB-PRS is a novel method that leverages information for effect sizes across all the markers to improve the prediction accuracy. No parameter tuning is needed in the method, and no external information is needed. This R-package provides the calculation of polygenic risk scores from the given training summary statistics and testing data. We can use EB-PRS to extract main information, estimate Empirical Bayes parameters, derive polygenic risk scores for each individual in testing data, and evaluate the PRS according to AUC and predictive r2.
Author: Shuang Song [aut, cre], Wei Jiang [aut], Lin Hou [aut] and Hongyu Zhao [aut]
Maintainer: Shuang Song <song-s19@mails.tsinghua.edu.cn>
Diff between EBPRS versions 1.2.1 dated 2019-10-12 and 1.2.2 dated 2019-11-07
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/agtc.R | 38 ++++++++++++++++++++------------------ 3 files changed, 25 insertions(+), 23 deletions(-)
Title: Music Chords Extraction
Description: Extracts music chords from the 'CifraClub' website <https://www.cifraclub.com.br/>.
The package also has functions for cleaning the extracted data and
feature extraction.
Author: Bruna Wundervald
Maintainer: Bruna Wundervald <brunadaviesw@gmail.com>
Diff between chorrrds versions 0.1.9.1 dated 2019-05-19 and 0.1.9.2 dated 2019-11-07
chorrrds-0.1.9.1/chorrrds/README.md |only chorrrds-0.1.9.2/chorrrds/DESCRIPTION | 6 ++-- chorrrds-0.1.9.2/chorrrds/MD5 | 11 +++---- chorrrds-0.1.9.2/chorrrds/R/get_chords.R | 41 +++++++++++++++++++--------- chorrrds-0.1.9.2/chorrrds/R/get_songs.R | 13 +++++--- chorrrds-0.1.9.2/chorrrds/R/utils.R | 2 - chorrrds-0.1.9.2/chorrrds/man/get_chords.Rd | 4 +- 7 files changed, 47 insertions(+), 30 deletions(-)
Title: Reliably Return the Source and Call Location of a Command
Description: Robust and reliable functions to return informative outputs to
console with the run or source location of a command. This can be from
the 'RScript'/R terminal commands or 'RStudio' console, source editor,
'Rmarkdown' document and a Shiny application.
Author: Jonathan Sidi [aut, cre] (<https://orcid.org/0000-0002-4222-1819>),
Colin Fay [ctb] (<https://orcid.org/0000-0001-7343-1846>),
Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>)
Maintainer: Jonathan Sidi <yonicd@gmail.com>
Diff between whereami versions 0.1.8.1 dated 2019-05-05 and 0.1.9 dated 2019-11-07
whereami-0.1.8.1/whereami/inst/doc/cat_where.R |only whereami-0.1.8.1/whereami/inst/doc/cat_where.Rmd |only whereami-0.1.8.1/whereami/inst/doc/cat_where.html |only whereami-0.1.8.1/whereami/vignettes/cat_where.Rmd |only whereami-0.1.8.1/whereami/vignettes/cat_where.png |only whereami-0.1.9/whereami/DESCRIPTION | 8 whereami-0.1.9/whereami/MD5 | 62 ++--- whereami-0.1.9/whereami/NAMESPACE | 10 whereami-0.1.9/whereami/NEWS.md | 9 whereami-0.1.9/whereami/R/counter.R | 171 +++++++++++++-- whereami-0.1.9/whereami/R/thisfile.R | 2 whereami-0.1.9/whereami/R/utils.R | 6 whereami-0.1.9/whereami/R/whereami.R | 19 - whereami-0.1.9/whereami/R/zzz.R |only whereami-0.1.9/whereami/README.md | 7 whereami-0.1.9/whereami/build/vignette.rds |binary whereami-0.1.9/whereami/inst/doc/counters.R |only whereami-0.1.9/whereami/inst/doc/counters.Rmd |only whereami-0.1.9/whereami/inst/doc/counters.html |only whereami-0.1.9/whereami/inst/doc/plots.html | 15 - whereami-0.1.9/whereami/inst/doc/printing.R |only whereami-0.1.9/whereami/inst/doc/printing.Rmd |only whereami-0.1.9/whereami/inst/doc/printing.html |only whereami-0.1.9/whereami/inst/doc/shiny.Rmd | 2 whereami-0.1.9/whereami/inst/doc/shiny.html | 13 - whereami-0.1.9/whereami/inst/doc/tables.html | 19 + whereami-0.1.9/whereami/inst/doc/tests_and_coverage.html | 9 whereami-0.1.9/whereami/man/counter.Rd | 57 +++-- whereami-0.1.9/whereami/man/figures/README-plot-1.png |binary whereami-0.1.9/whereami/man/figures/printing.png |only whereami-0.1.9/whereami/man/set_whereami_log.Rd |only whereami-0.1.9/whereami/man/whereami.Rd | 4 whereami-0.1.9/whereami/tests/README.md | 58 ++--- whereami-0.1.9/whereami/tests/testthat/scripts/cat.R | 2 whereami-0.1.9/whereami/tests/testthat/scripts/print.R | 2 whereami-0.1.9/whereami/tests/testthat/test-console.R | 2 whereami-0.1.9/whereami/tests/testthat/test-counter.R | 1 whereami-0.1.9/whereami/vignettes/counters.Rmd |only whereami-0.1.9/whereami/vignettes/printing.Rmd |only whereami-0.1.9/whereami/vignettes/shiny.Rmd | 2 40 files changed, 353 insertions(+), 127 deletions(-)
Title: Create Details HTML Tag for Markdown and Package Documentation
Description: Create a details HTML tag around R objects to place
in a Markdown, 'Rmarkdown' and 'roxygen2' documentation.
Author: Jonathan Sidi [aut, cre]
Maintainer: Jonathan Sidi <yonicd@gmail.com>
Diff between details versions 0.1.1 dated 2019-10-16 and 0.1.2 dated 2019-11-07
DESCRIPTION | 25 +++++---- MD5 | 37 +++++++------ NAMESPACE | 4 + NEWS.md | 6 ++ R/details.R | 2 R/read.R | 9 ++- R/use.R |only R/utils.R | 2 README.md | 105 +++++++++++++++++++-------------------- inst/doc/custom.html | 2 inst/doc/objects.R | 2 inst/doc/objects.Rmd | 2 inst/doc/sessioninfo.html | 80 +++++++++++++++-------------- inst/doc/tests_and_coverage.html | 2 man/details.Rd | 3 + man/use_details.Rd |only tests/testthat/helpers.R | 16 +++++ tests/testthat/test-basic.R | 11 +++- tests/testthat/test-device.R | 1 tests/testthat/test-use.R |only vignettes/objects.Rmd | 2 21 files changed, 181 insertions(+), 130 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre],
Mike Johnson [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 0.3.10 dated 2019-10-17 and 0.3.11 dated 2019-11-07
DESCRIPTION | 6 MD5 | 28 +-- NEWS.md | 6 R/get_nldi.R | 8 - R/nhdplusTools.R | 2 README.md | 4 inst/doc/nhdplusTools.R | 304 ++++++++++++++++++++--------------------- inst/doc/nhdplusTools.html | 168 ++++++++++++++++++++++ inst/doc/plot_nhdplus.R | 208 ++++++++++++++-------------- inst/doc/plot_nhdplus.Rmd | 10 - inst/doc/plot_nhdplus.html | 72 +++++++++ inst/doc/point_indexing.R | 128 ++++++++--------- inst/doc/point_indexing.html | 16 ++ tests/testthat/test_get_nldi.R | 5 vignettes/plot_nhdplus.Rmd | 10 - 15 files changed, 625 insertions(+), 350 deletions(-)
Title: Incidence Estimation Tools
Description: Tools for estimating incidence from biomarker data in cross-
sectional surveys, and for calibrating tests for recent infection.
Implements and extends the method of Kassanjee et al. (2012)
<doi:10.1097/EDE.0b013e3182576c07>.
Author: Eduard Grebe [cre, aut],
Alex Welte [aut],
Avery McIntosh [aut],
Petra Bäumler [aut],
Reshma Kassanjee [ctb],
Hilmarie Brand [ctb],
Cari Van Schalkwyk [ctb],
Yuruo Li [ctb],
Simon Daniel [ctb],
Stefano Ongarello [aut],
Yusuke Asai [ctb],
Jeffrey Eaton [ctb]
Maintainer: Eduard Grebe <Eduard.Grebe@ucsf.edu>
Diff between inctools versions 1.0.14 dated 2018-09-21 and 1.0.15 dated 2019-11-07
DESCRIPTION | 20 +- MD5 | 28 +-- R/calibration_frr.R | 25 ++- R/calibration_mdri.R | 25 +-- R/incidence.R | 3 build/vignette.rds |binary inst/doc/EstimatingIncidence.html | 95 ++++++++----- inst/doc/Introduction.html | 9 + inst/doc/SurveyDesign.html | 95 ++++++++----- inst/doc/TestCalibration.R | 23 --- inst/doc/TestCalibration.Rmd | 34 ---- inst/doc/TestCalibration.html | 267 ++++++++++++++++++++------------------ man/frrcal.Rd | 5 man/mdrical.Rd | 6 vignettes/TestCalibration.Rmd | 34 ---- 15 files changed, 354 insertions(+), 315 deletions(-)
Title: Direction Analysis for Pathways and Kinases
Description: Direction analysis is a set of tools designed to identify
combinatorial effects of multiple treatments/conditions on pathways
and kinases profiled by microarray, RNA-seq, proteomics, or phosphoproteomics
data. See Yang P et al (2014) <doi:10.1093/bioinformatics/btt616>; and Yang P et al. (2016) <doi:10.1002/pmic.201600068>.
Author: Pengyi Yang & Ellis Patrick
Maintainer: Pengyi Yang <yangpy7@gmail.com>
Diff between directPA versions 1.3 dated 2016-03-23 and 1.4 dated 2019-11-07
DESCRIPTION | 17 +-- MD5 | 58 ++++++----- NAMESPACE | 31 +++--- R/directExplorer2d.R | 207 +++++++++++++++++++++++------------------ R/directPA.R | 232 +++++++++++++++++++++++------------------------ R/geneStats.R | 86 ++++++++--------- R/kinasePA.R | 118 +++++++++++------------ R/pathwayStats.R | 126 ++++++++++++------------- R/perturbPlot2d.R | 139 ++++++++++++++-------------- R/perturbPlot3d.R |only R/rotate2d.R | 52 +++++----- R/rotate3d.R | 88 ++++++++--------- README.md | 76 +++++++-------- man/HEK.Rd | 16 +-- man/PM.Rd | 16 +-- man/Pathways.KEGG.Rd | 14 +- man/Pathways.reactome.Rd | 14 +- man/PhosphoELM.human.Rd | 18 +-- man/PhosphoELM.mouse.Rd | 18 +-- man/PhosphoSite.human.Rd | 16 +-- man/PhosphoSite.mouse.Rd | 16 +-- man/directExplorer2d.Rd | 123 ++++++++++++------------ man/directPA-package.Rd | 58 +++++------ man/directPA.Rd | 145 ++++++++++++++--------------- man/geneStats.Rd | 73 +++++++------- man/kinasePA.Rd | 137 +++++++++++++-------------- man/pathwayStats.Rd | 101 ++++++++++---------- man/perturbPlot2d.Rd | 77 +++++++-------- man/perturbPlot3d.Rd |only man/rotate2d.Rd | 63 ++++++------ man/rotate3d.Rd | 63 ++++++------ 31 files changed, 1111 insertions(+), 1087 deletions(-)
Title: Read, Write and Edit xlsx Files
Description: Simplifies the creation of Excel .xlsx files by
providing a high level interface to writing, styling and editing
worksheets. Through the use of 'Rcpp', read/write times are comparable
to the 'xlsx' and 'XLConnect' packages with the added benefit of
removing the dependency on Java.
Author: Philipp Schauberger [aut, cre],
Alexander Walker [aut],
Luca Braglia [ctb]
Maintainer: Philipp Schauberger <philipp@schauberger.co.at>
Diff between openxlsx versions 4.1.2 dated 2019-10-29 and 4.1.3 dated 2019-11-07
DESCRIPTION | 49 ++++++++++++++++++++++++++++------------------ MD5 | 16 +++++++-------- NEWS | 21 +++++++++++++++++++ README.md | 2 - inst/doc/Introduction.pdf |binary inst/doc/formatting.pdf |binary man/readWorkbook.Rd | 2 + src/helper_functions.cpp | 2 - src/write_data.cpp | 1 9 files changed, 64 insertions(+), 29 deletions(-)
Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>)
and new ones from the current literature on landscape metrics.
This package supports 'raster' spatial objects and takes
RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the
'raster' package as input arguments. It further provides utility functions
to visualize patches, select metrics and building blocks to develop new
metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
Sebastian Hanss [aut] (<https://orcid.org/0000-0002-3990-4897>),
Laura J. Graham [ctb] (Input on package structure),
Jeffrey Hollister [ctb] (Input on package structure),
Kimberly A. With [ctb] (Input on package structure),
Florian Privé [ctb] (Original author of underlying C++ code for
get_nearestneighbour() function),
Jeremy VanDerWal [ctb] (Original author of underlying C code for
get_patches() function),
Matt Strimas-Mackey [ctb] (Bugfix in sample_metrics())
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between landscapemetrics versions 1.2.2 dated 2019-09-10 and 1.3 dated 2019-11-07
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NEWS.md | 4 ++++ R/lsm_c_shape_cv.R | 3 ++- R/lsm_c_shape_mn.R | 3 ++- R/lsm_c_shape_sd.R | 3 ++- R/lsm_l_shape_cv.R | 5 +++-- R/lsm_l_shape_mn.R | 2 +- R/lsm_l_shape_sd.R | 2 +- R/lsm_p_shape.R | 14 +++++++++----- inst/CITATION | 4 ++-- inst/doc/getstarted.html | 4 ++-- man/figures/README-unnamed-chunk-1-1.png |binary man/lsm_l_shape_cv.Rd | 2 +- 14 files changed, 45 insertions(+), 33 deletions(-)
More information about landscapemetrics at CRAN
Permanent link
Title: Smoothed Bootstrap and Random Generation from Kernel Densities
Description: Smoothed bootstrap and functions for random generation from
univariate and multivariate kernel densities. It does not
estimate kernel densities.
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+kernelboot@gmail.com>
Diff between kernelboot versions 0.1.5 dated 2018-07-04 and 0.1.6 dated 2019-11-07
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- R/kernelboot.R | 2 +- README.md |only 4 files changed, 8 insertions(+), 7 deletions(-)
Title: Generalized Estimation Equation Solver
Description: Generalized Estimation Equation solver.
Author: Vincent J Carey. Ported to R by Thomas Lumley (versions 3.13 and 4.4)
and Brian Ripley <ripley@stats.ox.ac.uk> (version 4.13).
Files src/dgedi.f and src/dgefa.f are for LINPACK authored by
Cleve Moler.
Note that maintainers are not available to give advice on using a
package they did not author.
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between gee versions 4.13-19 dated 2015-06-29 and 4.13-20 dated 2019-11-07
ChangeLog | 5 +++++ DESCRIPTION | 10 ++++++---- MD5 | 6 +++--- src/ugee.c | 1 + 4 files changed, 15 insertions(+), 7 deletions(-)
Title: Graph Theory Analysis of Brain MRI Data
Description: A set of tools for performing graph theory analysis of brain MRI
data. It works with data from a Freesurfer analysis (cortical thickness,
volumes, local gyrification index, surface area), diffusion tensor
tractography data (e.g., from FSL) and resting-state fMRI data (e.g., from
DPABI). It contains a graphical user interface for graph visualization and
data exploration, along with several functions for generating useful
figures.
Author: Christopher G. Watson [aut, cre]
(<https://orcid.org/0000-0002-7082-7631>)
Maintainer: Christopher G. Watson <cgwatson@bu.edu>
Diff between brainGraph versions 2.7.2 dated 2019-11-06 and 2.7.3 dated 2019-11-07
brainGraph-2.7.2/brainGraph/R/atlas.R |only brainGraph-2.7.2/brainGraph/R/auc.R |only brainGraph-2.7.2/brainGraph/R/distances.R |only brainGraph-2.7.2/brainGraph/R/glm_design.R |only brainGraph-2.7.2/brainGraph/R/glm_methods.R |only brainGraph-2.7.2/brainGraph/R/glm_randomise.R |only brainGraph-2.7.2/brainGraph/R/glm_stats.R |only brainGraph-2.7.2/brainGraph/R/list.R |only brainGraph-2.7.2/brainGraph/R/method_helpers.R |only brainGraph-2.7.2/brainGraph/R/methods.R |only brainGraph-2.7.2/brainGraph/R/zzz.R |only brainGraph-2.7.2/brainGraph/man/atlas_helpers.Rd |only brainGraph-2.7.2/brainGraph/man/attributes.Rd |only brainGraph-2.7.2/brainGraph/man/brainGraph.Rd |only brainGraph-2.7.2/brainGraph/man/brainGraphList.Rd |only brainGraph-2.7.2/brainGraph/man/brain_atlases.Rd |only brainGraph-2.7.2/brainGraph/man/check_attributes.Rd |only brainGraph-2.7.2/brainGraph/man/correlation_matrices.Rd |only brainGraph-2.7.2/brainGraph/man/dir2files.Rd |only brainGraph-2.7.2/brainGraph/man/get_metadata.Rd |only brainGraph-2.7.2/brainGraph/man/get_rand_attrs.Rd |only brainGraph-2.7.2/brainGraph/man/get_thresholds.Rd |only brainGraph-2.7.2/brainGraph/man/glm_brainGraphList.Rd |only brainGraph-2.7.2/brainGraph/man/glm_fit.Rd |only brainGraph-2.7.2/brainGraph/man/glm_graph_plots.Rd |only brainGraph-2.7.2/brainGraph/man/glm_influence.Rd |only brainGraph-2.7.2/brainGraph/man/glm_info.Rd |only brainGraph-2.7.2/brainGraph/man/glm_model_select.Rd |only brainGraph-2.7.2/brainGraph/man/glm_stats.Rd |only brainGraph-2.7.2/brainGraph/man/is_binary.Rd |only brainGraph-2.7.2/brainGraph/man/make_auc_brainGraph.Rd |only brainGraph-2.7.2/brainGraph/man/matrix2list.Rd |only brainGraph-2.7.2/brainGraph/man/mean_distance_wt.Rd |only brainGraph-2.7.2/brainGraph/man/methods.Rd |only brainGraph-2.7.2/brainGraph/man/plot.brainGraphList.Rd |only brainGraph-2.7.2/brainGraph/man/plot_mni.Rd |only brainGraph-2.7.2/brainGraph/man/rename_levels.Rd |only brainGraph-2.7.2/brainGraph/man/set_graph_colors.Rd |only brainGraph-2.7.2/brainGraph/man/simpleCap.Rd |only brainGraph-2.7.2/brainGraph/man/split_string.Rd |only brainGraph-2.7.2/brainGraph/man/vif.bg_GLM.Rd |only brainGraph-2.7.3/brainGraph/DESCRIPTION | 16 brainGraph-2.7.3/brainGraph/MD5 | 262 +-- brainGraph-2.7.3/brainGraph/NAMESPACE | 111 - brainGraph-2.7.3/brainGraph/R/NBS.R | 227 +- brainGraph-2.7.3/brainGraph/R/analysis_random_graphs.R | 211 +- brainGraph-2.7.3/brainGraph/R/boot_global.R | 99 - brainGraph-2.7.3/brainGraph/R/brainGraph_GLM.R | 1105 +++++++------ brainGraph-2.7.3/brainGraph/R/brainGraph_mediate.R | 274 +-- brainGraph-2.7.3/brainGraph/R/centr_lev.R | 19 brainGraph-2.7.3/brainGraph/R/communicability.R | 38 brainGraph-2.7.3/brainGraph/R/contract_brainGraph.R | 64 brainGraph-2.7.3/brainGraph/R/corr_matrix.R | 282 --- brainGraph-2.7.3/brainGraph/R/count_edges.R | 29 brainGraph-2.7.3/brainGraph/R/create_graphs.R | 709 ++++---- brainGraph-2.7.3/brainGraph/R/create_mats.R | 286 +-- brainGraph-2.7.3/brainGraph/R/data.R | 177 -- brainGraph-2.7.3/brainGraph/R/data_tables.R | 133 - brainGraph-2.7.3/brainGraph/R/edge_asymmetry.R | 11 brainGraph-2.7.3/brainGraph/R/get_resid.R | 212 +- brainGraph-2.7.3/brainGraph/R/graph_efficiency.R | 62 brainGraph-2.7.3/brainGraph/R/hubs.R | 57 brainGraph-2.7.3/brainGraph/R/import.R | 51 brainGraph-2.7.3/brainGraph/R/individ_contrib.R | 362 +--- brainGraph-2.7.3/brainGraph/R/mtpc.R | 148 - brainGraph-2.7.3/brainGraph/R/permute_group.R | 174 +- brainGraph-2.7.3/brainGraph/R/plot_brainGraph.R | 564 +++--- brainGraph-2.7.3/brainGraph/R/plot_brainGraph_gui.R | 20 brainGraph-2.7.3/brainGraph/R/plot_brainGraph_list.R |only brainGraph-2.7.3/brainGraph/R/plot_brainGraph_multi.R | 244 +- brainGraph-2.7.3/brainGraph/R/plot_corr_mat.R |only brainGraph-2.7.3/brainGraph/R/plot_global.R | 121 - brainGraph-2.7.3/brainGraph/R/plot_group_means.R | 10 brainGraph-2.7.3/brainGraph/R/plot_rich_norm.R | 68 brainGraph-2.7.3/brainGraph/R/plot_vertex_measures.R | 62 brainGraph-2.7.3/brainGraph/R/random_graphs.R | 148 - brainGraph-2.7.3/brainGraph/R/rich_club.R | 178 +- brainGraph-2.7.3/brainGraph/R/robustness.R | 121 - brainGraph-2.7.3/brainGraph/R/s_core.R | 13 brainGraph-2.7.3/brainGraph/R/set_brainGraph_attributes.R | 415 +--- brainGraph-2.7.3/brainGraph/R/small_world.R | 91 - brainGraph-2.7.3/brainGraph/R/spatial_dist.R | 17 brainGraph-2.7.3/brainGraph/R/sysdata.rda |binary brainGraph-2.7.3/brainGraph/R/update_brainGraph_gui.R | 43 brainGraph-2.7.3/brainGraph/R/utils.R | 382 ++-- brainGraph-2.7.3/brainGraph/R/vertex_roles.R | 44 brainGraph-2.7.3/brainGraph/R/vulnerability.R | 48 brainGraph-2.7.3/brainGraph/R/write_brainnet.R | 72 brainGraph-2.7.3/brainGraph/man/Bootstrapping.Rd | 33 brainGraph-2.7.3/brainGraph/man/NBS.Rd | 73 brainGraph-2.7.3/brainGraph/man/aal.Rd |only brainGraph-2.7.3/brainGraph/man/apply_thresholds.Rd | 13 brainGraph-2.7.3/brainGraph/man/auc_diff.Rd | 2 brainGraph-2.7.3/brainGraph/man/brainGraph_GLM_fit.Rd |only brainGraph-2.7.3/brainGraph/man/brainGraph_permute.Rd | 27 brainGraph-2.7.3/brainGraph/man/brainsuite.Rd |only brainGraph-2.7.3/brainGraph/man/centr_betw_comm.Rd | 8 brainGraph-2.7.3/brainGraph/man/centr_lev.Rd | 12 brainGraph-2.7.3/brainGraph/man/check_degree.Rd |only brainGraph-2.7.3/brainGraph/man/check_strength.Rd |only brainGraph-2.7.3/brainGraph/man/check_weights.Rd |only brainGraph-2.7.3/brainGraph/man/choose.edges.Rd | 7 brainGraph-2.7.3/brainGraph/man/coeff_var.Rd | 3 brainGraph-2.7.3/brainGraph/man/color_vertices_edges.Rd |only brainGraph-2.7.3/brainGraph/man/communicability.Rd | 10 brainGraph-2.7.3/brainGraph/man/contract_brainGraph.Rd | 23 brainGraph-2.7.3/brainGraph/man/cor.diff.test.Rd | 27 brainGraph-2.7.3/brainGraph/man/corr.matrix.Rd |only brainGraph-2.7.3/brainGraph/man/count_edges.Rd | 11 brainGraph-2.7.3/brainGraph/man/craddock200.Rd |only brainGraph-2.7.3/brainGraph/man/create_mats.Rd | 61 brainGraph-2.7.3/brainGraph/man/data_tables.Rd | 32 brainGraph-2.7.3/brainGraph/man/delete_all_attr.Rd | 2 brainGraph-2.7.3/brainGraph/man/dosenbach160.Rd |only brainGraph-2.7.3/brainGraph/man/edge_asymmetry.Rd | 5 brainGraph-2.7.3/brainGraph/man/efficiency.Rd | 26 brainGraph-2.7.3/brainGraph/man/freesurfer_atlases.Rd |only brainGraph-2.7.3/brainGraph/man/get_lm_vars.Rd | 4 brainGraph-2.7.3/brainGraph/man/glm.Rd | 245 -- brainGraph-2.7.3/brainGraph/man/glm_design.Rd | 87 - brainGraph-2.7.3/brainGraph/man/glm_helpers.Rd | 81 brainGraph-2.7.3/brainGraph/man/hoa112.Rd |only brainGraph-2.7.3/brainGraph/man/hubness.Rd | 35 brainGraph-2.7.3/brainGraph/man/individ_contrib.Rd | 63 brainGraph-2.7.3/brainGraph/man/is.brainGraph.Rd |only brainGraph-2.7.3/brainGraph/man/lpba40.Rd |only brainGraph-2.7.3/brainGraph/man/make_brainGraph.Rd | 220 -- brainGraph-2.7.3/brainGraph/man/make_ego_brainGraph.Rd | 10 brainGraph-2.7.3/brainGraph/man/make_empty_brainGraph.Rd |only brainGraph-2.7.3/brainGraph/man/make_glm_brainGraph.Rd |only brainGraph-2.7.3/brainGraph/man/make_mediate_brainGraph.Rd |only brainGraph-2.7.3/brainGraph/man/make_nbs_brainGraph.Rd |only brainGraph-2.7.3/brainGraph/man/mediation.Rd | 79 brainGraph-2.7.3/brainGraph/man/mtpc.Rd | 69 brainGraph-2.7.3/brainGraph/man/partition.Rd | 19 brainGraph-2.7.3/brainGraph/man/plot.brainGraph.Rd | 119 - brainGraph-2.7.3/brainGraph/man/plot.brainGraph_GLM.Rd |only brainGraph-2.7.3/brainGraph/man/plot.brainGraph_NBS.Rd |only brainGraph-2.7.3/brainGraph/man/plot.brainGraph_mediate.Rd |only brainGraph-2.7.3/brainGraph/man/plot.brainGraph_mtpc.Rd |only brainGraph-2.7.3/brainGraph/man/plot_brainGraph_gui.Rd | 9 brainGraph-2.7.3/brainGraph/man/plot_brainGraph_list.Rd |only brainGraph-2.7.3/brainGraph/man/plot_brainGraph_multi.Rd | 130 - brainGraph-2.7.3/brainGraph/man/plot_corr_mat.Rd |only brainGraph-2.7.3/brainGraph/man/plot_global.Rd | 47 brainGraph-2.7.3/brainGraph/man/plot_rich_norm.Rd | 16 brainGraph-2.7.3/brainGraph/man/plot_vertex_measures.Rd | 32 brainGraph-2.7.3/brainGraph/man/plot_volumetric.Rd | 4 brainGraph-2.7.3/brainGraph/man/random_graphs.Rd | 92 - brainGraph-2.7.3/brainGraph/man/randomise.Rd | 58 brainGraph-2.7.3/brainGraph/man/residuals.Rd | 64 brainGraph-2.7.3/brainGraph/man/rich_club.Rd | 70 brainGraph-2.7.3/brainGraph/man/rich_club_attrs.Rd | 22 brainGraph-2.7.3/brainGraph/man/robustness.Rd | 25 brainGraph-2.7.3/brainGraph/man/rotation.Rd | 2 brainGraph-2.7.3/brainGraph/man/s_core.Rd | 9 brainGraph-2.7.3/brainGraph/man/set_brainGraph_attr.Rd |only brainGraph-2.7.3/brainGraph/man/small.world.Rd | 28 brainGraph-2.7.3/brainGraph/man/spatial_dist.Rd | 11 brainGraph-2.7.3/brainGraph/man/subset_graph.Rd | 2 brainGraph-2.7.3/brainGraph/man/symm_mean.Rd |only brainGraph-2.7.3/brainGraph/man/symmetrize_mats.Rd | 18 brainGraph-2.7.3/brainGraph/man/update_fs_names.Rd | 2 brainGraph-2.7.3/brainGraph/man/vertex_roles.Rd | 26 brainGraph-2.7.3/brainGraph/man/vulnerability.Rd | 9 brainGraph-2.7.3/brainGraph/man/write_brainnet.Rd | 38 brainGraph-2.7.3/brainGraph/man/xfm.weights.Rd |only 167 files changed, 4580 insertions(+), 5320 deletions(-)
Title: Retrieving Information of Proteins from Uniprot
Description: Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information.
Author: Mohamed Soudy [aut, cre],
Ali Mostafa [aut]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>
Diff between UniprotR versions 1.1.0 dated 2019-11-05 and 1.1.1 dated 2019-11-07
UniprotR-1.1.0/UniprotR/R/ConstructPhylogeny.R |only UniprotR-1.1.0/UniprotR/man/ConstructPhylogeny.Rd |only UniprotR-1.1.1/UniprotR/DESCRIPTION | 11 +++++------ UniprotR-1.1.1/UniprotR/MD5 | 6 ++---- UniprotR-1.1.1/UniprotR/NAMESPACE | 5 ----- 5 files changed, 7 insertions(+), 15 deletions(-)
Title: Disciplined Convex Optimization
Description: An object-oriented modeling language for disciplined convex
programming (DCP). It allows the user to formulate convex optimization problems
in a natural way following mathematical convention and DCP rules. The system
analyzes the problem, verifies its convexity, converts it into a canonical form,
and hands it off to an appropriate solver to obtain the solution.
Author: Anqi Fu [aut, cre],
Balasubramanian Narasimhan [aut],
Steven Diamond [aut],
John Miller [aut],
Stephen Boyd [ctb],
Paul Kunsberg Rosenfield [ctb]
Maintainer: Anqi Fu <anqif@stanford.edu>
Diff between CVXR versions 0.99-6 dated 2019-06-01 and 0.99-7 dated 2019-11-07
DESCRIPTION | 12 ++++----- MD5 | 14 +++++----- R/solver.R | 3 ++ README.md | 6 ++-- build/vignette.rds |binary inst/doc/cvxr_intro.html | 40 +++++++++++++++--------------- tests/testthat/test-g01-non_optimal.R | 3 +- tests/testthat/test-g01-nonlinear_atoms.R | 5 ++- 8 files changed, 45 insertions(+), 38 deletions(-)
Title: Representation Tool For Output Of Connectivity Map (CMap)
Analysis
Description: Automatically displays graphical visualization for exported data table (permutated results) from Connectivity Map (CMap) (2006) <doi:10.1126/science.1132939>.
It allows the representation of the statistics (p-value and enrichment) according to each cell lines in the form of a bubble plot.
Author: Raphaël Bonnet [aut, cre], Jean-François Peyron[aut,ths]
Maintainer: Raphaël Bonnet <raphael.bonnet@univ-cotedazur.fr>
Diff between CMapViz versions 0.0.4 dated 2019-11-06 and 0.1.0 dated 2019-11-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/bubble_plot.R | 6 +++--- inst/WORDLIST | 1 + inst/extdata/example.xls |binary man/bubble_plot.Rd | 2 +- tests/spelling.R | 9 +++------ 7 files changed, 18 insertions(+), 20 deletions(-)
Title: Uncertainty Decomposition
Description: If a procedure consists of several stages and there are several models that can be selected for each stage,
uncertainty of the procedure can be decomposed by stages or models.
This package includes the ANOVA-based method, the cumulative uncertainty-based method, and the balanced decomposition method.
Yongdai Kim et al. (2019) <doi:10.1016/j.hydroa.2019.100024> is a related paper which is accessible via the URL below.
Author: Seonghyeon Kim [aut, cre],
Yongdai Kim [aut],
Ilsang Ohn [aut]
Maintainer: Seonghyeon Kim <shkim93@snu.ac.kr>
Diff between UncDecomp versions 1.0.0 dated 2019-10-31 and 1.0.1 dated 2019-11-07
DESCRIPTION | 7 ++-- MD5 | 66 ++++++++++++++++++++++---------------------- R/UD_ANOVA_model.R | 16 ++++++---- R/UD_ANOVA_stage.R | 13 ++++---- R/UD_bal_model.R | 13 ++++---- R/UD_bal_stage.R | 11 ++++--- R/UD_cum_stage.R | 11 ++++--- R/UDtable.R | 5 ++- R/apply_sweep.R | 6 ++-- R/cum_uncertainty.R | 3 +- R/drange.R | 5 ++- R/model2stage.R | 11 ++++--- R/plotUDlist.R | 7 ++-- R/printUD.R | 5 ++- R/scenario_uncertainty.R | 3 +- R/stage_uncertainty.R | 3 +- R/unc_postprocess.R | 9 +++--- R/var0.R | 3 +- man/UD_ANOVA_model.Rd | 16 ++++++---- man/UD_ANOVA_stage.Rd | 11 ++++--- man/UD_bal_model.Rd | 13 ++++---- man/UD_bal_stage.Rd | 11 ++++--- man/UD_cum_stage.Rd | 11 ++++--- man/UD_model2stage.Rd | 11 ++++--- man/UDtable.Rd | 5 ++- man/apply_sweep.Rd | 6 ++-- man/cum_uncertainty.Rd | 3 +- man/drange.Rd | 5 ++- man/plotUDlist.Rd | 7 ++-- man/printUD.Rd | 5 ++- man/scenario_uncertainty.Rd | 3 +- man/stage_uncertainty.Rd | 3 +- man/unc_postprocess.Rd | 9 +++--- man/var0.Rd | 3 +- 34 files changed, 176 insertions(+), 143 deletions(-)
Title: Enhanced Database Interactivity
Description: Facilitates interaction with ODBC data sources, by hiding communications, and supporting parameterised multi-statement SQL with embedded R.
Author: Mike Lee
Maintainer: Mike Lee <random.deviate@gmail.com>
Diff between SQRL versions 0.6.3 dated 2019-07-07 and 0.7.0 dated 2019-11-07
DESCRIPTION | 12 MD5 | 24 R/SQRL.R | 3754 ++++++++++++++++++++++++++++++++------------------- man/SQRL-package.Rd | 62 man/sqrlAll.Rd | 11 man/sqrlConfig.Rd | 87 - man/sqrlInterface.Rd | 42 man/sqrlOff.Rd | 6 man/sqrlParams.Rd | 171 +- man/sqrlScript.Rd | 980 ++++++++++--- man/sqrlSource.Rd | 62 man/sqrlSources.Rd | 8 man/sqrlUsage.Rd | 420 +++-- 13 files changed, 3733 insertions(+), 1906 deletions(-)
Title: Parametric Mortality Models, Life Tables and HMD
Description: Fit the most popular human mortality 'laws', and construct
full and abridge life tables given various input indices. A mortality
law is a parametric function that describes the dying-out process of
individuals in a population during a significant portion of their
life spans. For a comprehensive review of the most important mortality
laws see Tabeau (2001) <doi:10.1007/0-306-47562-6_1>.
Practical functions for downloading data from various human mortality
databases are provided as well.
Author: Marius D. Pascariu [aut, cre, cph]
(<https://orcid.org/0000-0002-2568-6489>),
Vladimir Canudas-Romo [ctb]
Maintainer: Marius D. Pascariu <mpascariu@outlook.com>
Diff between MortalityLaws versions 1.8.0 dated 2019-06-18 and 1.8.1 dated 2019-11-07
DESCRIPTION | 6 +-- MD5 | 24 +++++++-------- NEWS | 5 +++ R/LifeTable.R | 1 R/readJMD.R | 11 +++---- README.md | 2 - inst/doc/Installation.pdf |binary inst/doc/Intro.pdf |binary man/ReadJMD.Rd | 8 ++--- tests/testthat/test_LifeTable.R | 3 + tests/testthat/test_MortalityLaws.R | 54 +++++++++++++++++++++++++---------- tests/testthat/test_MortalityLaws2.R | 17 +++++++---- tests/testthat/test_ReadHMD.R | 45 +++++++++++++++++++---------- 13 files changed, 115 insertions(+), 61 deletions(-)
More information about fastlogranktest at CRAN
Permanent link
Title: Dynamic Simulation and Testing for Single-Equation ARDL Models
Description: While autoregressive distributed lag (ARDL) models allow for extremely flexible dynamics, interpreting substantive significance of complex lag structures remains difficult. This package is designed to assist users in dynamically simulating and plotting the results of various ARDL models. It also contains post-estimation diagnostics, including a test for cointegration when estimating the error-correction variant of the autoregressive distributed lag model (Pesaran, Shin, and Smith 2001 <doi:10.1002/jae.616>).
Author: Soren Jordan [aut, cre, cph],
Andrew Q. Philips [aut]
Maintainer: Soren Jordan <sorenjordanpols@gmail.com>
Diff between dynamac versions 0.1.9 dated 2019-09-27 and 0.1.10 dated 2019-11-07
DESCRIPTION | 6 - MD5 | 12 +- R/dynamac.R | 174 ++++++++++++++++++++++++++--------------- inst/doc/dynamac-vignette.html | 8 - inst/dynamac-manual.pdf |binary man/dynardl.all.plots.Rd | 7 + man/dynardl.simulation.plot.Rd | 10 +- 7 files changed, 139 insertions(+), 78 deletions(-)
Title: Loading Screen for 'Shiny'
Description: Full screen splash loading screens for 'Shiny'.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between waiter versions 0.0.1 dated 2019-03-13 and 0.0.6 dated 2019-11-07
waiter-0.0.1/waiter/inst/assets/custom.js |only waiter-0.0.1/waiter/inst/assets/please-wait.css |only waiter-0.0.1/waiter/inst/assets/please-wait.min.js |only waiter-0.0.1/waiter/inst/assets/spinkit.css |only waiter-0.0.1/waiter/inst/examples |only waiter-0.0.6/waiter/DESCRIPTION | 12 waiter-0.0.6/waiter/MD5 | 42 +- waiter-0.0.6/waiter/NAMESPACE | 33 ++ waiter-0.0.6/waiter/R/butler.R |only waiter-0.0.6/waiter/R/print.R |only waiter-0.0.6/waiter/R/spinners.R | 186 +++++++++++ waiter-0.0.6/waiter/R/utils-pipe.R |only waiter-0.0.6/waiter/R/utils.R |only waiter-0.0.6/waiter/R/waiter.R | 174 ++++++++++ waiter-0.0.6/waiter/R/waitress.R |only waiter-0.0.6/waiter/README.md | 333 ++++++++++++++++++++- waiter-0.0.6/waiter/inst/assets/butler |only waiter-0.0.6/waiter/inst/assets/waiter |only waiter-0.0.6/waiter/inst/assets/waitress |only waiter-0.0.6/waiter/inst/waiter |only waiter-0.0.6/waiter/inst/waitress |only waiter-0.0.6/waiter/man/butler.Rd |only waiter-0.0.6/waiter/man/dot-random_name.Rd |only waiter-0.0.6/waiter/man/figures/butler.gif |only waiter-0.0.6/waiter/man/figures/waitress.gif |only waiter-0.0.6/waiter/man/pipe.Rd |only waiter-0.0.6/waiter/man/spinners.Rd | 48 +++ waiter-0.0.6/waiter/man/waiter.Rd | 157 +++++++++ waiter-0.0.6/waiter/man/waitress.Rd |only 29 files changed, 939 insertions(+), 46 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-31 0.3.0
2018-06-24 0.2.1
2017-11-03 0.2
2016-12-20 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-21 0.1.2
2019-10-16 0.1.1
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt'. Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Hothorn, 2019, <arxiv:1910.09219>).
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 0.3-0 dated 2019-10-22 and 0.3-1 dated 2019-11-07
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/methods.R | 2 +- R/tram.R | 6 +++++- build/partial.rdb |binary inst/NEWS.Rd | 9 +++++++++ inst/doc/mtram.pdf |binary inst/doc/tram.pdf |binary src/init.c | 4 ++-- tests/bugfixes.R | 19 +++++++++++++++++++ 10 files changed, 50 insertions(+), 18 deletions(-)
Title: Constructs Simple Feature Objects
Description: Converts R and 'Rcpp' objects to Simple Features 'sf', without depending
on the Simple Feature library. Conversion functions are available at both the R level,
and through 'Rcpp'.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <david.cooley.au@gmail.com>
Diff between sfheaders versions 0.0.1 dated 2019-10-03 and 0.0.2 dated 2019-11-07
DESCRIPTION | 7 ++++--- MD5 | 11 ++++++----- NEWS.md |only R/sf.R | 22 +++++++++++++++++----- README.md | 3 +++ inst/include/sfheaders/sfc/sfc_attributes.hpp | 4 ++-- inst/include/sfheaders/sfc/sfc_types.hpp | 2 +- 7 files changed, 33 insertions(+), 16 deletions(-)
Title: Colour Palettes for Data
Description: Colour palettes for data, based on some well known public data
sets. Includes helper functions to map absolute values to known palettes, and
capture the work of image colour mapping as raster data sets.
Author: Michael D. Sumner [aut, cre],
Abigael Proctor [ctb] (Named the package),
Tomas Remenyi [ctb] (Provided colours for element_pal),
R Core Team and contributors worldwide [ctb] (source code of
image.default)
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between palr versions 0.0.6 dated 2016-07-26 and 0.1.0 dated 2019-11-07
palr-0.0.6/palr/NEWS |only palr-0.0.6/palr/R/elemenPal.R |only palr-0.0.6/palr/man/bathyDeepPal.Rd |only palr-0.0.6/palr/man/chlPal.Rd |only palr-0.0.6/palr/man/icePal.Rd |only palr-0.0.6/palr/man/sstPal.Rd |only palr-0.1.0/palr/DESCRIPTION | 30 palr-0.1.0/palr/MD5 | 60 - palr-0.1.0/palr/NAMESPACE | 31 palr-0.1.0/palr/NEWS.md |only palr-0.1.0/palr/R/bathy.R | 86 - palr-0.1.0/palr/R/element_pal.R |only palr-0.1.0/palr/R/image_pal.R |only palr-0.1.0/palr/R/palr-package.r | 58 - palr-0.1.0/palr/R/palr.R | 1413 ++++++++++++++-------------- palr-0.1.0/palr/R/timePal.R | 72 - palr-0.1.0/palr/R/utils.R | 4 palr-0.1.0/palr/README.md | 119 +- palr-0.1.0/palr/build/vignette.rds |binary palr-0.1.0/palr/inst/doc/nasa_chla.R | 36 palr-0.1.0/palr/inst/doc/nasa_chla.Rmd | 93 - palr-0.1.0/palr/inst/doc/nasa_chla.html | 459 ++++++--- palr-0.1.0/palr/inst/doc/palr.R | 89 + palr-0.1.0/palr/inst/doc/palr.Rmd | 203 ++-- palr-0.1.0/palr/inst/doc/palr.html | 693 +++++++++---- palr-0.1.0/palr/man/bathy_deep_pal.Rd |only palr-0.1.0/palr/man/chl_pal.Rd |only palr-0.1.0/palr/man/col2hex.Rd | 47 palr-0.1.0/palr/man/ice_pal.Rd |only palr-0.1.0/palr/man/image_pal.Rd |only palr-0.1.0/palr/man/mk_timePal.Rd | 65 - palr-0.1.0/palr/man/oisst.Rd | 51 - palr-0.1.0/palr/man/palr.Rd | 21 palr-0.1.0/palr/man/sst_pal.Rd |only palr-0.1.0/palr/tests/testthat.R | 8 palr-0.1.0/palr/tests/testthat/test-basic.R | 93 + palr-0.1.0/palr/vignettes/nasa_chla.Rmd | 93 - palr-0.1.0/palr/vignettes/palr.Rmd | 203 ++-- 38 files changed, 2399 insertions(+), 1628 deletions(-)
Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii)
Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v)
Matrix functions, (vi) Projector and canonical efficiency functions, and (vii)
Miscellaneous functions. There is a vignette describing how to use the
design functions for randomizing and assessing designs available as a
vignette called 'DesignNotes'. The ANOVA functions facilitate the extraction of
information when the 'Error' function has been used in the call to 'aov'.
The package 'dae' can also be installed from
<http://chris.brien.name/rpackages/>.
Author: Chris Brien [aut, cre] (<https://orcid.org/0000-0003-0581-1817>)
Maintainer: Chris Brien <chris.brien@unisa.edu.au>
Diff between dae versions 3.0-32 dated 2019-05-15 and 3.1-16 dated 2019-11-07
dae-3.0-32/dae/R/fac.layout.v3.r |only dae-3.0-32/dae/data/Exp249.mplot.des.rda |only dae-3.0-32/dae/man/Exp249.mplot.des.Rd |only dae-3.0-32/dae/man/fac.layout.Rd |only dae-3.1-16/dae/DESCRIPTION | 10 dae-3.1-16/dae/MD5 | 69 +-- dae-3.1-16/dae/NAMESPACE | 3 dae-3.1-16/dae/R/S3methodsDeprecations.r | 6 dae-3.1-16/dae/R/dae.utilties.r | 6 dae-3.1-16/dae/R/daeAttach.r | 1 dae-3.1-16/dae/R/designGGPlot.v1.r |only dae-3.1-16/dae/R/designPlot.v2.r | 4 dae-3.1-16/dae/R/designRandomize.v2.r | 292 ++++++++------- dae-3.1-16/dae/R/fac.gen.r | 4 dae-3.1-16/dae/R/mat.functions.r | 27 - dae-3.1-16/dae/build/partial.rdb |binary dae-3.1-16/dae/build/vignette.rds |binary dae-3.1-16/dae/data/Cabinet1.des.rda |only dae-3.1-16/dae/data/Exp249.munit.des.rda |only dae-3.1-16/dae/inst/NEWS.Rd | 33 + dae-3.1-16/dae/inst/doc/DesignNotes.pdf |binary dae-3.1-16/dae/inst/doc/dae-manual.pdf |binary dae-3.1-16/dae/man/Cabinet1.des.Rd |only dae-3.1-16/dae/man/Exp249.munit.des.Rd |only dae-3.1-16/dae/man/dae-package.Rd | 6 dae-3.1-16/dae/man/designBlocksGGPlot.Rd |only dae-3.1-16/dae/man/designGGPlot.Rd |only dae-3.1-16/dae/man/designPlotlabels.Rd | 2 dae-3.1-16/dae/man/designRandomize.Rd | 48 +- dae-3.1-16/dae/man/mat.Vpredicts.Rd | 10 dae-3.1-16/dae/tests/testthat/data/EucPulp2x2.rda |binary dae-3.1-16/dae/tests/testthat/data/Exp249.mplot.sys.rda |binary dae-3.1-16/dae/tests/testthat/data/FAME.rda |binary dae-3.1-16/dae/tests/testthat/data/LS4.CC4x4.1a.rda |binary dae-3.1-16/dae/tests/testthat/data/LSRepeatHwife.dat.rda |binary dae-3.1-16/dae/tests/testthat/data/Need3.dat.rda |binary dae-3.1-16/dae/tests/testthat/data/Oats.dat.rda |binary dae-3.1-16/dae/tests/testthat/data/PiephoLSDRand.rda |binary dae-3.1-16/dae/tests/testthat/data/gwall.lay.rda |binary dae-3.1-16/dae/tests/testthat/testAmeasures.r | 6 dae-3.1-16/dae/tests/testthat/testRandomize.r | 76 +++ 41 files changed, 381 insertions(+), 222 deletions(-)
Title: Multiple Locus Association Mapping on a Genome-Wide Scale
Description: An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred and outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. For users unfamiliar with R, to perform an analysis, run 'OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.
Author: Andrew George [aut, cre],
Joshua Bowden [ctb],
Ryan Stephenson [ctb],
Hyun Kang [ctb],
Noah Zaitlen [ctb],
Claire Wade [ctb],
Andrew Kirby [ctb],
David Heckerman [ctb],
Mark Daly [ctb],
Eleazar Eskin [ctb]
Maintainer: Andrew George <andrew.george@csiro.au>
Diff between Eagle versions 1.5.2 dated 2019-08-22 and 2.0.0 dated 2019-11-07
Eagle-1.5.2/Eagle/R/ReadMarker.R |only Eagle-2.0.0/Eagle/DESCRIPTION | 12 Eagle-2.0.0/Eagle/MD5 | 88 ++- Eagle-2.0.0/Eagle/NAMESPACE | 2 Eagle-2.0.0/Eagle/NEWS |only Eagle-2.0.0/Eagle/R/AM.R | 291 ++++++++---- Eagle-2.0.0/Eagle/R/FPR4AM.R | 318 +++++++++----- Eagle-2.0.0/Eagle/R/RcppExports.R | 24 - Eagle-2.0.0/Eagle/R/ReadMarkerBin.R |only Eagle-2.0.0/Eagle/R/build_design_matrix.R | 28 - Eagle-2.0.0/Eagle/R/calcMMt.R | 6 Eagle-2.0.0/Eagle/R/calcVC.R | 10 Eagle-2.0.0/Eagle/R/calc_extBIC.R | 8 Eagle-2.0.0/Eagle/R/calc_extBIC_MLE.R |only Eagle-2.0.0/Eagle/R/calculateH.R | 1 Eagle-2.0.0/Eagle/R/calculateMMt.R | 2 Eagle-2.0.0/Eagle/R/calculate_a_and_vara.R | 34 + Eagle-2.0.0/Eagle/R/calculate_a_and_vara_batch.R | 17 Eagle-2.0.0/Eagle/R/calculate_reduced_a.R | 3 Eagle-2.0.0/Eagle/R/calculate_reduced_a_batch.R | 7 Eagle-2.0.0/Eagle/R/check_for_NA_in_trait.R | 6 Eagle-2.0.0/Eagle/R/check_inputs_mlam.R | 4 Eagle-2.0.0/Eagle/R/constructX.R | 11 Eagle-2.0.0/Eagle/R/create_bin.R |only Eagle-2.0.0/Eagle/R/emma_REMLE.R | 7 Eagle-2.0.0/Eagle/R/emma_misc.R | 122 ----- Eagle-2.0.0/Eagle/R/extract_geno_Mt.R |only Eagle-2.0.0/Eagle/R/find_qtl.R | 51 +- Eagle-2.0.0/Eagle/R/onAttach.R | 2 Eagle-2.0.0/Eagle/R/summary_am.R | 106 ++++ Eagle-2.0.0/Eagle/inst/shiny_app/app.R | 14 Eagle-2.0.0/Eagle/inst/shiny_app/faq.rmd |only Eagle-2.0.0/Eagle/man/AM.Rd | 34 - Eagle-2.0.0/Eagle/man/FPR4AM.Rd | 12 Eagle-2.0.0/Eagle/man/ReadMarker.Rd | 2 Eagle-2.0.0/Eagle/man/SummaryAM.Rd | 2 Eagle-2.0.0/Eagle/src/CreateBIN.cpp |only Eagle-2.0.0/Eagle/src/CreateBIN_PLINK.cpp |only Eagle-2.0.0/Eagle/src/RcppExports.cpp | 86 +++ Eagle-2.0.0/Eagle/src/ReadBlock.cpp | 6 Eagle-2.0.0/Eagle/src/ReadBlockBin.cpp |only Eagle-2.0.0/Eagle/src/ReshapeM_rcpp.cpp | 2 Eagle-2.0.0/Eagle/src/calculateMMt_rcpp.cpp | 20 Eagle-2.0.0/Eagle/src/calculate_a_and_vara_batch_rcpp.cpp | 44 + Eagle-2.0.0/Eagle/src/calculate_a_and_vara_rcpp.cpp | 63 ++ Eagle-2.0.0/Eagle/src/calculate_reduced_a_rcpp.cpp | 4 Eagle-2.0.0/Eagle/src/createM_BIN_rcpp.cpp |only Eagle-2.0.0/Eagle/src/createM_BIN_rcpp.h |only Eagle-2.0.0/Eagle/src/createMt_BIN_rcpp.cpp |only Eagle-2.0.0/Eagle/src/extract_geno_Mt_rcpp.cpp |only Eagle-2.0.0/Eagle/src/extract_geno_rcpp.cpp | 4 Eagle-2.0.0/Eagle/src/readblock.h | 5 52 files changed, 910 insertions(+), 548 deletions(-)