Title: Sparse Three-Dimensional Arrays and Linear Algebra Utilities
Description: Defines sparse three-dimensional arrays
and supports standard operations on them.
The package also includes utility functions for
matrix calculations that are common in
statistics, such as quadratic forms.
Author: Adrian Baddeley [aut, cre, cph]
(<https://orcid.org/0000-0001-9499-8382>),
Rolf Turner [aut, cph] (<https://orcid.org/0000-0001-5521-5218>),
Ege Rubak [aut, cph] (<https://orcid.org/0000-0002-6675-533X>)
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.sparse versions 2.0-0 dated 2021-03-16 and 2.1-0 dated 2021-12-16
DESCRIPTION | 9 +++----- MD5 | 17 ++++++++------- NEWS | 29 ++++++++++++++++++++++++++ R/linalg.R | 20 +++++++++--------- inst/doc/packagesizes.txt | 1 man/bind.sparse3Darray.Rd |only man/sparse3Darray.Rd | 2 - man/spatstat.sparse-internal.Rd | 2 - man/sumouter.Rd | 22 +++++++++++++++++--- tests/linalgeb.R | 44 +++++++++++++++++++++------------------- 10 files changed, 97 insertions(+), 49 deletions(-)
More information about spatstat.sparse at CRAN
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Title: Datasets for 'spatstat' Family
Description: Contains all the datasets for the 'spatstat' family of packages.
Author: Adrian Baddeley [aut, cre] (<https://orcid.org/0000-0001-9499-8382>),
Rolf Turner [aut] (<https://orcid.org/0000-0001-5521-5218>),
Ege Rubak [aut] (<https://orcid.org/0000-0002-6675-533X>),
W Aherne [ctb],
Freda Alexander [ctb],
Qi Wei Ang [ctb],
Sourav Banerjee [ctb],
Mark Berman [ctb],
R Bernhardt [ctb],
Thomas Berndtsen [ctb],
Andrew Bevan [ctb],
Jeffrey Betts [ctb],
Ray Cartwright [ctb],
Richard Condit [ctb],
Francis Crick [ctb],
Marcelino de la Cruz Rot [ctb],
Jack Cuzick [ctb],
Tilman Davies [ctb],
Peter Diggle [ctb],
Michael Drinkwater [ctb],
Stephen Eglen [ctb],
Robert Edwards [ctb],
AE Esler [ctb],
Gregory Evans [ctb],
Bernard Fingleton [ctb],
Olivier Flores [ctb],
David Ford [ctb],
Robin Foster [ctb],
Janet Franklin [ctb],
Neba Funwi-Gabga [ctb],
DJ Gerrard [ctb],
Andy Green [ctb],
Tim Griffin [ctb],
Ute Hahn [ctb],
RD Harkness [ctb],
Arthur Hickman [ctb],
Stephen Hubbell [ctb],
Austin Hughes [ctb],
Jonathan Huntington [ctb],
MJ Hutchings [ctb],
Jackie Inwald [ctb],
Valerie Isham [ctb],
Aruna Jammalamadaka [ctb],
Carl Knox-Robinson [ctb],
Mahdieh Khanmohammadi [ctb],
Tero Kokkila [ctb],
Bas Kooijman [ctb],
Kenneth Kosik [ctb],
Peter Kovesi [ctb],
Lily Kozmian-Ledward [ctb],
Robert Lamb [ctb],
NA Laskurain [ctb],
George Leser [ctb],
Marie-Colette van Lieshout [ctb],
AF Mark [ctb],
Jorge Mateu [ctb],
Annikki Makela [ctb],
Enrique Miranda [ctb],
Nicoletta Nava [ctb],
M Numata [ctb],
Matti Nummelin [ctb],
Jens Randel Nyengaard [ctb],
Yosihiko Ogata [ctb],
Si Palmer [ctb],
Antti Penttinen [ctb],
Sandra Pereira [ctb],
Nicolas Picard [ctb],
William Platt [ctb],
Stephen Rathbun [ctb],
Brian Ripley [ctb],
Roger Sainsbury [ctb],
Dietrich Stoyan [ctb],
David Strauss [ctb],
L Strand [ctb],
Masaharu Tanemura [ctb],
Graham Upton [ctb],
Bill Venables [ctb],
Sasha Voss [ctb],
Rasmus Waagepetersen [ctb],
Keith Watkins [ctb],
H Wendrock [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.data versions 2.1-0 dated 2021-03-21 and 2.1-2 dated 2021-12-16
DESCRIPTION | 8 +- MD5 | 129 ++++++++++++++++++++++++------------------------ NEWS |only data/Kovesi.rda |binary data/amacrine.rda |binary data/anemones.rda |binary data/ants.rda |binary data/austates.rda |binary data/bdspots.rda |binary data/bei.rda |binary data/betacells.rda |binary data/bramblecanes.rda |binary data/bronzefilter.rda |binary data/btb.rda |binary data/cells.rda |binary data/cetaceans.rda |binary data/chicago.rda |binary data/chorley.rda |binary data/clmfires.rda |binary data/concrete.rda |binary data/copper.rda |binary data/demohyper.rda |binary data/demopat.rda |binary data/dendrite.rda |binary data/finpines.rda |binary data/flu.rda |binary data/ganglia.rda |binary data/gordon.rda |binary data/gorillas.rda |binary data/hamster.rda |binary data/heather.rda |binary data/humberside.rda |binary data/hyytiala.rda |binary data/japanesepines.rda |binary data/lansing.rda |binary data/letterR.rda |binary data/longleaf.rda |binary data/mucosa.rda |binary data/murchison.rda |binary data/nbfires.rda |binary data/nztrees.rda |binary data/osteo.rda |binary data/paracou.rda |binary data/ponderosa.rda |binary data/pyramidal.rda |binary data/redwood.rda |binary data/redwood3.rda |binary data/redwoodfull.rda |binary data/residualspaper.rda |binary data/shapley.rda |binary data/simba.rda |binary data/simdat.rda |binary data/simplenet.rda |binary data/spiders.rda |binary data/sporophores.rda |binary data/spruces.rda |binary data/swedishpines.rda |binary data/urkiola.rda |binary data/vesicles.rda |binary data/waka.rda |binary data/waterstriders.rda |binary man/gordon.Rd | 2 man/japanesepines.Rd | 5 + man/nbfires.Rd | 2 man/redwood.Rd | 6 -- man/redwoodfull.Rd | 4 + 66 files changed, 79 insertions(+), 77 deletions(-)
Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data, including densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.
Author: Tarn Duong [aut, cre] (<https://orcid.org/0000-0002-1198-3482>),
Matt Wand [ctb] (<https://orcid.org/0000-0003-2555-896X>),
Jose Chacon [ctb],
Artur Gramacki [ctb] (<https://orcid.org/0000-0002-1610-9743>)
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.13.2 dated 2021-07-01 and 1.13.3 dated 2021-12-16
CHANGELOG | 29 ++++- DESCRIPTION | 22 ++-- MD5 | 76 ++++++------- NAMESPACE | 9 - R/binning.R | 4 R/hist.R | 8 - R/integrate-kde.R | 36 ------ R/kcde.R | 48 ++++---- R/kcopula.R | 10 - R/kda.R | 152 ++++++++++++--------------- R/kdde.R | 43 +++---- R/kde-boundary.R | 9 - R/kde-test.R | 34 +++--- R/kde.R | 128 ++++++++++------------- R/kdr.R | 252 +++++++++++++++++++++++++++++++++++++++++++-- R/kfe.R | 14 +- R/kfs.R | 19 +-- R/kms.R | 102 ++++++++++-------- R/ksupp.R | 33 +++++- R/mise.R | 160 +++++++++++++---------------- R/normal.R | 167 ++++++++++++------------------ R/prelim.R | 223 +++++++++++++++++++++++----------------- R/selector.R | 263 +++++++++++++++++++++++++----------------------- R/vkde.R | 2 build/vignette.rds |binary inst/doc/kde.pdf |binary man/kde.Rd | 4 man/kdr.Rd | 41 ++++--- man/kms.Rd | 2 man/ksupp.Rd | 29 +++-- man/plot.histde.Rd | 10 - man/plot.kcde.Rd | 6 - man/plot.kda.Rd | 6 - man/plot.kdde.Rd | 7 - man/plot.kde.Rd | 13 +- man/plot.kde.loctest.Rd | 4 man/plot.kde.part.Rd | 4 man/plot.kfs.Rd | 3 man/plot.kroc.Rd | 4 39 files changed, 1112 insertions(+), 864 deletions(-)
Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between parallelly versions 1.29.0 dated 2021-11-21 and 1.30.0 dated 2021-12-16
DESCRIPTION | 6 - MD5 | 20 +++--- NEWS | 39 ++++++++++++ R/makeClusterPSOCK.R | 149 +++++++++++++++++++++++++++++++++++++++-------- R/zzz.R | 16 ++--- README.md | 3 inst/WORDLIST | 1 man/as.cluster.Rd | 2 man/autoStopCluster.Rd | 2 man/makeClusterPSOCK.Rd | 68 ++++++++++++++------- tests/makeClusterPSOCK.R | 76 +++++++++++++++++++++++ 11 files changed, 310 insertions(+), 72 deletions(-)
Title: Download and Tidy Time Series Data from the Australian Bureau of
Statistics
Description: Downloads, imports, and tidies time series data from the
Australian Bureau of Statistics <https://www.abs.gov.au/>.
Author: Matt Cowgill [aut, cre] (<https://orcid.org/0000-0003-0422-3300>),
Zoe Meers [aut],
Jaron Lee [aut],
David Diviny [aut],
Hugh Parsonage [ctb]
Maintainer: Matt Cowgill <mattcowgill@gmail.com>
Diff between readabs versions 0.4.10 dated 2021-10-28 and 0.4.11 dated 2021-12-16
DESCRIPTION | 10 +++++----- MD5 | 23 ++++++++++++----------- NEWS.md | 5 +++++ R/extract_abs_sheets.R | 2 +- R/read_abs_local.R | 16 ++++++++-------- R/read_payrolls.R | 24 +++++++++++++++++++----- R/sysdata.rda |binary build/vignette.rds |binary man/read_abs_local.Rd | 6 +++--- man/read_payrolls.Rd | 9 +++++++-- tests/testdata/6202021.xlsx |only tests/testthat/test-local-files.R | 8 ++++++++ tests/testthat/test-read_payrolls.R | 4 +++- 13 files changed, 71 insertions(+), 36 deletions(-)
Title: Mediterranean Forest Simulation
Description: Functions to simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Author: Miquel De Cáceres [aut, cre],
Shengli Huang [aut],
Víctor Granda [aut],
Antoine Cabon [aut],
Jordi Martínez-Vilalta [ctb],
Maurizio Mencuccini [ctb],
Nicolas Martin-StPaul [ctb]
Maintainer: Miquel De Cáceres <miquelcaceres@gmail.com>
Diff between medfate versions 2.2.3 dated 2021-06-18 and 2.3.7 dated 2021-12-16
medfate-2.2.3/medfate/vignettes/SensitivityCalibration.html |only medfate-2.2.3/medfate/vignettes/mcmc_out.rds |only medfate-2.2.3/medfate/vignettes/opt_cal.rds |only medfate-2.2.3/medfate/vignettes/sa_eval.rds |only medfate-2.2.3/medfate/vignettes/sa_stress.rds |only medfate-2.2.3/medfate/vignettes/sa_transp.rds |only medfate-2.3.7/medfate/DESCRIPTION | 12 medfate-2.3.7/medfate/MD5 | 167 - medfate-2.3.7/medfate/NAMESPACE | 2 medfate-2.3.7/medfate/R/RcppExports.R | 44 medfate-2.3.7/medfate/R/defaultControl.R | 3 medfate-2.3.7/medfate/R/evaluation.R | 79 medfate-2.3.7/medfate/R/extractSubdaily.R | 10 medfate-2.3.7/medfate/R/fordyn.R | 10 medfate-2.3.7/medfate/R/hydrology_interceptionPlot.R | 2 medfate-2.3.7/medfate/R/plot.fordyn.R |only medfate-2.3.7/medfate/R/plot.spwb.R | 171 + medfate-2.3.7/medfate/R/plotutils.R | 43 medfate-2.3.7/medfate/R/shinyplot.R |only medfate-2.3.7/medfate/R/sysdata.rda |only medfate-2.3.7/medfate/build/vignette.rds |binary medfate-2.3.7/medfate/data/SpParamsDefinition.rda |only medfate-2.3.7/medfate/data/SpParamsMED.rda |binary medfate-2.3.7/medfate/data/SpParamsUS.rda |binary medfate-2.3.7/medfate/data/exampleforestMED.rda |binary medfate-2.3.7/medfate/data/exampleobs.rda |binary medfate-2.3.7/medfate/inst/doc/AdvancedWaterEnergyBalance.R | 3 medfate-2.3.7/medfate/inst/doc/AdvancedWaterEnergyBalance.Rmd | 5 medfate-2.3.7/medfate/inst/doc/AdvancedWaterEnergyBalance.html | 508 ++--- medfate-2.3.7/medfate/inst/doc/BasicWaterBalance.R | 5 medfate-2.3.7/medfate/inst/doc/BasicWaterBalance.Rmd | 7 medfate-2.3.7/medfate/inst/doc/BasicWaterBalance.html | 276 +-- medfate-2.3.7/medfate/inst/doc/ForestDynamics.R | 6 medfate-2.3.7/medfate/inst/doc/ForestDynamics.Rmd | 14 medfate-2.3.7/medfate/inst/doc/ForestDynamics.html | 133 - medfate-2.3.7/medfate/inst/doc/ForestGrowth.R | 3 medfate-2.3.7/medfate/inst/doc/ForestGrowth.Rmd | 6 medfate-2.3.7/medfate/inst/doc/ForestGrowth.html | 130 - medfate-2.3.7/medfate/inst/doc/PackageOverview.Rmd | 2 medfate-2.3.7/medfate/inst/doc/PackageOverview.html | 6 medfate-2.3.7/medfate/inst/doc/PreparingInputs.R | 4 medfate-2.3.7/medfate/inst/doc/PreparingInputs.Rmd | 17 medfate-2.3.7/medfate/inst/doc/PreparingInputs.html | 916 ++++++++-- medfate-2.3.7/medfate/man/SpParams.Rd | 171 - medfate-2.3.7/medfate/man/TaxonTraitMeans.Rd |only medfate-2.3.7/medfate/man/defaultControl.Rd | 7 medfate-2.3.7/medfate/man/evaluation.Rd | 6 medfate-2.3.7/medfate/man/exampleobs.Rd | 12 medfate-2.3.7/medfate/man/fuel_properties.Rd | 2 medfate-2.3.7/medfate/man/growth.Rd | 1 medfate-2.3.7/medfate/man/hydraulics_conductancefunctions.Rd | 4 medfate-2.3.7/medfate/man/modifySpParams.Rd | 15 medfate-2.3.7/medfate/man/optimization.Rd | 10 medfate-2.3.7/medfate/man/plant_values.Rd | 3 medfate-2.3.7/medfate/man/plot.spwb.Rd | 87 medfate-2.3.7/medfate/man/shinyplot.Rd |only medfate-2.3.7/medfate/man/species_values.Rd | 9 medfate-2.3.7/medfate/man/spwb.Rd | 1 medfate-2.3.7/medfate/man/summary.spwb.Rd |only medfate-2.3.7/medfate/src/RcppExports.cpp | 152 - medfate-2.3.7/medfate/src/firebehaviour.cpp | 11 medfate-2.3.7/medfate/src/forestutils.cpp | 168 - medfate-2.3.7/medfate/src/forestutils.h | 10 medfate-2.3.7/medfate/src/fuelstructure.cpp | 65 medfate-2.3.7/medfate/src/growth.cpp | 190 +- medfate-2.3.7/medfate/src/growth.h | 10 medfate-2.3.7/medfate/src/hydraulics.cpp | 13 medfate-2.3.7/medfate/src/hydraulics.h | 2 medfate-2.3.7/medfate/src/lightextinction.cpp | 21 medfate-2.3.7/medfate/src/modelInput.cpp | 489 +---- medfate-2.3.7/medfate/src/modelInput.h | 2 medfate-2.3.7/medfate/src/paramutils.cpp |only medfate-2.3.7/medfate/src/paramutils.h |only medfate-2.3.7/medfate/src/phenology.cpp | 9 medfate-2.3.7/medfate/src/spwb.cpp | 137 + medfate-2.3.7/medfate/src/spwb.h | 10 medfate-2.3.7/medfate/src/tissuemoisture.cpp | 1 medfate-2.3.7/medfate/src/transpiration.cpp | 57 medfate-2.3.7/medfate/src/transpiration.h | 7 medfate-2.3.7/medfate/src/windKatul.cpp | 5 medfate-2.3.7/medfate/vignettes/AdvancedWaterEnergyBalance.Rmd | 5 medfate-2.3.7/medfate/vignettes/BasicWaterBalance.Rmd | 7 medfate-2.3.7/medfate/vignettes/ForestDynamics.Rmd | 14 medfate-2.3.7/medfate/vignettes/ForestGrowth.Rmd | 6 medfate-2.3.7/medfate/vignettes/PackageOverview.Rmd | 2 medfate-2.3.7/medfate/vignettes/PreparingInputs.Rmd | 17 medfate-2.3.7/medfate/vignettes/evaluation |only medfate-2.3.7/medfate/vignettes/modelanalysis |only medfate-2.3.7/medfate/vignettes/parametrization |only medfate-2.3.7/medfate/vignettes/workedexamples |only 90 files changed, 2587 insertions(+), 1735 deletions(-)
More information about covid19srilanka at CRAN
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Title: Functional Singular Spectrum Analysis
Description: Methods and tools for implementing univariate and multivariate functional singular spectrum analysis for functional time series whose variables might be observed over different dimensional domains. The univariate fssa algorithm is described in Haghbin H., Najibi, S.M., Mahmoudvand R., Trinka J., Maadooliat M. (2021) and the multivariate fssa over different dimensional domains technique may be found in Trinka J., Haghbin H., and Maadooliat M. (Accepted). In addition, one may perform forecasting of univariate and multivariate fts whose variables are observed over one-dimensional domains as described in the dissertation of Trinka J. (2021) and the manuscript of Trinka J., Haghbin H., Maadooliat M. (2020) where the manuscript is to be submitted to a journal for publication.
Author: Hossein Haghbin [aut, cre],
Jordan Trinka [aut],
Seyed Morteza Najibi [aut],
Mehdi Maadooliat [aut]
Maintainer: Hossein Haghbin <haghbinh@gmail.com>
Diff between Rfssa versions 1.0.0 dated 2019-09-12 and 2.0.0 dated 2021-12-16
Rfssa-1.0.0/Rfssa/data |only Rfssa-2.0.0/Rfssa/DESCRIPTION | 25 Rfssa-2.0.0/Rfssa/MD5 | 99 +- Rfssa-2.0.0/Rfssa/NAMESPACE | 22 Rfssa-2.0.0/Rfssa/NEWS.md | 88 +- Rfssa-2.0.0/Rfssa/R/Callcenter.R | 9 Rfssa-2.0.0/Rfssa/R/FTSclass.R | 470 +++++++++++- Rfssa-2.0.0/Rfssa/R/Jambi.R | 4 Rfssa-2.0.0/Rfssa/R/Montana.R |only Rfssa-2.0.0/Rfssa/R/RcppExports.R | 10 Rfssa-2.0.0/Rfssa/R/Rfssa.R | 108 +- Rfssa-2.0.0/Rfssa/R/fforecast.R |only Rfssa-2.0.0/Rfssa/R/freconstruct.r | 18 Rfssa-2.0.0/Rfssa/R/fssa.r | 192 ++--- Rfssa-2.0.0/Rfssa/R/fssaplot.R | 352 +++++---- Rfssa-2.0.0/Rfssa/R/ftsarithmetic.R | 594 ++++++++++------ Rfssa-2.0.0/Rfssa/R/ftscor.R | 72 - Rfssa-2.0.0/Rfssa/R/ftsplot.r | 239 +++--- Rfssa-2.0.0/Rfssa/R/launchApp.R | 17 Rfssa-2.0.0/Rfssa/R/load_github_data.R |only Rfssa-2.0.0/Rfssa/R/mfforecast.R |only Rfssa-2.0.0/Rfssa/R/mfreconstruct.R | 68 + Rfssa-2.0.0/Rfssa/R/mfssa.R | 66 + Rfssa-2.0.0/Rfssa/R/shinyFSSA.R | 987 ++++++++++++++++++-------- Rfssa-2.0.0/Rfssa/R/shinyMFSSA.R | 1110 ++++++++++++++++++++---------- Rfssa-2.0.0/Rfssa/R/ufforecast.R |only Rfssa-2.0.0/Rfssa/R/ufreconstruct.r | 37 - Rfssa-2.0.0/Rfssa/R/ufssa.R | 37 - Rfssa-2.0.0/Rfssa/R/utils.R | 125 ++- Rfssa-2.0.0/Rfssa/R/wcor.r | 141 +-- Rfssa-2.0.0/Rfssa/R/wplot.R | 34 Rfssa-2.0.0/Rfssa/README.md | 116 +-- Rfssa-2.0.0/Rfssa/man/Callcenter.Rd | 108 +- Rfssa-2.0.0/Rfssa/man/Jambi.Rd | 73 - Rfssa-2.0.0/Rfssa/man/Montana.Rd |only Rfssa-2.0.0/Rfssa/man/Rfssa.Rd | 100 +- Rfssa-2.0.0/Rfssa/man/cor.fts.Rd | 38 - Rfssa-2.0.0/Rfssa/man/dot-fts.Rd | 27 Rfssa-2.0.0/Rfssa/man/fforecast.Rd |only Rfssa-2.0.0/Rfssa/man/freconstruct.Rd | 16 Rfssa-2.0.0/Rfssa/man/fssa.Rd | 171 ++-- Rfssa-2.0.0/Rfssa/man/fts.Rd | 20 Rfssa-2.0.0/Rfssa/man/fwcor.Rd | 77 -- Rfssa-2.0.0/Rfssa/man/launchApp.Rd | 6 Rfssa-2.0.0/Rfssa/man/load_github_data.Rd |only Rfssa-2.0.0/Rfssa/man/plot.fssa.Rd | 79 -- Rfssa-2.0.0/Rfssa/man/plot.fts.Rd | 60 - Rfssa-2.0.0/Rfssa/man/plus-.fts.Rd | 28 Rfssa-2.0.0/Rfssa/man/sub-.fts.Rd | 32 Rfssa-2.0.0/Rfssa/man/times-.fts.Rd | 27 Rfssa-2.0.0/Rfssa/man/wplot.Rd | 6 Rfssa-2.0.0/Rfssa/src/RcppExports.cpp | 31 Rfssa-2.0.0/Rfssa/src/Utils.cpp | 29 Rfssa-2.0.0/Rfssa/src/winprod.cpp | 2 54 files changed, 3771 insertions(+), 2199 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Abhraneel Sarma [ctb],
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
Ben Baumer [ctb],
Brian Diggs [ctb],
Brian Zhang [ctb],
Bulat Yapparov [ctb],
Cassio Pereira [ctb],
Christophe Dervieux [ctb],
David Hall [ctb],
David Hugh-Jones [ctb],
David Robinson [ctb],
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Elio Campitelli [ctb],
Ellis Hughes [ctb],
Emily Riederer [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Forest Fang [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Garrick Aden-Buie [ctb],
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Hao Zhu [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Ian Lyttle [ctb],
Hodges Daniel [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Javier Luraschi [ctb],
Jeff Arnold [ctb],
Jenny Bryan [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Jonathan Sidi [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kamil Slowikowski [ctb],
Karl Forner [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Lorenz Walthert [ctb],
Lucas Gallindo [ctb],
Marius Hofert [ctb],
Martin Modrák [ctb],
Michael Chirico [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Miller Patrick [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Niels Richard Hansen [ctb],
Noam Ross [ctb],
Obada Mahdi [ctb],
Pavel N. Krivitsky [ctb] (<https://orcid.org/0000-0002-9101-3362>),
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Ruaridh Williamson [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Sylvain Rousseau [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tim Mastny [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.36 dated 2021-09-29 and 1.37 dated 2021-12-16
knitr-1.36/knitr/vignettes/knitr-refcard.lyx |only knitr-1.37/knitr/DESCRIPTION | 8 knitr-1.37/knitr/MD5 | 43 ++-- knitr-1.37/knitr/R/block.R | 10 - knitr-1.37/knitr/R/cache.R | 2 knitr-1.37/knitr/R/citation.R | 9 knitr-1.37/knitr/R/engine.R | 75 +++++++ knitr-1.37/knitr/R/output.R | 2 knitr-1.37/knitr/R/parser.R | 86 ++++++--- knitr-1.37/knitr/R/themes.R | 3 knitr-1.37/knitr/R/utils-sweave.R | 5 knitr-1.37/knitr/R/utils-vignettes.R | 15 - knitr-1.37/knitr/R/utils.R | 32 +-- knitr-1.37/knitr/build/vignette.rds |binary knitr-1.37/knitr/inst/doc/knit_expand.html | 4 knitr-1.37/knitr/inst/doc/knit_print.html | 248 +++++++++++++++++++++++++- knitr-1.37/knitr/inst/doc/knitr-intro.html | 246 ++++++++++++++++++++++++- knitr-1.37/knitr/inst/doc/knitr-markdown.html | 2 knitr-1.37/knitr/inst/doc/knitr-refcard.pdf |binary knitr-1.37/knitr/inst/misc/knitr.sty | 8 knitr-1.37/knitr/man/output_type.Rd | 3 knitr-1.37/knitr/man/write_bib.Rd | 3 knitr-1.37/knitr/tests/testit/test-cache.R | 10 - 23 files changed, 692 insertions(+), 122 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>),
Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>),
Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>),
Jeff Farrell [ctb],
Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>),
Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>),
Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>),
Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>),
Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>),
Patrick Roelli [ctb],
Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>),
Karthik Shekhar [ctb],
Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>),
Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>),
Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>),
Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>),
Satija Lab and Collaborators [fnd]
Maintainer: Paul Hoffman <seurat@nygenome.org>
Diff between Seurat versions 4.0.5 dated 2021-10-17 and 4.0.6 dated 2021-12-16
DESCRIPTION | 15 LICENSE | 676 -------------------------------------------- MD5 | 55 ++- NAMESPACE | 24 + NEWS.md | 25 + R/RcppExports.R | 12 R/differential_expression.R | 15 R/dimensional_reduction.R | 173 ++++++++++- R/generics.R | 23 + R/integration.R | 33 +- R/objects.R | 6 R/preprocessing.R | 16 - R/reexports.R | 66 ---- R/utilities.R | 220 +++++++++----- R/visualization.R | 465 +++++++++++++++--------------- build/partial.rdb |binary man/AutoPointSize.Rd |only man/DimHeatmap.Rd | 2 man/FeaturePlot.Rd | 3 man/FindConservedMarkers.Rd | 3 man/PercentAbove.Rd |only man/ProjectUMAP.Rd | 6 man/RunSLSI.Rd |only man/RunSPCA.Rd | 2 man/SetQuantile.Rd |only man/SingleCorPlot.Rd |only man/SingleDimPlot.Rd |only man/SingleExIPlot.Rd |only man/SingleImageMap.Rd |only man/SingleRasterMap.Rd |only man/SingleSpatialPlot.Rd |only man/VlnPlot.Rd | 5 src/RcppExports.cpp | 45 ++ src/stats.cpp |only 34 files changed, 787 insertions(+), 1103 deletions(-)
Title: Mail Sender Using 'Sendgrid' Service
Description: Send email using 'Sendgrid' <https://sendgrid.com/>
mail API(v3) <https://docs.sendgrid.com/api-reference/how-to-use-the-sendgrid-v3-api/authentication>.
Author: Chanyub Park [aut, cre] (<https://orcid.org/0000-0001-6474-2570>)
Maintainer: Chanyub Park <mrchypark@gmail.com>
Diff between sendgridr versions 0.3.3 dated 2021-10-06 and 0.4.2 dated 2021-12-16
sendgridr-0.3.3/sendgridr/R/style.R |only sendgridr-0.3.3/sendgridr/R/utils.R |only sendgridr-0.4.2/sendgridr/DESCRIPTION | 12 sendgridr-0.4.2/sendgridr/MD5 | 42 + sendgridr-0.4.2/sendgridr/NAMESPACE | 32 - sendgridr-0.4.2/sendgridr/NEWS.md | 18 sendgridr-0.4.2/sendgridr/R/auth.R | 27 - sendgridr-0.4.2/sendgridr/R/dynamic-templates.R |only sendgridr-0.4.2/sendgridr/R/embed_rmd.R |only sendgridr-0.4.2/sendgridr/R/helpers.R | 99 ---- sendgridr-0.4.2/sendgridr/R/print.R | 240 ++++++----- sendgridr-0.4.2/sendgridr/R/sendgridr-package.R | 1 sendgridr-0.4.2/sendgridr/R/set_mail.R | 119 ++--- sendgridr-0.4.2/sendgridr/R/sysdata.rda |binary sendgridr-0.4.2/sendgridr/R/utils-pipe.R | 25 - sendgridr-0.4.2/sendgridr/README.md | 363 +++++++---------- sendgridr-0.4.2/sendgridr/inst |only sendgridr-0.4.2/sendgridr/man/attachments.Rd | 4 sendgridr-0.4.2/sendgridr/man/dynamic_template.Rd |only sendgridr-0.4.2/sendgridr/man/dynamic_template_data.Rd | 7 sendgridr-0.4.2/sendgridr/man/embed_rmd.Rd |only sendgridr-0.4.2/sendgridr/man/pipe.Rd | 10 sendgridr-0.4.2/sendgridr/man/print.sg_mail.Rd |only sendgridr-0.4.2/sendgridr/man/sendgridr-package.Rd | 3 sendgridr-0.4.2/sendgridr/man/template_id.Rd | 52 +- sendgridr-0.4.2/sendgridr/tests/testthat/test-send.R | 10 26 files changed, 489 insertions(+), 575 deletions(-)
Title: Power Calculation for Stepped Wedge Designs
Description: Tools for power and sample size
calculation as well as design diagnostics for
longitudinal mixed model settings, with a focus on stepped wedge designs.
All calculations are oracle estimates i.e. assume random effect variances
to be known (or guessed) in advance.
The method is introduced in Hussey and Hughes (2007) <doi:10.1016/j.cct.2006.05.007>,
extensions are discussed in Li et al. (2020) <doi:10.1177/0962280220932962>.
Author: Philipp Mildenberger [aut, cre]
(<https://orcid.org/0000-0002-7367-1708>),
Federico Marini [ctb] (<https://orcid.org/0000-0003-3252-7758>)
Maintainer: Philipp Mildenberger <pmildenb@uni-mainz.de>
Diff between SteppedPower versions 0.2.0 dated 2021-07-07 and 0.3.1 dated 2021-12-16
DESCRIPTION | 10 MD5 | 65 - NAMESPACE | 91 - NEWS.md | 20 R/SteppedPower-pkg.R | 41 R/construct_CovMat.R | 66 - R/construct_DesMat.R | 89 + R/wlsPower.R | 404 ++++-- README.md | 2 build/vignette.rds |binary inst/doc/Getting_Started.R | 21 inst/doc/Getting_Started.Rmd | 74 - inst/doc/Getting_Started.html | 2603 ++++-------------------------------------- man/RandEff_to_alpha012.Rd | 68 - man/SteppedPower-pkg.Rd | 32 man/VarClosed_Kasza.Rd | 114 - man/VarClosed_Li.Rd | 72 - man/alpha012_to_RandEff.Rd | 74 - man/compute_wlsPower.Rd | 180 +- man/construct_CovBlk.Rd | 2 man/construct_CovMat.Rd | 184 +- man/construct_CovSubMat.Rd | 4 man/construct_DesMat.Rd | 6 man/construct_incompMat.Rd |only man/construct_trtMat.Rd | 72 - man/plot.wlsPower.Rd | 27 man/plot_CellWeights.Rd |only man/plot_CovMat.Rd | 2 man/plot_InfoContent.Rd |only man/print.DesMat.Rd | 38 man/print.wlsPower.Rd | 40 man/tTestPwr.Rd | 58 man/wlsPower.Rd | 528 ++++---- vignettes/Getting_Started.Rmd | 74 - vignettes/references.bib | 15 35 files changed, 1679 insertions(+), 3397 deletions(-)
Title: Meta-Analysis of Significance Values
Description: The canonical way to perform meta-analysis involves using effect sizes.
When they are not available this package provides a number of methods for
meta-analysis of significance values including the methods of Edgington, Fisher,
Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results;
and routines for graphical display.
Author: Michael Dewey [aut, cre] (<https://orcid.org/0000-0002-7522-3677>)
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between metap versions 1.6 dated 2021-11-05 and 1.7 dated 2021-12-16
DESCRIPTION | 10 +++++----- MD5 | 31 +++++++++++++++++-------------- NAMESPACE | 5 +++-- NEWS | 11 +++++++++-- R/albatros.R |only R/allmetap.R | 17 ++++++++++++++--- R/docontours.R |only build/metap.pdf |binary build/partial.rdb |binary build/vignette.rds |binary data/dat.metap.rda |binary inst/REFERENCES.bib | 25 +++++++++++++++++++++++++ inst/doc/compare.pdf |binary inst/doc/metap.pdf |binary man/albatros.Rd |only man/allmetap.Rd | 3 ++- man/dat.metap.Rd | 27 ++++++++++++++++++++++++++- man/metap-package.Rd | 2 ++ 18 files changed, 103 insertions(+), 28 deletions(-)
Title: Build a Package from Rmarkdown File
Description: Use Rmarkdown First method to build your package. Start your
package with documentation, functions, examples and tests in the same
unique file. Everything can be set from the Rmarkdown template file
provided in your project, then inflated as a package. Inflating the
template copies the relevant chunks and sections in the appropriate
files required for package development.
Author: Sebastien Rochette [aut, cre] (<https://orcid.org/0000-0002-1565-9313>),
ThinkR [cph]
Maintainer: Sebastien Rochette <sebastien@thinkr.fr>
Diff between fusen versions 0.2.4 dated 2021-08-04 and 0.3.0 dated 2021-12-16
fusen-0.2.4/fusen/inst/dev-template-minimal.Rmd |only fusen-0.3.0/fusen/DESCRIPTION | 35 fusen-0.3.0/fusen/MD5 | 98 - fusen-0.3.0/fusen/NAMESPACE | 10 fusen-0.3.0/fusen/NEWS.md | 65 fusen-0.3.0/fusen/R/add_dev_history.R | 123 - fusen-0.3.0/fusen/R/add_flat_template.R |only fusen-0.3.0/fusen/R/addins.R |only fusen-0.3.0/fusen/R/build_fusen_chunks.R |only fusen-0.3.0/fusen/R/create_fusen_rsproject.R |only fusen-0.3.0/fusen/R/fill_description.R | 14 fusen-0.3.0/fusen/R/fusen-package.R |only fusen-0.3.0/fusen/R/globals.R | 2 fusen-0.3.0/fusen/R/inflate-utils.R |only fusen-0.3.0/fusen/R/inflate.R | 452 ++--- fusen-0.3.0/fusen/README.md | 134 - fusen-0.3.0/fusen/build/vignette.rds |binary fusen-0.3.0/fusen/inst/dev-template-additional.Rmd | 15 fusen-0.3.0/fusen/inst/dev-template-full.Rmd | 10 fusen-0.3.0/fusen/inst/dev-template-teaching.Rmd | 9 fusen-0.3.0/fusen/inst/doc/How-to-use-fusen.R | 62 fusen-0.3.0/fusen/inst/doc/How-to-use-fusen.Rmd | 117 - fusen-0.3.0/fusen/inst/doc/How-to-use-fusen.html | 401 +++- fusen-0.3.0/fusen/inst/doc/Maintain-packages-with-fusen.R | 3 fusen-0.3.0/fusen/inst/doc/Maintain-packages-with-fusen.Rmd | 57 fusen-0.3.0/fusen/inst/doc/Maintain-packages-with-fusen.html | 286 ++- fusen-0.3.0/fusen/inst/doc/tips-and-tricks.R |only fusen-0.3.0/fusen/inst/doc/tips-and-tricks.Rmd |only fusen-0.3.0/fusen/inst/doc/tips-and-tricks.html |only fusen-0.3.0/fusen/inst/flat-template-additional.Rmd |only fusen-0.3.0/fusen/inst/flat-template-full.Rmd |only fusen-0.3.0/fusen/inst/flat-template-minimal.Rmd |only fusen-0.3.0/fusen/inst/flat-template-teaching.Rmd |only fusen-0.3.0/fusen/inst/rstudio |only fusen-0.3.0/fusen/inst/tests-templates/dev-template-empty-not-function.Rmd |only fusen-0.3.0/fusen/inst/tests-templates/dev-template-no-example-no-tests.Rmd | 2 fusen-0.3.0/fusen/inst/tests-templates/dev-template-nord-but-example.Rmd |only fusen-0.3.0/fusen/inst/tests-templates/dev-template-r6class.Rmd |only fusen-0.3.0/fusen/inst/tests-templates/dev-template-stop-duplicate-fun.Rmd | 2 fusen-0.3.0/fusen/inst/tests-templates/dev-template-stop-duplicate-label.Rmd | 2 fusen-0.3.0/fusen/inst/tests-templates/dev-template-test-parse-nothing.Rmd | 2 fusen-0.3.0/fusen/inst/tests-templates/dev-template-tests-special-char.Rmd | 6 fusen-0.3.0/fusen/inst/tests-templates/dev-template-tests.Rmd | 90 + fusen-0.3.0/fusen/inst/tests-templates/dev-template-two-fun-same-title.Rmd |only fusen-0.3.0/fusen/inst/the-dev-history.Rmd |only fusen-0.3.0/fusen/man/add_dev_history.Rd | 28 fusen-0.3.0/fusen/man/add_flat_template.Rd |only fusen-0.3.0/fusen/man/add_fusen_chunks.Rd |only fusen-0.3.0/fusen/man/create_fusen.Rd |only fusen-0.3.0/fusen/man/figures/create_fusen_rstudio.png |only fusen-0.3.0/fusen/man/figures/fusen_inflate_functions.png |only fusen-0.3.0/fusen/man/figures/fusen_rstudio_project.png |only fusen-0.3.0/fusen/man/fill_description.Rd | 3 fusen-0.3.0/fusen/man/fusen-package.Rd |only fusen-0.3.0/fusen/man/inflate.Rd | 34 fusen-0.3.0/fusen/tests/testthat/test-add_dev_history.R | 109 - fusen-0.3.0/fusen/tests/testthat/test-add_flat_template.R |only fusen-0.3.0/fusen/tests/testthat/test-build_fusen_chunks.R |only fusen-0.3.0/fusen/tests/testthat/test-create_fusen_rsproject.R |only fusen-0.3.0/fusen/tests/testthat/test-fill_description.R | 82 fusen-0.3.0/fusen/tests/testthat/test-inflate.R | 845 +++++++++- fusen-0.3.0/fusen/tests/testthat/test-inflate_utils.R |only fusen-0.3.0/fusen/vignettes/How-to-use-fusen.Rmd | 117 - fusen-0.3.0/fusen/vignettes/Maintain-packages-with-fusen.Rmd | 57 fusen-0.3.0/fusen/vignettes/tips-and-tricks.Rmd |only 65 files changed, 2319 insertions(+), 953 deletions(-)
Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut],
Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>
Diff between rpact versions 3.1.1 dated 2021-08-27 and 3.2.0 dated 2021-12-16
rpact-3.1.1/rpact/src/f_simulation_survival.cpp |only rpact-3.2.0/rpact/DESCRIPTION | 36 rpact-3.2.0/rpact/MD5 | 313 rpact-3.2.0/rpact/NAMESPACE | 5 rpact-3.2.0/rpact/NEWS.md | 23 rpact-3.2.0/rpact/R/RcppExports.R | 16 rpact-3.2.0/rpact/R/class_analysis_dataset.R | 703 rpact-3.2.0/rpact/R/class_analysis_results.R | 40 rpact-3.2.0/rpact/R/class_analysis_stage_results.R | 50 rpact-3.2.0/rpact/R/class_core_parameter_set.R | 587 rpact-3.2.0/rpact/R/class_core_plot_settings.R | 42 rpact-3.2.0/rpact/R/class_design.R | 38 rpact-3.2.0/rpact/R/class_design_plan.R | 38 rpact-3.2.0/rpact/R/class_design_power_and_asn.R | 38 rpact-3.2.0/rpact/R/class_design_set.R | 38 rpact-3.2.0/rpact/R/class_event_probabilities.R | 38 rpact-3.2.0/rpact/R/class_simulation_results.R | 590 rpact-3.2.0/rpact/R/class_summary.R | 1179 - rpact-3.2.0/rpact/R/class_time.R | 38 rpact-3.2.0/rpact/R/data.R | 67 rpact-3.2.0/rpact/R/f_analysis_base.R | 3625 ++-- rpact-3.2.0/rpact/R/f_analysis_base_means.R | 3430 ++- rpact-3.2.0/rpact/R/f_analysis_base_rates.R | 3359 +-- rpact-3.2.0/rpact/R/f_analysis_base_survival.R | 2476 +- rpact-3.2.0/rpact/R/f_analysis_enrichment.R | 695 rpact-3.2.0/rpact/R/f_analysis_enrichment_means.R | 2474 +- rpact-3.2.0/rpact/R/f_analysis_enrichment_rates.R | 2196 +- rpact-3.2.0/rpact/R/f_analysis_enrichment_survival.R | 2011 +- rpact-3.2.0/rpact/R/f_analysis_multiarm.R | 2137 +- rpact-3.2.0/rpact/R/f_analysis_multiarm_means.R | 2613 +- rpact-3.2.0/rpact/R/f_analysis_multiarm_rates.R | 2485 +- rpact-3.2.0/rpact/R/f_analysis_multiarm_survival.R | 2131 +- rpact-3.2.0/rpact/R/f_analysis_utilities.R | 250 rpact-3.2.0/rpact/R/f_core_assertions.R | 202 rpact-3.2.0/rpact/R/f_core_constants.R | 217 rpact-3.2.0/rpact/R/f_core_output_formats.R | 38 rpact-3.2.0/rpact/R/f_core_plot.R | 123 rpact-3.2.0/rpact/R/f_core_utilities.R | 323 rpact-3.2.0/rpact/R/f_design_fisher_combination_test.R | 1534 - rpact-3.2.0/rpact/R/f_design_group_sequential.R | 3732 ++-- 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rpact-3.2.0/rpact/build/partial.rdb |binary rpact-3.2.0/rpact/build/vignette.rds |binary rpact-3.2.0/rpact/data/rawDataTwoArmNormal.RData |only rpact-3.2.0/rpact/inst/doc/rpact_getting_started.Rmd | 20 rpact-3.2.0/rpact/inst/doc/rpact_getting_started.html | 19 rpact-3.2.0/rpact/inst/tests/testthat/test-rpact.R | 56 rpact-3.2.0/rpact/man/DatasetRates.Rd | 4 rpact-3.2.0/rpact/man/DatasetSurvival.Rd | 4 rpact-3.2.0/rpact/man/ParameterSet_summary.Rd | 8 rpact-3.2.0/rpact/man/SimulationResultsEnrichmentMeans.Rd |only rpact-3.2.0/rpact/man/SimulationResultsEnrichmentRates.Rd |only rpact-3.2.0/rpact/man/SimulationResultsEnrichmentSurvival.Rd |only rpact-3.2.0/rpact/man/getAnalysisResults.Rd | 77 rpact-3.2.0/rpact/man/getClosedConditionalDunnettTestResults.Rd | 4 rpact-3.2.0/rpact/man/getConditionalPower.Rd | 14 rpact-3.2.0/rpact/man/getConditionalRejectionProbabilities.Rd | 18 rpact-3.2.0/rpact/man/getData.Rd | 3 rpact-3.2.0/rpact/man/getDataset.Rd | 17 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Title: The Gaussian Covariate Method for Variable Selection
Description: Given the standard linear model the traditional way of deciding whether to include the jth covariate is to apply the F-test to decide whether the corresponding beta coefficient is zero. The Gaussian covariate method is completely different. The question as to whether the beta coefficient is or is not zero is replaced by the question as to whether the covariate is better or worse than i.i.d. Gaussian noise. The P-value for the covariate is the probability that Gaussian noise is better. Surprisingly this can be given exactly and it is the same a the P-value for the classical model based on the F-distribution. The Gaussian covariate P-value is model free, it is the same for any data set. Using the idea it is possible to do covariate selection for a small number of covariates 25 by considering all subsets. Post selection inference causes no problems as the P-values hold whatever the data. The idea extends to stepwise regression again with exact probabilities. In the simplest version the only parameter is a specified cut-off P-value which can be interpreted as the probability of a false positive being included in the final selection. For more information see the web site below and the accompanying papers: L. Davies and L. Duembgen, "Covariate Selection Based on a Assumption -free Approach to Linear Regression with Exact Probabilities", 2020, <arXiv:1906.01990>. L. Davies, "Lasso, Knockoff and Gaussian covariates: A comparison", 2018, <arXiv:1807.09633>.
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <laurie.davies@uni-due.de>
Diff between gausscov versions 0.1.1 dated 2021-04-30 and 0.1.2 dated 2021-12-16
gausscov-0.1.1/gausscov/R/fmch.R |only gausscov-0.1.1/gausscov/R/frmch.R |only gausscov-0.1.1/gausscov/R/frobreg.R |only gausscov-0.1.1/gausscov/R/frobregp.R |only gausscov-0.1.1/gausscov/R/frst.R |only gausscov-0.1.1/gausscov/R/fsimords.R |only gausscov-0.1.1/gausscov/man/fmch.Rd |only gausscov-0.1.1/gausscov/man/frmch.Rd |only gausscov-0.1.1/gausscov/man/frobreg.Rd |only gausscov-0.1.1/gausscov/man/frobregp.Rd |only gausscov-0.1.1/gausscov/man/frst.Rd |only gausscov-0.1.1/gausscov/man/fsimords.Rd |only gausscov-0.1.2/gausscov/DESCRIPTION | 10 gausscov-0.1.2/gausscov/MD5 | 82 +-- gausscov-0.1.2/gausscov/NAMESPACE | 2 gausscov-0.1.2/gausscov/R/decode.R | 2 gausscov-0.1.2/gausscov/R/decomp.R | 14 gausscov-0.1.2/gausscov/R/f1st.R | 138 ++--- gausscov-0.1.2/gausscov/R/f2st.R | 39 - gausscov-0.1.2/gausscov/R/fasb.R |only gausscov-0.1.2/gausscov/R/fgeninter.R | 36 + gausscov-0.1.2/gausscov/R/fgentrig.R | 6 gausscov-0.1.2/gausscov/R/fgr1st.R | 76 +- gausscov-0.1.2/gausscov/R/fgr2st.R | 74 -- gausscov-0.1.2/gausscov/R/fgrall.R |only gausscov-0.1.2/gausscov/R/flag.R | 6 gausscov-0.1.2/gausscov/R/fnfp.R |only gausscov-0.1.2/gausscov/R/fpsired.R |only gausscov-0.1.2/gausscov/R/fpval.R | 62 +- gausscov-0.1.2/gausscov/R/fr1st.R |only gausscov-0.1.2/gausscov/R/frasb.R |only gausscov-0.1.2/gausscov/R/frpval.R |only gausscov-0.1.2/gausscov/R/fselect.R | 8 gausscov-0.1.2/gausscov/R/fundr.R |only gausscov-0.1.2/gausscov/data/nufp.rda |only gausscov-0.1.2/gausscov/man/decode.Rd | 6 gausscov-0.1.2/gausscov/man/decomp.Rd | 15 gausscov-0.1.2/gausscov/man/dentx.Rd | 2 gausscov-0.1.2/gausscov/man/f1st.Rd | 19 gausscov-0.1.2/gausscov/man/f2st.Rd | 21 gausscov-0.1.2/gausscov/man/fasb.Rd |only gausscov-0.1.2/gausscov/man/fgeninter.Rd | 8 gausscov-0.1.2/gausscov/man/fgentrig.Rd | 10 gausscov-0.1.2/gausscov/man/fgr1st.Rd | 20 gausscov-0.1.2/gausscov/man/fgr2st.Rd | 14 gausscov-0.1.2/gausscov/man/fgrall.Rd |only gausscov-0.1.2/gausscov/man/flag.Rd | 8 gausscov-0.1.2/gausscov/man/fnfp.Rd |only gausscov-0.1.2/gausscov/man/fpsired.Rd |only gausscov-0.1.2/gausscov/man/fpval.Rd | 12 gausscov-0.1.2/gausscov/man/fr1st.Rd |only gausscov-0.1.2/gausscov/man/frasb.Rd |only gausscov-0.1.2/gausscov/man/frpval.Rd |only gausscov-0.1.2/gausscov/man/fselect.Rd | 10 gausscov-0.1.2/gausscov/man/fundr.Rd |only gausscov-0.1.2/gausscov/man/nufp.Rd |only gausscov-0.1.2/gausscov/src/gaucov.f | 819 +++++++++++++++++++++++-------- 57 files changed, 1010 insertions(+), 509 deletions(-)
Title: Structural Equation Modeling and Twin Modeling in R
Description: Quickly create, run, and report structural equation models, and twin models.
See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R.
Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
Author: Timothy C. Bates [aut, cre] (<https://orcid.org/0000-0002-1153-9007>),
Gillespie Nathan [wit],
Michael Zakharin [wit],
Brenton Wiernik [ctb],
Luis De Araujo [ctb],
Joshua N. Pritikin [ctb],
Michael C. Neale [ctb],
Hermine Maes [ctb]
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>
Diff between umx versions 4.10.10 dated 2021-11-29 and 4.10.50 dated 2021-12-16
DESCRIPTION | 14 - MD5 | 220 ++++++++------- NAMESPACE | 3 NEWS.md | 20 + R/build_run_modify.R | 43 ++- R/datasets.R | 9 R/fit_and_reporting.R | 237 +++++++++++++++-- R/lavanify2ram.R | 7 R/misc_and_utility.R | 487 ++++++++++++++++------------------- R/umxDoC.R | 52 ++- R/umxPower.R | 71 +++-- R/umx_build_high_level_models.R | 2 R/umx_build_polychoricMatrix3.R | 3 R/umx_build_umxSimplex.R | 4 R/xmu.R | 169 ++++++++---- build/partial.rdb |binary inst/WORDLIST | 2 man/Fischbein_wt.Rd | 2 man/GFF.Rd | 3 man/RMSEA.summary.mxmodel.Rd | 1 man/figures/DoC.pdf |binary man/figures/DoC.png |binary man/figures/umx_help_figures.graffle |binary man/fin_percent.Rd | 11 man/iqdat.Rd | 2 man/loadings.MxModel.Rd | 2 man/plot.percent.Rd | 2 man/power.ACE.test.Rd | 2 man/umx.Rd | 3 man/umxACE.Rd | 2 man/umxAPA.Rd | 3 man/umxAlgebra.Rd | 3 man/umxCompare.Rd | 4 man/umxConfint.Rd | 2 man/umxDiagnose.Rd | 2 man/umxDoC.Rd | 19 + man/umxEquate.Rd | 2 man/umxExpCov.Rd | 3 man/umxExpMeans.Rd | 3 man/umxFactorScores.Rd | 3 man/umxFixAll.Rd | 3 man/umxGetLatents.Rd |only man/umxGetManifests.Rd |only man/umxGetModel.Rd |only man/umxGetParameters.Rd | 5 man/umxGxE.Rd | 2 man/umxGxE_window.Rd | 2 man/umxLav2RAM.Rd | 2 man/umxMI.Rd | 4 man/umxMatrix.Rd | 3 man/umxModify.Rd | 3 man/umxParameters.Rd | 6 man/umxPlotACE.Rd | 2 man/umxPlotACEcov.Rd | 2 man/umxPlotDoC.Rd | 8 man/umxPlotGxE.Rd | 2 man/umxPower.Rd | 7 man/umxRAM.Rd | 2 man/umxRAM2Lav.Rd | 2 man/umxRenameMatrix.Rd | 7 man/umxRotate.MxModelCP.Rd | 2 man/umxRun.Rd | 4 man/umxSetParameters.Rd | 3 man/umxSummary.MxModel.Rd | 3 man/umxSummaryACE.Rd | 6 man/umxSummaryACEcov.Rd | 5 man/umxSummaryGxE.Rd | 2 man/umxSummaryIP.Rd | 2 man/umxSuperModel.Rd | 1 man/umxTwoStage.Rd | 2 man/umxVersion.Rd | 7 man/umx_aggregate.Rd | 3 man/umx_check_model.Rd | 4 man/umx_explode_twin_names.Rd | 2 man/umx_get_bracket_addresses.Rd | 3 man/umx_get_checkpoint.Rd | 3 man/umx_has_CIs.Rd | 2 man/umx_has_been_run.Rd | 5 man/umx_has_means.Rd | 3 man/umx_is_RAM.Rd | 2 man/umx_is_endogenous.Rd | 3 man/umx_is_exogenous.Rd | 3 man/umx_make.Rd | 6 man/umx_make_TwinData.Rd | 17 - man/umx_polychoric.Rd | 3 man/umx_score_scale.Rd | 93 ++++-- man/umx_stack.Rd | 4 man/umx_str_chars.Rd | 2 man/umx_time.Rd | 5 man/us_skinfold_data.Rd | 2 man/xmuLabel.Rd | 2 man/xmuValues.Rd | 3 man/xmu_cell_is_on.Rd | 6 man/xmu_lavaan_process_group.Rd | 3 man/xmu_make_mxData.Rd | 3 man/xmu_print_algebras.Rd | 1 man/xmu_safe_run_summary.Rd | 9 man/xmu_standardize_ACEcov.Rd | 2 man/xmu_standardize_RAM.Rd | 3 man/xmu_twin_get_var_names.Rd | 6 tests |only 101 files changed, 1129 insertions(+), 590 deletions(-)
Title: Prediction and Clustering on the Torus by Conformal Prediction
Description: Provides various tools of for clustering multivariate angular
data on the torus. The package provides angular
adaptations of usual clustering methods such as the k-means
clustering, pairwise angular distances, which can be used as an
input for distance-based clustering algorithms, and implements
clustering based on the conformal prediction framework. Options
for the conformal scores include scores based on a kernel density
estimate, multivariate von Mises mixtures, and naive k-means clusters.
Moreover, the package provides some basic data handling tools for
angular data.
Author: Sungkyu Jung [aut, cph],
Seungki Hong [aut, cre],
Kiho Park [ctb],
Byungwon Kim [ctb]
Maintainer: Seungki Hong <skgaboja@snu.ac.kr>
Diff between ClusTorus versions 0.1.3 dated 2021-07-26 and 0.2.0 dated 2021-12-16
ClusTorus-0.1.3/ClusTorus/R/kmeans.kspheres.R |only ClusTorus-0.1.3/ClusTorus/man/icp.torus.score.Rd |only ClusTorus-0.1.3/ClusTorus/man/kmeans.kspheres.Rd |only ClusTorus-0.1.3/ClusTorus/man/pred.kmeans.torus.Rd |only ClusTorus-0.2.0/ClusTorus/DESCRIPTION | 10 ClusTorus-0.2.0/ClusTorus/MD5 | 80 ++-- ClusTorus-0.2.0/ClusTorus/NAMESPACE | 25 + ClusTorus-0.2.0/ClusTorus/R/Ainv.R | 2 ClusTorus-0.2.0/ClusTorus/R/EMsinvMmix.R | 8 ClusTorus-0.2.0/ClusTorus/R/ang.pdist.R | 2 ClusTorus-0.2.0/ClusTorus/R/clus.torus.R |only ClusTorus-0.2.0/ClusTorus/R/cluster.assign.torus.R | 162 ++++----- ClusTorus-0.2.0/ClusTorus/R/cp.torus.kde.R | 36 +- ClusTorus-0.2.0/ClusTorus/R/data.R | 32 - ClusTorus-0.2.0/ClusTorus/R/ehat.eval.R | 4 ClusTorus-0.2.0/ClusTorus/R/ellip.kmeans.torus.R |only ClusTorus-0.2.0/ClusTorus/R/hcluster.torus.R | 7 ClusTorus-0.2.0/ClusTorus/R/hyperparam.J.R | 128 +++---- ClusTorus-0.2.0/ClusTorus/R/hyperparam.alpha.R | 26 - ClusTorus-0.2.0/ClusTorus/R/hyperparam.torus.R | 248 ++++----------- ClusTorus-0.2.0/ClusTorus/R/icp.torus.R | 294 +++++++++--------- ClusTorus-0.2.0/ClusTorus/R/kde.torus.R | 7 ClusTorus-0.2.0/ClusTorus/R/kmeans.torus.R | 35 +- ClusTorus-0.2.0/ClusTorus/R/methods.R |only ClusTorus-0.2.0/ClusTorus/R/plot.ellipsoids.R | 2 ClusTorus-0.2.0/ClusTorus/R/predict.kmeans.torus.R | 76 ++-- ClusTorus-0.2.0/ClusTorus/build/partial.rdb |binary ClusTorus-0.2.0/ClusTorus/data/SARS_CoV_2.rda |binary ClusTorus-0.2.0/ClusTorus/inst/doc/ClusTorus.R | 36 -- ClusTorus-0.2.0/ClusTorus/inst/doc/ClusTorus.Rmd | 36 -- ClusTorus-0.2.0/ClusTorus/inst/doc/ClusTorus.html | 129 ++++--- ClusTorus-0.2.0/ClusTorus/man/EMsinvMmix.Rd | 8 ClusTorus-0.2.0/ClusTorus/man/ILE.Rd | 6 ClusTorus-0.2.0/ClusTorus/man/SARS_CoV_2.Rd | 26 - ClusTorus-0.2.0/ClusTorus/man/ang.pdist.Rd | 2 ClusTorus-0.2.0/ClusTorus/man/clus.torus.Rd |only ClusTorus-0.2.0/ClusTorus/man/cluster.assign.torus.Rd | 69 ++-- ClusTorus-0.2.0/ClusTorus/man/cp.torus.kde.Rd | 11 ClusTorus-0.2.0/ClusTorus/man/ellip.kmeans.torus.Rd |only ClusTorus-0.2.0/ClusTorus/man/hyperparam.J.Rd | 38 +- ClusTorus-0.2.0/ClusTorus/man/hyperparam.alpha.Rd | 17 - ClusTorus-0.2.0/ClusTorus/man/hyperparam.torus.Rd | 123 +------ ClusTorus-0.2.0/ClusTorus/man/icp.torus.Rd |only ClusTorus-0.2.0/ClusTorus/man/icp.torus.eval.Rd | 10 ClusTorus-0.2.0/ClusTorus/man/kmeans.torus.Rd | 34 +- ClusTorus-0.2.0/ClusTorus/vignettes/ClusTorus.Rmd | 36 -- 46 files changed, 816 insertions(+), 949 deletions(-)
Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager
from Facebook Marketing API into R. For more details see official documents by Facebook
Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>)
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rfacebookstat versions 2.4.0 dated 2021-07-27 and 2.5.0 dated 2021-12-16
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 8 ++++++++ R/authorization.R | 10 +++++++--- R/fbGetMarketingStat.R | 4 ++++ R/fbParsers.R | 6 ++---- R/zzz.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/rfacebookstat-cost-data.html | 4 ++-- inst/doc/rfacebookstat-get-statistics.html | 6 +++--- man/fbAuth.Rd | 6 ++++++ man/fbGetToken.Rd | 10 +++++++++- 13 files changed, 58 insertions(+), 30 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
Author: Emmanuel Paradis [aut, cre, cph]
(<https://orcid.org/0000-0003-3092-2199>),
Thibaut Jombart [aut, cph] (<https://orcid.org/0000-0003-2226-8692>),
Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>),
Brian Knaus [aut, cph] (<https://orcid.org/0000-0003-1665-4343>),
Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>),
Alastair Potts [aut, cph] (<https://orcid.org/0000-0003-0919-7279>),
David Winter [aut, cph] (<https://orcid.org/0000-0002-6165-0029>)
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between pegas versions 1.0-1 dated 2021-05-17 and 1.1 dated 2021-12-16
DESCRIPTION | 12 ++--- MD5 | 24 +++++----- NAMESPACE | 4 - NEWS | 17 ++++++- R/haplotype.R | 106 +++++++++++++++++++++++----------------------- R/zzz.R | 5 -- build/partial.rdb |binary build/vignette.rds |binary inst/doc/PlotHaploNet.pdf |binary inst/doc/ReadingFiles.pdf |binary man/haploNet.Rd | 7 +-- man/hw.test.Rd | 6 +- vignettes/ape.sty | 6 +- 13 files changed, 100 insertions(+), 87 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.1-1 dated 2021-12-07 and 1.1-2 dated 2021-12-16
DESCRIPTION | 8 ++-- MD5 | 8 ++-- inst/NEWS.Rd | 6 +++ inst/doc/mlt.pdf |binary tests/truncreg-Ex.Rout.save | 74 ++++++++++++++++++++++---------------------- 5 files changed, 52 insertions(+), 44 deletions(-)
Title: Analyze Cricket Performances Based on Data from Cricsheet
Description: Analyzing performances of cricketers and cricket teams
based on 'yaml' match data from Cricsheet <https://cricsheet.org/>.
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>
Diff between yorkr versions 0.0.29 dated 2021-12-13 and 0.0.30 dated 2021-12-16
DESCRIPTION | 8 +- MD5 | 62 +++++++++++----------- R/overallRunsSRDeathOversPlotT20.R | 4 - R/overallRunsSRPPowerplayPlotT20.R | 4 - R/overallRunsSRPlotT20.R | 4 - R/overallWicketsERDeathOversPlotT20.R | 4 - R/overallWicketsERPlotT20.R | 4 - R/teamRunSRDeathOversPlotAllOppnAllMatches.R | 4 - R/teamRunSRDeathOversPlotMatch.R | 4 - R/teamRunSRDeathOversPlotOppnAllMatches.R | 4 - R/teamRunsSRMiddleOversPlotAllOppnAllMatches.R | 4 - R/teamRunsSRMiddleOversPlotMatch.R | 4 - R/teamRunsSRMiddleOversPlotOppnAllMatches.R | 4 - R/teamRunsSRPlotAllOppnAllMatches.R | 4 - R/teamRunsSRPlotMatch.R | 4 - R/teamRunsSRPlotOppnAllMatches.R | 4 - R/teamRunsSRPowerPlayPlotAllOppnAllMatches.R | 4 - R/teamRunsSRPowerPlayPlotMatch.R | 5 - R/teamRunsSRPowerPlayPlotOppnAllMatches.R | 4 - R/teamWicketsERDeathOversPlotAllOppnAllMatches.R | 4 - R/teamWicketsERDeathOversPlotMatch.R | 4 - R/teamWicketsERDeathOversPlotOppnAllMatches.R | 4 - R/teamWicketsERMiddleOversPlotAllOppnAllMatches.R | 4 - R/teamWicketsERMiddleOversPlotMatch.R | 4 - R/teamWicketsERMiddleOversPlotOppnAllMatches.R | 4 - R/teamWicketsERPlotAllOppnAllMatches.R | 4 - R/teamWicketsERPlotMatch.R | 4 - R/teamWicketsERPlotOppnAllMatches.R | 4 - R/teamWicketsERPowerPlayPlotAllOppnAllMatches.R | 4 - R/teamWicketsERPowerPlayPlotMatch.R | 4 - R/teamWicketsERPowerPlayPlotOppnAllMatches.R | 4 - R/topERBowlerAcrossOversAllOppnAllMatches.R | 6 +- 32 files changed, 96 insertions(+), 97 deletions(-)
Title: Fitting RT-MPT Models
Description: Fit response-time extended multinomial processing tree (RT-MPT) models by Klauer and
Kellen (2018) <doi:10.1016/j.jmp.2017.12.003>. The RT-MPT class not only incorporate
frequencies like traditional multinomial processing tree (MPT) models, but also latencies. This enables it
to estimate process completion times and encoding plus motor execution times next to the process probabilities
of traditional MPTs. 'rtmpt' is a Bayesian framework and posterior samples are sampled using a Metropolis-Gibbs
sampler like the one described in the Klauer and Kellen (2018), but with some modifications. Other than in
the original C++ program we use the free and open source GNU Scientific Library (GSL). There is also the
possibility to suppress single process completion times.
Author: Raphael Hartmann [aut, cre],
Karl C. Klauer [cph, aut, ctb, ths],
Henrik Singmann [ctb, aut],
Jean Marie Linhart [ctb],
Frederick Novomestky [ctb]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between rtmpt versions 0.2-2 dated 2021-10-11 and 0.2-3 dated 2021-12-16
DESCRIPTION | 12 MD5 | 22 NAMESPACE | 2 R/call_rtmpt.R | 26 R/get_infofile.R | 1360 +++++++++++++++++++++++----------------------- R/get_model.R | 378 ++++++------ R/make_models.R | 32 + R/print_RTMPT.R | 6 R/simulate_rtmpt.R | 12 build/partial.rdb |binary inst/doc/rtmpt_intro.html | 212 ++++++- man/fit_rtmpt.Rd | 2 12 files changed, 1165 insertions(+), 899 deletions(-)
Title: Rendering Word Documents with R Inline Code
Description: Serves for rendering MS Word documents with R inline code and inserting tables and plots.
Author: Tomas Hovorka
Maintainer: Tomas Hovorka <tomashovorka@seznam.cz>
Diff between WordR versions 0.3.1 dated 2018-07-23 and 0.3.2 dated 2021-12-16
WordR-0.3.1/WordR/man/WordR.Rd |only WordR-0.3.2/WordR/DESCRIPTION | 11 WordR-0.3.2/WordR/MD5 | 29 - WordR-0.3.2/WordR/NAMESPACE | 11 WordR-0.3.2/WordR/NEWS.md | 4 WordR-0.3.2/WordR/R/WordR.R | 2 WordR-0.3.2/WordR/R/addPlots.R | 24 - WordR-0.3.2/WordR/R/body_add_flextables.R | 9 WordR-0.3.2/WordR/R/misc.R | 118 ++++++ WordR-0.3.2/WordR/R/renderInlineCode.R | 7 WordR-0.3.2/WordR/build/vignette.rds |binary WordR-0.3.2/WordR/inst/doc/WordR.html | 266 ++++++++++++++- WordR-0.3.2/WordR/inst/examples/resultFT.docx |only WordR-0.3.2/WordR/inst/examples/results/result1.docx |binary WordR-0.3.2/WordR/inst/examples/results/resultPlots.docx |binary WordR-0.3.2/WordR/inst/examples/results/templateAll.docx |only WordR-0.3.2/WordR/man/addPlots.Rd | 13 17 files changed, 448 insertions(+), 46 deletions(-)
Title: Spatial Early Warning Signals of Ecosystem Degradation
Description: Tools to compute and assess significance of early-warnings signals (EWS) of ecosystem degradation on raster data sets. EWS are metrics derived from the observed spatial structure of an ecosystem -- e.g. spatial autocorrelation -- that increase before an ecosystem undergoes a non-linear transition (Genin et al. (2018) <doi:10.1111/2041-210X.13058>).
Author: Alain Danet, Alexandre Genin, Vishwesha Guttal, Sonia Kefi,
Sabiha Majumder, Sumithra Sankaran, Florian Schneider
Maintainer: Alexandre Genin <a.a.h.genin@uu.nl>
Diff between spatialwarnings versions 3.0.0 dated 2021-05-19 and 3.0.2 dated 2021-12-16
DESCRIPTION | 10 +-- MD5 | 42 +++++++------- NEWS | 20 +++++- R/RcppExports.R | 10 +++ R/indictest.R | 7 +- R/null_model_helpers.R | 9 ++- R/simple_indic.R | 4 - R/simple_indic_indictest.R | 4 + build/partial.rdb |binary man/create_indicator.Rd | 4 - man/indictest.Rd | 7 +- man/raw_moran.Rd | 10 +++ src/RcppExports.cpp | 13 +++- src/coarse_graining.cpp | 13 +++- src/label.cpp | 4 - src/moran_correlation.cpp | 73 ++++++++++++++++++++----- src/norm_constants.cpp | 10 +-- src/rspectrum.cpp | 2 src/skewness.cpp | 7 +- tests/testthat/rodriguez2018/read_sd.m |only tests/testthat/test-indicator_values-plosone.R | 10 +++ tests/testthat/test-moran.R |only tests/testthat/test-skewness.R | 2 23 files changed, 188 insertions(+), 73 deletions(-)
More information about spatialwarnings at CRAN
Permanent link
Title: Compute and Illustrate the Multiple Facets of Functional
Diversity
Description: Computing functional traits-based distances between pairs of
species for species gathered in assemblages allowing to build several
functional spaces. The package allows to compute functional diversity
indices assessing the distribution of species (and of their dominance) in a
given functional space for each assemblage and the overlap between
assemblages in a given functional space, see: Chao et al. (2018)
<doi:10.1002/ecm.1343>, Maire et al. (2015) <doi:10.1111/geb.12299>,
Mouillot et al. (2013) <doi:10.1016/j.tree.2012.10.004>, Mouillot et al.
(2014) <doi:10.1073/pnas.1317625111>, Ricotta and Szeidl (2009)
<doi:10.1016/j.tpb.2009.10.001>. Graphical outputs are included.
Visit the 'mFD' website for more information, documentation and examples.
Author: Camille Magneville [aut, cre, cph]
(<https://orcid.org/0000-0003-0489-3822>),
Nicolas Loiseau [aut] (<https://orcid.org/0000-0002-2469-1980>),
Camille Albouy [aut] (<https://orcid.org/0000-0003-1629-2389>),
Nicolas Casajus [aut] (<https://orcid.org/0000-0002-5537-5294>),
Thomas Claverie [aut] (<https://orcid.org/0000-0002-6258-4991>),
Arthur Escalas [aut] (<https://orcid.org/0000-0002-6450-5716>),
Fabien Leprieur [aut] (<https://orcid.org/0000-0001-6869-342X>),
Eva Maire [aut] (<https://orcid.org/0000-0002-1032-3394>),
David Mouillot [aut] (<https://orcid.org/0000-0003-0402-2605>),
Sebastien Villeger [aut] (<https://orcid.org/0000-0002-2362-7178>)
Maintainer: Camille Magneville <camille.magneville@gmail.com>
Diff between mFD versions 1.0.0 dated 2021-11-05 and 1.0.1 dated 2021-12-16
DESCRIPTION | 8 +-- MD5 | 22 +++++----- NEWS.md | 7 +++ R/quality_fspaces.R | 3 + README.md | 8 ++- build/vignette.rds |binary inst/doc/Compute_and_interpret_quality_of_functional_spaces.html | 10 ++-- inst/doc/Compute_functional_hill_indices.html | 4 - inst/doc/Continuous_traits_framework.html | 4 - inst/doc/How_to_deal_with_Functional_Entities.html | 4 - inst/doc/mFD_general_workflow.html | 8 +-- man/mFD-package.Rd | 12 ----- 12 files changed, 46 insertions(+), 44 deletions(-)
Title: Estimation and Prediction Methods for High-Dimensional Mixed
Frequency Time Series Data
Description: The 'midasml' package implements estimation and prediction methods for high-dimensional mixed-frequency (MIDAS) time-series and panel data regression models. The regularized MIDAS models are estimated using orthogonal (e.g. Legendre) polynomials and sparse-group LASSO (sg-LASSO) estimator. For more information on the 'midasml' approach see Babii, Ghysels, and Striaukas (2021, JBES forthcoming) <doi:10.1080/07350015.2021.1899933>. The package is equipped with the fast implementation of the sg-LASSO estimator by means of proximal block coordinate descent. High-dimensional mixed frequency time-series data can also be easily manipulated with functions provided in the package.
Author: Jonas Striaukas [cre, aut],
Andrii Babii [aut],
Eric Ghysels [aut],
Alex Kostrov [ctb] (Contributions to analytical gradients for
non-linear low-dimensional MIDAS estimation code)
Maintainer: Jonas Striaukas <jonas.striaukas@gmail.com>
Diff between midasml versions 0.1.7 dated 2021-12-08 and 0.1.8 dated 2021-12-16
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/cv.sglfit.R | 2 +- R/ic.sglfit.R | 2 +- R/reg.sgl.R | 39 ++++++++++++++++++++++++++++++++++----- R/tscv.sglfit.R | 24 ++++++++++++------------ man/tscv.sglfit.Rd | 6 +++--- 7 files changed, 60 insertions(+), 31 deletions(-)
Title: Interface with Google Cloud Storage API
Description: Interact with Google Cloud Storage <https://cloud.google.com/storage/>
API in R. Part of the 'cloudyr' <https://cloudyr.github.io/> project.
Author: Mark Edmondson [aut, cre] (<https://orcid.org/0000-0002-8434-3881>)
Maintainer: Mark Edmondson <r@sunholo.com>
Diff between googleCloudStorageR versions 0.6.0 dated 2021-01-05 and 0.7.0 dated 2021-12-16
googleCloudStorageR-0.6.0/googleCloudStorageR/tests/testthat/test-gcs.R |only googleCloudStorageR-0.7.0/googleCloudStorageR/DESCRIPTION | 20 googleCloudStorageR-0.7.0/googleCloudStorageR/MD5 | 51 googleCloudStorageR-0.7.0/googleCloudStorageR/NAMESPACE | 6 googleCloudStorageR-0.7.0/googleCloudStorageR/NEWS.md | 10 googleCloudStorageR-0.7.0/googleCloudStorageR/R/auth.R | 11 googleCloudStorageR-0.7.0/googleCloudStorageR/R/buckets.R | 47 googleCloudStorageR-0.7.0/googleCloudStorageR/R/download.R | 21 googleCloudStorageR-0.7.0/googleCloudStorageR/R/objects.R | 120 + googleCloudStorageR-0.7.0/googleCloudStorageR/R/options.R | 2 googleCloudStorageR-0.7.0/googleCloudStorageR/R/upload.R | 37 googleCloudStorageR-0.7.0/googleCloudStorageR/R/utilities.R | 22 googleCloudStorageR-0.7.0/googleCloudStorageR/build/vignette.rds |binary googleCloudStorageR-0.7.0/googleCloudStorageR/inst/doc/googleCloudStorageR.Rmd | 23 googleCloudStorageR-0.7.0/googleCloudStorageR/inst/doc/googleCloudStorageR.html | 764 +++------- googleCloudStorageR-0.7.0/googleCloudStorageR/man/gcs_auth.Rd | 11 googleCloudStorageR-0.7.0/googleCloudStorageR/man/gcs_delete_bucket.Rd | 12 googleCloudStorageR-0.7.0/googleCloudStorageR/man/gcs_delete_object.Rd | 2 googleCloudStorageR-0.7.0/googleCloudStorageR/man/gcs_get_object.Rd | 21 googleCloudStorageR-0.7.0/googleCloudStorageR/man/gcs_list_objects.Rd | 5 googleCloudStorageR-0.7.0/googleCloudStorageR/man/gcs_parse_download.Rd | 6 googleCloudStorageR-0.7.0/googleCloudStorageR/tests/testthat/_snaps |only googleCloudStorageR-0.7.0/googleCloudStorageR/tests/testthat/setup-helpers.R |only googleCloudStorageR-0.7.0/googleCloudStorageR/tests/testthat/test-aauth.R |only googleCloudStorageR-0.7.0/googleCloudStorageR/tests/testthat/test-buckets.R |only googleCloudStorageR-0.7.0/googleCloudStorageR/tests/testthat/test-downloads.R |only googleCloudStorageR-0.7.0/googleCloudStorageR/tests/testthat/test-objects.R |only googleCloudStorageR-0.7.0/googleCloudStorageR/tests/testthat/test-pubsub.R |only googleCloudStorageR-0.7.0/googleCloudStorageR/tests/testthat/test-sessions.R |only googleCloudStorageR-0.7.0/googleCloudStorageR/tests/testthat/test-zz-access-control.R |only googleCloudStorageR-0.7.0/googleCloudStorageR/tests/testthat/test-zz-deleting.R |only googleCloudStorageR-0.7.0/googleCloudStorageR/vignettes/googleCloudStorageR.Rmd | 23 32 files changed, 648 insertions(+), 566 deletions(-)
More information about googleCloudStorageR at CRAN
Permanent link
Title: R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal 'RPC' protocols and file formats. Additional documentation
is available in two included vignettes one of which corresponds to our 'JSS'
paper (2016, <doi:10.18637/jss.v071.i02>. Either version 2 or 3 of the
'Protocol Buffers' 'API' is supported.
Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RProtoBuf versions 0.4.17 dated 2020-03-28 and 0.4.18 dated 2021-12-16
RProtoBuf-0.4.17/RProtoBuf/R/http.handler.R |only RProtoBuf-0.4.17/RProtoBuf/R/rpc.R |only RProtoBuf-0.4.17/RProtoBuf/man/RpcHTTP-class.Rd |only RProtoBuf-0.4.17/RProtoBuf/man/invokeLocally.Rd |only RProtoBuf-0.4.18/RProtoBuf/ChangeLog | 86 ++++++++++- RProtoBuf-0.4.18/RProtoBuf/DESCRIPTION | 13 - RProtoBuf-0.4.18/RProtoBuf/MD5 | 61 +++---- RProtoBuf-0.4.18/RProtoBuf/NAMESPACE | 6 RProtoBuf-0.4.18/RProtoBuf/R/00classes.R | 28 +-- RProtoBuf-0.4.18/RProtoBuf/R/debug_string.R | 11 - RProtoBuf-0.4.18/RProtoBuf/README.md | 18 +- RProtoBuf-0.4.18/RProtoBuf/build/vignette.rds |binary RProtoBuf-0.4.18/RProtoBuf/cleanup | 4 RProtoBuf-0.4.18/RProtoBuf/inst/NEWS.Rd | 45 ++++- RProtoBuf-0.4.18/RProtoBuf/inst/doc/RProtoBuf-intro.pdf |binary RProtoBuf-0.4.18/RProtoBuf/inst/doc/RProtoBuf-paper.pdf |binary RProtoBuf-0.4.18/RProtoBuf/inst/doc/RProtoBuf-quickref.pdf |binary RProtoBuf-0.4.18/RProtoBuf/man/ArrayInputStream-class.Rd | 2 RProtoBuf-0.4.18/RProtoBuf/man/ArrayOutputStream-class.Rd | 2 RProtoBuf-0.4.18/RProtoBuf/man/Descriptor-class.Rd | 2 RProtoBuf-0.4.18/RProtoBuf/man/EnumValueDescriptor-class.Rd | 2 RProtoBuf-0.4.18/RProtoBuf/man/FileDescriptor-class.Rd | 2 RProtoBuf-0.4.18/RProtoBuf/man/FileInputStream-class.Rd | 2 RProtoBuf-0.4.18/RProtoBuf/man/FileOutputStream-class.Rd | 2 RProtoBuf-0.4.18/RProtoBuf/man/Message-class.Rd | 8 - RProtoBuf-0.4.18/RProtoBuf/man/ZeroCopyInputStream-class.Rd | 2 RProtoBuf-0.4.18/RProtoBuf/man/ZeroCopyOutputStream-class.Rd | 2 RProtoBuf-0.4.18/RProtoBuf/man/swap.Rd | 2 RProtoBuf-0.4.18/RProtoBuf/src/Makevars.ucrt |only RProtoBuf-0.4.18/RProtoBuf/src/Makevars.win | 2 RProtoBuf-0.4.18/RProtoBuf/src/RcppMacros.h | 11 + RProtoBuf-0.4.18/RProtoBuf/src/init.c | 4 RProtoBuf-0.4.18/RProtoBuf/src/wrapper_Message.cpp | 8 - RProtoBuf-0.4.18/RProtoBuf/src/wrapper_ServiceDescriptor.cpp | 4 34 files changed, 227 insertions(+), 102 deletions(-)
Title: Permutation Tests for Time Series Data
Description: Helps you determine the analysis window to use when analyzing densely-sampled
time-series data, such as EEG data, using permutation testing (Maris & Oostenveld, 2007)
<doi:10.1016/j.jneumeth.2007.03.024>. These permutation tests can help identify the timepoints
where significance of an effect begins and ends, and the results can be plotted in various
types of heatmap for reporting. Mixed-effects models are supported using an implementation of
the approach by Lee & Braun (2012) <doi:10.1111/j.1541-0420.2011.01675.x>.
Author: Cesko C. Voeten [aut, cre]
Maintainer: Cesko C. Voeten <cvoeten@gmail.com>
Diff between permutes versions 2.2 dated 2021-10-13 and 2.3.2 dated 2021-12-16
DESCRIPTION | 6 - MD5 | 12 +- R/buildmer.R | 215 ++++++++++++++++++++++-------------------------- build/vignette.rds |binary inst/doc/buildmer.pdf |binary inst/doc/permutes.pdf |binary man/clusterperm.lmer.Rd | 2 7 files changed, 109 insertions(+), 126 deletions(-)
Title: Estimation and Use of the Generalised (Tukey) Lambda
Distribution
Description: The generalised lambda distribution, or Tukey lambda distribution,
provides a wide variety of shapes with one functional form.
This package provides random numbers, quantiles, probabilities,
densities and density quantiles for four different types of the distribution,
the FKML (Freimer et al 1988), RS (Ramberg and Schmeiser 1974), GPD (van Staden
and Loots 2009) and FM5 - see documentation for details.
It provides the density function, distribution function, and Quantile-Quantile
plots.
It implements a variety of estimation methods for the distribution,
including diagnostic plots.
Estimation methods include the starship (all 4 types),
method of L-Moments for the GPD and FKML types, and a
number of methods for only the FKML type.
These include maximum likelihood, maximum product of spacings,
Titterington's method, Moments, Trimmed L-Moments and
Distributional Least Absolutes.
Author: Robert King [aut, cre] (<https://orcid.org/0000-0001-7495-6599>),
Benjamin Dean [aut],
Sigbert Klinke [aut],
Paul van Staden [aut] (<https://orcid.org/0000-0002-5710-5984>)
Maintainer: Robert King <Robert.King.Newcastle@gmail.com>
Diff between gld versions 2.6.3 dated 2021-11-24 and 2.6.4 dated 2021-12-16
gld-2.6.3/gld/man/fit.fkml.moments.val.Rd |only gld-2.6.4/gld/Changelog | 6 ++++++ gld-2.6.4/gld/DESCRIPTION | 15 ++++++++------- gld-2.6.4/gld/MD5 | 28 ++++++++++++++-------------- gld-2.6.4/gld/NAMESPACE | 2 +- gld-2.6.4/gld/NEWS | 4 ++++ gld-2.6.4/gld/R/CheckParameters.R | 1 + gld-2.6.4/gld/R/e1071wrap.R | 9 +++++---- gld-2.6.4/gld/R/fit.fkml.R | 4 ++-- gld-2.6.4/gld/R/fit.gpd.R | 5 ++++- gld-2.6.4/gld/R/moment.R | 5 ++++- gld-2.6.4/gld/R/rgld.R | 5 ++++- gld-2.6.4/gld/build/partial.rdb |binary gld-2.6.4/gld/man/fit.fkml.Rd | 4 ++-- gld-2.6.4/gld/man/fit.fkml.moments.Rd |only gld-2.6.4/gld/man/fit.gpd.Rd | 5 ++++- 16 files changed, 59 insertions(+), 34 deletions(-)
Title: Easily Downloads a Gene Expression Dataset from a GEO Code and
Retrieves the Gene Symbols of Its Probesets
Description: A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, <doi:10.1007/978-1-0716-1839-4_12>.
Author: Davide Chicco [aut, cre] (<https://orcid.org/0000-0001-9655-7142>)
Maintainer: Davide Chicco <davidechicco@davidechicco.it>
Diff between geneExpressionFromGEO versions 0.8 dated 2021-11-06 and 0.9 dated 2021-12-16
DESCRIPTION | 11 - MD5 | 8 R/geneExpressionFromGEO.r | 18 - build/vignette.rds |binary inst/doc/geneExpressionFromGEOvignette.html | 298 ++++++++++------------------ 5 files changed, 130 insertions(+), 205 deletions(-)
More information about geneExpressionFromGEO at CRAN
Permanent link
Title: Univariate Analysis of Cluster Trials with Multiple Outcomes
Description: Frequentist statistical inference for cluster randomised trials with
multiple outcomes that controls the family-wise error rate and provides nominal
coverage of confidence sets. A full description of the methods can be found
in Watson et al. (2021) <arXiv:2107.10017>.
Author: Sam Watson [aut, cre] (<https://orcid.org/0000-0002-8972-769X>)
Maintainer: Sam Watson <s.i.watson@bham.ac.uk>
Diff between crctStepdown versions 0.1 dated 2021-08-03 and 0.2.1 dated 2021-12-16
DESCRIPTION | 6 MD5 | 40 +-- NAMESPACE | 45 ++-- R/confint.R | 322 +++++++++++++++++------------- R/crctStepdown-package.R | 16 - R/permutations.R | 340 ++++++++++++++++---------------- R/sims.R | 128 ++++++------ R/stepdown.R | 468 ++++++++++++++++++++++++++------------------- R/teststats.R | 288 +++++++++++++-------------- man/conf_int_search.Rd | 184 +++++++++-------- man/est_null_model.Rd | 96 ++++----- man/gen_rand_order.Rd | 42 ++-- man/lme_permute2.Rd | 120 +++++------ man/outname_fit.Rd | 50 ++-- man/perm_dist.Rd | 42 ++-- man/permute.Rd | 126 ++++++------ man/qscore_stat.Rd | 96 ++++----- man/stepdown.Rd | 157 +++++++-------- man/twoarm_sim.Rd | 86 ++++---- tests/testthat.R | 8 tests/testthat/test-test.R | 56 ++--- 21 files changed, 1421 insertions(+), 1295 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-08 0.4.0
2018-10-04 0.3.0
2017-09-07 0.2.0
2017-01-28 0.1.11
2017-01-16 0.1.0
Title: PC Algorithm with the Principle of Mendelian Randomization
Description: A PC Algorithm with the Principle of Mendelian Randomization. This package implements the MRPC
(PC with the principle of Mendelian randomization) algorithm to infer causal graphs. It also
contains functions to simulate data under a certain topology, to visualize a graph in different
ways, and to compare graphs and quantify the differences.
See Badsha and Fu (2019) <doi:10.3389/fgene.2019.00460>; Badsha, Martin and Fu (2021) <doi:10.3389/fgene.2021.651812>.
Author: Md Bahadur Badsha [aut,cre],Evan A Martin [ctb] and Audrey Qiuyan Fu [aut]
Maintainer: Md Bahadur Badsha <mbbadshar@gmail.com>
Diff between MRPC versions 2.3.1 dated 2021-05-02 and 3.0.0 dated 2021-12-16
DESCRIPTION | 14 - MD5 | 81 ++--- NAMESPACE | 2 R/Classes.R | 25 + R/EdgeOrientation.R | 522 +++++++++++++++++++++++++++++++++----- R/MRPC.R | 80 +++-- R/ModiSkeleton.R | 315 ++++++++++++++++------ R/RecallPrecision.R | 43 +-- R/addis.R |only man/CompareMethodsNodeOrdering.Rd | 11 man/CompareMethodsVStructure.Rd | 8 man/CutModules.Rd | 2 man/Data_GEUVADIS.Rd | 2 man/EdgeOrientation.Rd | 36 ++ man/IdentifyAssociatedPCs.Rd | 6 man/MRPC.Rd | 95 ++++-- man/MRPCclass.Rd | 23 + man/MRPCtruth.Rd | 2 man/ModiSkeleton.Rd | 28 +- man/PlotGraphWithModules.Rd | 2 man/RecallPrecision.Rd | 6 man/RobustCor.Rd | 2 man/SeqFDR.Rd | 2 man/SimulateData.Rd | 2 man/SimulateData2P.Rd | 2 man/SimulateData3P.Rd | 2 man/SimulateDataNP.Rd | 2 man/aSHD.Rd | 2 man/data_GEUVADIS_combined.Rd | 21 - man/data_examples.Rd | 69 +++-- man/data_with_outliers.Rd | 10 man/data_without_outliers.Rd | 4 man/empty.Rd | 2 man/mpinv.Rd | 2 man/simu_data_M0.Rd | 2 man/simu_data_M1.Rd | 2 man/simu_data_M2.Rd | 2 man/simu_data_M3.Rd | 2 man/simu_data_M4.Rd | 2 man/simu_data_layered.Rd | 2 man/simu_data_multiparent.Rd | 2 man/simu_data_starshaped.Rd | 2 42 files changed, 1060 insertions(+), 381 deletions(-)