Title: Sunburst 'Htmlwidget'
Description: Make interactive 'd3.js' sequence sunburst diagrams in R with the
convenience and infrastructure of an 'htmlwidget'.
Author: Mike Bostock [aut, cph] (d3.js library, http://d3js.org),
Kerry Rodden [aut, cph] (sequences library in htmlwidgets/lib,
https://gist.github.com/kerryrodden/7090426),
Kevin Warne [aut, cph] (d2b sunburst library in htmlwidgets/lib,
https://github.com/d2bjs/d2b),
Kent Russell [aut, cre] (R interface),
Florian Breitwieser [ctb] (R interface),
CJ Yetman [ctb] (R interface, <https://orcid.org/0000-0001-5099-9500>)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between sunburstR versions 2.1.3 dated 2019-11-05 and 2.1.4 dated 2020-07-06
DESCRIPTION | 10 - MD5 | 22 +-- NEWS.md | 4 R/d2b.R | 5 build/vignette.rds |binary inst/doc/sunburst-2-0-0.html | 230 ++++++++++++++++++++++++++++------------- inst/examples/example_sund2b.R | 40 ++++--- inst/htmlwidgets/sund2b.js | 6 + man/sunburst.Rd | 26 +++- man/sund2b.Rd | 59 ++++++---- man/sund2bBreadcrumb.Rd | 2 man/sund2bTooltip.Rd | 5 12 files changed, 273 insertions(+), 136 deletions(-)
Title: Rounding to Decimal Digits
Description: Decimal rounding is non-trivial in binary arithmetic. ISO
standard round to even is more rare than typically assumed as most decimal fractions
are not exactly representable in binary. Our roundX() versions explore differences
between current and potential future versions of round() in R.
Further, provides (some partly related) C99 math lib functions not in base R.
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
R-core [ctb] ("r1.C" only)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between round versions 0.12-1 dated 2020-01-24 and 0.12-2 dated 2020-07-06
DESCRIPTION | 11 - MD5 | 24 +-- R/round.R | 6 build/round.pdf |binary build/vignette.rds |binary inst/NEWS.Rd | 18 ++ inst/doc/Rounding.Rmd | 227 ++++++++++++++++++++++++-------- inst/doc/Rounding.html | 340 +++++++++++++++++++++++++++---------------------- man/roundX.Rd | 17 +- src/fround.c | 5 tests/round-tst.R | 58 +++++--- vignettes/Rounding.Rmd | 227 ++++++++++++++++++++++++-------- vignettes/style.css | 2 13 files changed, 623 insertions(+), 312 deletions(-)
Title: R Functions for Chapter 3,4,6,7,9,10,11,12,14,15 of Sample Size
Calculation in Clinical Research
Description: Functions and Examples in Sample Size Calculation in
Clinical Research.
Author: Ed Zhang ; Vicky Qian Wu ; Shein-Chung Chow ; Harry G.Zhang
(Quality check) <ed.zhang.jr@gmail.com>
Maintainer: Vicky Qian Wu <wuqian7@gmail.com>
Diff between TrialSize versions 1.3 dated 2013-06-03 and 1.4 dated 2020-07-06
TrialSize-1.3/TrialSize/data |only TrialSize-1.3/TrialSize/man/Example.3.1.4.Rd |only TrialSize-1.4/TrialSize/DESCRIPTION | 13 TrialSize-1.4/TrialSize/MD5 | 212 ++++------ TrialSize-1.4/TrialSize/NAMESPACE | 1 TrialSize-1.4/TrialSize/R/Cox.Equality.R | 9 TrialSize-1.4/TrialSize/R/Cox.Equivalence.R | 9 TrialSize-1.4/TrialSize/R/Cox.NIS.R | 9 TrialSize-1.4/TrialSize/R/OneSampleMean.Equality.R | 4 TrialSize-1.4/TrialSize/R/OneSampleMean.Equivalence.R | 7 TrialSize-1.4/TrialSize/R/OneSampleMean.NIS.R | 4 TrialSize-1.4/TrialSize/R/OneSampleProportion.Equality.R | 6 TrialSize-1.4/TrialSize/R/OneSampleProportion.Equivalence.R | 6 TrialSize-1.4/TrialSize/R/OneSampleProportion.NIS.R | 6 TrialSize-1.4/TrialSize/R/TwoSampleCrossOver.Equality.R | 4 TrialSize-1.4/TrialSize/R/TwoSampleCrossOver.Equivalence.R | 6 TrialSize-1.4/TrialSize/R/TwoSampleCrossOver.NIS.R | 5 TrialSize-1.4/TrialSize/R/TwoSampleMean.Equality.R | 7 TrialSize-1.4/TrialSize/R/TwoSampleMean.Equivalence.R | 7 TrialSize-1.4/TrialSize/R/TwoSampleMean.NIS.R | 7 TrialSize-1.4/TrialSize/R/TwoSampleProportion.Equality.R | 9 TrialSize-1.4/TrialSize/R/TwoSampleProportion.Equivalence.R | 6 TrialSize-1.4/TrialSize/R/TwoSampleProportion.NIS.R | 7 TrialSize-1.4/TrialSize/man/AB.withDescalation.Rd | 5 TrialSize-1.4/TrialSize/man/AB.withoutDescalation.Rd | 4 TrialSize-1.4/TrialSize/man/ABE.Rd | 4 TrialSize-1.4/TrialSize/man/ANOVA.Repeat.Measure.Rd | 7 TrialSize-1.4/TrialSize/man/Carry.Over.Rd | 4 TrialSize-1.4/TrialSize/man/Cochran.Armitage.Trend.Rd | 4 TrialSize-1.4/TrialSize/man/Cox.Equality.Rd | 11 TrialSize-1.4/TrialSize/man/Cox.Equivalence.Rd | 15 TrialSize-1.4/TrialSize/man/Cox.NIS.Rd | 11 TrialSize-1.4/TrialSize/man/CrossOver.ISV.Equality.Rd | 4 TrialSize-1.4/TrialSize/man/CrossOver.ISV.Equivalence.Rd | 6 TrialSize-1.4/TrialSize/man/CrossOver.ISV.NIS.Rd | 4 TrialSize-1.4/TrialSize/man/Dose.Min.Effect.Rd | 4 TrialSize-1.4/TrialSize/man/Dose.Response.Linear.Rd | 4 TrialSize-1.4/TrialSize/man/Dose.Response.binary.Rd | 4 TrialSize-1.4/TrialSize/man/Dose.Response.time.to.event.Rd | 4 TrialSize-1.4/TrialSize/man/IBE.Rd | 7 TrialSize-1.4/TrialSize/man/ISCV.Equality.Rd | 5 TrialSize-1.4/TrialSize/man/ISCV.Equivalence.Rd | 6 TrialSize-1.4/TrialSize/man/ISCV.NIS.Rd | 4 TrialSize-1.4/TrialSize/man/ISV.Equality.Rd | 5 TrialSize-1.4/TrialSize/man/ISV.Equivalence.Rd | 4 TrialSize-1.4/TrialSize/man/ISV.NIS.Rd | 7 TrialSize-1.4/TrialSize/man/InterSV.Equality.Rd | 4 TrialSize-1.4/TrialSize/man/InterSV.NIS.Rd | 4 TrialSize-1.4/TrialSize/man/MeanWilliamsDesign.Equality.Rd | 4 TrialSize-1.4/TrialSize/man/MeanWilliamsDesign.Equivalence.Rd | 4 TrialSize-1.4/TrialSize/man/MeanWilliamsDesign.NIS.Rd | 5 TrialSize-1.4/TrialSize/man/Multiple.Testing.Rd | 6 TrialSize-1.4/TrialSize/man/Nonpara.Independ.Rd | 4 TrialSize-1.4/TrialSize/man/Nonpara.One.Sample.Rd | 4 TrialSize-1.4/TrialSize/man/Nonpara.Two.Sample.Rd | 4 TrialSize-1.4/TrialSize/man/OneSampleMean.Equality.Rd | 6 TrialSize-1.4/TrialSize/man/OneSampleMean.Equivalence.Rd | 6 TrialSize-1.4/TrialSize/man/OneSampleMean.NIS.Rd | 6 TrialSize-1.4/TrialSize/man/OneSampleProportion.Equality.Rd | 10 TrialSize-1.4/TrialSize/man/OneSampleProportion.Equivalence.Rd | 8 TrialSize-1.4/TrialSize/man/OneSampleProportion.NIS.Rd | 8 TrialSize-1.4/TrialSize/man/OneSide.fixEffect.Rd | 4 TrialSize-1.4/TrialSize/man/OneSide.varyEffect.Rd | 6 TrialSize-1.4/TrialSize/man/OneWayANOVA.PairwiseComparison.Rd | 4 TrialSize-1.4/TrialSize/man/OneWayANOVA.pairwise.Rd | 5 TrialSize-1.4/TrialSize/man/PBE.Rd | 4 TrialSize-1.4/TrialSize/man/Propensity.Score.nostrata.Rd | 4 TrialSize-1.4/TrialSize/man/Propensity.Score.strata.Rd | 4 TrialSize-1.4/TrialSize/man/QOL.Rd | 4 TrialSize-1.4/TrialSize/man/QT.PK.crossover.Rd | 4 TrialSize-1.4/TrialSize/man/QT.PK.parallel.Rd | 4 TrialSize-1.4/TrialSize/man/QT.crossover.Rd | 5 TrialSize-1.4/TrialSize/man/QT.parallel.Rd | 4 TrialSize-1.4/TrialSize/man/RelativeRisk.Equality.Rd | 4 TrialSize-1.4/TrialSize/man/RelativeRisk.Equivalence.Rd | 4 TrialSize-1.4/TrialSize/man/RelativeRisk.NIS.Rd | 4 TrialSize-1.4/TrialSize/man/RelativeRiskCrossOver.Equality.Rd | 5 TrialSize-1.4/TrialSize/man/RelativeRiskCrossOver.Equivalence.Rd | 5 TrialSize-1.4/TrialSize/man/RelativeRiskCrossOver.NIS.Rd | 4 TrialSize-1.4/TrialSize/man/Sensitivity.Index.Rd | 4 TrialSize-1.4/TrialSize/man/Stuart.Maxwell.Test.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSampleCrossOver.Equality.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSampleCrossOver.Equivalence.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSampleCrossOver.NIS.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSampleMean.Equality.Rd | 5 TrialSize-1.4/TrialSize/man/TwoSampleMean.Equivalence.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSampleMean.NIS.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSampleProportion.Equality.Rd | 11 TrialSize-1.4/TrialSize/man/TwoSampleProportion.Equivalence.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSampleProportion.NIS.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSampleSeqCrossOver.Equality.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSampleSeqCrossOver.Equivalence.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSampleSeqCrossOver.NIS.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSampleSurvival.Conditional.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSampleSurvival.Equality.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSampleSurvival.Equivalence.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSampleSurvival.NIS.Rd | 4 TrialSize-1.4/TrialSize/man/TwoSide.fixEffect.Rd | 2 TrialSize-1.4/TrialSize/man/TwoSide.varyEffect.Rd | 4 TrialSize-1.4/TrialSize/man/Vaccine.CEM.Rd | 4 TrialSize-1.4/TrialSize/man/Vaccine.ELDI.Rd | 4 TrialSize-1.4/TrialSize/man/Vaccine.RDI.Rd | 4 TrialSize-1.4/TrialSize/man/Vitro.BE.Rd | 4 TrialSize-1.4/TrialSize/man/WilliamsDesign.Equality.Rd | 4 TrialSize-1.4/TrialSize/man/WilliamsDesign.Equivalence.Rd | 4 TrialSize-1.4/TrialSize/man/WilliamsDesign.NIS.Rd | 4 TrialSize-1.4/TrialSize/man/gof.Pearson.Rd | 4 TrialSize-1.4/TrialSize/man/gof.Pearson.twoway.Rd | 5 108 files changed, 199 insertions(+), 562 deletions(-)
Title: Download DBnomics Data
Description: R access to hundreds of millions data series from DBnomics API
(<https://db.nomics.world/>).
Author: Sebastien Galais [cre, ctb],
Thomas Brand [aut]
Maintainer: Sebastien Galais <s915.stem@gmail.com>
Diff between rdbnomics versions 0.6.1 dated 2020-04-23 and 0.6.2 dated 2020-07-06
rdbnomics-0.6.1/rdbnomics/tests/testthat |only rdbnomics-0.6.1/rdbnomics/tests/testthat.R |only rdbnomics-0.6.2/rdbnomics/DESCRIPTION | 12 rdbnomics-0.6.2/rdbnomics/MD5 | 43 rdbnomics-0.6.2/rdbnomics/NEWS.md | 5 rdbnomics-0.6.2/rdbnomics/R/dbnomics.R | 100 rdbnomics-0.6.2/rdbnomics/R/dot_rdb.R | 82 rdbnomics-0.6.2/rdbnomics/R/rdb_datasets.R | 8 rdbnomics-0.6.2/rdbnomics/R/rdb_dimensions.R | 17 rdbnomics-0.6.2/rdbnomics/R/rdb_last_updates.R | 5 rdbnomics-0.6.2/rdbnomics/R/rdb_series.R | 24 rdbnomics-0.6.2/rdbnomics/R/rdbnomics.R | 2 rdbnomics-0.6.2/rdbnomics/R/utils.R | 145 rdbnomics-0.6.2/rdbnomics/README.md | 28 rdbnomics-0.6.2/rdbnomics/build/vignette.rds |binary rdbnomics-0.6.2/rdbnomics/inst/doc/rdbnomics.R | 983 ++++-- rdbnomics-0.6.2/rdbnomics/inst/doc/rdbnomics.Rmd | 986 ++++-- rdbnomics-0.6.2/rdbnomics/inst/doc/rdbnomics.html | 3233 +++------------------- rdbnomics-0.6.2/rdbnomics/inst/tinytest |only rdbnomics-0.6.2/rdbnomics/man/dbnomics.Rd | 2 rdbnomics-0.6.2/rdbnomics/man/figures |only rdbnomics-0.6.2/rdbnomics/tests/tinytest.R |only rdbnomics-0.6.2/rdbnomics/vignettes/rdbnomics.Rmd | 986 ++++-- 23 files changed, 2714 insertions(+), 3947 deletions(-)
Title: Fast Imputations Using 'Rcpp' and 'Armadillo'
Description: Fast imputations under the object-oriented programming paradigm.
Moreover there are offered a few functions built to work with popular R packages such as 'data.table' or 'dplyr'.
The biggest improvement in time performance could be achieve for a calculation where a grouping variable have to be used.
A single evaluation of a quantitative model for the multiple imputations is another major enhancement.
A new major improvement is one of the fastest predictive mean matching in the R world because of presorting and binary search.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>
Diff between miceFast versions 0.5.1 dated 2019-08-19 and 0.6.1 dated 2020-07-06
miceFast-0.5.1/miceFast/inst/extdata/images |only miceFast-0.6.1/miceFast/DESCRIPTION | 24 miceFast-0.6.1/miceFast/MD5 | 91 miceFast-0.6.1/miceFast/NAMESPACE | 108 miceFast-0.6.1/miceFast/NEWS.md | 83 miceFast-0.6.1/miceFast/R/RcppExports.R | 68 miceFast-0.6.1/miceFast/R/VIF.R | 306 +- miceFast-0.6.1/miceFast/R/data.R | 98 miceFast-0.6.1/miceFast/R/fill_NA.R | 791 +++-- miceFast-0.6.1/miceFast/R/fill_NA_N.R | 812 +++-- miceFast-0.6.1/miceFast/R/miceFast.R |only miceFast-0.6.1/miceFast/R/naive_fill_NA.R |only miceFast-0.6.1/miceFast/R/pmm.R |only miceFast-0.6.1/miceFast/R/zzz.R | 29 miceFast-0.6.1/miceFast/build/vignette.rds |binary miceFast-0.6.1/miceFast/data/air_miss.rda |binary miceFast-0.6.1/miceFast/inst/doc/miceFast-intro.R | 617 ++-- miceFast-0.6.1/miceFast/inst/doc/miceFast-intro.Rmd | 1003 +++--- miceFast-0.6.1/miceFast/inst/doc/miceFast-intro.html | 1817 ++++++------ miceFast-0.6.1/miceFast/inst/extdata/performance_validity.R | 1127 +++---- miceFast-0.6.1/miceFast/man/VIF.Rd | 40 miceFast-0.6.1/miceFast/man/air_miss.Rd | 32 miceFast-0.6.1/miceFast/man/figures |only miceFast-0.6.1/miceFast/man/fill_NA.Rd | 368 +- miceFast-0.6.1/miceFast/man/fill_NA_N.Rd | 414 +- miceFast-0.6.1/miceFast/man/naive_fill_NA.Rd |only miceFast-0.6.1/miceFast/man/neibo.Rd |only miceFast-0.6.1/miceFast/man/neibo_index.Rd |only miceFast-0.6.1/miceFast/src/R_funs.cpp | 57 miceFast-0.6.1/miceFast/src/RcppExports.cpp | 65 miceFast-0.6.1/miceFast/src/miceFast.h | 56 miceFast-0.6.1/miceFast/src/miceFast_additfunc.cpp | 44 miceFast-0.6.1/miceFast/src/miceFast_class.cpp | 88 miceFast-0.6.1/miceFast/src/miceFast_quantmodels.cpp | 375 ++ miceFast-0.6.1/miceFast/tests/testthat.R | 14 miceFast-0.6.1/miceFast/tests/testthat/test-corrData_fill.R | 125 miceFast-0.6.1/miceFast/tests/testthat/test-impute.R | 563 +-- miceFast-0.6.1/miceFast/tests/testthat/test-impute_N.R | 66 miceFast-0.6.1/miceFast/tests/testthat/test-imputes_funcs.R | 744 +++- miceFast-0.6.1/miceFast/tests/testthat/test-naive_fill_NA.R |only miceFast-0.6.1/miceFast/tests/testthat/test-vif.R | 81 miceFast-0.6.1/miceFast/vignettes/miceFast-intro.Rmd | 1003 +++--- 42 files changed, 6238 insertions(+), 4871 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-29 0.1.4
2019-05-08 0.1.1
2019-04-09 0.1.0.0
Title: Install the 'Natverse' Packages from Scratch
Description: Provides streamlined installation for packages from the 'natverse',
a suite of R packages for computational neuroanatomy built on top of the
'nat' 'NeuroAnatomy Toolbox' package. Installation of the complete
'natverse' suite requires a 'GitHub' user account and personal access token
'GITHUB_PAT'. 'natmanager' will help the end user set this up if necessary.
Author: Sridhar Jagannathan [aut, cre]
(<https://orcid.org/0000-0002-2078-1145>),
Gregory Jefferis [aut] (<https://orcid.org/0000-0002-0587-9355>)
Maintainer: Sridhar Jagannathan <j.sridharrajan@gmail.com>
Diff between natmanager versions 0.4.0 dated 2020-03-11 and 0.4.6 dated 2020-07-06
DESCRIPTION | 8 +++---- MD5 | 16 +++++++-------- NEWS.md | 30 ++++++++++++++++++++++++++++ R/install.R | 56 ++++++++++++++++++++++++++++++++++++++---------------- R/update.R | 50 +++++++++++++++++++++++++++++++++--------------- R/utils.R | 27 ++++++++++++++++++++++++++ README.md | 9 ++++++++ man/install.Rd | 16 ++++++++++++--- man/selfupdate.Rd | 13 +++++++++++- 9 files changed, 178 insertions(+), 47 deletions(-)
Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing
with 'Stan' <https://mc-stan.org>, including functions to set up the required
package structure, S3 generics and default methods to unify function naming
across 'Stan'-based R packages, and vignettes with recommendations for
developers.
Author: Jonah Gabry [aut, cre],
Ben Goodrich [aut],
Martin Lysy [aut],
Stefan Siegert [ctb],
Trustees of Columbia University [cph]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between rstantools versions 2.1.0 dated 2020-06-01 and 2.1.1 dated 2020-07-06
DESCRIPTION | 10 - MD5 | 20 +-- NEWS.md | 6 - inst/doc/developer-guidelines.html | 2 inst/doc/minimal-rstan-package.R | 14 +- inst/doc/minimal-rstan-package.Rmd | 18 +-- inst/doc/minimal-rstan-package.html | 172 ++++++++++++++++++++--------- inst/include/sys/Makevars | 4 inst/include/sys/Makevars.win | 4 tests/testthat/test-rstan_create_package.R | 8 - vignettes/minimal-rstan-package.Rmd | 18 +-- 11 files changed, 175 insertions(+), 101 deletions(-)
Title: Ocean Biodiversity Information System (OBIS) Client
Description: Client for the Ocean Biodiversity Information System (<https://obis.org>).
Author: Pieter Provoost [cre, aut],
Samuel Bosch [aut],
Ward Appeltans [ctb],
OBIS [cph]
Maintainer: Pieter Provoost <pieterprovoost@gmail.com>
Diff between robis versions 2.1.8 dated 2019-06-03 and 2.3.9 dated 2020-07-06
robis-2.1.8/robis/inst |only robis-2.3.9/robis/DESCRIPTION | 17 +-- robis-2.3.9/robis/MD5 | 41 ++++---- robis-2.3.9/robis/NAMESPACE | 7 + robis-2.3.9/robis/NEWS.md | 52 ++++++++++ robis-2.3.9/robis/R/area.R | 2 robis-2.3.9/robis/R/checklist.R | 27 +++-- robis-2.3.9/robis/R/dataset.R | 7 + robis-2.3.9/robis/R/map.R | 18 +++ robis-2.3.9/robis/R/mof.R |only robis-2.3.9/robis/R/node.R | 2 robis-2.3.9/robis/R/occurrence.R | 91 ++++++++++++++----- robis-2.3.9/robis/R/robis.R | 3 robis-2.3.9/robis/R/util.R | 23 +++- robis-2.3.9/robis/man/checklist.Rd | 6 + robis-2.3.9/robis/man/dataset.Rd | 4 robis-2.3.9/robis/man/get_geometry.Rd |only robis-2.3.9/robis/man/map_leaflet.Rd | 2 robis-2.3.9/robis/man/measurements.Rd |only robis-2.3.9/robis/man/occurrence.Rd | 32 ++++++ robis-2.3.9/robis/man/robis.Rd | 1 robis-2.3.9/robis/tests/testthat/test_checklist.R | 7 + robis-2.3.9/robis/tests/testthat/test_measurements.R |only robis-2.3.9/robis/tests/testthat/test_occurrence.R | 7 + 24 files changed, 277 insertions(+), 72 deletions(-)
Title: Nonparametric Regression via Smoothing Splines
Description: Multiple and generalized nonparametric regression using smoothing spline ANOVA models and generalized additive models, as described in Helwig (2020) <doi:10.4135/9781526421036885885>. Includes support for Gaussian and non-Gaussian responses, smoothers for multiple types of predictors, interactions between smoothers of mixed types, and eight different methods for smoothing parameter selection.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between npreg versions 1.0-2 dated 2020-05-04 and 1.0-3 dated 2020-07-06
ChangeLog | 34 ++++++++ DESCRIPTION | 10 +- MD5 | 37 ++++---- NAMESPACE | 8 - R/NegBin.R |only R/check_control.R | 18 +++- R/check_family.R | 12 +- R/fit_gsm.R | 203 +++++++++++++++++++++++++++++++------------------ R/gsm.R | 20 ++++ R/predict.gsm.R | 4 R/predict.sm.R | 4 R/sm.R | 6 - R/ss.R | 6 - R/summary.gsm.R | 14 +-- R/tune.theta.R |only man/NegBin.Rd |only man/gsm.Rd | 112 ++++++++++++++++++--------- man/npreg-internals.Rd | 1 man/predict.gsm.Rd | 4 man/sm.Rd | 6 - man/ss.Rd | 4 21 files changed, 333 insertions(+), 170 deletions(-)
Title: Kernel Learning Integrative Clustering
Description: Kernel Learning Integrative Clustering (KLIC) is an algorithm that allows to combine multiple kernels, each representing a different measure of the similarity between a set of observations. The contribution of each kernel on the final clustering is weighted according to the amount of information carried by it. As well as providing the functions required to perform the kernel-based clustering, this package also allows the user to simply give the data as input: the kernels are then built using consensus clustering. Different strategies to choose the best number of clusters are also available. For further details please see Cabassi and Kirk (2020) <doi:10.1093/bioinformatics/btaa593>.
Author: Alessandra Cabassi [aut, cre] (<https://orcid.org/0000-0003-1605-652X>),
Paul DW Kirk [ths] (<https://orcid.org/0000-0002-5931-7489>),
Mehmet Gonen [ctb] (<https://orcid.org/0000-0002-2483-075X>)
Maintainer: Alessandra Cabassi <alessandra.cabassi@mrc-bsu.cam.ac.uk>
Diff between klic versions 1.0.2 dated 2020-04-03 and 1.0.4 dated 2020-07-06
DESCRIPTION | 14 ++--- MD5 | 20 +++---- R/klic.R | 27 +++++++--- R/lmkkmeans.R | 10 +++ README.md | 9 ++- build/vignette.rds |binary inst/CITATION | 8 +- inst/doc/klic-vignette.html | 16 ++--- man/klic.Rd | 3 - vignettes/klic-vignette_files/figure-html/consensus_cluster-1.png |binary vignettes/klic-vignette_files/figure-html/spectrum_shift-1.png |binary 11 files changed, 66 insertions(+), 41 deletions(-)
Title: Input Output Analysis
Description: Calculates fundamental IO matrices (Leontief, Wassily W. (1951) <doi:10.1038/scientificamerican1051-15>); within period analysis via various rankings and coefficients (Sonis and Hewings (2006) <doi:10.1080/09535319200000013>, Blair and Miller (2009) <ISBN:978-0-521-73902-3>, Antras et al (2012) <doi:10.3386/w17819>, Hummels, Ishii, and Yi (2001) <doi:10.1016/S0022-1996(00)00093-3>); across period analysis with impact analysis (Dietzenbacher, van der Linden, and Steenge (2006) <doi:10.1080/09535319300000017>, Sonis, Hewings, and Guo (2006) <doi:10.1080/09535319600000002>); and a variety of table operators.
Author: John Wade [aut, cre],
Ignacio Sarmiento-Barbieri [aut]
Maintainer: John Wade <jjpwade2@illinois.edu>
Diff between ioanalysis versions 0.3.2 dated 2020-06-08 and 0.3.3 dated 2020-07-06
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- R/multipliers.R | 4 ++-- R/ras.R | 2 +- man/ioanalysis.Rd |only man/multipliers.Rd | 6 +++--- 6 files changed, 15 insertions(+), 14 deletions(-)
Title: Cluster-of-Clusters Analysis
Description: Contains the R functions needed to perform Cluster-Of-Clusters Analysis (COCA) and Consensus Clustering (CC). For further details please see Cabassi and Kirk (2020) <doi:10.1093/bioinformatics/btaa593>.
Author: Alessandra Cabassi [aut, cre] (<https://orcid.org/0000-0003-1605-652X>),
Paul DW Kirk [ths] (<https://orcid.org/0000-0002-5931-7489>)
Maintainer: Alessandra Cabassi <alessandra.cabassi@mrc-bsu.cam.ac.uk>
Diff between coca versions 1.0.4 dated 2020-03-26 and 1.1.0 dated 2020-07-06
DESCRIPTION | 12 - MD5 | 16 +- R/consensus-cluster.R | 71 ++++++---- README.md | 10 + build/vignette.rds |binary inst/CITATION | 8 - inst/doc/coca-vignette.html | 8 - man/consensusCluster.Rd | 18 ++ vignettes/coca-vignette_files/figure-html/coca_unknownK-1.png |binary 9 files changed, 91 insertions(+), 52 deletions(-)
Title: Empirical Dynamic Modeling ('EDM')
Description: An implementation of 'EDM' algorithms based on research software developed for internal use at the Sugihara Lab ('UCSD/SIO'). The package is implemented with 'Rcpp' wrappers around the 'cppEDM' library. It implements the 'simplex' projection method from Sugihara & May (1990) <doi:10.1038/344734a0>, the 'S-map' algorithm from Sugihara (1994) <doi:10.1098/rsta.1994.0106>, convergent cross mapping described in Sugihara et al. (2012) <doi:10.1126/science.1227079>, and, 'multiview embedding' described in Ye & Sugihara (2016) <doi:10.1126/science.aag0863>.
Author: Joseph Park [aut, cre] (ORCID:0000-0001-5411-1409),
Cameron Smith [aut],
George Sugihara [aut, ccp] (ORCID:0000-0002-2863-6946),
Ethan Deyle [aut] (ORCID:0000-0001-8704-8434),
Erik Saberski [ctb] (ORCID:0000-0002-6475-6187),
Hao Ye [ctb] (<https://orcid.org/0000-0002-8630-1458>),
The Regents of the University of California [cph]
Maintainer: Joseph Park <JosephPark@IEEE.org>
Diff between rEDM versions 1.3.8.5 dated 2020-06-23 and 1.5.0 dated 2020-07-06
rEDM-1.3.8.5/rEDM/src/cppEDM/src/AuxFunc.cc |only rEDM-1.3.8.5/rEDM/src/cppEDM/src/AuxFunc.h |only rEDM-1.3.8.5/rEDM/src/cppEDM/src/DateTimeUtil.cc |only rEDM-1.3.8.5/rEDM/src/cppEDM/src/Embed.cc |only rEDM-1.3.8.5/rEDM/src/cppEDM/src/Embed.h |only rEDM-1.3.8.5/rEDM/src/cppEDM/src/Interface.cc |only rEDM-1.3.8.5/rEDM/src/cppEDM/src/Neighbors.cc |only rEDM-1.3.8.5/rEDM/src/cppEDM/src/Neighbors.h |only rEDM-1.5.0/rEDM/DESCRIPTION | 9 rEDM-1.5.0/rEDM/MD5 | 82 - rEDM-1.5.0/rEDM/NEWS | 6 rEDM-1.5.0/rEDM/R/EDM.R | 5 rEDM-1.5.0/rEDM/R/LegacyInterface.R | 9 rEDM-1.5.0/rEDM/build/vignette.rds |binary rEDM-1.5.0/rEDM/data/paramecium_didinium.RData |only rEDM-1.5.0/rEDM/inst/doc/rEDM-tutorial.Rmd | 11 rEDM-1.5.0/rEDM/inst/doc/rEDM-tutorial.pdf |binary rEDM-1.5.0/rEDM/man/MakeBlock.Rd | 4 rEDM-1.5.0/rEDM/man/paramecium_didinium.Rd |only rEDM-1.5.0/rEDM/src/Embed.cpp | 18 rEDM-1.5.0/rEDM/src/Makevars | 2 rEDM-1.5.0/rEDM/src/Multiview.cpp | 8 rEDM-1.5.0/rEDM/src/RcppEDMCommon.cpp | 9 rEDM-1.5.0/rEDM/src/RcppEDMCommon.h | 5 rEDM-1.5.0/rEDM/src/cppEDM/src/API.cc |only rEDM-1.5.0/rEDM/src/cppEDM/src/API.h |only rEDM-1.5.0/rEDM/src/cppEDM/src/CCM.cc | 863 +++--------- rEDM-1.5.0/rEDM/src/cppEDM/src/CCM.h |only rEDM-1.5.0/rEDM/src/cppEDM/src/Common.cc | 94 - rEDM-1.5.0/rEDM/src/cppEDM/src/Common.h | 335 ---- rEDM-1.5.0/rEDM/src/cppEDM/src/DataFrame.h | 263 +-- rEDM-1.5.0/rEDM/src/cppEDM/src/DateTime.cc |only rEDM-1.5.0/rEDM/src/cppEDM/src/DateTime.h | 15 rEDM-1.5.0/rEDM/src/cppEDM/src/EDM.cc |only rEDM-1.5.0/rEDM/src/cppEDM/src/EDM.h |only rEDM-1.5.0/rEDM/src/cppEDM/src/EDM_Formatting.cc |only rEDM-1.5.0/rEDM/src/cppEDM/src/EDM_Neighbors.cc |only rEDM-1.5.0/rEDM/src/cppEDM/src/EDM_Neighbors.h |only rEDM-1.5.0/rEDM/src/cppEDM/src/Eval.cc | 415 ++--- rEDM-1.5.0/rEDM/src/cppEDM/src/Multiview.cc | 706 ++++------ rEDM-1.5.0/rEDM/src/cppEDM/src/Multiview.h |only rEDM-1.5.0/rEDM/src/cppEDM/src/Parameter.cc | 278 +--- rEDM-1.5.0/rEDM/src/cppEDM/src/Parameter.h | 142 -- rEDM-1.5.0/rEDM/src/cppEDM/src/SMap.cc | 389 +---- rEDM-1.5.0/rEDM/src/cppEDM/src/SMap.h |only rEDM-1.5.0/rEDM/src/cppEDM/src/Simplex.cc | 303 +--- rEDM-1.5.0/rEDM/src/cppEDM/src/Simplex.h |only rEDM-1.5.0/rEDM/src/cppEDM/src/Version.h | 3 rEDM-1.5.0/rEDM/src/cppEDM/src/makefile | 83 - rEDM-1.5.0/rEDM/src/cppEDM/src/makefile.mingw | 85 - rEDM-1.5.0/rEDM/src/cppEDM/src/makefile.windows | 71 - rEDM-1.5.0/rEDM/vignettes/rEDM-tutorial.Rmd | 11 rEDM-1.5.0/rEDM/vignettes/rEDM-tutorial.html | 1594 +++++++++++------------ 53 files changed, 2384 insertions(+), 3434 deletions(-)
More information about mrgsim.parallel at CRAN
Permanent link
Title: Hybrid Bayesian Networks Using R and JAGS
Description: Facilities for easy implementation of hybrid Bayesian networks
using R. Bayesian networks are directed acyclic graphs representing joint
probability distributions, where each node represents a random variable and
each edge represents conditionality. The full joint distribution is therefore
factorized as a product of conditional densities, where each node is assumed
to be independent of its non-descendents given information on its parent nodes.
Since exact, closed-form algorithms are computationally burdensome for inference
within hybrid networks that contain a combination of continuous and discrete
nodes, particle-based approximation techniques like Markov Chain Monte Carlo
are popular. We provide a user-friendly interface to constructing these networks
and running inference using the 'rjags' package. Econometric analyses (maximum
expected utility under competing policies, value of information) involving
decision and utility nodes are also supported.
Author: Jarrod E. Dalton <daltonj@ccf.org> and Benjamin Nutter
<benjamin.nutter@gmail.com>
Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>
Diff between HydeNet versions 0.10.10 dated 2020-05-15 and 0.10.11 dated 2020-07-06
DESCRIPTION | 6 MD5 | 26 +-- NAMESPACE | 1 R/bindPosterior.R | 47 ++--- R/chain.R | 4 R/cpt.R | 9 - R/plot.HydeNetwork.R | 22 +- inst/doc/DecisionNetworks.html | 260 +++++++++++++++++--------------- inst/doc/GettingStartedWithHydeNet.html | 38 ++-- inst/doc/HydeNetPlots.html | 4 inst/doc/WorkingWithHydeNetObjects.html | 6 man/bindSim.Rd | 2 man/chain.Rd | 4 tests/testthat/test-plot.HydeNetwork.R | 5 14 files changed, 227 insertions(+), 207 deletions(-)
Title: Automated Spectral Deconvolution, Alignment, and Metabolite
Identification in GC/MS-Based Untargeted Metabolomics
Description: Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. Outputs a table with compound names, matching scores and the integrated area of the compound for each sample. Package implementation is described in Domingo-Almenara et al. (2016) <doi:10.1021/acs.analchem.6b02927>.
Author: Xavier Domingo-Almenara [aut, cre, cph], Jasen P. Finch [ctb], Sara Samino [aut], Maria Vinaixa [aut], Alexandre Perera [aut, ths], Jesus Brezmes [aut, ths], Oscar Yanes [aut, ths]
Maintainer: Xavier Domingo-Almenara <xavier.domingoa@eurecat.org>
Diff between erah versions 1.1.0 dated 2018-07-11 and 1.1.1 dated 2020-07-06
erah-1.1.0/erah/inst/doc/eRahManual.pdf.asis |only erah-1.1.0/erah/vignettes/eRahManual.pdf.asis |only erah-1.1.1/erah/DESCRIPTION | 18 ++++---- erah-1.1.1/erah/MD5 | 55 +++++++++++++------------- erah-1.1.1/erah/R/MSimport.R | 16 ++++++- erah-1.1.1/erah/R/alignment.R | 4 - erah-1.1.1/erah/R/identification.R | 29 ++++++------- erah-1.1.1/erah/R/missingCompRecovery.R | 15 +++---- erah-1.1.1/erah/R/plotting.R | 13 ++++-- erah-1.1.1/erah/R/processing.R | 12 ++++- erah-1.1.1/erah/R/zzz.R | 2 erah-1.1.1/erah/build/vignette.rds |binary erah-1.1.1/erah/data/mslib.rda |binary erah-1.1.1/erah/inst/NEWS | 4 + erah-1.1.1/erah/inst/doc/eRahManual.Rnw |only erah-1.1.1/erah/inst/doc/eRahManual.pdf |binary erah-1.1.1/erah/man/alignComp.Rd | 2 erah-1.1.1/erah/man/computeRIerror.Rd | 6 +- erah-1.1.1/erah/man/createdt.Rd | 2 erah-1.1.1/erah/man/deconvolveComp.Rd | 4 - erah-1.1.1/erah/man/identifyComp.Rd | 2 erah-1.1.1/erah/man/newExp.Rd | 4 - erah-1.1.1/erah/man/plotAlign.Rd | 2 erah-1.1.1/erah/man/plotChr.Rd | 2 erah-1.1.1/erah/man/plotProfile.Rd | 2 erah-1.1.1/erah/man/plotSpectra.Rd | 2 erah-1.1.1/erah/man/recMissComp.Rd | 2 erah-1.1.1/erah/man/setAlPar.Rd | 2 erah-1.1.1/erah/man/setDecPar.Rd | 2 erah-1.1.1/erah/vignettes/eRahManual.Rnw |only erah-1.1.1/erah/vignettes/eem.pdf |only 31 files changed, 115 insertions(+), 87 deletions(-)
Title: Testing Neighbor Effects in Marker-Based Regressions
Description: To incorporate neighbor genotypic identity into genome-wide association studies, the package provides a set of functions for variation partitioning and association mapping. The theoretical background of the method is described in Sato et al. (2019) <doi:10.1101/845735>.
Author: Yasuhiro Sato [aut, cre] (<https://orcid.org/0000-0002-6466-723X>),
Eiji Yamamoto [aut],
Kentaro K. Shimizu [aut] (<https://orcid.org/0000-0002-6483-1781>),
Atsushi J. Nagano [aut] (<https://orcid.org/0000-0001-7891-5049>)
Maintainer: Yasuhiro Sato <sato.yasuhiro.36c@kyoto-u.jp>
Diff between rNeighborGWAS versions 1.0.0 dated 2020-04-15 and 1.2.0 dated 2020-07-06
DESCRIPTION | 16 +-- MD5 | 58 +++++++----- NAMESPACE | 2 R/calc_PVEnei.R | 71 ++++++-------- R/delta_PVE.R | 7 - R/gaston2neiGWAS.R |only R/min_dist.R | 34 +++++-- R/neiGWAS.R | 52 +++++----- R/nei_coval.R | 90 ++++++++++++------ R/nei_lmm.R |only R/nei_simu.R | 18 ++- R/qtl_pheno_simu.R | 35 ++++--- R/rNeighborGWAS-package.R | 2 R/w.R | 11 +- README.md |only inst/doc/rNeighborGWAS.R | 69 +++++++++++--- inst/doc/rNeighborGWAS.Rmd | 207 ++++++++++++++++++++++++++----------------- inst/doc/rNeighborGWAS.html | 178 ++++++++++++++++++++++++------------ man/calc_PVEnei.Rd | 14 +- man/delta_PVE.Rd | 2 man/gaston2neiGWAS.Rd |only man/min_dist.Rd | 4 man/neiGWAS.Rd | 8 - man/nei_coval.Rd | 18 ++- man/nei_lmm.Rd |only man/nei_simu.Rd | 10 +- man/qtl_pheno_simu.Rd | 26 ++--- man/rNeighborGWAS-package.Rd | 2 man/w.Rd | 4 tests |only vignettes/rNeighborGWAS.Rmd | 207 ++++++++++++++++++++++++++----------------- 31 files changed, 708 insertions(+), 437 deletions(-)
Title: Tables, Labels and Some Useful Functions from Spreadsheets and
'SPSS' Statistics
Description: Package computes and displays tables with support for 'SPSS'-style
labels, multiple and nested banners, weights, multiple-response variables
and significance testing. There are facilities for nice output of tables
in 'knitr', 'Shiny', '*.xlsx' files, R and 'Jupyter' notebooks. Methods
for labelled variables add value labels support to base R functions and to
some functions from other packages. Additionally, the package brings
popular data transformation functions from 'SPSS' Statistics and 'Excel':
'RECODE', 'COUNT', 'COMPUTE', 'DO IF', 'COUNTIF', 'VLOOKUP' and etc.
These functions are very useful for data processing in marketing research
surveys. Package intended to help people to move data
processing from 'Excel' and 'SPSS' to R.
Author: Gregory Demin [aut, cre],
Sebastian Jeworutzki [ctb] (<https://orcid.org/0000-0002-2671-5253>)
Maintainer: Gregory Demin <gdemin@gmail.com>
Diff between expss versions 0.10.2 dated 2020-03-25 and 0.10.5 dated 2020-07-06
DESCRIPTION | 8 MD5 | 210 NAMESPACE | 2 NEWS | 355 R/S3_methods.R | 916 R/add_rows.R | 351 R/as_hux.R | 65 R/caption.R | 15 R/compute.R | 22 R/criteria_functions.R | 14 R/custom_tables.R | 2 R/expss_options.R | 351 R/fctr.R | 12 R/html_datatable.R | 11 R/html_table.R | 1077 - R/labels.R | 17 R/selectors.R | 4 R/vlookup.R | 722 R/write_labelled.R | 3 build/vignette.rds |binary inst/doc/examples.R | 636 inst/doc/examples.html |16242 ++++++++--------- inst/doc/labels-support.R | 266 inst/doc/labels-support.html | 1384 - inst/doc/tables-with-labels.R | 950 inst/doc/tables-with-labels.html |12198 ++++++------ inst/doc/xlsx-export.R | 146 inst/doc/xlsx-export.html | 1526 - man/add_rows.Rd | 9 man/as.datatable_widget.Rd | 8 man/compute.Rd | 22 man/criteria.Rd | 14 man/fctr.Rd | 12 man/htmlTable.etable.Rd | 117 man/reexports.Rd | 6 man/tables.Rd | 2 man/var_lab.Rd | 5 man/vars.Rd | 4 man/write_labelled_csv.Rd | 2 tests/testthat.R | 12 tests/testthat/rds/as_hux1.rds |binary tests/testthat/rds/as_hux10.rds |binary tests/testthat/rds/as_hux11.rds |binary tests/testthat/rds/as_hux12.rds |binary tests/testthat/rds/as_hux12single.rds |binary tests/testthat/rds/as_hux12single2.rds |binary tests/testthat/rds/as_hux13.rds |binary tests/testthat/rds/as_hux14.rds |binary tests/testthat/rds/as_hux14_2.rds |binary tests/testthat/rds/as_hux15.rds |binary tests/testthat/rds/as_hux16.rds |binary tests/testthat/rds/as_hux17.rds |binary tests/testthat/rds/as_hux18.rds |binary tests/testthat/rds/as_hux19.rds |binary tests/testthat/rds/as_hux1_caption.rds |binary tests/testthat/rds/as_hux2.rds |binary tests/testthat/rds/as_hux2empty1.rds |binary tests/testthat/rds/as_hux2single1.rds |binary tests/testthat/rds/as_hux3_no_rowgroups_caption.rds |binary tests/testthat/rds/cro_mean_out.txt | 14 tests/testthat/rds/htmlTable1.rds |binary tests/testthat/rds/htmlTable10.rds |binary tests/testthat/rds/htmlTable11.rds |binary tests/testthat/rds/htmlTable12.rds |binary tests/testthat/rds/htmlTable12_no_rowgroups.rds |binary tests/testthat/rds/htmlTable12single.rds |binary tests/testthat/rds/htmlTable12single2.rds |binary tests/testthat/rds/htmlTable13.rds |binary tests/testthat/rds/htmlTable13_1.rds |binary tests/testthat/rds/htmlTable14.rds |binary tests/testthat/rds/htmlTable14_1.rds |binary tests/testthat/rds/htmlTable14_2.rds |binary tests/testthat/rds/htmlTable14_3.rds |binary tests/testthat/rds/htmlTable15.rds |binary tests/testthat/rds/htmlTable16.rds |binary tests/testthat/rds/htmlTable17.rds |binary tests/testthat/rds/htmlTable18.rds |binary tests/testthat/rds/htmlTable19.rds |binary tests/testthat/rds/htmlTable1_caption.rds |binary tests/testthat/rds/htmlTable1_list.rds |binary tests/testthat/rds/htmlTable1_list_norogroups.rds |binary tests/testthat/rds/htmlTable2.rds |binary tests/testthat/rds/htmlTable20.rds |binary tests/testthat/rds/htmlTable21.rds |binary tests/testthat/rds/htmlTable2empty1.rds |binary tests/testthat/rds/htmlTable2single1.rds |binary tests/testthat/rds/htmlTable3.rds |binary tests/testthat/rds/htmlTable3_no_rowgroups.rds |binary tests/testthat/rds/htmlTable3_no_rowgroups_caption.rds |binary tests/testthat/rds/print_etable.txt | 46 tests/testthat/rds/print_etable_2.txt | 92 tests/testthat/rds/print_etable_custom_label.txt | 46 tests/testthat/rds/print_etable_digits2.txt | 46 tests/testthat/rds/print_etable_digits2_2.txt | 92 tests/testthat/rds/print_etable_raw.txt | 36 tests/testthat/rds/print_etable_rnotebook.txt | 410 tests/testthat/rds/print_etable_rnotebook_caption.txt | 207 tests/testthat/rds/print_etable_single_column.txt | 40 tests/testthat/rds/print_etable_unrounded.txt | 46 tests/testthat/rds/print_etable_unrounded2.txt | 92 tests/testthat/rds/print_etable_zero.txt | 2 tests/testthat/rds/print_etable_zero_columns.txt | 2 tests/testthat/rds/print_etable_zero_rows.txt | 12 tests/testthat/test_huxtable.R | 49 tests/testthat/test_labels.R | 13 tests/testthat/test_split_labels.R | 720 106 files changed, 19857 insertions(+), 19826 deletions(-)
Title: Data Science for Psychologists
Description: All datasets and functions required for the examples and exercises of the book "Data Science for Psychologists" (by Hansjoerg Neth, Konstanz University, 2020), available at <https://bookdown.org/hneth/ds4psy/>. The book and course introduce principles and methods of data science to students of psychology and other biological or social sciences. The 'ds4psy' package primarily provides datasets, but also functions for data generation and manipulation (e.g., of text and time data) and graphics that are used in the book and its exercises. All functions included in 'ds4psy' are designed to be instructive and entertaining, rather than elegant or efficient.
Author: Hansjoerg Neth [aut, cre] (<https://orcid.org/0000-0001-5427-3141>)
Maintainer: Hansjoerg Neth <h.neth@uni.kn>
Diff between ds4psy versions 0.3.0 dated 2020-06-15 and 0.4.0 dated 2020-07-06
DESCRIPTION | 10 MD5 | 129 ++++--- NAMESPACE | 3 NEWS.md | 111 ++---- R/data.R | 430 ++++++++++++++++--------- R/data_fun.R | 79 +++- R/plot_fun.R | 19 - R/text_fun.R | 18 - R/time_fun.R | 824 ++++++++++++++++++++++++++++++++++++++++++++----- R/util_fun.R | 22 - README.md | 239 +++----------- data/dt_10.rda |only data/exp_num_dt.rda |only data/fruits.rda |binary inst/CITATION | 4 inst/WORDLIST | 12 inst/doc/ds4psy.R | 2 inst/doc/ds4psy.Rmd | 4 inst/doc/ds4psy.html | 294 ++--------------- man/Bushisms.Rd | 2 man/Trumpisms.Rd | 2 man/change_time.Rd |only man/change_tz.Rd |only man/countries.Rd | 2 man/cur_date.Rd | 35 +- man/cur_time.Rd | 27 + man/data_1.Rd | 2 man/data_2.Rd | 2 man/data_t1.Rd | 2 man/data_t1_de.Rd | 2 man/data_t1_tab.Rd | 2 man/data_t2.Rd | 2 man/data_t3.Rd | 2 man/data_t4.Rd | 2 man/dt_10.Rd |only man/exp_num_dt.Rd |only man/exp_wide.Rd | 2 man/falsePosPsy_all.Rd | 2 man/fame.Rd | 2 man/flowery.Rd | 2 man/fruits.Rd | 2 man/is.wholenumber.Rd | 12 man/is_leap_year.Rd |only man/outliers.Rd | 2 man/pi_100k.Rd | 2 man/plot_n.Rd | 17 - man/posPsy_AHI_CESD.Rd | 2 man/posPsy_long.Rd | 2 man/posPsy_p_info.Rd | 2 man/posPsy_wide.Rd | 2 man/sample_date.Rd | 2 man/sample_time.Rd | 43 ++ man/t3.Rd | 2 man/t4.Rd | 2 man/t_1.Rd | 2 man/t_2.Rd | 2 man/t_3.Rd | 2 man/t_4.Rd | 2 man/table6.Rd | 2 man/table7.Rd | 2 man/table8.Rd | 2 man/tb.Rd | 6 man/what_date.Rd | 66 +++ man/what_day.Rd | 23 - man/what_month.Rd | 12 man/what_time.Rd | 53 ++- man/what_week.Rd | 21 - man/what_year.Rd | 10 vignettes/ds4psy.Rmd | 4 69 files changed, 1674 insertions(+), 919 deletions(-)
Title: Clustering of Weighted Data
Description: Clusters state sequences and weighted data. It provides an optimized weighted PAM algorithm as well as functions for aggregating replicated cases, computing cluster quality measures for a range of clustering solutions and plotting clusters of state sequences.
Author: Matthias Studer [aut, cre]
Maintainer: Matthias Studer <matthias.studer@unige.ch>
Diff between WeightedCluster versions 1.4 dated 2019-03-21 and 1.4-1 dated 2020-07-06
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 6 ++++++ R/clusterquality.R | 2 +- build/vignette.rds |binary inst/doc/WeightedCluster.pdf |binary inst/doc/WeightedClusterFR.pdf |binary inst/doc/WeightedClusterPreview.pdf |binary src/init.c | 4 ++-- 9 files changed, 21 insertions(+), 15 deletions(-)
More information about WeightedCluster at CRAN
Permanent link
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
<doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou,
Nathan Russell, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 1.0.4.6 dated 2020-04-09 and 1.0.5 dated 2020-07-06
ChangeLog | 836 ++++++++++++++++------------- DESCRIPTION | 13 MD5 | 60 +- R/Rcpp.package.skeleton.R | 11 README.md | 38 - build/vignette.rds |binary inst/NEWS.Rd | 40 + inst/bib/Rcpp.bib | 72 ++ inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-jss-2011.pdf |binary inst/doc/Rcpp-libraries.Rnw |only inst/doc/Rcpp-libraries.pdf |only inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.pdf |binary inst/include/Rcpp/DataFrame.h | 2 inst/include/Rcpp/String.h | 9 inst/include/Rcpp/config.h | 8 inst/include/Rcpp/exceptions.h | 4 inst/include/Rcpp/macros/debug.h | 36 - inst/include/Rcpp/macros/macros.h | 19 inst/include/Rcpp/sugar/functions/sample.h | 4 inst/include/RcppCommon.h | 19 inst/tinytest/test_exceptions.R | 2 src/api.cpp | 8 tests/tinytest.R | 8 vignettes/Rcpp-libraries.Rnw |only vignettes/pdf/Rcpp-jss-2011.pdf |binary vignettes/pdf/Rcpp-libraries.pdf |only 33 files changed, 707 insertions(+), 482 deletions(-)
Title: Parsing Command-Line Arguments and Simple Variable Interpolation
Description: This is a command-line argument parser which wraps the
powerful Perl module Getopt::Long and with some adaptations for easier use
in R. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between GetoptLong versions 1.0.1 dated 2020-07-05 and 1.0.2 dated 2020-07-06
DESCRIPTION | 8 +++---- MD5 | 12 +++++----- inst/doc/GetoptLong.R | 39 ++++++++++++++++++++++++++--------- inst/doc/GetoptLong.Rmd | 39 ++++++++++++++++++++++++++--------- inst/doc/GetoptLong.html | 12 +++++----- inst/doc/variable_interpolation.html | 10 ++++---- vignettes/GetoptLong.Rmd | 39 ++++++++++++++++++++++++++--------- 7 files changed, 111 insertions(+), 48 deletions(-)
Title: Low-Level R to Java Interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
Author: Simon Urbanek <simon.urbanek@r-project.org>
Maintainer: Simon Urbanek <simon.urbanek@r-project.org>
Diff between rJava versions 0.9-12 dated 2020-03-24 and 0.9-13 dated 2020-07-06
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Title: Bayesian Network Meta-Analysis using 'JAGS'
Description: Network meta-analyses using Bayesian framework following Dias et al. (2013) <DOI:10.1177/0272989X12458724>. Based on the data input, creates prior, model file, and initial values needed to run models in 'rjags'. Able to handle binomial, normal and multinomial arm-based data. Can handle multi-arm trials and includes methods to incorporate covariate and baseline risk effects. Includes standard diagnostics and visualization tools to evaluate the results.
Author: Michael Seo [aut, cre],
Christopher Schmid [aut]
Maintainer: Michael Seo <swj8874@gmail.com>
Diff between bnma versions 1.1.2 dated 2020-04-26 and 1.2.0 dated 2020-07-06
DESCRIPTION | 7 MD5 | 19 +- NEWS.md | 5 R/network.rjags.R | 20 ++ R/network.summary.R | 241 ++++++++++++++++-------------- inst/CITATION |only inst/doc/my-vignette.html | 328 +++++++++++++++++++++--------------------- man/network.autocorr.diag.Rd | 2 man/network.forest.plot.Rd | 5 man/network.gelman.diag.Rd | 4 man/relative.effects.table.Rd | 2 11 files changed, 337 insertions(+), 296 deletions(-)
Title: Interface to the 'SymEngine' Library
Description: Provides an R interface to 'SymEngine' <https://github.com/symengine/>,
a standalone 'C++' library for fast symbolic manipulation. The package has functionalities
for symbolic computation like calculating exact mathematical expressions, solving
systems of linear equations and code generation.
Author: Jialin Ma [cre, aut],
Isuru Fernando [aut],
Xin Chen [aut]
Maintainer: Jialin Ma <marlin@inventati.org>
Diff between symengine versions 0.1.3 dated 2020-05-07 and 0.1.5 dated 2020-07-06
DESCRIPTION | 6 - MD5 | 41 +++++----- R/language_conversion.R | 28 +++--- R/matrix.R | 4 configure | 11 ++ src/Makevars.in | 2 src/upstream/CMakeLists.txt | 16 +-- src/upstream/CMakeLists.txt.orig | 16 +-- src/upstream/symengine/CMakeLists.txt | 1 src/upstream/symengine/cwrapper.cpp | 4 src/upstream/symengine/diophantine.cpp | 3 src/upstream/symengine/expand.cpp | 2 src/upstream/symengine/functions.cpp | 2 src/upstream/symengine/ntheory.cpp | 2 src/upstream/symengine/parser/parser.cpp | 13 ++- src/upstream/symengine/polys/basic_conversions.h | 10 +- src/upstream/symengine/utilities/matchpycpp/autogen_tests/CMakeLists.txt | 5 + src/upstream/symengine/utilities/matchpycpp/generate_tests.py | 5 + tests/testthat/test-matrix.R | 9 ++ tests/testthat/test-solve.R |only tests/testthat/test-vecbasic_s4bindings.R | 9 ++ tools/bundle_symengine_source.sh | 3 22 files changed, 121 insertions(+), 71 deletions(-)
Title: Easily Install and Load the 'mlr3' Package Family
Description: The 'mlr3' package family is a set of packages for
machine-learning purposes built in a modular fashion. This wrapper
package is aimed to simplify the installation and loading of the core
'mlr3' packages. Get more information about the 'mlr3' project at
<https://mlr3book.mlr-org.com/>.
Author: Patrick Schratz [cre, aut] (<https://orcid.org/0000-0003-0748-6624>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between mlr3verse versions 0.1.1 dated 2020-01-19 and 0.1.3 dated 2020-07-06
DESCRIPTION | 14 ++-- MD5 | 13 ++- NAMESPACE | 25 +++---- NEWS.md | 15 +++- R/mlr3verse_info.R | 2 R/zzz.R | 26 ++++--- README.md | 174 ++++++++++++++++++++++++++--------------------------- inst |only 8 files changed, 139 insertions(+), 130 deletions(-)
Title: Linear Mixed Models
Description: It implements Expectation/Conditional Maximization Either (ECME)
and rapidly converging algorithms as well as
Bayesian inference for linear mixed models,
which is described in Schafer, J.L. (1998)
"Some improved procedures for linear mixed models".
Dept. of Statistics, The Pennsylvania State University.
Author: Original by Joseph L. Schafer
Maintainer: Jing hua Zhao <jinghuazhao@hotmail.com>
Diff between lmm versions 1.2 dated 2018-06-30 and 1.3 dated 2020-07-06
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/lmm-tr.pdf |binary src/package_native_routine_registration_skeleton.c | 18 +++++++++--------- 6 files changed, 26 insertions(+), 18 deletions(-)
Title: Fast Row by Row Data Processing Tool, Using 'Sailr' Script
Description: A fast row by row data processing tool. You can write data processing code in 'Sailr' scripting language which is specially intended for data manipulation. The package uses 'libsailr' (C/C++ library) for its 'Sailr' code parsing and its execution.
Author: Toshihiro Umehara [aut, cre],
Troy Hanson [cph, ctb] (uthash),
Howard Hinnant [cph, ctb] (date.h),
Adrian Colomitchi [cph, ctb] (date.h),
Florian Dang [cph, ctb] (date.h),
Paul Thompson [cph, ctb] (date.h),
Tomasz Kamiński [cph, ctb] (date.h),
Nemanja Trifunovic [cph, ctb] (utfcpp),
Kim Grasman [cph, ctb] (getopt_port),
Jon Clayden [cph, ctb] (ore package),
K.Kosako [cph, ctb] (onigmo author),
K.Takata [cph, ctb] (onigmo author),
Byte [cph, ctb] (onigmo contributor),
KUBO Takehiro [cph, ctb] (onigmo contributor),
Free Software Foundation, Inc [cph],
X Consortium [cph]
Maintainer: Toshihiro Umehara <toshi@niceume.com>
Diff between datasailr versions 0.8.4 dated 2020-06-25 and 0.8.5 dated 2020-07-06
DESCRIPTION | 10 ++++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ configure | 53 ++++++++++++++++++++++++++++++++++++++--------------- configure.ac | 37 ++++++++++++++++++++++++++++++------- 5 files changed, 83 insertions(+), 30 deletions(-)
Title: Find, Download and Process Sentinel-2 Data
Description: Functions to download Sentinel-2 optical images
and perform preliminary processing operations.
'sen2r' provides the instruments required to easily perform
(and eventually automate) the steps necessary to build a complete
Sentinel-2 processing chain.
A Graphical User Interface to facilitate data processing is also provided.
For additional documentation refer to the following article:
Ranghetti et al. (2020) <doi:10.1016/j.cageo.2020.104473>.
Author: Luigi Ranghetti [aut, cre] (<https://orcid.org/0000-0001-6207-5188>),
Lorenzo Busetto [aut] (<https://orcid.org/0000-0001-9634-6038>)
Maintainer: Luigi Ranghetti <luigi@ranghetti.info>
Diff between sen2r versions 1.3.6 dated 2020-06-04 and 1.3.7 dated 2020-07-06
DESCRIPTION | 8 MD5 | 139 ++++++------- NEWS.md | 19 + R/calcindex.R | 2 R/check_param_list.R | 5 R/check_sen2r_deps.R | 28 +- R/compute_s2_paths.R | 112 +++++----- R/create_indices_db.R | 40 +++ R/gdalwarp_grid.R | 4 R/gipp.R | 11 - R/s2_calcindices.R | 13 - R/s2_defNA.R | 4 R/s2_download.R | 8 R/s2_gui.R | 311 ++++++++++++++++++------------ R/s2_list.R | 2 R/s2_mask.R | 6 R/s2_merge.R | 11 - R/s2_order.R | 2 R/s2_rgb.R | 10 R/s2_thumbnails.R | 38 ++- R/s2_translate.R | 9 R/safe_getMetadata.R | 12 - R/safe_shortname.R | 2 R/sen2r.R | 79 +++---- R/str_pad2.R | 3 inst/WORDLIST | 4 inst/doc/installation.R | 20 + inst/doc/installation.Rmd | 131 ++++++------ inst/doc/installation.html | 135 +++++-------- inst/doc/outstructure.Rmd | 56 +++++ inst/doc/outstructure.html | 58 +++++ inst/doc/sen2r_gui.html | 10 inst/extdata/palettes/WVP.cpt |only inst/extdata/palettes/bw.cpt |only inst/extdata/settings/indices.json | 40 +++ inst/www/images/irea_logo.png |only man/compute_s2_paths.Rd | 5 man/figures/sen2r_gui_sheet1.png |binary man/figures/sen2r_gui_sheet1_small.png |binary man/figures/sen2r_gui_sheet2.png |binary man/figures/sen2r_gui_sheet2_small.png |binary man/figures/sen2r_gui_sheet3.png |binary man/figures/sen2r_gui_sheet3_small.png |binary man/figures/sen2r_gui_sheet4.png |binary man/figures/sen2r_gui_sheet4_small.png |binary man/figures/sen2r_gui_sheet5.png |binary man/figures/sen2r_gui_sheet5_small.png |binary man/gdalwarp_grid.Rd | 13 + man/s2_calcindices.Rd | 8 man/s2_rgb.Rd | 7 man/s2_thumbnails.Rd | 7 man/stack2rgb.Rd | 4 man/str_pad2.Rd | 3 tests/testthat/setup-commons.R |only tests/testthat/setup-scihub_creds.R |only tests/testthat/test-s2_calcindices.R | 3 tests/testthat/test-s2_download.R | 11 - tests/testthat/test-s2_list.R | 42 +--- tests/testthat/test-s2_mask.R | 1 tests/testthat/test-s2_order.R | 18 - tests/testthat/test-s2_rgb.R | 2 tests/testthat/test-safelist-class.R | 3 tests/testthat/test-scihub_login.R | 7 tests/testthat/test-sen2cor.R | 2 tests/testthat/test-sen2r-00_connection.R | 3 tests/testthat/test-sen2r-01_merge.R | 10 tests/testthat/test-sen2r-02_warp.R | 82 ++++--- tests/testthat/test-sen2r-03_mask.R | 66 ++++-- tests/testthat/test-sen2r-04_indices.R | 6 tests/testthat/test-sen2r-05_rgb.R | 6 tests/testthat/test-sen2r-06_ignorelist.R | 6 vignettes/installation.Rmd | 131 ++++++------ vignettes/outstructure.Rmd | 56 +++++ 73 files changed, 1135 insertions(+), 699 deletions(-)
Title: Non-Negative Garrote Estimation with Penalized Initial
Estimators
Description: Functions to compute the non-negative garrote estimator as
proposed by Breiman (1995) <https://www.jstor.org/stable/1269730>
with the penalized initial estimators extension as proposed by
Yuan and Lin (2007) <https://www.jstor.org/stable/4623260>.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Stefan Van Aelst <stefan.vanaelst@kuleuven.be>,
Ruben Zamar <ruben@stat.ubc.ca>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between nnGarrote versions 1.0.2 dated 2020-03-16 and 1.0.3 dated 2020-07-06
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 3 +++ R/coef.nnGarrote.R | 3 +-- R/nnGarrote.R | 3 +-- R/predict.nnGarrote.R | 3 +-- README.md | 2 +- man/coef.nnGarrote.Rd | 3 +-- man/nnGarrote.Rd | 3 +-- man/predict.nnGarrote.Rd | 3 +-- 10 files changed, 23 insertions(+), 26 deletions(-)
Title: Decipher Mutational Signatures from Somatic Mutational Catalogs
Description: Cancer cells accumulate DNA mutations as result of DNA damage and DNA repair processes. This computational framework is aimed at deciphering DNA mutational signatures operating in cancer. The framework includes modules that support raw data import and processing, mutational signature extraction, and results interpretation and visualization. The framework accepts widely used file formats storing information about DNA variants, such as Variant Call Format files. The framework performs Non-Negative Matrix Factorization to extract mutational signatures explaining the observed set of DNA mutations. Bootstrapping is performed as part of the analysis. The framework supports parallelization and is optimized for use on multi-core systems. The software is based on a custom R-based implementation of the original MATLAB WTSI framework by Alexandrov LB et al (2013) <doi:10.1016/j.celrep.2012.12.008>.
Author: Damiano Fantini, Vania Vidimar, Joshua J Meeks
Maintainer: Damiano Fantini <damiano.fantini@gmail.com>
Diff between mutSignatures versions 1.2 dated 2017-01-24 and 2.0.1 dated 2020-07-06
mutSignatures-1.2/mutSignatures/R/addWeak.R |only mutSignatures-1.2/mutSignatures/R/bootstrapCancerGenomes.R |only mutSignatures-1.2/mutSignatures/R/citation.R |only mutSignatures-1.2/mutSignatures/R/decipherMutationalProcesses.R |only mutSignatures-1.2/mutSignatures/R/deconvoluteMutCounts.R |only mutSignatures-1.2/mutSignatures/R/do.nmf.R |only mutSignatures-1.2/mutSignatures/R/evaluateStability.R |only mutSignatures-1.2/mutSignatures/R/extractSignatures.R |only mutSignatures-1.2/mutSignatures/R/filterOutIterations.R |only mutSignatures-1.2/mutSignatures/R/getTestRunArgs.R |only mutSignatures-1.2/mutSignatures/R/leadZeros.R |only mutSignatures-1.2/mutSignatures/R/mutSignatures-internal.R |only mutSignatures-1.2/mutSignatures/R/plotSignatureExposures.R |only mutSignatures-1.2/mutSignatures/R/removeWeak.R |only mutSignatures-1.2/mutSignatures/R/setMutClusterParams.R |only mutSignatures-1.2/mutSignatures/R/setMutCountObject.R |only mutSignatures-1.2/mutSignatures/R/silhouetteMLB.R |only mutSignatures-1.2/mutSignatures/man/citation.Rd |only mutSignatures-1.2/mutSignatures/man/do.nmf.Rd |only mutSignatures-1.2/mutSignatures/man/plotSignatureExposures.Rd |only mutSignatures-1.2/mutSignatures/man/setMutCountObject.Rd |only mutSignatures-2.0.1/mutSignatures/DESCRIPTION | 25 +- mutSignatures-2.0.1/mutSignatures/MD5 | 114 ++++++---- mutSignatures-2.0.1/mutSignatures/NAMESPACE | 102 ++++++++ mutSignatures-2.0.1/mutSignatures/R/s01_all_classes.R |only mutSignatures-2.0.1/mutSignatures/R/s02_all_methods.R |only mutSignatures-2.0.1/mutSignatures/R/s03_all_functions.R |only mutSignatures-2.0.1/mutSignatures/R/s04_all_extra.R |only mutSignatures-2.0.1/mutSignatures/build |only mutSignatures-2.0.1/mutSignatures/data |only mutSignatures-2.0.1/mutSignatures/inst |only mutSignatures-2.0.1/mutSignatures/man/addWeak.Rd | 64 ++--- mutSignatures-2.0.1/mutSignatures/man/alexaNMF.Rd |only mutSignatures-2.0.1/mutSignatures/man/as.data.frame-mutSignExposures-method.Rd |only mutSignatures-2.0.1/mutSignatures/man/as.data.frame-mutationCounts-method.Rd |only mutSignatures-2.0.1/mutSignatures/man/as.data.frame-mutationSignatures-method.Rd |only mutSignatures-2.0.1/mutSignatures/man/as.list-mutFrameworkParams-method.Rd |only mutSignatures-2.0.1/mutSignatures/man/as.list-mutationSignatures-method.Rd |only mutSignatures-2.0.1/mutSignatures/man/as.matrix-mutationCounts-method.Rd |only mutSignatures-2.0.1/mutSignatures/man/as.mutation.counts.Rd |only mutSignatures-2.0.1/mutSignatures/man/as.mutation.signatures.Rd |only mutSignatures-2.0.1/mutSignatures/man/as.mutsign.exposures.Rd |only mutSignatures-2.0.1/mutSignatures/man/attachContext.Rd |only mutSignatures-2.0.1/mutSignatures/man/attachMutType.Rd |only mutSignatures-2.0.1/mutSignatures/man/bootstrapCancerGenomes.Rd | 54 +++- mutSignatures-2.0.1/mutSignatures/man/cbind2.Rd |only mutSignatures-2.0.1/mutSignatures/man/chihJenNMF.Rd |only mutSignatures-2.0.1/mutSignatures/man/coerceObj-methods.Rd |only mutSignatures-2.0.1/mutSignatures/man/countMutTypes.Rd |only mutSignatures-2.0.1/mutSignatures/man/custom_cssls.Rd |only mutSignatures-2.0.1/mutSignatures/man/custom_fcnnls.Rd |only mutSignatures-2.0.1/mutSignatures/man/decipherMutationalProcesses.Rd | 55 +++- mutSignatures-2.0.1/mutSignatures/man/deconvoluteMutCounts.Rd | 58 +++-- mutSignatures-2.0.1/mutSignatures/man/evaluateStability.Rd | 60 +++-- mutSignatures-2.0.1/mutSignatures/man/extractSignatures.Rd | 62 +++-- mutSignatures-2.0.1/mutSignatures/man/extractXvarlinkData.Rd |only mutSignatures-2.0.1/mutSignatures/man/filterOutIterations.Rd | 57 ++--- mutSignatures-2.0.1/mutSignatures/man/filterSNV.Rd |only mutSignatures-2.0.1/mutSignatures/man/frequencize.Rd |only mutSignatures-2.0.1/mutSignatures/man/getCosmicSignatures.Rd |only mutSignatures-2.0.1/mutSignatures/man/getCounts.Rd |only mutSignatures-2.0.1/mutSignatures/man/getFwkParam.Rd |only mutSignatures-2.0.1/mutSignatures/man/getMutationTypes.Rd |only mutSignatures-2.0.1/mutSignatures/man/getSampleIdentifiers.Rd |only mutSignatures-2.0.1/mutSignatures/man/getSignatureIdentifiers.Rd |only mutSignatures-2.0.1/mutSignatures/man/getTestRunArgs.Rd | 41 ++- mutSignatures-2.0.1/mutSignatures/man/importVCFfiles.Rd |only mutSignatures-2.0.1/mutSignatures/man/leadZeros.Rd | 60 +++-- mutSignatures-2.0.1/mutSignatures/man/matchSignatures.Rd |only mutSignatures-2.0.1/mutSignatures/man/msigPlot.Rd |only mutSignatures-2.0.1/mutSignatures/man/mutFrameworkParams-class.Rd |only mutSignatures-2.0.1/mutSignatures/man/mutFrameworkParams-show.Rd |only mutSignatures-2.0.1/mutSignatures/man/mutSigData.Rd |only mutSignatures-2.0.1/mutSignatures/man/mutSignExposures-class.Rd |only mutSignatures-2.0.1/mutSignatures/man/mutSignExposures-show.Rd |only mutSignatures-2.0.1/mutSignatures/man/mutSignatures-package.Rd | 46 ++-- mutSignatures-2.0.1/mutSignatures/man/mutationCounts-class.Rd |only mutSignatures-2.0.1/mutSignatures/man/mutationCounts-show.Rd |only mutSignatures-2.0.1/mutSignatures/man/mutationSignatures-class.Rd |only mutSignatures-2.0.1/mutSignatures/man/mutationSignatures-show.Rd |only mutSignatures-2.0.1/mutSignatures/man/plotMutTypeProfile.Rd |only mutSignatures-2.0.1/mutSignatures/man/plotSignExposures.Rd |only mutSignatures-2.0.1/mutSignatures/man/prelimProcessAssess.Rd |only mutSignatures-2.0.1/mutSignatures/man/processVCFdata.Rd |only mutSignatures-2.0.1/mutSignatures/man/removeMismatchMut.Rd |only mutSignatures-2.0.1/mutSignatures/man/removeWeak.Rd | 55 +++- mutSignatures-2.0.1/mutSignatures/man/resolveMutSignatures.Rd |only mutSignatures-2.0.1/mutSignatures/man/revCompl.Rd |only mutSignatures-2.0.1/mutSignatures/man/setFwkParam.Rd |only mutSignatures-2.0.1/mutSignatures/man/setMutClusterParams.Rd | 105 ++++++--- mutSignatures-2.0.1/mutSignatures/man/silhouetteMLB.Rd | 48 ++-- mutSignatures-2.0.1/mutSignatures/man/simplifySignatures.Rd |only mutSignatures-2.0.1/mutSignatures/man/sortByMutations.Rd |only mutSignatures-2.0.1/mutSignatures/man/sub-mutSignExposures-numeric-method.Rd |only mutSignatures-2.0.1/mutSignatures/man/sub-mutationCounts-numeric-method.Rd |only mutSignatures-2.0.1/mutSignatures/man/sub-mutationSignatures-numeric-method.Rd |only mutSignatures-2.0.1/mutSignatures/man/table2df.Rd |only mutSignatures-2.0.1/mutSignatures/vignettes |only 98 files changed, 667 insertions(+), 339 deletions(-)
Title: Monotonic Optimal Binning
Description: Generate the monotonic binning and
perform the woe (weight of evidence) transformation for the logistic regression
used in the consumer credit scorecard development. The woe transformation is a piecewise
transformation that is linear to the log odds. For a numeric variable, all of its monotonic
functional transformations will converge to the same woe transformation.
Author: WenSui Liu
Maintainer: WenSui Liu <liuwensui@gmail.com>
Diff between mob versions 0.2.0 dated 2020-07-05 and 0.2.1 dated 2020-07-06
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 1 + R/kmn_bin.R | 3 ++- R/manual_bin.R | 1 - R/rng_bin.R | 3 ++- 6 files changed, 13 insertions(+), 11 deletions(-)
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Title: Import Surface Meteorological Data from NOAA Integrated Surface
Database (ISD)
Description: Functions to import data from more than 30,000 surface
meteorological sites around the world managed by the National Oceanic and Atmospheric Administration (NOAA) Integrated Surface
Database (ISD, see <https://www.ncdc.noaa.gov/isd>).
Author: David Carslaw [aut, cre]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between worldmet versions 0.8.8 dated 2020-02-12 and 0.9.0 dated 2020-07-06
DESCRIPTION | 14 - MD5 | 15 - NAMESPACE | 1 R/getMeta.R | 18 - R/metNOAA.R | 559 +++++++++++++++++++++++--------------------------- R/sysdata.rda |binary R/zzz.R |only data/weatherCodes.rda |binary man/importNOAA.Rd | 39 +-- 9 files changed, 309 insertions(+), 337 deletions(-)
Title: Adaptive Multivariate Integration over Hypercubes
Description: R wrappers around the cubature C library of Steven
G. Johnson for adaptive multivariate integration over hypercubes
and the Cuba C library of Thomas Hahn for deterministic and
Monte Carlo integration. Scalar and vector interfaces for
cubature and Cuba routines are provided; the vector interfaces
are highly recommended as demonstrated in the package
vignette.
Author: Balasubramanian Narasimhan [aut, cre],
Manuel Koller [ctb],
Steven G. Johnson [aut],
Thomas Hahn [aut],
Annie Bouvier [aut],
Kiên Kiêu [aut],
Simen Gaure [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.stanford.edu>
Diff between cubature versions 2.0.4 dated 2019-12-04 and 2.0.4.1 dated 2020-07-06
cubature-2.0.4.1/cubature/DESCRIPTION | 6 ++--- cubature-2.0.4.1/cubature/MD5 | 16 ++------------ cubature-2.0.4.1/cubature/cleanup |only cubature-2.0.4.1/cubature/src/Makevars | 5 ++-- cubature-2.0.4/cubature/src/Cuba-4.2/config.h |only cubature-2.0.4/cubature/src/Cuba-4.2/config.log |only cubature-2.0.4/cubature/src/Cuba-4.2/config.status |only cubature-2.0.4/cubature/src/Cuba-4.2/makefile |only cubature-2.0.4/cubature/src/Cuba-4.2/src/common/CSample.c |only cubature-2.0.4/cubature/src/Cuba-4.2/src/common/Fork.c |only cubature-2.0.4/cubature/src/Cuba-4.2/src/common/Global.c |only cubature-2.0.4/cubature/src/Cuba-4.2/src/common/Random.c |only cubature-2.0.4/cubature/src/Cuba-4.2/src/common/sock.h |only cubature-2.0.4/cubature/src/Cuba-4.2/src/common/stddecl.h |only cubature-2.0.4/cubature/src/Cuba-4.2/src/cuhre/common.c |only 15 files changed, 9 insertions(+), 18 deletions(-)
Title: Compact and Flexible Summaries of Data
Description: A simple to use summary function that can be used buttskyle96@gmail.comwith pipes
and displays nicely in the console. The default summary statistics may
be modified by the user as can the default formatting. Support for
data frames and vectors is included, and users can implement their own
skim methods for specific object types as described in a vignette.
Default summaries include support for inline spark graphs.
Instructions for managing these on specific operating systems are
given in the "Using skimr" vignette and the README.
Author: Elin Waring [cre, aut],
Michael Quinn [aut],
Amelia McNamara [aut],
Eduardo Arino de la Rubia [aut],
Hao Zhu [aut],
Julia Lowndes [ctb],
Shannon Ellis [aut],
Hope McLeod [ctb],
Hadley Wickham [ctb],
Kirill Müller [ctb],
RStudio, Inc. [cph] (Spark functions),
Connor Kirkpatrick [ctb],
Scott Brenstuhl [ctb],
Patrick Schratz [ctb],
lbusett [ctb],
Mikko Korpela [ctb],
Jennifer Thompson [ctb],
Harris McGehee [ctb],
Mark Roepke [ctb],
Patrick Kennedy [ctb],
Daniel Possenriede [ctb],
David Zimmermann [ctb],
Kyle Butts [ctb]
Maintainer: Elin Waring <elin.waring@gmail.com>
Diff between skimr versions 2.1.1 dated 2020-04-16 and 2.1.2 dated 2020-07-06
DESCRIPTION | 30 +- MD5 | 50 +-- NAMESPACE | 1 NEWS.md | 11 R/get_skimmers.R | 7 R/stats.R | 2 build/vignette.rds |binary inst/doc/Skimr_defaults.html | 9 inst/doc/Supporting_additional_objects.R | 58 --- inst/doc/Supporting_additional_objects.Rmd | 125 +++----- inst/doc/Supporting_additional_objects.html | 268 +++++++++--------- inst/doc/Using_fonts.html | 2 inst/doc/skimr.html | 28 + man/get_skimmers.Rd | 6 man/mutate.skim_df.Rd | 4 man/print.Rd | 6 man/reexports.Rd | 4 man/sfl.Rd | 2 tests/testthat/print/knit_print-old_knitr.txt |only tests/testthat/print/knit_print-summary-old_knitr.txt |only tests/testthat/print/knit_print-summary.txt | 2 tests/testthat/print/knit_print.txt | 2 tests/testthat/test-get_skimmers.R | 3 tests/testthat/test-skim.R | 41 ++ tests/testthat/test-skim_print.R | 17 - tests/testthat/test-stats.R | 4 vignettes/Supporting_additional_objects.Rmd | 125 +++----- 27 files changed, 415 insertions(+), 392 deletions(-)
Title: Interact with BioUML Server
Description: Functions for connecting to BioUML server, querying BioUML repository and launching BioUML analyses.
Author: Ivan Yevshin [aut, cre],
Tagir Valeev [aut]
Maintainer: Ivan Yevshin <ivan@dote.ru>
Diff between rbiouml versions 1.9 dated 2019-11-26 and 1.10 dated 2020-07-06
ChangeLog | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/biouml.R | 14 +++++++++++++- inst/doc/rbiouml.pdf |binary 5 files changed, 23 insertions(+), 9 deletions(-)
Title: Scale Mixture of Skew-Normal Linear Mixed Models
Description: It fits scale mixture of skew-normal linear mixed models using an expectation–maximization (EM) type algorithm, including some possibilities for modeling the within-subject dependence. Details can be found in Schumacher, Lachos and Matos (2020) <arXiv:2002.01040>.
Author: Fernanda L. Schumacher [aut, cre],
Larissa A. Matos [aut],
Victor H. Lachos [aut]
Maintainer: Fernanda L. Schumacher <fernandalschumacher@gmail.com>
Diff between skewlmm versions 0.2.0 dated 2020-05-15 and 0.2.1 dated 2020-07-06
DESCRIPTION | 8 ++-- MD5 | 14 ++++---- NAMESPACE | 3 + R/auxfunctions-sim.R | 46 ++++++++++++---------------- R/auxfunctions.R | 82 ++++++++++++++++++++++++++------------------------ R/mainfunctions-sim.R | 26 +++++++++++---- R/mainfunctions.R | 30 +++++++++++++----- R/residuals.R | 2 - 8 files changed, 120 insertions(+), 91 deletions(-)
Title: Phonetic Spelling Algorithms
Description: Provides a collection of phonetic algorithms including
Soundex, Metaphone, NYSIIS, Caverphone, and others.
Author: James Howard [aut, cre] (<https://orcid.org/0000-0003-4530-1547>),
Kyle Haynes [ctb],
Amanda Hood [ctb],
Os Keyes [ctb]
Maintainer: James Howard <jh@jameshoward.us>
Diff between phonics versions 1.3.2 dated 2019-06-21 and 1.3.6 dated 2020-07-06
DESCRIPTION | 21 ++++++----- MD5 | 36 +++++++++---------- README.md | 7 ++- build/vignette.rds |binary inst/CITATION | 4 +- inst/doc/phonics.R | 8 ++-- inst/doc/phonics.html | 91 +++++++++++++++++++++++++------------------------- man/caverphone.Rd | 18 ++++++--- man/cologne.Rd | 18 ++++++--- man/lein.Rd | 18 ++++++--- man/metaphone.Rd | 18 ++++++--- man/mra.Rd | 18 ++++++--- man/nysiis.Rd | 18 ++++++--- man/onca.Rd | 21 +++++++---- man/phonex.Rd | 18 ++++++--- man/phonics.Rd | 18 ++++++--- man/rogerroot.Rd | 18 ++++++--- man/soundex.Rd | 18 ++++++--- man/statcan.Rd | 18 ++++++--- 19 files changed, 231 insertions(+), 155 deletions(-)
Title: Bifactor Indices Calculator
Description: The calculator computes bifactor indices such as explained common variance (ECV), hierarchical Omega (OmegaH), percentage of uncontaminated correlations (PUC), item explained common variance (I-ECV), and more. This package is an R version of the 'Excel' based 'Bifactor Indices Calculator' (Dueber, 2017) <doi:10.13023/edp.tool.01> with added convenience features for directly utilizing output from several programs that can fit confirmatory factor analysis or item response models.
Author: David Dueber [aut, cre]
Maintainer: David Dueber <david.dueber@uky.edu>
Diff between BifactorIndicesCalculator versions 0.2.0 dated 2020-04-11 and 0.2.1 dated 2020-07-06
DESCRIPTION | 12 MD5 | 59 NAMESPACE | 3 R/BifactorIndices.R | 3 R/BifactorIndicesCalculator.R | 5 R/ECV_Indices.R | 538 ++--- R/Exploratory_BifactorIndices.R | 64 R/Omega_Indices.R | 224 +- R/Other_Indices.R | 370 +-- R/UtilityFunctions.R | 408 ++-- R/data.R | 54 build/partial.rdb |binary man/BifactorIndicesCalculator.Rd | 6 man/MTMM_data.Rd | 6 man/SRS_data.Rd | 6 man/bifactorIndices.Rd | 11 man/bifactorIndicesMplus.Rd | 8 man/bifactorIndicesMplus_ESEM.Rd | 12 man/bifactorIndicesMplus_expl.Rd |only man/bifactorIndices_expl.Rd | 5 tests/testthat.R | 8 tests/testthat/bifactorData.csv | 2014 ++++++++++----------- tests/testthat/bifactor_continuous_wrongfacvar.out | 570 ++--- tests/testthat/bifactor_efa.out | 700 +++---- tests/testthat/bifactor_esem.out | 1116 +++++------ tests/testthat/bifactor_esem_nostd.out | 688 +++---- tests/testthat/categorical.out | 1380 +++++++------- tests/testthat/continuous.out | 570 ++--- tests/testthat/exploratory_bindices_SRS_fixed.rds |binary tests/testthat/lav_indices.rds |binary tests/testthat/test-BifactorIndicesCalculator.R | 73 31 files changed, 4497 insertions(+), 4416 deletions(-)
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