Title: Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC; Dimitris Rizopoulos (2016) <doi:10.18637/jss.v072.i07>.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes versions 0.8-83 dated 2019-03-25 and 0.8-85 dated 2020-01-08
DESCRIPTION | 8 +-- MD5 | 16 +++--- R/aucJM.JMbayes.R | 87 +++++++++++++++----------------------- R/aucJM.coxph.R | 24 ++++++++-- R/jointModelBayes.R | 4 - R/mvJointModelBayes.R | 20 ++++---- R/prederrJM.coxph.R | 6 ++ R/supportFuns_mvJointModelBayes.R | 3 + man/JMbayes.Rd | 4 - 9 files changed, 90 insertions(+), 82 deletions(-)
Title: Weighted Mixed-Effects Models Using Multilevel Pseudo Maximum
Likelihood Estimation
Description: Run mixed-effects models that include weights at every level. The WeMix package fits a weighted mixed model, also known as a multilevel, mixed, or hierarchical linear model (HLM). The weights could be inverse selection probabilities, such as those developed for an education survey where schools are sampled probabilistically, and then students inside of those schools are sampled probabilistically. Although mixed-effects models are already available in R, WeMix is unique in implementing methods for mixed models using weights at multiple levels. Both linear and logit models are supported. Models may have up to three levels.
Author: Paul Bailey [aut, cre], Claire Kelley [aut], Trang Nguyen [aut], Huade Huo [aut], Christian Kjeldsen [ctb] (tests with TIMSS data).
Maintainer: Paul Bailey <pbailey@air.org>
Diff between WeMix versions 3.1.1 dated 2019-06-27 and 3.1.3 dated 2020-01-08
WeMix-3.1.1/WeMix/inst/doc/Introduction_to_Mixed_Effects_Models_With_WeMix.pdf |only WeMix-3.1.1/WeMix/inst/doc/Weighted_Linear_Mixed_Effects_Models.pdf |only WeMix-3.1.3/WeMix/DESCRIPTION | 10 WeMix-3.1.3/WeMix/MD5 | 18 - WeMix-3.1.3/WeMix/R/adaptiveQuad.R | 2 WeMix-3.1.3/WeMix/R/analyticSolve.R | 16 + WeMix-3.1.3/WeMix/R/helpers.R | 102 +++++----- WeMix-3.1.3/WeMix/build/vignette.rds |binary WeMix-3.1.3/WeMix/inst/NEWS.Rd | 9 WeMix-3.1.3/WeMix/inst/doc/Introduction_to_Mixed_Effects_Models_With_WeMix.html |only WeMix-3.1.3/WeMix/inst/doc/Weighted_Linear_Mixed_Effects_Models.html |only WeMix-3.1.3/WeMix/tests/testthat/test-1-main.R | 59 +++++ 12 files changed, 145 insertions(+), 71 deletions(-)
Title: Overlays on Static Maps
Description: Serves two purposes: (i) Provide a
comfortable R interface to query the Google server for static
maps, and (ii) Use the map as a background image to overlay
plots within R. This requires proper coordinate scaling.
Author: Markus Loecher
Maintainer: Markus Loecher <markus.loecher@gmail.com>
Diff between RgoogleMaps versions 1.4.5 dated 2019-12-11 and 1.4.5.1 dated 2020-01-08
RgoogleMaps-1.4.5.1/RgoogleMaps/DESCRIPTION | 15 -- RgoogleMaps-1.4.5.1/RgoogleMaps/MD5 | 14 - RgoogleMaps-1.4.5.1/RgoogleMaps/R/GetMap.R | 4 RgoogleMaps-1.4.5.1/RgoogleMaps/R/GetMapTiles.R | 2 RgoogleMaps-1.4.5.1/RgoogleMaps/R/plotmap.R | 13 + RgoogleMaps-1.4.5.1/RgoogleMaps/man/plotmap.Rd | 174 ++++++++++++++++-------- RgoogleMaps-1.4.5/RgoogleMaps/inst |only 7 files changed, 141 insertions(+), 81 deletions(-)
Title: Functions for Clustering and Testing of Presence-Absence,
Abundance and Multilocus Genetic Data
Description: Distance-based parametric bootstrap tests for clustering with
spatial neighborhood information. Some distance measures,
Clustering of presence-absence, abundance and multilocus genetic data
for species delimitation, nearest neighbor
based noise detection. Genetic distances between communities.
Tests whether various distance-based regressions
are equal. Try package?prabclus for on overview.
Author: Christian Hennig <christian.hennig@unibo.it>,
Bernhard Hausdorf <Hausdorf@zoologie.uni-hamburg.de>
Maintainer: Christian Hennig <christian.hennig@unibo.it>
Diff between prabclus versions 2.3-1 dated 2019-06-04 and 2.3-2 dated 2020-01-08
DESCRIPTION | 10 MD5 | 16 - data/kykladspecreg.rda |binary data/waterdist.rda |binary man/alleleinit.Rd | 4 man/communitydist.Rd | 26 + man/regeqdist.Rd | 2 tests/Examples/prabclus-Ex.Rout.save | 499 +++++++++++++++-------------------- tests/prabclustests.Rout.save | 18 - 9 files changed, 265 insertions(+), 310 deletions(-)
Title: The Poisson Binomial Distribution
Description: Implementation of both the exact and approximation methods for computing the cdf of the Poisson binomial distribution as described in Hong (2013) <doi: 10.1016/j.csda.2012.10.006>. It also provides the pmf, quantile function, and random number generation for the Poisson binomial distribution. The C code for fast Fourier transformation (FFT) is written by R Core Team (2019)<https://www.R-project.org/>, which implements the FFT algorithm in Singleton (1969) <doi: 10.1109/TAU.1969.1162042>.
Author: Yili Hong [aut, cre],
R Core Team [aut, cph]
Maintainer: Yili Hong <yilihong@vt.edu>
Diff between poibin versions 1.4 dated 2019-12-13 and 1.5 dated 2020-01-08
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- build/partial.rdb |binary man/poibin-package.Rd | 4 ++++ man/ppoibin.Rd | 2 +- 5 files changed, 17 insertions(+), 13 deletions(-)
Title: Easily Visualize Data from 'ERDDAP' Servers via the 'rerddap'
Package
Description: Easily visualize and animate 'tabledap' and 'griddap' objects obtained via the 'rerddap' package in a simple one-line command, using either base graphics or 'ggplot2' graphics. 'plotdap' handles extracting and reshaping the data, map projections and continental outlines. Optionally the data can be animated through time using the 'gganmiate' package.
Author: Carson Sievert [aut],
Roy Mendelssohn [aut, ctb, cre]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between plotdap versions 0.0.4 dated 2019-10-15 and 0.0.5 dated 2020-01-08
DESCRIPTION | 16 +++--- MD5 | 26 +++++----- NEWS.md | 5 + R/add_griddap.R | 26 ++++++++-- R/add_tabledap.R | 14 ++++- R/utils.R | 1 build/vignette.rds |binary inst/doc/using_plotdap.R | 111 ++++++++++++++++++++++---------------------- inst/doc/using_plotdap.Rmd | 43 ++++++++--------- inst/doc/using_plotdap.html | 94 ++++++++++++++++++------------------- man/add_griddap.Rd | 18 +++++-- man/add_tabledap.Rd | 15 ++++- man/plotdap.Rd | 13 +++-- vignettes/using_plotdap.Rmd | 43 ++++++++--------- 14 files changed, 244 insertions(+), 181 deletions(-)
Title: Producing and Reproducing Results
Description: A system for embedded scientific computing and reproducible research with R.
The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange
with R. This provides a reliable and scalable foundation for statistical services or
building R web applications. The OpenCPU server runs either as a single-user development
server within the interactive R session, or as a multi-user Linux stack based on Apache2.
The entire system is fully open source and permissively licensed. The OpenCPU website
has detailed documentation and example apps.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between opencpu versions 2.1.4 dated 2019-09-26 and 2.1.5 dated 2020-01-08
opencpu-2.1.4/opencpu/R/loadPackageFrom.R |only opencpu-2.1.5/opencpu/DESCRIPTION | 6 +++--- opencpu-2.1.5/opencpu/MD5 | 17 ++++++++--------- opencpu-2.1.5/opencpu/NEWS | 4 ++++ opencpu-2.1.5/opencpu/R/httpget.R | 4 ++-- opencpu-2.1.5/opencpu/R/httpget_library.R | 9 +++++++-- opencpu-2.1.5/opencpu/R/httpget_package_data.R | 2 +- opencpu-2.1.5/opencpu/R/httpget_package_r.R | 2 +- opencpu-2.1.5/opencpu/build/vignette.rds |binary opencpu-2.1.5/opencpu/inst/doc/opencpu-paper.pdf |binary 10 files changed, 26 insertions(+), 18 deletions(-)
Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series. 'mvMORPH' also proposes high-dimensional multivariate comparative tools (linear models using Generalized Least Squares and multivariate tests) based on penalized likelihood. See
Clavel et al. (2015) <DOI:10.1111/2041-210X.12420> and Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>.
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel <julien.clavel@hotmail.fr>
Diff between mvMORPH versions 1.1.0 dated 2018-08-04 and 1.1.1 dated 2020-01-08
DESCRIPTION | 16 +- MD5 | 59 ++++--- NAMESPACE | 16 +- NEWS.md | 9 + R/classes_methods.r | 293 ++++++++++++++++++++++++++++++++++++--- R/estim.r | 24 +-- R/multivariate.stat.r |only R/mvBM.r | 10 - R/mvBMTS.r | 2 R/mvSIM.r | 2 R/mvgls.pca.r | 4 R/mvgls.r | 46 +++--- R/penalized.r | 35 ++-- R/utils.r | 14 + R/zzz.r | 2 README.md | 13 - build/vignette.rds |binary data |only inst/doc/How_to_use_mvMORPH.R | 74 ++++----- inst/doc/How_to_use_mvMORPH.Rmd | 2 inst/doc/How_to_use_mvMORPH.pdf |binary inst/doc/tutorial_mvMORPH.R | 26 +-- inst/doc/tutorial_mvMORPH.pdf |binary man/EIC.Rd |only man/GIC.Rd | 4 man/manova.gls.Rd |only man/mvLL.Rd | 4 man/mvMORPH-package.Rd | 6 man/mvgls.Rd | 27 ++- man/mvgls.pca.Rd | 7 man/phyllostomid.Rd |only man/residuals.mvgls.Rd | 2 vignettes/How_to_use_mvMORPH.Rmd | 2 33 files changed, 499 insertions(+), 200 deletions(-)
Title: Data Sets and Functions Used in Multivariate Statistics: Old
School by John Marden
Description: Multivariate Analysis methods and data sets used
in John Marden's book Multivariate Statistics: Old School (2015) <ISBN:978-1456538835>.
This also serves as a companion package for the
STAT 571: Multivariate Analysis course offered by the Department of Statistics
at the University of Illinois at Urbana-Champaign ('UIUC').
Author: John Marden [aut, cph],
James Balamuta [cre, ctb, com]
(<https://orcid.org/0000-0003-2826-8458>)
Maintainer: James Balamuta <james.balamuta@gmail.com>
Diff between msos versions 1.1.0 dated 2017-04-27 and 1.1.1 dated 2020-01-08
msos-1.1.0/msos/R/msos-internal.R |only msos-1.1.1/msos/DESCRIPTION | 36 msos-1.1.1/msos/LICENSE | 2 msos-1.1.1/msos/MD5 | 160 +-- msos-1.1.1/msos/NAMESPACE | 72 - msos-1.1.1/msos/NEWS.md | 69 - msos-1.1.1/msos/R/bothsidesmodel.R | 202 ++-- msos-1.1.1/msos/R/bothsidesmodel.chisquare.R | 85 - msos-1.1.1/msos/R/bothsidesmodel.df.R | 114 +- msos-1.1.1/msos/R/bothsidesmodel.hotelling.R | 124 +- msos-1.1.1/msos/R/bothsidesmodel.lrt.R | 105 +- msos-1.1.1/msos/R/bothsidesmodel.mle.R | 215 ++-- msos-1.1.1/msos/R/bsm.fit.R | 165 +-- msos-1.1.1/msos/R/bsm.simple.R | 117 +- msos-1.1.1/msos/R/datasets-doc.R | 1201 +++++++++++------------- msos-1.1.1/msos/R/fillout.R | 61 - msos-1.1.1/msos/R/imax.R | 38 msos-1.1.1/msos/R/lda.R | 109 +- msos-1.1.1/msos/R/logdet.R | 32 msos-1.1.1/msos/R/msos-package.R |only msos-1.1.1/msos/R/negent.R | 41 msos-1.1.1/msos/R/negent2D.R | 75 - msos-1.1.1/msos/R/negent3D.R | 121 +- msos-1.1.1/msos/R/pcbic.R | 88 - msos-1.1.1/msos/R/pcbic.stepwise.R | 97 + msos-1.1.1/msos/R/pcbic.subpatterns.R | 73 - msos-1.1.1/msos/R/pcbic.unite.R | 63 - msos-1.1.1/msos/R/predict_qda.R | 92 - msos-1.1.1/msos/R/qda.R | 112 +- msos-1.1.1/msos/R/reverse.kronecker.R | 71 - msos-1.1.1/msos/R/silhouette.km.R | 76 - msos-1.1.1/msos/R/sort_silhouette.R | 66 - msos-1.1.1/msos/R/tr.R | 35 msos-1.1.1/msos/README.md | 60 + msos-1.1.1/msos/man/SAheart.Rd | 88 - msos-1.1.1/msos/man/Spam.Rd | 182 +-- msos-1.1.1/msos/man/births.Rd | 46 msos-1.1.1/msos/man/bothsidesmodel.Rd | 108 +- msos-1.1.1/msos/man/bothsidesmodel.chisquare.Rd | 100 + msos-1.1.1/msos/man/bothsidesmodel.df.Rd | 86 - msos-1.1.1/msos/man/bothsidesmodel.hotelling.Rd | 111 +- msos-1.1.1/msos/man/bothsidesmodel.lrt.Rd | 123 +- msos-1.1.1/msos/man/bothsidesmodel.mle.Rd | 121 +- msos-1.1.1/msos/man/bsm.fit.Rd | 106 +- msos-1.1.1/msos/man/bsm.simple.Rd | 118 +- msos-1.1.1/msos/man/caffeine.Rd | 62 - msos-1.1.1/msos/man/cars.Rd | 80 - msos-1.1.1/msos/man/cereal.Rd | 76 - msos-1.1.1/msos/man/crabs.Rd | 76 - msos-1.1.1/msos/man/decathlon08.Rd | 64 - msos-1.1.1/msos/man/decathlon12.Rd | 62 - msos-1.1.1/msos/man/election.Rd | 52 - msos-1.1.1/msos/man/exams.Rd | 48 msos-1.1.1/msos/man/fillout.Rd | 56 - msos-1.1.1/msos/man/grades.Rd | 52 - msos-1.1.1/msos/man/histamine.Rd | 70 - msos-1.1.1/msos/man/imax.Rd | 54 - msos-1.1.1/msos/man/lda.Rd | 72 - msos-1.1.1/msos/man/leprosy.Rd | 54 - msos-1.1.1/msos/man/logdet.Rd | 50 msos-1.1.1/msos/man/mouths.Rd | 60 - msos-1.1.1/msos/man/msos-package.Rd | 64 - msos-1.1.1/msos/man/negent.Rd | 54 - msos-1.1.1/msos/man/negent2D.Rd | 75 - msos-1.1.1/msos/man/negent3D.Rd | 98 - msos-1.1.1/msos/man/painters.Rd | 98 - msos-1.1.1/msos/man/pcbic.Rd | 86 - msos-1.1.1/msos/man/pcbic.stepwise.Rd | 84 - msos-1.1.1/msos/man/pcbic.subpatterns.Rd | 70 - msos-1.1.1/msos/man/pcbic.unite.Rd | 54 - msos-1.1.1/msos/man/planets.Rd | 56 - msos-1.1.1/msos/man/predict_qda.Rd | 91 - msos-1.1.1/msos/man/prostaglandin.Rd | 56 - msos-1.1.1/msos/man/qda.Rd | 97 - msos-1.1.1/msos/man/reverse.kronecker.Rd | 83 - msos-1.1.1/msos/man/silhouette.km.Rd | 77 - msos-1.1.1/msos/man/skulls.Rd | 54 - msos-1.1.1/msos/man/softdrinks.Rd | 56 - msos-1.1.1/msos/man/sort_silhouette.Rd | 71 - msos-1.1.1/msos/man/sportsranks.Rd | 58 - msos-1.1.1/msos/man/states.Rd | 76 - msos-1.1.1/msos/man/tr.Rd | 53 - 82 files changed, 3921 insertions(+), 3744 deletions(-)
Title: Multilevel Exponential-Family Random Graph Models
Description: Estimates exponential-family random graph models for multilevel network data, assuming the multilevel structure is observed. The scope, at present, covers multilevel models where the set of nodes is nested within known blocks. The estimation method uses Monte-Carlo maximum likelihood estimation (MCMLE) methods to estimate a variety of canonical or curved exponential family models for binary random graphs. MCMLE methods for curved exponential-family random graph models can be found in Hunter and Handcock (2006) <DOI: 10.1198/106186006X133069>. The package supports parallel computing, and provides methods for assessing goodness-of-fit of models and visualization of networks.
Author: Jonathan Stewart [cre, aut],
Michael Schweinberger [ctb]
Maintainer: Jonathan Stewart <jonathan.stewart@rice.edu>
Diff between mlergm versions 0.4 dated 2019-11-04 and 0.5 dated 2020-01-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/estimate_between_block.R | 33 ++++++++++++++++++++++++--------- R/step_to_chull.R | 4 ++-- R/summary.mlergm.R | 21 +++++++++++++++------ inst/doc/mlergm_tutorial.html | 36 ++++++++++++++++++++---------------- 6 files changed, 69 insertions(+), 41 deletions(-)
Title: Weighted Metrics, Scoring Functions and Performance Measures for
Machine Learning
Description: Provides weighted versions of several metrics,
scoring functions and performance measures used in machine learning,
including average unit deviances of the Bernoulli, Tweedie, Poisson,
and Gamma distributions, see Jorgensen B. (1997, ISBN:
978-0412997112). The package also contains a weighted version of
generalized R-squared, see e.g. Cohen, J. et al. (2002, ISBN:
978-0805822236). Furthermore, 'dplyr' chains are supported.
Author: Michael Mayer [aut, cre, cph],
Christian Lorentzen [ctb, rev]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between MetricsWeighted versions 0.4.0 dated 2019-12-02 and 0.5.0 dated 2020-01-08
DESCRIPTION | 18 ++++++----- MD5 | 25 +++++++++------ NAMESPACE | 3 + NEWS.md | 8 ++++ R/elementary_score.R |only R/multi_metric.R |only build/vignette.rds |binary inst/doc/MetricsWeighted.R | 18 +++++++++++ inst/doc/MetricsWeighted.Rmd | 46 ++++++++++++++++++++++------ inst/doc/MetricsWeighted.html | 68 ++++++++++++++++++++++++++++++++++-------- man/elementary_score.Rd |only man/multi_metric.Rd |only man/performance.Rd | 24 +++++++------- man/weighted_mean.Rd | 2 - vignettes/MetricsWeighted.Rmd | 46 ++++++++++++++++++++++------ vignettes/biblio.bib |only 16 files changed, 195 insertions(+), 63 deletions(-)
More information about MetricsWeighted at CRAN
Permanent link
Title: Utility Functions for Production R Code
Description: A suite of utility functions providing functionality commonly
needed for production level projects such as logging, error handling,
and cache management.
Author: Jonathan Callahan [aut, cre],
Spencer Pease [aut],
Thomas Bergamaschi [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaCoreUtils versions 0.4.0 dated 2019-11-06 and 0.4.2 dated 2020-01-08
DESCRIPTION | 8 MD5 | 42 +- NEWS.md | 9 R/dateRange.R | 49 ++ R/loadDataFile.R | 4 R/timeRange.R | 17 build/vignette.rds |binary inst/doc/cache-management.html | 589 +++++++++++++------------------ inst/doc/date-parsing.html | 422 ++++++++++------------ inst/doc/error-handling.html | 652 +++++++++++++++------------------- inst/doc/logging.html | 751 ++++++++++++++++++---------------------- man/MazamaCoreUtils.Rd | 1 man/dateRange.Rd | 24 - man/dateSequence.Rd | 8 man/lintFunctionArgs.Rd | 3 man/logger.setup.Rd | 10 man/manageCache.Rd | 9 man/parseDatetime.Rd | 11 man/timeRange.Rd | 20 - man/timeStamp.Rd | 3 tests/testthat/test-dateRange.R | 31 + tests/testthat/test-timeRange.R | 18 22 files changed, 1272 insertions(+), 1409 deletions(-)
More information about MazamaCoreUtils at CRAN
Permanent link
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc]
(<https://orcid.org/0000-0002-0734-2199>),
Christoph Burow [aut, trl, dtc]
(<https://orcid.org/0000-0002-5023-4046>),
Michael Dietze [aut] (<https://orcid.org/0000-0001-6063-1726>),
Margret C. Fuchs [aut],
Christoph Schmidt [aut] (<https://orcid.org/0000-0002-2309-3209>),
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] (<https://orcid.org/0000-0002-0805-9547>),
Norbert Mercier [ctb] (<https://orcid.org/0000-0002-6375-9108>),
Rachel K. Smedley [ctb] (<https://orcid.org/0000-0001-7773-5193>),
Claire Christophe [ctb],
Antoine Zink [ctb] (<https://orcid.org/0000-0001-7146-1101>),
Julie Durcan [ctb] (<https://orcid.org/0000-0001-8724-8022>),
Georgina E. King [ctb, dtc] (<https://orcid.org/0000-0003-1059-8192>),
Anne Philippe [ctb],
Guillaume Guerin [ctb] (<https://orcid.org/0000-0001-6298-5579>),
Svenja Riedesel [ctb] (<https://orcid.org/0000-0003-2936-8776>),
Martin Autzen [ctb],
Pierre Guibert [ctb] (<https://orcid.org/0000-0001-8969-8684>),
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Diff between Luminescence versions 0.9.6 dated 2019-12-04 and 0.9.7 dated 2020-01-08
DESCRIPTION | 8 MD5 | 262 ++++++++++++++--------------- NEWS.md | 36 +++ R/Luminescence-package.R | 5 R/analyse_Al2O3C_Measurement.R | 16 - R/analyse_baSAR.R | 1 R/convert_Activity2Concentration.R | 2 R/get_Quote.R | 5 R/internal_as.latex.table.R | 28 +-- R/plot_AbanicoPlot.R | 70 +++++-- R/plot_GrowthCurve.R | 8 R/plot_RadialPlot.R | 10 - R/read_BIN2R.R | 14 - README.md | 2 build/partial.rdb |binary man/Analyse_SAR.OSLdata.Rd | 2 man/CW2pHMi.Rd | 2 man/CW2pLM.Rd | 2 man/CW2pLMi.Rd | 2 man/CW2pPMi.Rd | 2 man/GitHub-API.Rd | 2 man/Luminescence-package.Rd | 4 man/PSL2Risoe.BINfileData.Rd | 2 man/RLum-class.Rd | 2 man/RLum.Analysis-class.Rd | 2 man/RLum.Data.Curve-class.Rd | 2 man/RLum.Data.Image-class.Rd | 2 man/RLum.Data.Spectrum-class.Rd | 2 man/RLum.Results-class.Rd | 2 man/Risoe.BINfileData-class.Rd | 2 man/Risoe.BINfileData2RLum.Analysis.Rd | 2 man/Second2Gray.Rd | 2 man/analyse_Al2O3C_CrossTalk.Rd | 2 man/analyse_Al2O3C_ITC.Rd | 2 man/analyse_Al2O3C_Measurement.Rd | 7 man/analyse_FadingMeasurement.Rd | 2 man/analyse_IRSAR.RF.Rd | 2 man/analyse_SAR.CWOSL.Rd | 2 man/analyse_SAR.TL.Rd | 2 man/analyse_baSAR.Rd | 2 man/analyse_pIRIRSequence.Rd | 2 man/analyse_portableOSL.Rd | 2 man/app_RLum.Rd | 2 man/apply_CosmicRayRemoval.Rd | 2 man/apply_EfficiencyCorrection.Rd | 2 man/bin_RLum.Data.Rd | 2 man/calc_AliquotSize.Rd | 2 man/calc_AverageDose.Rd | 2 man/calc_CentralDose.Rd | 2 man/calc_CommonDose.Rd | 2 man/calc_CosmicDoseRate.Rd | 2 man/calc_FadingCorr.Rd | 2 man/calc_FastRatio.Rd | 2 man/calc_FiniteMixture.Rd | 2 man/calc_FuchsLang2001.Rd | 2 man/calc_HomogeneityTest.Rd | 2 man/calc_Huntley2006.Rd | 2 man/calc_IEU.Rd | 2 man/calc_Kars2008.Rd | 2 man/calc_Lamothe2003.Rd | 2 man/calc_MaxDose.Rd | 2 man/calc_MinDose.Rd | 2 man/calc_OSLLxTxRatio.Rd | 2 man/calc_SourceDoseRate.Rd | 2 man/calc_Statistics.Rd | 2 man/calc_TLLxTxRatio.Rd | 2 man/calc_ThermalLifetime.Rd | 2 man/calc_WodaFuchs2008.Rd | 2 man/calc_gSGC.Rd | 2 man/convert_Activity2Concentration.Rd | 4 man/convert_BIN2CSV.Rd | 2 man/convert_Daybreak2CSV.Rd | 2 man/convert_PSL2CSV.Rd | 2 man/convert_RLum2Risoe.BINfileData.Rd | 2 man/convert_Wavelength2Energy.Rd | 2 man/convert_XSYG2CSV.Rd | 2 man/extract_IrradiationTimes.Rd | 2 man/fit_CWCurve.Rd | 2 man/fit_LMCurve.Rd | 2 man/fit_OSLLifeTimes.Rd | 2 man/fit_SurfaceExposure.Rd | 2 man/fit_ThermalQuenching.Rd | 2 man/get_Layout.Rd | 2 man/get_Quote.Rd | 4 man/get_RLum.Rd | 2 man/get_Risoe.BINfileData.Rd | 2 man/get_rightAnswer.Rd | 2 man/length_RLum.Rd | 2 man/merge_RLum.Analysis.Rd | 2 man/merge_RLum.Data.Curve.Rd | 2 man/merge_RLum.Rd | 2 man/merge_RLum.Results.Rd | 2 man/merge_Risoe.BINfileData.Rd | 2 man/names_RLum.Rd | 2 man/plot_AbanicoPlot.Rd | 2 man/plot_DRCSummary.Rd | 2 man/plot_DRTResults.Rd | 2 man/plot_DetPlot.Rd | 2 man/plot_FilterCombinations.Rd | 2 man/plot_GrowthCurve.Rd | 10 - man/plot_Histogram.Rd | 2 man/plot_KDE.Rd | 2 man/plot_NRt.Rd | 2 man/plot_RLum.Analysis.Rd | 2 man/plot_RLum.Data.Curve.Rd | 2 man/plot_RLum.Data.Image.Rd | 2 man/plot_RLum.Data.Spectrum.Rd | 2 man/plot_RLum.Rd | 2 man/plot_RLum.Results.Rd | 2 man/plot_RadialPlot.Rd | 2 man/plot_Risoe.BINfileData.Rd | 2 man/plot_ViolinPlot.Rd | 2 man/read_BIN2R.Rd | 4 man/read_Daybreak2R.Rd | 2 man/read_PSL2R.Rd | 2 man/read_SPE2R.Rd | 2 man/read_XSYG2R.Rd | 2 man/replicate_RLum.Rd | 2 man/report_RLum.Rd | 2 man/sTeve.Rd | 2 man/scale_GammaDose.Rd | 2 man/set_RLum.Rd | 2 man/set_Risoe.BINfileData.Rd | 2 man/smooth_RLum.Rd | 2 man/structure_RLum.Rd | 2 man/template_DRAC.Rd | 2 man/tune_Data.Rd | 2 man/use_DRAC.Rd | 2 man/verify_SingleGrainData.Rd | 2 man/write_R2BIN.Rd | 2 man/write_RLum2CSV.Rd | 2 tests/testthat/test_calc_ThermalLifetime.R | 59 ++---- 132 files changed, 427 insertions(+), 352 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] (Reviews the documentation),
Florian De Boissieu [ctb] (Fixed bugs and improved catalog features),
Andrew Sánchez Meador [ctb] (Implemented wing2015 for lassnags),
Bourdon Jean-François [ctb] (Implemented sensor_tracking)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between lidR versions 2.1.4 dated 2019-10-15 and 2.2.0 dated 2020-01-08
lidR-2.1.4/lidR/R/grid_hexametrics.r |only lidR-2.1.4/lidR/R/grid_metrics3d.r |only lidR-2.1.4/lidR/R/lasmetrics.r |only lidR-2.1.4/lidR/man/grid_hexametrics.Rd |only lidR-2.1.4/lidR/man/grid_metrics3d.Rd |only lidR-2.1.4/lidR/man/lasmetrics.Rd |only lidR-2.1.4/lidR/man/lmfauto.Rd |only lidR-2.1.4/lidR/src/QuadTree.cpp |only lidR-2.1.4/lidR/src/QuadTree.h |only lidR-2.1.4/lidR/src/Triangulation.cpp |only lidR-2.1.4/lidR/src/Triangulation.h |only lidR-2.1.4/lidR/tests/testthat/test-grid_hexametrics.R |only lidR-2.1.4/lidR/tests/testthat/test-grid_metrics3d.R |only lidR-2.2.0/lidR/DESCRIPTION | 54 - lidR-2.2.0/lidR/MD5 | 354 +++++----- lidR-2.2.0/lidR/NAMESPACE | 17 lidR-2.2.0/lidR/NEWS.md | 156 ++++ lidR-2.2.0/lidR/R/Class-LAS.r | 16 lidR-2.2.0/lidR/R/Class-LAScatalog.r | 30 lidR-2.2.0/lidR/R/Class-LAScluster.r | 5 lidR-2.2.0/lidR/R/RcppExports.R | 24 lidR-2.2.0/lidR/R/algorithm-dsm.r | 96 +- lidR-2.2.0/lidR/R/algorithm-gnd.r | 3 lidR-2.2.0/lidR/R/algorithm-itd.R | 110 --- lidR-2.2.0/lidR/R/algorithm-spi.r | 64 + lidR-2.2.0/lidR/R/catalog_apply.r | 87 +- lidR-2.2.0/lidR/R/catalog_fakerun.r | 2 lidR-2.2.0/lidR/R/catalog_index.r | 19 lidR-2.2.0/lidR/R/catalog_makecluster.r | 90 +- lidR-2.2.0/lidR/R/catalog_merge_results.R | 117 ++- lidR-2.2.0/lidR/R/catalog_select.r | 22 lidR-2.2.0/lidR/R/cloud_metrics.r |only lidR-2.2.0/lidR/R/clusters_apply.r | 22 lidR-2.2.0/lidR/R/deprecated.R |only lidR-2.2.0/lidR/R/grid_canopy.r | 6 lidR-2.2.0/lidR/R/grid_metrics.r | 7 lidR-2.2.0/lidR/R/grid_terrain.r | 58 + lidR-2.2.0/lidR/R/hexbin_metrics.r |only lidR-2.2.0/lidR/R/io_readLAS.r | 10 lidR-2.2.0/lidR/R/lascheck.r | 58 - lidR-2.2.0/lidR/R/lasclip.r | 37 - lidR-2.2.0/lidR/R/lasfilterdecimate.r | 3 lidR-2.2.0/lidR/R/lasfilterduplicates.r | 3 lidR-2.2.0/lidR/R/lasfiltersurfacepoints.r | 3 lidR-2.2.0/lidR/R/lasground.r | 17 lidR-2.2.0/lidR/R/lasindentify.r | 14 lidR-2.2.0/lidR/R/lasmergespatial.r | 6 lidR-2.2.0/lidR/R/lasnormalize.r | 60 + lidR-2.2.0/lidR/R/lasrangecorrection.R |only lidR-2.2.0/lidR/R/lassnags.r | 3 lidR-2.2.0/lidR/R/lastrees.r | 3 lidR-2.2.0/lidR/R/lasupdateheader.r | 12 lidR-2.2.0/lidR/R/methods-LAS.r | 25 lidR-2.2.0/lidR/R/methods-LAScatalog.r | 12 lidR-2.2.0/lidR/R/plot.r | 109 ++- lidR-2.2.0/lidR/R/plot.s3.r | 36 - lidR-2.2.0/lidR/R/point_metrics.R |only lidR-2.2.0/lidR/R/print.r | 8 lidR-2.2.0/lidR/R/sensor_tracking.R |only lidR-2.2.0/lidR/R/tree_detection.r | 21 lidR-2.2.0/lidR/R/tree_hulls.r | 5 lidR-2.2.0/lidR/R/tree_metrics.r | 6 lidR-2.2.0/lidR/R/utils_assertive.r | 2 lidR-2.2.0/lidR/R/utils_catalog_options.r | 8 lidR-2.2.0/lidR/R/utils_colors.r | 50 + lidR-2.2.0/lidR/R/utils_define_constant.R | 19 lidR-2.2.0/lidR/R/utils_delaunay.R | 117 ++- lidR-2.2.0/lidR/R/utils_is.r | 6 lidR-2.2.0/lidR/R/utils_metrics.r | 19 lidR-2.2.0/lidR/R/utils_misc.r | 51 - lidR-2.2.0/lidR/R/utils_raster.r | 2 lidR-2.2.0/lidR/R/voxel_metrics.r |only lidR-2.2.0/lidR/R/zzz.r | 12 lidR-2.2.0/lidR/README.md | 7 lidR-2.2.0/lidR/build/vignette.rds |binary lidR-2.2.0/lidR/inst/WORDLIST | 15 lidR-2.2.0/lidR/inst/doc/lidR-LAS-class.R | 24 lidR-2.2.0/lidR/inst/doc/lidR-LAS-class.Rmd | 4 lidR-2.2.0/lidR/inst/doc/lidR-LAS-class.html | 17 lidR-2.2.0/lidR/inst/doc/lidR-LAScatalog-class.R | 26 lidR-2.2.0/lidR/inst/doc/lidR-LAScatalog-class.Rmd | 21 lidR-2.2.0/lidR/inst/doc/lidR-LAScatalog-class.html | 188 ++--- lidR-2.2.0/lidR/inst/doc/lidR-catalog-apply-examples.Rmd | 20 lidR-2.2.0/lidR/inst/doc/lidR-catalog-apply-examples.html | 27 lidR-2.2.0/lidR/inst/doc/lidR-computation-speed-LAScatalog.R | 47 + lidR-2.2.0/lidR/inst/doc/lidR-computation-speed-LAScatalog.Rmd | 41 + lidR-2.2.0/lidR/inst/doc/lidR-computation-speed-LAScatalog.html | 30 lidR-2.2.0/lidR/inst/extdata/Topography.laz |binary lidR-2.2.0/lidR/man/LAS-class.Rd | 20 lidR-2.2.0/lidR/man/LAScatalog-class.Rd | 25 lidR-2.2.0/lidR/man/area.Rd | 1 lidR-2.2.0/lidR/man/catalog_apply.Rd | 57 - lidR-2.2.0/lidR/man/catalog_select.Rd | 11 lidR-2.2.0/lidR/man/cloud_metrics.Rd |only lidR-2.2.0/lidR/man/csf.Rd | 17 lidR-2.2.0/lidR/man/dalponte2016.Rd | 24 lidR-2.2.0/lidR/man/deprecated.Rd |only lidR-2.2.0/lidR/man/dsmtin.Rd | 5 lidR-2.2.0/lidR/man/extent.Rd | 1 lidR-2.2.0/lidR/man/grid_canopy.Rd | 21 lidR-2.2.0/lidR/man/grid_density.Rd | 21 lidR-2.2.0/lidR/man/grid_metrics.Rd | 30 lidR-2.2.0/lidR/man/grid_terrain.Rd | 34 lidR-2.2.0/lidR/man/hexbin_metrics.Rd |only lidR-2.2.0/lidR/man/highest.Rd | 5 lidR-2.2.0/lidR/man/homogenize.Rd | 5 lidR-2.2.0/lidR/man/knnidw.Rd | 5 lidR-2.2.0/lidR/man/kriging.Rd | 5 lidR-2.2.0/lidR/man/lasaddattribute.Rd | 12 lidR-2.2.0/lidR/man/lasclip.Rd | 21 lidR-2.2.0/lidR/man/lasfilter.Rd | 7 lidR-2.2.0/lidR/man/lasfilterdecimate.Rd | 8 lidR-2.2.0/lidR/man/lasfilterduplicates.Rd | 14 lidR-2.2.0/lidR/man/lasfilters.Rd | 79 +- lidR-2.2.0/lidR/man/lasfiltersurfacepoints.Rd | 14 lidR-2.2.0/lidR/man/lasground.Rd | 18 lidR-2.2.0/lidR/man/lasnormalize.Rd | 12 lidR-2.2.0/lidR/man/lasrangecorrection.Rd |only lidR-2.2.0/lidR/man/lassmooth.Rd | 9 lidR-2.2.0/lidR/man/lassnags.Rd | 4 lidR-2.2.0/lidR/man/lastrees.Rd | 3 lidR-2.2.0/lidR/man/lasvoxelize.Rd | 4 lidR-2.2.0/lidR/man/li2012.Rd | 9 lidR-2.2.0/lidR/man/lidR-package.Rd | 3 lidR-2.2.0/lidR/man/lmf.Rd | 3 lidR-2.2.0/lidR/man/manual.Rd | 3 lidR-2.2.0/lidR/man/p2r.Rd | 5 lidR-2.2.0/lidR/man/pitfree.Rd | 8 lidR-2.2.0/lidR/man/plot.Rd | 40 - lidR-2.2.0/lidR/man/plot.lasmetrics3d.Rd | 15 lidR-2.2.0/lidR/man/plot_3d.Rd | 7 lidR-2.2.0/lidR/man/pmf.Rd | 3 lidR-2.2.0/lidR/man/point_metrics.Rd |only lidR-2.2.0/lidR/man/print.Rd | 1 lidR-2.2.0/lidR/man/projection.Rd | 1 lidR-2.2.0/lidR/man/random.Rd | 5 lidR-2.2.0/lidR/man/redefined_behaviors.Rd | 1 lidR-2.2.0/lidR/man/sensor_tracking.Rd |only lidR-2.2.0/lidR/man/set.colors.Rd | 2 lidR-2.2.0/lidR/man/silva2016.Rd | 16 lidR-2.2.0/lidR/man/stdmetrics.Rd | 19 lidR-2.2.0/lidR/man/tin.Rd | 5 lidR-2.2.0/lidR/man/tree_detection.Rd | 2 lidR-2.2.0/lidR/man/tree_hulls.Rd | 14 lidR-2.2.0/lidR/man/tree_metrics.Rd | 13 lidR-2.2.0/lidR/man/util_makeZhangParam.Rd | 10 lidR-2.2.0/lidR/man/voxel_metrics.Rd |only lidR-2.2.0/lidR/man/watershed.Rd | 11 lidR-2.2.0/lidR/man/wing2015.Rd | 9 lidR-2.2.0/lidR/src/C_delaunay.cpp |only lidR-2.2.0/lidR/src/GridPartition.cpp |only lidR-2.2.0/lidR/src/GridPartition.h |only lidR-2.2.0/lidR/src/LAS.cpp | 229 +++++- lidR-2.2.0/lidR/src/LAS.h | 7 lidR-2.2.0/lidR/src/Makevars | 2 lidR-2.2.0/lidR/src/Makevars.win | 2 lidR-2.2.0/lidR/src/Progress.cpp | 9 lidR-2.2.0/lidR/src/RcppExports.cpp | 92 ++ lidR-2.2.0/lidR/src/RcppFunction.cpp | 44 - lidR-2.2.0/lidR/tests/testthat/Rplots.pdf |binary lidR-2.2.0/lidR/tests/testthat/test-LAS.R | 6 lidR-2.2.0/lidR/tests/testthat/test-assertions.R |only lidR-2.2.0/lidR/tests/testthat/test-catalog_apply.R | 174 ++++ lidR-2.2.0/lidR/tests/testthat/test-cloud_metrics.R |only lidR-2.2.0/lidR/tests/testthat/test-delaunay.R |only lidR-2.2.0/lidR/tests/testthat/test-grid_canopy.R | 12 lidR-2.2.0/lidR/tests/testthat/test-grid_metrics.R | 10 lidR-2.2.0/lidR/tests/testthat/test-grid_terrain.R | 68 + lidR-2.2.0/lidR/tests/testthat/test-hexbin_metrics.R |only lidR-2.2.0/lidR/tests/testthat/test-internal_quadtree.R | 4 lidR-2.2.0/lidR/tests/testthat/test-lasadddata.R |only lidR-2.2.0/lidR/tests/testthat/test-lascheck.R |only lidR-2.2.0/lidR/tests/testthat/test-lasclip.R | 41 + lidR-2.2.0/lidR/tests/testthat/test-lasdetectedshape.R | 21 lidR-2.2.0/lidR/tests/testthat/test-lasfilterdecimate.R | 13 lidR-2.2.0/lidR/tests/testthat/test-lasfilterduplicates.R |only lidR-2.2.0/lidR/tests/testthat/test-lasgrid.R | 2 lidR-2.2.0/lidR/tests/testthat/test-lasground.R | 37 - lidR-2.2.0/lidR/tests/testthat/test-lasidentify.R | 64 + lidR-2.2.0/lidR/tests/testthat/test-lasmergespatial.R | 26 lidR-2.2.0/lidR/tests/testthat/test-lasnormalize.R | 26 lidR-2.2.0/lidR/tests/testthat/test-lasrangecorrection.R |only lidR-2.2.0/lidR/tests/testthat/test-lasrescale.R |only lidR-2.2.0/lidR/tests/testthat/test-lasupdateheader.R | 31 lidR-2.2.0/lidR/tests/testthat/test-plot.R |only lidR-2.2.0/lidR/tests/testthat/test-point_metrics.R |only lidR-2.2.0/lidR/tests/testthat/test-print.R |only lidR-2.2.0/lidR/tests/testthat/test-progress.R |only lidR-2.2.0/lidR/tests/testthat/test-projection.R | 12 lidR-2.2.0/lidR/tests/testthat/test-sensor_tracking.R |only lidR-2.2.0/lidR/tests/testthat/test-stdmetric.R | 6 lidR-2.2.0/lidR/tests/testthat/test-tree_detection.R | 29 lidR-2.2.0/lidR/tests/testthat/test-tree_hulls.R | 33 lidR-2.2.0/lidR/tests/testthat/test-utils_colors.R | 7 lidR-2.2.0/lidR/tests/testthat/test-utils_geometry.R | 1 lidR-2.2.0/lidR/tests/testthat/test-utils_metrics.R |only lidR-2.2.0/lidR/tests/testthat/test-voxel_metrics.R |only lidR-2.2.0/lidR/vignettes/lidR-LAS-class.Rmd | 4 lidR-2.2.0/lidR/vignettes/lidR-LAScatalog-class.Rmd | 21 lidR-2.2.0/lidR/vignettes/lidR-catalog-apply-examples.Rmd | 20 lidR-2.2.0/lidR/vignettes/lidR-computation-speed-LAScatalog.Rmd | 41 + 201 files changed, 2959 insertions(+), 1395 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 0.9.1 dated 2019-12-05 and 0.9.2 dated 2020-01-08
DESCRIPTION | 8 ++--- MD5 | 10 +++---- NEWS.md | 7 +++++ R/CreateTableOneJS.R | 2 - R/svyCreateTableOneJS.R | 2 - inst/doc/jstable.html | 65 +++++++++++++++++++++++++----------------------- 6 files changed, 53 insertions(+), 41 deletions(-)
Title: Calls Copy Number Variants from Targeted Sequence Data
Description: Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
Author: Vincent Plagnol [aut, cre]
Maintainer: Vincent Plagnol <v.plagnol@ucl.ac.uk>
Diff between ExomeDepth versions 1.1.12 dated 2019-08-30 and 1.1.15 dated 2020-01-08
DESCRIPTION | 10 +++---- MD5 | 44 ++++++++++++++++----------------- R/countBamInGranges.R | 39 +++++++++++++++-------------- R/optimize_reference_set.R | 2 - build/vignette.rds |binary data/Conrad.hg19.RData |binary data/ExomeCount.RData |binary data/exons.hg19.RData |binary data/exons.hg19.X.RData |binary data/genes.hg19.RData |binary inst/doc/ExomeDepth-vignette.R | 40 +++++++++++++++--------------- inst/doc/ExomeDepth-vignette.pdf |binary man/AnnotateExtra-ExomeDepth-method.Rd | 6 +--- man/CallCNVs-ExomeDepth-method.Rd | 12 ++++++--- man/TestCNV-ExomeDepth-method.Rd | 1 man/count.everted.reads.Rd | 10 ++++++- man/countBamInGRanges.exomeDepth.Rd | 9 +++++- man/get.power.betabinom.Rd | 11 ++++++-- man/getBamCounts.Rd | 13 +++++++-- man/initialize-ExomeDepth-method.Rd | 15 ++++++++--- man/plot-methods.Rd | 18 ++++++++++--- man/select.reference.set.Rd | 12 ++++++--- man/somatic.CNV.call.Rd | 3 -- 23 files changed, 149 insertions(+), 96 deletions(-)
Title: Dynamical Systems Approach to Infectious Disease Epidemiology
(Ecology/Evolution)
Description: Exploration of simulation models (apps) of various infectious disease transmission dynamics scenarios.
The purpose of the package is to help individuals learn
about infectious disease epidemiology (ecology/evolution) from a dynamical systems perspective.
All apps include explanations of the underlying models and instructions on what to do with the models.
Author: Andreas Handel [aut, cre] (<https://orcid.org/0000-0002-4622-1146>),
Christine Casey [ctb] (Parasite model app),
Isaac Chun-Hai Fung [ctb],
Ronald Galiwango [ctb] (ID surveillance app),
Chase Golden [ctb] (Maternal Immunity app),
Spencer Hall [ctb],
Ben Listyg [ctb],
Brian McKay [ctb],
John Rossow [ctb],
Sina Solaimanpour [ctb],
Kevin Spiegel [ctb] (Global warming app),
Henok Woldu [ctb]
Maintainer: Andreas Handel <ahandel@uga.edu>
Diff between DSAIDE versions 0.8.2 dated 2019-07-04 and 0.8.3 dated 2020-01-08
DSAIDE-0.8.2/DSAIDE/inst/docsfordevelopers/documentation.html |only DSAIDE-0.8.3/DSAIDE/DESCRIPTION | 44 - DSAIDE-0.8.3/DSAIDE/MD5 | 218 ++++---- DSAIDE-0.8.3/DSAIDE/NAMESPACE | 2 DSAIDE-0.8.3/DSAIDE/NEWS.md | 4 DSAIDE-0.8.3/DSAIDE/R/data.R | 10 DSAIDE-0.8.3/DSAIDE/R/generate_documentation.R | 2 DSAIDE-0.8.3/DSAIDE/R/generate_fctcall.R | 74 +- DSAIDE-0.8.3/DSAIDE/R/generate_ggplot.R | 104 ++-- DSAIDE-0.8.3/DSAIDE/R/generate_plotly.R | 4 DSAIDE-0.8.3/DSAIDE/R/generate_shinyinput.R | 152 +++--- DSAIDE-0.8.3/DSAIDE/R/simulate_idcontrolmultioutbreak_ode.R | 248 +++++----- DSAIDE-0.8.3/DSAIDE/R/simulate_idsurveillance_ode.R | 172 +++--- DSAIDE-0.8.3/DSAIDE/R/simulate_modelexploration_sir.R | 224 ++++----- DSAIDE-0.8.3/DSAIDE/R/simulate_parasites_ode.R | 170 +++--- DSAIDE-0.8.3/DSAIDE/R/simulate_reproductivenumber1_ode.R | 122 ++-- DSAIDE-0.8.3/DSAIDE/R/simulate_reproductivenumber2_ode.R | 174 +++---- DSAIDE-0.8.3/DSAIDE/R/simulate_sir_discrete.R | 118 ++-- DSAIDE-0.8.3/DSAIDE/R/simulate_usanalysis_sir.R | 234 ++++----- DSAIDE-0.8.3/DSAIDE/build/vignette.rds |binary DSAIDE-0.8.3/DSAIDE/inst/DSAIDE/app.R | 9 DSAIDE-0.8.3/DSAIDE/inst/DSAIDE/rsconnect/shinyapps.io/epibiouga |only DSAIDE-0.8.3/DSAIDE/inst/DSAIDE/rsconnect/shinyapps.io/handelgroup/dsaide.dcf | 4 DSAIDE-0.8.3/DSAIDE/inst/appinformation/basicsir_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/directtransmission_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/environmentaltransmission_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/evolutionarydynamics_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/fitflu_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/fitnoro_documentation.Rmd | 4 DSAIDE-0.8.3/DSAIDE/inst/appinformation/fitnoro_documentation.html | 8 DSAIDE-0.8.3/DSAIDE/inst/appinformation/hostheterogeneity_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/idcharacteristics_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/idcontrolcomplex_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/idcontrolcomplex_settings.R | 54 +- DSAIDE-0.8.3/DSAIDE/inst/appinformation/idcontrolmultioutbreak_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/idcontrolmultioutbreak_settings.R | 64 +- DSAIDE-0.8.3/DSAIDE/inst/appinformation/idcontrolvaccine_documentation.Rmd | 240 ++++----- DSAIDE-0.8.3/DSAIDE/inst/appinformation/idcontrolvaccine_documentation.html | 9 DSAIDE-0.8.3/DSAIDE/inst/appinformation/idcontrolvaccine_settings.R | 2 DSAIDE-0.8.3/DSAIDE/inst/appinformation/idpatterns_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/idsurveillance_documentation.Rmd | 34 - DSAIDE-0.8.3/DSAIDE/inst/appinformation/idsurveillance_documentation.html | 41 - DSAIDE-0.8.3/DSAIDE/inst/appinformation/idsurveillance_settings.R | 54 +- DSAIDE-0.8.3/DSAIDE/inst/appinformation/maternalimmunity_documentation.Rmd | 46 + DSAIDE-0.8.3/DSAIDE/inst/appinformation/maternalimmunity_documentation.html | 55 +- DSAIDE-0.8.3/DSAIDE/inst/appinformation/modelexploration_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/modelexploration_settings.R | 58 +- DSAIDE-0.8.3/DSAIDE/inst/appinformation/multipathogen_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/parasitemodel_documentation.Rmd | 4 DSAIDE-0.8.3/DSAIDE/inst/appinformation/parasitemodel_documentation.html | 13 DSAIDE-0.8.3/DSAIDE/inst/appinformation/reproductivenumber1_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/reproductivenumber2_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/stochasticseir_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/stochasticsir_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/usanalysis_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/appinformation/usanalysis_settings.R | 66 +- DSAIDE-0.8.3/DSAIDE/inst/appinformation/vectortransmission_documentation.html | 7 DSAIDE-0.8.3/DSAIDE/inst/doc/DSAIDE.R | 32 - DSAIDE-0.8.3/DSAIDE/inst/doc/DSAIDE.Rmd | 8 DSAIDE-0.8.3/DSAIDE/inst/doc/DSAIDE.html | 18 DSAIDE-0.8.3/DSAIDE/inst/docsfordevelopers/documentation.md | 91 ++- DSAIDE-0.8.3/DSAIDE/inst/simulatorfunctions/simulate_idcontrolmultioutbreak_ode.R | 248 +++++----- DSAIDE-0.8.3/DSAIDE/inst/simulatorfunctions/simulate_idsurveillance_ode.R | 172 +++--- DSAIDE-0.8.3/DSAIDE/inst/simulatorfunctions/simulate_modelexploration_sir.R | 224 ++++----- DSAIDE-0.8.3/DSAIDE/inst/simulatorfunctions/simulate_parasites_ode.R | 170 +++--- DSAIDE-0.8.3/DSAIDE/inst/simulatorfunctions/simulate_reproductivenumber1_ode.R | 122 ++-- DSAIDE-0.8.3/DSAIDE/inst/simulatorfunctions/simulate_reproductivenumber2_ode.R | 174 +++---- DSAIDE-0.8.3/DSAIDE/inst/simulatorfunctions/simulate_sir_discrete.R | 118 ++-- DSAIDE-0.8.3/DSAIDE/inst/simulatorfunctions/simulate_usanalysis_sir.R | 234 ++++----- DSAIDE-0.8.3/DSAIDE/inst/simulatorfunctions/simulatorfunctions.zip |binary DSAIDE-0.8.3/DSAIDE/man/DSAIDE.Rd | 41 - DSAIDE-0.8.3/DSAIDE/man/dsaidemenu.Rd | 38 - DSAIDE-0.8.3/DSAIDE/man/flu1918data.Rd | 54 +- DSAIDE-0.8.3/DSAIDE/man/generate_documentation.Rd | 50 +- DSAIDE-0.8.3/DSAIDE/man/generate_fctcall.Rd | 46 - DSAIDE-0.8.3/DSAIDE/man/generate_ggplot.Rd | 100 ++-- DSAIDE-0.8.3/DSAIDE/man/generate_plotly.Rd | 98 +-- DSAIDE-0.8.3/DSAIDE/man/generate_shinyinput.Rd | 68 +- DSAIDE-0.8.3/DSAIDE/man/generate_text.Rd | 66 +- DSAIDE-0.8.3/DSAIDE/man/norodata.Rd | 56 +- DSAIDE-0.8.3/DSAIDE/man/run_model.Rd | 68 +- DSAIDE-0.8.3/DSAIDE/man/simulate_directtransmission_ode.Rd | 154 +++--- DSAIDE-0.8.3/DSAIDE/man/simulate_environmentaltransmission_ode.Rd | 129 ++--- DSAIDE-0.8.3/DSAIDE/man/simulate_evolution_stochastic.Rd | 174 +++---- DSAIDE-0.8.3/DSAIDE/man/simulate_fit_flu.Rd | 197 ++++--- DSAIDE-0.8.3/DSAIDE/man/simulate_fit_noro.Rd | 169 +++--- DSAIDE-0.8.3/DSAIDE/man/simulate_heterogeneity_ode.Rd | 160 +++--- DSAIDE-0.8.3/DSAIDE/man/simulate_idcharacteristics_ode.Rd | 172 +++--- DSAIDE-0.8.3/DSAIDE/man/simulate_idcontrol_ode.Rd | 234 +++++---- DSAIDE-0.8.3/DSAIDE/man/simulate_idcontrolmultioutbreak_ode.Rd | 159 +++--- DSAIDE-0.8.3/DSAIDE/man/simulate_idpatterns_ode.Rd | 193 ++++--- DSAIDE-0.8.3/DSAIDE/man/simulate_idsurveillance_ode.Rd | 166 +++--- DSAIDE-0.8.3/DSAIDE/man/simulate_maternalimmunity_ode.Rd | 145 +++-- DSAIDE-0.8.3/DSAIDE/man/simulate_modelexploration_sir.Rd | 191 ++++--- DSAIDE-0.8.3/DSAIDE/man/simulate_multipathogen_ode.Rd | 155 +++--- DSAIDE-0.8.3/DSAIDE/man/simulate_parasites_ode.Rd | 163 +++--- DSAIDE-0.8.3/DSAIDE/man/simulate_reproductivenumber1_ode.Rd | 102 ++-- DSAIDE-0.8.3/DSAIDE/man/simulate_reproductivenumber2_ode.Rd | 158 +++--- DSAIDE-0.8.3/DSAIDE/man/simulate_seir_stochastic.Rd | 156 +++--- DSAIDE-0.8.3/DSAIDE/man/simulate_sir_discrete.Rd | 98 ++- DSAIDE-0.8.3/DSAIDE/man/simulate_sir_ode.Rd | 98 ++- DSAIDE-0.8.3/DSAIDE/man/simulate_sirdemographic_ode.Rd | 108 ++-- DSAIDE-0.8.3/DSAIDE/man/simulate_sirdemographic_stochastic.Rd | 151 +++--- DSAIDE-0.8.3/DSAIDE/man/simulate_usanalysis_sir.Rd | 199 ++++---- DSAIDE-0.8.3/DSAIDE/man/simulate_vectortransmission_ode.Rd | 135 ++--- DSAIDE-0.8.3/DSAIDE/tests/testthat/Rplots.pdf |binary DSAIDE-0.8.3/DSAIDE/tests/testthat/test-generate_ggplot.R | 58 +- DSAIDE-0.8.3/DSAIDE/tests/testthat/test-generate_plotly.R | 58 +- DSAIDE-0.8.3/DSAIDE/tests/testthat/test-generate_usplot.R | 114 ++-- DSAIDE-0.8.3/DSAIDE/tests/testthat/test-modelexploration.R | 74 +- DSAIDE-0.8.3/DSAIDE/vignettes/DSAIDE.Rmd | 8 111 files changed, 4889 insertions(+), 4452 deletions(-)
Title: Interpolation Methods
Description: Bivariate data interpolation on regular and irregular
grids, either linear or using splines are the main part of this
package. It is intended to provide FOSS replacement functions for
the ACM licensed akima::interp and tripack::tri.mesh functions.
Currently the piecewise linear interpolation part of akima::interp
(and also akima::interpp) is implemented in interp::interp, this
corresponds to the call akima::interp(..., linear=TRUE) which is the
default setting and covers most of akima::interp use cases in
depending packages. A re-implementation of Akimas spline
interpolation (akima::interp(..., linear=FALSE)) is currently under
development and will complete this package in a later
version. Estimators for partial derivatives are already available,
these are a prerequisite for the spline interpolation. The basic
part is currently a GPLed triangulation algorithm (sweep hull
algorithm by David Sinclair) providing the starting point for the
piecewise linear interpolator. As side effect this algorithm is also
used to provide replacements for the basic functions of the tripack
package which also suffer from the ACM restrictions. All functions
are designed to be backward compatible with their akima / tripack
counterparts.
Author: Albrecht Gebhardt [aut, cre, cph] (...),
Roger Bivand [aut],
David Sinclair [aut, cph]
Maintainer: Albrecht Gebhardt <albrecht.gebhardt@aau.at>
Diff between interp versions 1.0-32 dated 2019-05-04 and 1.0-33 dated 2020-01-08
ChangeLog | 24 ++++++++++++++++++++++-- DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/in.convex.hull.R | 4 +++- man/on.convex.hull.Rd | 12 +++++++++++- src/shullDeltri.cpp | 33 +++++++++++++++++++++++---------- 6 files changed, 68 insertions(+), 23 deletions(-)
Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Like 'xtable', creates styled tables. Export to HTML, LaTeX, 'Word',
'Excel', 'PowerPoint' and RTF. Simple, modern interface to manipulate
borders, size, position, captions, colours, text styles and number formatting.
Table cells can span multiple rows and/or columns.
Includes a 'huxreg' function for creation of regression tables, and 'quick_*'
one-liners to print data to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 4.7.0 dated 2019-10-03 and 4.7.1 dated 2020-01-08
huxtable-4.7.0/huxtable/tests/testthat/huxtable.aux |only huxtable-4.7.0/huxtable/tests/testthat/libs |only huxtable-4.7.1/huxtable/DESCRIPTION | 6 huxtable-4.7.1/huxtable/MD5 | 146 -- huxtable-4.7.1/huxtable/NEWS.md | 10 huxtable-4.7.1/huxtable/R/flextable.R | 9 huxtable-4.7.1/huxtable/R/mapping-functions.R | 68 huxtable-4.7.1/huxtable/R/quick-functions.R | 5 huxtable-4.7.1/huxtable/build/vignette.rds |binary huxtable-4.7.1/huxtable/inst/doc/design-principles.R | 2 huxtable-4.7.1/huxtable/inst/doc/design-principles.html | 8 huxtable-4.7.1/huxtable/inst/doc/huxreg.R | 36 huxtable-4.7.1/huxtable/inst/doc/huxreg.html | 15 huxtable-4.7.1/huxtable/inst/doc/huxtable.R | 92 - huxtable-4.7.1/huxtable/inst/doc/huxtable.html | 56 huxtable-4.7.1/huxtable/inst/doc/themes.R | 20 huxtable-4.7.1/huxtable/inst/doc/themes.html | 16 huxtable-4.7.1/huxtable/man/align.Rd | 2 huxtable-4.7.1/huxtable/man/background_color.Rd | 2 huxtable-4.7.1/huxtable/man/bold.Rd | 2 huxtable-4.7.1/huxtable/man/by_colorspace.Rd | 9 huxtable-4.7.1/huxtable/man/by_quantiles.Rd | 15 huxtable-4.7.1/huxtable/man/caption.Rd | 2 huxtable-4.7.1/huxtable/man/col_width.Rd | 2 huxtable-4.7.1/huxtable/man/font.Rd | 2 huxtable-4.7.1/huxtable/man/font_size.Rd | 2 huxtable-4.7.1/huxtable/man/height.Rd | 2 huxtable-4.7.1/huxtable/man/label.Rd | 2 huxtable-4.7.1/huxtable/man/latex_float.Rd | 2 huxtable-4.7.1/huxtable/man/left_border.Rd | 2 huxtable-4.7.1/huxtable/man/left_padding.Rd | 2 huxtable-4.7.1/huxtable/man/na_string.Rd | 2 huxtable-4.7.1/huxtable/man/position.Rd | 2 huxtable-4.7.1/huxtable/man/rotation.Rd | 2 huxtable-4.7.1/huxtable/man/row_height.Rd | 2 huxtable-4.7.1/huxtable/man/rowspan.Rd | 2 huxtable-4.7.1/huxtable/man/tabular_environment.Rd | 2 huxtable-4.7.1/huxtable/man/text_color.Rd | 2 huxtable-4.7.1/huxtable/man/valign.Rd | 2 huxtable-4.7.1/huxtable/man/width.Rd | 2 huxtable-4.7.1/huxtable/tests/testthat/bookdown-test.log | 779 +++++----- huxtable-4.7.1/huxtable/tests/testthat/huxreg.log | 854 ++++++----- huxtable-4.7.1/huxtable/tests/testthat/huxtable.log | 859 ++++++----- huxtable-4.7.1/huxtable/tests/testthat/table-tester-2.log | 861 ++++++------ huxtable-4.7.1/huxtable/tests/testthat/test-flextable.R | 7 huxtable-4.7.1/huxtable/tests/testthat/test-map-interface.R | 18 huxtable-4.7.1/huxtable/tests/testthat/test-print.R | 1 huxtable-4.7.1/huxtable/tests/testthat/themes.log | 794 +++++------ 48 files changed, 2444 insertions(+), 2284 deletions(-)
Title: Pretty Time of Day
Description: Implements an S3 class for storing and formatting time-of-day
values, based on the 'difftime' class.
Author: Kirill Müller [aut, cre],
The R Consortium [fnd],
RStudio [fnd]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between hms versions 0.5.2 dated 2019-10-30 and 0.5.3 dated 2020-01-08
hms-0.5.2/hms/R/aaa-tools.R |only hms-0.5.3/hms/DESCRIPTION | 14 +++++++------- hms-0.5.3/hms/MD5 | 27 +++++++++++++-------------- hms-0.5.3/hms/NAMESPACE | 2 -- hms-0.5.3/hms/NEWS.md | 15 +++++++++++---- hms-0.5.3/hms/R/coerce.R | 8 +++----- hms-0.5.3/hms/R/hms.R | 7 +------ hms-0.5.3/hms/R/round.R | 6 +++--- hms-0.5.3/hms/build/hms.pdf |binary hms-0.5.3/hms/man/Deprecated.Rd | 6 ++---- hms-0.5.3/hms/man/hms-package.Rd | 3 ++- hms-0.5.3/hms/man/hms.Rd | 18 ------------------ hms-0.5.3/hms/man/round_hms.Rd | 6 +++--- hms-0.5.3/hms/man/vec_ptype2.hms.Rd | 4 ++-- hms-0.5.3/hms/tests/testthat/test-combine.R | 9 +++++++++ 15 files changed, 56 insertions(+), 69 deletions(-)
Title: Data Sets from the History of Statistics and Data Visualization
Description: The 'HistData' package provides a collection of small data sets
that are interesting and important in the history of statistics and data
visualization. The goal of the package is to make these available, both for
instructional use and for historical research. Some of these present interesting
challenges for graphics or analysis in R.
Author: Michael Friendly [aut, cre],
Stephane Dray [ctb],
Hadley Wickham [ctb],
James Hanley [ctb],
Dennis Murphy [ctb],
Peter Li [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between HistData versions 0.8-4 dated 2018-04-04 and 0.8-6 dated 2020-01-08
DESCRIPTION | 10 MD5 | 40 +-- NEWS | 9 build/vignette.rds |binary data/EdgeworthDeaths.RData |only inst/doc/Snow_deaths-duplicates.R | 18 - inst/doc/Snow_deaths-duplicates.html | 398 +++++++++++++++++++++++++++-------- man/Armada.Rd | 2 man/Cholera.Rd | 2 man/DrinksWages.Rd | 2 man/EdgeworthDeaths.Rd |only man/Galton.Rd | 4 man/GaltonFamilies.Rd | 2 man/Guerry.Rd | 2 man/HistData-package.Rd | 9 man/Langren.Rd | 11 man/Macdonell.Rd | 4 man/Minard.Rd | 9 man/OldMaps.Rd | 6 man/Quarrels.Rd | 10 man/SnowMap.Rd | 9 man/Wheat.Rd | 2 22 files changed, 400 insertions(+), 149 deletions(-)
Title: Construct Modeling Packages
Description: Building modeling packages is hard. A large amount of effort
generally goes into providing an implementation for a new method that is
efficient, fast, and correct, but often less emphasis is put on the user
interface. A good interface requires specialized knowledge about S3 methods
and formulas, which the average package developer might not have.
The goal of 'hardhat' is to reduce the burden around building new modeling
packages by providing functionality for preprocessing, predicting, and
validating input.
Author: Davis Vaughan [aut, cre],
Max Kuhn [aut],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between hardhat versions 0.1.0 dated 2019-12-16 and 0.1.1 dated 2020-01-08
DESCRIPTION | 12 ++++++------ MD5 | 11 ++++++----- NEWS.md |only R/blueprint-recipe-default.R | 16 +++++++++++++++- build/hardhat.pdf |binary tests/testthat/test-forge-recipe.R | 14 ++++++++++++++ tests/testthat/test-mold-recipe.R | 6 +----- 7 files changed, 42 insertions(+), 17 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 <Robert.King@newcastle.edu.au>,
Benjamin Dean <Benjamin.Dean@uon.edu.au>, Sigbert Klinke, Paul van Staden
Maintainer: Robert King <Robert.King@newcastle.edu.au>
Diff between gld versions 2.6.1 dated 2019-12-17 and 2.6.2 dated 2020-01-08
Changelog | 3 + DESCRIPTION | 8 ++-- MD5 | 38 +++++++++++----------- NEWS | 3 + R/CheckParameters.R | 58 +++++++++++++++++++---------------- man/BetaLambdaLambda.Rd | 4 +- man/GeneralisedLambdaDistribution.Rd | 4 +- man/StarshipClassDocs.Rd | 4 +- man/fit.fkml.Rd | 2 - man/fit.fkml.moments.val.Rd | 8 ++-- man/fit.gpd.Rd | 2 - man/gl.check.lambda.Rd | 4 +- man/gld.lmoments.Rd | 10 +++--- man/gld.moments.Rd | 8 ++-- man/plot.starship.Rd | 4 +- man/plotgl.Rd | 4 +- man/qqgl.Rd | 4 +- man/starship.Rd | 4 +- man/starship.adaptivegrid.Rd | 4 +- man/starship.obj.Rd | 4 +- 20 files changed, 96 insertions(+), 84 deletions(-)
Title: Parsing Command-Line Arguments and Variable Interpolation
Description: This is yet another command-line argument parser which wraps the
powerful Perl module Getopt::Long and with some adaptation 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 0.1.7 dated 2018-06-10 and 0.1.8 dated 2020-01-08
GetoptLong-0.1.7/GetoptLong/man/GetOptions.rd |only GetoptLong-0.1.7/GetoptLong/man/GetoptLong.options.rd |only GetoptLong-0.1.7/GetoptLong/man/GetoptLong.rd |only GetoptLong-0.1.7/GetoptLong/man/get_scriptdir.rd |only GetoptLong-0.1.7/GetoptLong/man/get_scriptname.rd |only GetoptLong-0.1.7/GetoptLong/man/qq.options.rd |only GetoptLong-0.1.7/GetoptLong/man/qq.rd |only GetoptLong-0.1.7/GetoptLong/man/qqcat.rd |only GetoptLong-0.1.8/GetoptLong/DESCRIPTION | 8 - GetoptLong-0.1.8/GetoptLong/LICENSE | 2 GetoptLong-0.1.8/GetoptLong/MD5 | 42 +++++----- GetoptLong-0.1.8/GetoptLong/NAMESPACE | 16 +-- GetoptLong-0.1.8/GetoptLong/NEWS | 6 + GetoptLong-0.1.8/GetoptLong/R/GetoptLong.R | 4 GetoptLong-0.1.8/GetoptLong/R/qq.R | 30 +++++-- GetoptLong-0.1.8/GetoptLong/build/vignette.rds |binary GetoptLong-0.1.8/GetoptLong/inst/doc/GetoptLong.html | 15 +-- GetoptLong-0.1.8/GetoptLong/inst/doc/variable_interpolation.R | 7 + GetoptLong-0.1.8/GetoptLong/inst/doc/variable_interpolation.Rmd | 10 ++ GetoptLong-0.1.8/GetoptLong/inst/doc/variable_interpolation.html | 36 +++++--- GetoptLong-0.1.8/GetoptLong/man/GetOptions.Rd |only GetoptLong-0.1.8/GetoptLong/man/GetoptLong.Rd |only GetoptLong-0.1.8/GetoptLong/man/GetoptLong.options.Rd |only GetoptLong-0.1.8/GetoptLong/man/get_scriptdir.Rd |only GetoptLong-0.1.8/GetoptLong/man/get_scriptname.Rd |only GetoptLong-0.1.8/GetoptLong/man/qq.Rd |only GetoptLong-0.1.8/GetoptLong/man/qq.options.Rd |only GetoptLong-0.1.8/GetoptLong/man/qqcat.Rd |only GetoptLong-0.1.8/GetoptLong/tests/testthat/test_qq.R | 15 ++- GetoptLong-0.1.8/GetoptLong/vignettes/variable_interpolation.Rmd | 10 ++ 30 files changed, 138 insertions(+), 63 deletions(-)
Title: ANSI Control Sequence Aware String Functions
Description: Counterparts to R string manipulation functions that account for
the effects of ANSI text formatting control sequences.
Author: Brodie Gaslam [aut, cre],
Elliott Sales De Andrade [ctb],
R Core Team [cph] (UTF8 byte length calcs from src/util.c)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between fansi versions 0.4.0 dated 2018-10-05 and 0.4.1 dated 2020-01-08
DESCRIPTION | 8 MD5 | 90 ++++----- NEWS.md | 8 R/constants.R | 2 R/fansi-package.R | 2 R/has.R | 2 R/internal.R | 2 R/load.R | 7 R/misc.R | 27 ++ R/nchar.R | 2 R/strip.R | 2 R/strsplit.R | 11 - R/strtrim.R | 2 R/strwrap.R | 2 R/substr2.R | 8 R/tohtml.R | 6 R/unhandled.R | 2 README.md | 314 ++++++++++++++++++---------------- build/vignette.rds |binary inst/doc/sgr-in-rmd.Rmd | 17 + inst/doc/sgr-in-rmd.html | 58 ++++-- man/set_knit_hooks.Rd | 19 +- man/sgr_to_html.Rd | 4 man/strsplit_ctl.Rd | 9 man/substr_ctl.Rd | 6 src/assumptions.c | 2 src/fansi.h | 2 src/has.c | 2 src/init.c | 4 src/nchar.c | 2 src/read.c | 2 src/rnchar.c | 2 src/state.c | 2 src/strip.c | 2 src/strsplit.c | 2 src/tabs.c | 2 src/tohtml.c | 16 + src/unhandled.c | 2 src/unique.c | 2 src/utf8.c | 2 src/utils.c | 2 src/wrap.c | 2 tests/unitizer/misc.R | 6 tests/unitizer/misc.unitizer/data.rds |binary vignettes/sgr-in-rmd.Rmd | 17 + vignettes/styles.css | 11 + 46 files changed, 426 insertions(+), 268 deletions(-)
Title: Uncertainty Propagation for R Vectors
Description: Support for measurement errors in R vectors, matrices and arrays:
automatic uncertainty propagation and reporting.
Documentation about 'errors' is provided in the paper by Ucar, Pebesma &
Azcorra (2018, <doi:10.32614/RJ-2018-075>), included in this package as a
vignette; see 'citation("errors")' for details.
Author: Iñaki Ucar [aut, cph, cre] (<https://orcid.org/0000-0001-6403-5550>)
Maintainer: Iñaki Ucar <iucar@fedoraproject.org>
Diff between errors versions 0.3.2 dated 2019-05-20 and 0.3.3 dated 2020-01-08
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 7 +++++-- R/plot.R | 35 ++++++++++++++++++++++++++++------- R/summary.R | 6 +++--- README.md | 1 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/rjournal.R | 26 +++++++++++++------------- inst/doc/rjournal.pdf |binary man/as.data.frame.errors.Rd | 7 +++---- man/cbind.errors.Rd | 2 +- man/plot.errors.Rd | 2 +- man/rep.errors.Rd | 2 +- tests/testthat/test-summary.R | 23 ++++++++++++++++++++--- 15 files changed, 94 insertions(+), 53 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>.
'entropart' provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.
Estimation-bias corrections are available.
Author: Eric Marcon [aut, cre] (<https://orcid.org/0000-0002-5249-321X>),
Bruno Herault [aut] (<https://orcid.org/0000-0002-6950-7286>)
Maintainer: Eric Marcon <eric.marcon@ecofog.gf>
Diff between entropart versions 1.6-1 dated 2019-04-11 and 1.6-3 dated 2020-01-08
DESCRIPTION | 8 MD5 | 24 +- NEWS.md | 13 + R/CheckentropartArguments.R | 22 ++ R/DivProfile.R | 3 R/Richness.R | 18 - R/SpeciesDistribution.R | 12 - build/vignette.rds |binary inst/doc/entropart.R | 38 +-- inst/doc/entropart.html | 427 ++++++++++++++++++++++++++++++++------------ man/PPtree.Rd | 2 man/Richness.Rd | 16 + man/SpeciesDistribution.Rd | 11 - 13 files changed, 427 insertions(+), 167 deletions(-)
Title: Wrapper Package for Design of Experiments Functionality
Description: Various kinds of designs for
(industrial) experiments can be created. The package uses, and sometimes enhances,
design generation routines from other packages.
So far, response surface designs from package rsm, latin hypercube
samples from packages lhs and DiceDesign, and
D-optimal designs from package AlgDesign have been implemented.
Author: Ulrike Groemping [aut, cre],
Lenth Russ [ctb]
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>
Diff between DoE.wrapper versions 0.10 dated 2019-05-11 and 0.11 dated 2020-01-08
DoE.wrapper-0.10/DoE.wrapper/tests/Dopt.test.Rout.save |only DoE.wrapper-0.10/DoE.wrapper/tests/bbd.test.Rout.save |only DoE.wrapper-0.10/DoE.wrapper/tests/ccd.augment.test.Rout.save |only DoE.wrapper-0.10/DoE.wrapper/tests/qua.design.test.Rout.save |only DoE.wrapper-0.11/DoE.wrapper/DESCRIPTION | 9 ++- DoE.wrapper-0.11/DoE.wrapper/MD5 | 24 ++++------ DoE.wrapper-0.11/DoE.wrapper/inst/NEWS | 7 ++ DoE.wrapper-0.11/DoE.wrapper/man/Dopt.augment.Rd | 4 + DoE.wrapper-0.11/DoE.wrapper/man/Dopt.design.Rd | 5 +- DoE.wrapper-0.11/DoE.wrapper/man/ccd.design.Rd | 3 - DoE.wrapper-0.11/DoE.wrapper/man/optimality.criteria.Rd | 8 ++- DoE.wrapper-0.11/DoE.wrapper/tests/Dopt.test.R | 12 ++--- DoE.wrapper-0.11/DoE.wrapper/tests/bbd.test.R | 2 DoE.wrapper-0.11/DoE.wrapper/tests/ccd.augment.test.R | 19 +++++-- DoE.wrapper-0.11/DoE.wrapper/tests/qua.design.test.R | 8 +-- 15 files changed, 57 insertions(+), 44 deletions(-)
Title: Block Diagonal Extraction or Replacement
Description: Several tools for handling block-matrix diagonals and similar
constructs are implemented. Block-diagonal matrices can be extracted or removed
using two small functions implemented here. In addition, non-square matrices
are supported. Block diagonal matrices occur when two dimensions of a data set
are combined along one edge of a matrix. For example, trade-flow data in the
'decompr' and 'gvc' packages have each country-industry combination occur along
both edges of the matrix.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between diagonals versions 0.4.0 dated 2015-10-05 and 1.0.1 dated 2020-01-08
diagonals-0.4.0/diagonals/R/matricise.R |only diagonals-0.4.0/diagonals/man/matricise.Rd |only diagonals-1.0.1/diagonals/DESCRIPTION | 18 diagonals-1.0.1/diagonals/MD5 | 30 diagonals-1.0.1/diagonals/NAMESPACE | 2 diagonals-1.0.1/diagonals/NEWS | 14 diagonals-1.0.1/diagonals/R/diagonals.R | 7 diagonals-1.0.1/diagonals/README.md | 15 diagonals-1.0.1/diagonals/build/vignette.rds |binary diagonals-1.0.1/diagonals/inst/doc/fatdiag.R | 10 diagonals-1.0.1/diagonals/inst/doc/fatdiag.Rmd | 2 diagonals-1.0.1/diagonals/inst/doc/fatdiag.html | 541 +++++++++------- diagonals-1.0.1/diagonals/man/diagonals.Rd | 18 diagonals-1.0.1/diagonals/man/fatdiag.Rd | 4 diagonals-1.0.1/diagonals/man/split_vector.Rd | 3 diagonals-1.0.1/diagonals/tests/testthat/test_fatdiag.R | 10 diagonals-1.0.1/diagonals/vignettes/fatdiag.Rmd | 2 17 files changed, 420 insertions(+), 256 deletions(-)
Title: Clustering of Variables Around Latent Variables
Description: Functions for the clustering of variables around Latent Variables, for 2-way or 3-way data. Each cluster of variables, which may be defined as a local or directional cluster, is associated with a latent variable. External variables measured on the same observations or/and additional information on the variables can be taken into account. A "noise" cluster or sparse latent variables can also be defined.
Author: Evelyne Vigneau [aut, cre], Mingkun Chen [ctb], Veronique Cariou [aut]
Maintainer: Evelyne Vigneau <evelyne.vigneau@oniris-nantes.fr>
Diff between ClustVarLV versions 2.0.0 dated 2019-06-28 and 2.0.1 dated 2020-01-08
DESCRIPTION | 6 MD5 | 20 +-- NAMESPACE | 3 R/RcppExports.R | 6 R/get_partition.R | 2 R/lm_CLV.R | 159 ++++++++++++++++++-------- R/predict.lmclv.R |only inst/doc/Getting_started_with_ClustVarLV.html | 8 - inst/doc/clv3w-vignette.html | 66 +++++----- man/lm_CLV.Rd | 15 +- man/predict.lmclv.Rd |only src/RcppExports.cpp | 22 +-- 12 files changed, 194 insertions(+), 113 deletions(-)
Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces
('CLIs'), from semantic elements: headings, lists, alerts, paragraphs,
etc. Supports custom themes via a 'CSS'-like language. It also contains a
number of lower level 'CLI' elements: rules, boxes, trees, and
'Unicode' symbols with 'ASCII' alternatives. It integrates with the
'crayon' package to support 'ANSI' terminal colors.
Author: Gábor Csárdi [aut, cre],
Hadley Wickham [ctb],
Kirill Müller [ctb]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between cli versions 2.0.0 dated 2019-12-09 and 2.0.1 dated 2020-01-08
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 10 ++++++++++ R/onload.R | 2 +- R/simple-theme.R | 16 ++++------------ R/sitrep.R | 2 +- R/status-bar.R | 1 + R/themes.R | 22 ++-------------------- inst/doc/pluralization.html | 4 ++-- man/figures/README/unnamed-chunk-3.svg | 2 +- man/figures/README/unnamed-chunk-7.svg | 2 +- man/figures/README/unnamed-chunk-8.svg | 2 +- man/figures/README/unnamed-chunk-9.svg | 2 +- 13 files changed, 41 insertions(+), 56 deletions(-)
Title: Censored Spatial Models
Description: It fits linear regression models for censored spatial data. It provides different estimation methods as the SAEM (Stochastic Approximation of Expectation Maximization) algorithm and seminaive that uses Kriging prediction to estimate the response at censored locations and predict new values at unknown locations. It also offers graphical tools for assessing the fitted model.
Author: Alejandro Ordonez, Christian E. Galarza, Victor H. Lachos
Maintainer: Alejandro Ordonez <ordonezjosealejandro@gmail.com>
Diff between CensSpatial versions 1.3 dated 2017-03-02 and 2.1 dated 2020-01-08
CensSpatial-1.3/CensSpatial/R/atypicalfin.R |only CensSpatial-1.3/CensSpatial/R/atypicalprin.R |only CensSpatial-1.3/CensSpatial/data/paranacens25.rda |only CensSpatial-1.3/CensSpatial/man/atypical.Rd |only CensSpatial-1.3/CensSpatial/man/paranacens25.Rd |only CensSpatial-2.1/CensSpatial/DESCRIPTION | 12 ++++---- CensSpatial-2.1/CensSpatial/MD5 | 32 +++++++++------------- CensSpatial-2.1/CensSpatial/NAMESPACE | 3 +- CensSpatial-2.1/CensSpatial/R/SAEMSCLfin.R | 2 - CensSpatial-2.1/CensSpatial/R/Seminaivefin.R | 21 ++++++-------- CensSpatial-2.1/CensSpatial/R/Seminaiveprin.R | 3 -- CensSpatial-2.1/CensSpatial/R/algnaive12fin.R | 18 ++++++------ CensSpatial-2.1/CensSpatial/R/algnaive12prin.R | 3 -- CensSpatial-2.1/CensSpatial/R/auxfunjustnorm2.R | 10 +++--- CensSpatial-2.1/CensSpatial/R/derivQfunprin.R | 2 - CensSpatial-2.1/CensSpatial/R/distmatrixprin.R | 2 - CensSpatial-2.1/CensSpatial/R/localinfmeasprin.R | 8 ++--- CensSpatial-2.1/CensSpatial/R/probility.R |only CensSpatial-2.1/CensSpatial/man/algnaive12.Rd | 15 +++++++--- CensSpatial-2.1/CensSpatial/man/seminaive_1.Rd | 9 ++++-- 20 files changed, 72 insertions(+), 68 deletions(-)
Title: Fluid Data Transformations
Description: Supplies higher-order coordinatized data specification and fluid transform operators that include pivot and anti-pivot as special cases.
The methodology is describe in 'Zumel', 2018, "Fluid data reshaping with 'cdata'", <http://winvector.github.io/FluidData/FluidDataReshapingWithCdata.html> , doi:10.5281/zenodo.1173299 .
This package introduces the idea of explicit control table specification of data transforms.
Works on in-memory data or on remote data using 'rquery' and 'SQL' database interfaces.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between cdata versions 1.1.3 dated 2019-10-29 and 1.1.4 dated 2020-01-08
DESCRIPTION | 12 ++-- MD5 | 71 +++++++++++++------------- NEWS.md | 4 + R/LocalOps.R | 6 +- inst/doc/blocksrecs.R | 10 +-- inst/doc/blocksrecs.html | 7 +- inst/doc/cdata.R | 12 ++-- inst/doc/cdata.html | 7 +- inst/doc/control_table_keys.R | 12 ++-- inst/doc/control_table_keys.html | 7 +- inst/doc/design.R | 10 +-- inst/doc/design.html | 7 +- inst/doc/exercises.R | 38 +++++++------- inst/doc/exercises.html | 7 +- inst/doc/general_transform.R | 18 +++--- inst/doc/general_transform.html | 68 ++++++++++++------------- inst/doc/operators.R | 22 ++++---- inst/doc/operators.html | 7 +- inst/unit_tests/test_not_seen_level.R |only man/blocks_to_rowrecs.Rd | 51 ++++++++++++++---- man/blocks_to_rowrecs_q.Rd | 25 +++++++-- man/blocks_to_rowrecs_spec.Rd | 13 +++- man/build_pivot_control.Rd | 40 ++++++++++---- man/build_pivot_control_q.Rd | 13 +++- man/build_unpivot_control.Rd | 8 ++ man/cdata.Rd | 1 man/convert_records.Rd | 19 +++++-- man/layout_specification.Rd | 13 +++- man/map_fields_q.Rd | 12 +++- man/pivot_to_rowrecs.Rd | 30 ++++++++--- man/qlook.Rd | 10 ++- man/reexports.Rd | 2 man/rowrecs_to_blocks.Rd | 48 +++++++++++++---- man/rowrecs_to_blocks_q.Rd | 24 ++++++-- man/rowrecs_to_blocks_spec.Rd | 13 +++- man/run_cdata_tests.Rd | 17 ++++-- man/unpivot_to_blocks.Rd | 92 +++++++++++++++++++++++++--------- 37 files changed, 487 insertions(+), 269 deletions(-)
Title: Compare Baseline Characteristics Between Groups
Description: Compare baseline characteristics between two or more groups. The variables being compared can be factor and numeric variables. The function will automatically judge the type and distribution of the variables, and make statistical description and bivariate analysis.
Author: Zhongheng Zhang,
Sir Run-Run Shaw hospital,
Zhejiang university school of medicine
Maintainer: Zhongheng Zhang <zh_zhang1984@zju.edu.cn>
Diff between CBCgrps versions 2.5 dated 2019-12-20 and 2.6 dated 2020-01-08
CBCgrps-2.5/CBCgrps/man/CBCgrps2.5-package.Rd |only CBCgrps-2.6/CBCgrps/DESCRIPTION | 8 ++++---- CBCgrps-2.6/CBCgrps/MD5 | 12 ++++++------ CBCgrps-2.6/CBCgrps/R/multigrps.R | 5 +++-- CBCgrps-2.6/CBCgrps/R/twogrps.R | 5 +++-- CBCgrps-2.6/CBCgrps/man/CBCgrps2.6-package.Rd |only CBCgrps-2.6/CBCgrps/man/multigrps.Rd | 2 +- CBCgrps-2.6/CBCgrps/man/twogrps.Rd | 2 +- 8 files changed, 18 insertions(+), 16 deletions(-)
Title: Inferring Causal Effects using Bayesian Structural Time-Series
Models
Description: Implements a Bayesian approach to causal impact estimation in time
series, as described in Brodersen et al. (2015) <DOI:10.1214/14-AOAS788>.
See the package documentation on GitHub
<https://google.github.io/CausalImpact/> to get started.
Author: Kay H. Brodersen <kbrodersen@google.com>,
Alain Hauser <alhauser@google.com>
Maintainer: Alain Hauser <alhauser@google.com>
Diff between CausalImpact versions 1.2.2 dated 2017-09-14 and 1.2.4 dated 2020-01-08
DESCRIPTION | 12 +++--- MD5 | 32 ++++++++--------- R/impact_analysis.R | 26 +++++++++++--- R/impact_inference.R | 21 ++++++----- R/impact_misc.R | 5 +- R/impact_model.R | 22 ++++++++---- R/impact_plot.R | 18 +++++----- build/vignette.rds |binary inst/doc/CausalImpact.R | 61 +++++++++++++++++----------------- inst/doc/CausalImpact.Rmd | 9 +++++ inst/doc/CausalImpact.html | 36 ++++++++++++-------- man/CausalImpact.Rd | 7 +++ tests/CausalImpact_import_test.R | 1 tests/testthat/test-impact-analysis.R | 41 +++++++++++++++++++++- tests/testthat/test-impact-misc.R | 9 +++-- tests/testthat/test-impact-model.R | 18 +++++++--- vignettes/CausalImpact.Rmd | 9 +++++ 17 files changed, 221 insertions(+), 106 deletions(-)
Title: Bayesian Regularization for Feed-Forward Neural Networks
Description: Bayesian regularization for feed-forward neural networks.
Author: Paulino Perez Rodriguez, Daniel Gianola
Maintainer: Paulino Perez Rodriguez <perpdgo@colpos.mx>
Diff between brnn versions 0.7 dated 2018-08-23 and 0.8 dated 2020-01-08
DESCRIPTION | 10 - MD5 | 40 ++-- NAMESPACE | 20 +- R/brnn.R | 380 ++++++++++++++++++++++++++++++++++++++-- R/methods.R | 116 +++++++++++- data/GLS.RData |only demo/00Index | 1 demo/Example_4.R | 127 ++++++------- demo/Example_6.R |only inst/history.txt | 4 man/G.Rd | 59 +++--- man/GOrd.Rd |only man/brnn.Rd | 16 - man/brnn_extended.Rd | 302 +++++++++++++++---------------- man/brnn_ordinal.Rd |only man/estimate.trace.Rd | 74 +++---- man/initnw.Rd | 128 ++++++------- man/pheno.Rd | 49 ++--- man/phenoOrd.Rd |only man/predictions.brnn_ordinal.Rd |only man/twoinput.Rd | 42 ++-- src/init.c | 6 src/unix/util_unix.c | 104 ++++++++++ src/win/util_win.c | 104 ++++++++++ 24 files changed, 1119 insertions(+), 463 deletions(-)
Title: Visualising Bipartite Networks and Calculating Some (Ecological)
Indices
Description: Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.
Author: Carsten F. Dormann, Jochen Fruend and Bernd Gruber, with additional code from Stephen Beckett, Mariano Devoto, Jose Iriondo, Tove Opsahl, Rouven Strauss and Diego Vazquez, also based on C-code developed by Nils Bluethgen, Aaron Clauset/Rouven Strauss and Miguel Rodriguez-Girones
Maintainer: Carsten F. Dormann <carsten.dormann@biom.uni-freiburg.de>
Diff between bipartite versions 2.13 dated 2019-05-21 and 2.14 dated 2020-01-08
DESCRIPTION | 8 MD5 | 48 +-- R/H2fun.R | 22 + R/as.tnet.R | 340 +++++++++++++-------------- R/betalinkr.R | 139 ++++++----- R/betalinkr_multi.R | 7 R/grouplevel.R | 520 +++++++++++++++++++++--------------------- R/networklevel.R | 10 R/robustness.r | 28 +- R/slope.bipartite.R | 70 ++--- R/webs2array.R | 2 inst/doc/Dormann2008Rnews.pdf |binary inst/doc/Intro2bipartite.R | 38 +-- inst/doc/Intro2bipartite.Rnw | 7 inst/doc/Intro2bipartite.pdf |binary man/ND.rd | 200 ++++++++-------- man/betalinkr.Rd | 73 +++-- man/bipartite-package.Rd | 11 man/czvalues.Rd | 15 + man/plotModuleWeb.Rd | 2 src/identifyModules.cc | 10 src/init.c | 2 vignettes/Intro2bipartite.Rnw | 7 vignettes/Sweavel.sty | 118 ++++----- vignettes/bipartite.bib | 159 ++++++++++++ 25 files changed, 1034 insertions(+), 802 deletions(-)
Title: N-Gram Analysis of Biological Sequences
Description: Tools for extraction and analysis of various
n-grams (k-mers) derived from biological sequences (proteins
or nucleic acids). Contains QuiPT (quick permutation test) for fast
feature-filtering of the n-gram data.
Author: Michal Burdukiewicz [cre, aut]
(<https://orcid.org/0000-0001-8926-582X>),
Piotr Sobczyk [aut],
Chris Lauber [aut],
Dominik Rafacz [aut]
Maintainer: Michal Burdukiewicz <michalburdukiewicz@gmail.com>
Diff between biogram versions 1.4 dated 2017-01-05 and 1.6.1 dated 2020-01-08
CHANGELOG | 66 DESCRIPTION | 20 MD5 | 215 +- NAMESPACE | 134 - R/aaprop.R | 1818 +++++++++++------------ R/add_remove_ngrams.R | 240 +-- R/biogram.R | 190 +- R/calc_ed.R | 478 +++--- R/calc_si.R | 108 - R/chi_square.R | 56 R/cluster_reg_exp.R | 198 +- R/construct_ngrams.R | 174 +- R/count_multigrams.R | 82 - R/count_ngrams.R | 360 ++-- R/count_specified.R | 178 +- R/create_encoding.R | 200 +- R/criterion_distribution.R | 186 +- R/criterions.R | 142 - R/data_manipulation.R | 112 - R/degenerate.R | 293 ++- R/distr_crit.R | 195 +- R/feature_test_class.R | 385 ++--- R/generate_encodings_dist_1.r |only R/generate_sequence.R |only R/human_cleave.R | 42 R/indices_and_positions.R | 194 +- R/information_gain.R | 104 - R/is_ngram.R | 88 - R/kl_divergence.R | 54 R/ngram_coding.R | 200 +- R/ngrams.R | 172 +- R/position_ngrams.R | 150 - R/read_fasta.R |only R/regenerate.R |only R/region.R |only R/seq2matrix.R | 50 R/simplify.R |only R/table_ngrams.R | 112 - R/test_features.R | 349 ++-- R/utilities.R | 176 +- R/write_enc.R |only README.md | 82 - build/vignette.rds |binary inst/CITATION | 48 inst/doc/overview.R | 220 +- inst/doc/overview.Rmd | 534 +++--- inst/doc/overview.html | 842 +++++++---- man/aaprop.Rd | 1833 +++++++++++------------- man/add_1grams.Rd | 73 man/as.data.frame.feature_test.Rd | 64 man/binarize.Rd | 37 man/biogram-package.Rd | 196 +- man/calc_criterion.Rd | 99 - man/calc_cs.Rd | 83 - man/calc_ed.Rd | 115 - man/calc_ig.Rd | 95 - man/calc_kl.Rd | 91 - man/calc_pi.Rd | 113 - man/calc_si.Rd | 105 - man/cluster_reg_exp.Rd | 77 - man/code_ngrams.Rd | 49 man/construct_ngrams.Rd | 122 - man/count_multigrams.Rd | 118 - man/count_ngrams.Rd | 170 +- man/count_specified.Rd | 75 man/count_total.Rd | 75 man/create_encoding.Rd | 77 - man/create_feature_target.Rd | 67 man/create_ngrams.Rd | 85 - man/criterion_distribution.Rd | 58 man/cut.feature_test.Rd | 66 man/decode_ngrams.Rd | 57 man/degenerate.Rd | 81 - man/distr_crit.Rd | 69 man/encoding2df.Rd | 71 man/fast_crosstable.Rd | 87 - man/feature_test.Rd | 65 man/full2simple.Rd |only man/gap_ngrams.Rd | 61 man/generate_sequence.Rd |only man/generate_single_region.Rd |only man/generate_single_unigram.Rd |only man/generate_unigrams.Rd |only man/get_ngrams_ind.Rd | 69 man/human_cleave.Rd | 63 man/is_ngram.Rd | 45 man/l2n.Rd | 59 man/list2matrix.Rd | 59 man/n2l.Rd | 59 man/ngrams2df.Rd | 49 man/plot.criterion_distribution.Rd | 97 - man/position_ngrams.Rd | 75 man/print.feature_test.Rd | 39 man/read_fasta.Rd |only man/regenerate.Rd |only man/regional_param.Rd |only man/seq2ngrams.Rd | 75 man/simple2full.Rd |only man/summary.feature_test.Rd | 47 man/table_ngrams.Rd | 75 man/test_features.Rd | 218 +- man/validate_encoding.Rd | 91 - man/write_encoding.Rd |only man/write_fasta.Rd |only tests/test-all.R | 4 tests/testthat/test_calc_ed.R | 230 +-- tests/testthat/test_count_ngrams.R | 150 - tests/testthat/test_create_ngrams.R | 42 tests/testthat/test_crosstable.R | 22 tests/testthat/test_generate_encodings_dist_1.r |only tests/testthat/test_get_ngrams_pos.R | 10 tests/testthat/test_is_ngram.R | 44 tests/testthat/test_position_ngrams.R | 64 tests/testthat/test_quipt_consistency.R | 50 tests/testthat/test_seq2grams.R | 54 tests/testthat/test_table_ngrams.R | 34 vignettes/biogram_pub.bib | 534 +++--- vignettes/overview.Rmd | 534 +++--- 118 files changed, 8446 insertions(+), 8127 deletions(-)
Title: Boost C++ Header Files
Description: Boost provides free peer-reviewed portable C++ source
libraries. A large part of Boost is provided as C++ template code
which is resolved entirely at compile-time without linking. This
package aims to provide the most useful subset of Boost libraries
for template use among CRAN packages. By placing these libraries in
this package, we offer a more efficient distribution system for CRAN
as replication of this code in the sources of other packages is
avoided. As of release 1.72.0-3, the following Boost libraries are
included: 'accumulators' 'algorithm' 'align' 'any' 'atomic' 'bimap'
'bind' 'circular_buffer' 'compute' 'concept' 'config' 'container'
'date_time' 'detail' 'dynamic_bitset' 'exception' 'flyweight'
'foreach' 'functional' 'fusion' 'geometry' 'graph' 'heap' 'icl'
'integer' 'interprocess' 'intrusive' 'io' 'iostreams' 'iterator'
'math' 'move' 'mp11' 'mpl' 'multiprcecision' 'numeric' 'pending'
'phoenix' 'polygon' 'preprocessor' 'propery_tree' 'random' 'range'
'scope_exit' 'smart_ptr' 'sort' 'spirit' 'tuple' 'type_traits'
'typeof' 'unordered' 'utility' 'uuid'.
Author: Dirk Eddelbuettel, John W. Emerson and Michael J. Kane
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between BH versions 1.72.0-2 dated 2019-12-17 and 1.72.0-3 dated 2020-01-08
ChangeLog | 7 + DESCRIPTION | 14 +- MD5 | 65 +++++++++- README.md | 15 +- build/partial.rdb |binary inst/NEWS.Rd | 6 inst/include/boost/accumulators/numeric/detail/function3.hpp |only inst/include/boost/accumulators/numeric/detail/function4.hpp |only inst/include/boost/accumulators/statistics.hpp |only inst/include/boost/accumulators/statistics/covariance.hpp |only inst/include/boost/accumulators/statistics/density.hpp |only inst/include/boost/accumulators/statistics/error_of.hpp |only inst/include/boost/accumulators/statistics/error_of_mean.hpp |only inst/include/boost/accumulators/statistics/extended_p_square.hpp |only inst/include/boost/accumulators/statistics/extended_p_square_quantile.hpp |only inst/include/boost/accumulators/statistics/kurtosis.hpp |only inst/include/boost/accumulators/statistics/max.hpp |only inst/include/boost/accumulators/statistics/median.hpp |only inst/include/boost/accumulators/statistics/min.hpp |only inst/include/boost/accumulators/statistics/p_square_cumul_dist.hpp |only inst/include/boost/accumulators/statistics/p_square_cumulative_distribution.hpp |only inst/include/boost/accumulators/statistics/p_square_quantile.hpp |only inst/include/boost/accumulators/statistics/parameters |only inst/include/boost/accumulators/statistics/peaks_over_threshold.hpp |only inst/include/boost/accumulators/statistics/pot_quantile.hpp |only inst/include/boost/accumulators/statistics/pot_tail_mean.hpp |only inst/include/boost/accumulators/statistics/rolling_count.hpp |only inst/include/boost/accumulators/statistics/rolling_mean.hpp |only inst/include/boost/accumulators/statistics/rolling_moment.hpp |only inst/include/boost/accumulators/statistics/rolling_sum.hpp |only inst/include/boost/accumulators/statistics/rolling_variance.hpp |only inst/include/boost/accumulators/statistics/rolling_window.hpp |only inst/include/boost/accumulators/statistics/skewness.hpp |only inst/include/boost/accumulators/statistics/sum_kahan.hpp |only inst/include/boost/accumulators/statistics/tail.hpp |only inst/include/boost/accumulators/statistics/tail_mean.hpp |only inst/include/boost/accumulators/statistics/tail_quantile.hpp |only inst/include/boost/accumulators/statistics/tail_variate.hpp |only inst/include/boost/accumulators/statistics/tail_variate_means.hpp |only inst/include/boost/accumulators/statistics/times2_iterator.hpp |only inst/include/boost/accumulators/statistics/variates |only inst/include/boost/accumulators/statistics/weighted_covariance.hpp |only inst/include/boost/accumulators/statistics/weighted_density.hpp |only inst/include/boost/accumulators/statistics/weighted_extended_p_square.hpp |only inst/include/boost/accumulators/statistics/weighted_kurtosis.hpp |only inst/include/boost/accumulators/statistics/weighted_mean.hpp |only inst/include/boost/accumulators/statistics/weighted_median.hpp |only inst/include/boost/accumulators/statistics/weighted_moment.hpp |only inst/include/boost/accumulators/statistics/weighted_p_square_cumul_dist.hpp |only inst/include/boost/accumulators/statistics/weighted_p_square_cumulative_distribution.hpp |only inst/include/boost/accumulators/statistics/weighted_p_square_quantile.hpp |only inst/include/boost/accumulators/statistics/weighted_peaks_over_threshold.hpp |only inst/include/boost/accumulators/statistics/weighted_skewness.hpp |only inst/include/boost/accumulators/statistics/weighted_sum.hpp |only inst/include/boost/accumulators/statistics/weighted_sum_kahan.hpp |only inst/include/boost/accumulators/statistics/weighted_tail_mean.hpp |only inst/include/boost/accumulators/statistics/weighted_tail_quantile.hpp |only inst/include/boost/accumulators/statistics/weighted_tail_variate_means.hpp |only inst/include/boost/accumulators/statistics/weighted_variance.hpp |only inst/include/boost/accumulators/statistics/with_error.hpp |only inst/include/boost/serialization/boost_array.hpp |only 61 files changed, 88 insertions(+), 19 deletions(-)
Title: Regression Analysis of Sparse Asynchronous Longitudinal Data
Description: Estimation of regression models for sparse asynchronous longitudinal observations, where time-dependent response and covariates are mismatched and observed intermittently within subjects. Kernel weighted estimating equations are used for generalized linear models with either time-invariant or time-dependent coefficients. Cao, H., Li, J., and Fine, J. P. (2016) <doi:10.1214/16-EJS1141>. Cao, H., Zeng, D., and Fine, J. P. (2015) <doi:10.1111/rssb.12086>.
Author: Hongyuan Cao, Donglin Zeng, Jialiang Li, Jason P. Fine, and Shannon T. Holloway
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
Diff between AsynchLong versions 2.0 dated 2016-01-22 and 2.1 dated 2020-01-08
AsynchLong-2.0/AsynchLong/R/zzz.R |only AsynchLong-2.1/AsynchLong/DESCRIPTION | 10 ++-- AsynchLong-2.1/AsynchLong/MD5 | 41 +++++++++----------- AsynchLong-2.1/AsynchLong/R/SD.R | 4 - AsynchLong-2.1/AsynchLong/R/asynchHK.R | 15 ++++--- AsynchLong-2.1/AsynchLong/R/asynchLV.R | 6 +- AsynchLong-2.1/AsynchLong/R/asynchTD.R | 15 ++++--- AsynchLong-2.1/AsynchLong/R/asynchTI.R | 11 +++-- AsynchLong-2.1/AsynchLong/R/asynchWLV.R | 11 +++-- AsynchLong-2.1/AsynchLong/R/betaHat.R | 2 AsynchLong-2.1/AsynchLong/R/kernelAuto.R | 9 ++-- AsynchLong-2.1/AsynchLong/R/kernelFixed.R | 10 ++-- AsynchLong-2.1/AsynchLong/R/preprocessX.R | 2 AsynchLong-2.1/AsynchLong/R/preprocessY.R | 2 AsynchLong-2.1/AsynchLong/man/AsynchLong-package.Rd | 6 +- AsynchLong-2.1/AsynchLong/man/asynchDataTD.Rd | 3 - AsynchLong-2.1/AsynchLong/man/asynchDataTI.Rd | 3 - AsynchLong-2.1/AsynchLong/man/asynchHK.Rd | 7 +-- AsynchLong-2.1/AsynchLong/man/asynchLV.Rd | 3 - AsynchLong-2.1/AsynchLong/man/asynchTD.Rd | 3 - AsynchLong-2.1/AsynchLong/man/asynchTI.Rd | 3 - AsynchLong-2.1/AsynchLong/man/asynchWLV.Rd | 7 +-- 22 files changed, 95 insertions(+), 78 deletions(-)
Title: Fast Generators and Iterators for Permutations, Combinations,
Integer Partitions and Compositions
Description: Fast generators and iterators for permutations, combinations,
integer partitions and compositions. The arrangements are in
lexicographical order and generated iteratively in a memory efficient manner.
It has been demonstrated that 'arrangements' outperforms most existing
packages of similar kind. Benchmarks could be found at
<https://randy3k.github.io/arrangements/articles/benchmark.html>.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between arrangements versions 1.1.7 dated 2019-11-02 and 1.1.8 dated 2020-01-08
arrangements-1.1.7/arrangements/R/utils.R |only arrangements-1.1.7/arrangements/src/combinations-multiset.h |only arrangements-1.1.7/arrangements/src/combinations-ordinary.h |only arrangements-1.1.7/arrangements/src/combinations-replacement.h |only arrangements-1.1.7/arrangements/src/next |only arrangements-1.1.7/arrangements/src/next.c |only arrangements-1.1.7/arrangements/src/next.h |only arrangements-1.1.7/arrangements/src/partitions-k.h |only arrangements-1.1.7/arrangements/src/partitions-ordinary.h |only arrangements-1.1.7/arrangements/src/partitions_utils.h |only arrangements-1.1.7/arrangements/src/permutations-k.h |only arrangements-1.1.7/arrangements/src/permutations-multiset.h |only arrangements-1.1.7/arrangements/src/permutations-ordinary.h |only arrangements-1.1.7/arrangements/src/permutations-replacement.h |only arrangements-1.1.7/arrangements/tests/testthat/test_combinations.R |only arrangements-1.1.7/arrangements/tests/testthat/test_k_partitions.R |only arrangements-1.1.7/arrangements/tests/testthat/test_k_permutations.R |only arrangements-1.1.7/arrangements/tests/testthat/test_multiset_combinations.R |only arrangements-1.1.7/arrangements/tests/testthat/test_multiset_permutations.R |only arrangements-1.1.7/arrangements/tests/testthat/test_partitions.R |only arrangements-1.1.7/arrangements/tests/testthat/test_permutations.R |only arrangements-1.1.7/arrangements/tests/testthat/test_replace_combinations.R |only arrangements-1.1.7/arrangements/tests/testthat/test_replace_permutations.R |only arrangements-1.1.8/arrangements/DESCRIPTION | 24 - arrangements-1.1.8/arrangements/MD5 | 130 +++++---- arrangements-1.1.8/arrangements/NAMESPACE | 4 arrangements-1.1.8/arrangements/R/arrangements.R | 5 arrangements-1.1.8/arrangements/R/combinations.R | 28 -- arrangements-1.1.8/arrangements/R/compositions.R |only arrangements-1.1.8/arrangements/R/partitions.R | 31 +- arrangements-1.1.8/arrangements/R/permutations.R | 30 -- arrangements-1.1.8/arrangements/README.md | 16 - arrangements-1.1.8/arrangements/man/arrangements-package.Rd | 15 - arrangements-1.1.8/arrangements/man/combinations.Rd | 11 arrangements-1.1.8/arrangements/man/compositions.Rd |only arrangements-1.1.8/arrangements/man/icombinations.Rd | 15 - arrangements-1.1.8/arrangements/man/icompositions.Rd |only arrangements-1.1.8/arrangements/man/ipartitions.Rd | 9 arrangements-1.1.8/arrangements/man/ipermutations.Rd | 15 - arrangements-1.1.8/arrangements/man/ncombinations.Rd | 13 arrangements-1.1.8/arrangements/man/ncompositions.Rd |only arrangements-1.1.8/arrangements/man/npartitions.Rd | 4 arrangements-1.1.8/arrangements/man/npermutations.Rd | 13 arrangements-1.1.8/arrangements/man/partitions.Rd | 10 arrangements-1.1.8/arrangements/man/permutations.Rd | 11 arrangements-1.1.8/arrangements/src/arrangements.c | 35 ++ arrangements-1.1.8/arrangements/src/combinations |only arrangements-1.1.8/arrangements/src/combinations.c | 81 ++--- arrangements-1.1.8/arrangements/src/combinations.h | 2 arrangements-1.1.8/arrangements/src/compositions |only arrangements-1.1.8/arrangements/src/compositions.c |only arrangements-1.1.8/arrangements/src/compositions.h |only arrangements-1.1.8/arrangements/src/macros.h | 64 +--- arrangements-1.1.8/arrangements/src/math.c |only arrangements-1.1.8/arrangements/src/math.h |only arrangements-1.1.8/arrangements/src/partitions |only arrangements-1.1.8/arrangements/src/partitions.c | 139 +++++++--- arrangements-1.1.8/arrangements/src/partitions.h | 4 arrangements-1.1.8/arrangements/src/permutations |only arrangements-1.1.8/arrangements/src/permutations.c | 85 ++---- arrangements-1.1.8/arrangements/src/permutations.h | 2 arrangements-1.1.8/arrangements/src/utils.c | 83 +---- arrangements-1.1.8/arrangements/src/utils.h | 12 arrangements-1.1.8/arrangements/tests/testthat/test-combinations.R |only arrangements-1.1.8/arrangements/tests/testthat/test-compositions.R |only arrangements-1.1.8/arrangements/tests/testthat/test-distinct-k_partitions.R |only arrangements-1.1.8/arrangements/tests/testthat/test-distinct-partitions.R |only arrangements-1.1.8/arrangements/tests/testthat/test-k_compositions.R |only arrangements-1.1.8/arrangements/tests/testthat/test-k_partitions.R |only arrangements-1.1.8/arrangements/tests/testthat/test-k_permutations.R |only arrangements-1.1.8/arrangements/tests/testthat/test-multiset_combinations.R |only arrangements-1.1.8/arrangements/tests/testthat/test-multiset_permutations.R |only arrangements-1.1.8/arrangements/tests/testthat/test-partitions.R |only arrangements-1.1.8/arrangements/tests/testthat/test-permutations.R |only arrangements-1.1.8/arrangements/tests/testthat/test-replace_combinations.R |only arrangements-1.1.8/arrangements/tests/testthat/test-replace_permutations.R |only 76 files changed, 458 insertions(+), 433 deletions(-)
Title: Aggregation Operators and Preordered Sets
Description: Tools supporting multi-criteria and group decision making,
including variable number of criteria, by means of
aggregation operators, spread measures,
fuzzy logic connectives, fusion functions,
and preordered sets. Possible applications include,
but are not limited to, quality management, scientometrics,
software engineering, etc.
Author: Marek Gagolewski [aut, cre] (<https://orcid.org/0000-0003-0637-6028>),
Anna Cena [ctb] (<https://orcid.org/0000-0001-8697-5383>)
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between agop versions 0.2-2 dated 2019-03-08 and 0.2-3 dated 2020-01-08
DESCRIPTION | 19 +++--- MD5 | 124 ++++++++++++++++++++-------------------- NEWS | 16 +++-- R/agop-package.R | 2 R/agops-classical.R | 2 R/agops-dispersion.R | 8 +- R/agops-impact.R | 28 ++++----- R/check-comonotonicity.R | 2 R/distrib-dpareto2-estimators.R | 10 +-- R/distrib-exp-adtest.R | 6 - R/distrib-pareto2-adtest.R | 2 R/distrib-pareto2-estimators.R | 8 +- R/distrib-pareto2-ftest.R | 12 +-- R/rel-assymetry.R | 2 R/rel-examples.R | 2 R/rel-hasse.R | 6 - R/rel-irreflexivity.R | 2 R/rel-other.R | 4 - R/rel-reflexivity.R | 6 - R/rel-totality.R | 2 R/rel-transitivity.R | 2 R/visualization.R | 10 +-- man/agop-package.Rd | 2 man/check_comonotonicity.Rd | 2 man/d2owa.Rd | 6 - man/dpareto2_estimate_mle.Rd | 10 +-- man/exp_test_ad.Rd | 6 - man/index_g.Rd | 4 - man/index_h.Rd | 4 - man/index_lp.Rd | 10 +-- man/index_maxprod.Rd | 4 - man/index_rp.Rd | 4 - man/index_w.Rd | 2 man/owa.Rd | 2 man/pareto2_estimate_mle.Rd | 8 +- man/pareto2_test_ad.Rd | 2 man/pareto2_test_f.Rd | 12 +-- man/plot_producer.Rd | 10 +-- man/pord_nd.Rd | 2 man/rel_asymmetric.Rd | 2 man/rel_graph.Rd | 4 - man/rel_hasse.Rd | 6 - man/rel_irreflexive.Rd | 2 man/rel_reflexive.Rd | 6 - man/rel_total.Rd | 2 man/rel_transitive.Rd | 2 src/adtest.cpp | 12 ++- src/agop.h | 10 +-- src/agops_classical.cpp | 50 ++++++++++------ src/agops_dispersion.cpp | 11 ++- src/agops_impact.cpp | 59 +++++++++++++------ src/check_comonotonicity.cpp | 22 +++++-- src/distrib_pareto2.cpp | 24 ++++--- src/rel_antisymmetry.cpp | 15 +++- src/rel_asymmetry.cpp | 11 ++- src/rel_cyclicity.cpp | 11 ++- src/rel_examples.cpp | 66 ++++++++++++++------- src/rel_hasse.cpp | 5 - src/rel_irreflexivity.cpp | 11 ++- src/rel_reflexivity.cpp | 21 ++++-- src/rel_symmetry.cpp | 16 +++-- src/rel_totality.cpp | 16 +++-- src/rel_transitivity.cpp | 28 ++++++--- 63 files changed, 466 insertions(+), 311 deletions(-)
Title: Distributional Semantic Models in R
Description: An interactive laboratory for research on distributional semantic models ('DSM',
see <https://en.wikipedia.org/wiki/Distributional_semantics> for more information).
Author: Stefan Evert [http://www.stefan-evert.de/]
Maintainer: Stefan Evert <stefan.evert@fau.de>
Diff between wordspace versions 0.2-5 dated 2019-07-13 and 0.2-6 dated 2020-01-08
wordspace-0.2-5/wordspace/tests/context_vectors.R |only wordspace-0.2-5/wordspace/tests/convenience.R |only wordspace-0.2-5/wordspace/tests/dist_matrix.R |only wordspace-0.2-5/wordspace/tests/dsm.R |only wordspace-0.2-5/wordspace/tests/dsm_projection.R |only wordspace-0.2-5/wordspace/tests/dsm_score.R |only wordspace-0.2-5/wordspace/tests/evaluation.R |only wordspace-0.2-5/wordspace/tests/export.R |only wordspace-0.2-5/wordspace/tests/file_formats.R |only wordspace-0.2-5/wordspace/tests/nearest_neighbours.R |only wordspace-0.2-5/wordspace/tests/norms.R |only wordspace-0.2-5/wordspace/tests/pair_distances.R |only wordspace-0.2-5/wordspace/tests/scale_margins.R |only wordspace-0.2-5/wordspace/tests/subset.R |only wordspace-0.2-6/wordspace/DESCRIPTION | 10 - wordspace-0.2-6/wordspace/MD5 | 73 ++++++------- wordspace-0.2-6/wordspace/NEWS | 7 + wordspace-0.2-6/wordspace/R/eval_multiple_choice.R | 5 wordspace-0.2-6/wordspace/build/vignette.rds |binary wordspace-0.2-6/wordspace/data/DSM_GoodsMatrix.rda |binary wordspace-0.2-6/wordspace/data/DSM_HieroglyphsMatrix.rda |binary wordspace-0.2-6/wordspace/data/DSM_SingularValues.rda |binary wordspace-0.2-6/wordspace/data/DSM_TermContext.rda |binary wordspace-0.2-6/wordspace/data/DSM_TermContextMatrix.rda |binary wordspace-0.2-6/wordspace/data/DSM_TermTerm.rda |binary wordspace-0.2-6/wordspace/data/DSM_TermTermMatrix.rda |binary wordspace-0.2-6/wordspace/data/DSM_Vectors.rda |binary wordspace-0.2-6/wordspace/data/DSM_VerbNounTriples_BNC.rda |binary wordspace-0.2-6/wordspace/data/ESSLLI08_Nouns.rda |binary wordspace-0.2-6/wordspace/data/RG65.rda |binary wordspace-0.2-6/wordspace/data/SemCorWSD.rda |binary wordspace-0.2-6/wordspace/data/WordSim353.rda |binary wordspace-0.2-6/wordspace/inst/doc/wordspace-intro.R | 62 +++++------ wordspace-0.2-6/wordspace/inst/doc/wordspace-intro.html | 39 +++--- wordspace-0.2-6/wordspace/inst/extdata/word2vec_hiero.txt | 2 wordspace-0.2-6/wordspace/src/parts/am.cpp | 2 wordspace-0.2-6/wordspace/src/wordspace.cpp | 2 wordspace-0.2-6/wordspace/tests/testthat |only wordspace-0.2-6/wordspace/tests/testthat.R |only 39 files changed, 107 insertions(+), 95 deletions(-)
Title: Quick and Dirty Estimates for Wildlife Populations
Description: Provides simple, fast functions for maximum likelihood and Bayesian estimates of wildlife population parameters, suitable for use with simulated data or bootstraps. Early versions were indeed quick and dirty, but optional error-checking routines and meaningful error messages have been added. Includes single and multi-season occupancy, closed capture population estimation, survival, species richness and distance measures.
Author: Mike Meredith
Maintainer: Mike Meredith <mmeredith@wcs.org>
Diff between wiqid versions 0.2.2 dated 2019-06-05 and 0.2.3 dated 2020-01-08
wiqid-0.2.2/wiqid/README |only wiqid-0.2.2/wiqid/data/GrandSkinks.rda |only wiqid-0.2.2/wiqid/data/KanhaTigers.rda |only wiqid-0.2.2/wiqid/data/KillarneyBirds.rda |only wiqid-0.2.2/wiqid/data/MeadowVoles.rda |only wiqid-0.2.2/wiqid/data/Temburong.rda |only wiqid-0.2.2/wiqid/data/dippers.rda |only wiqid-0.2.2/wiqid/data/distTestData.rda |only wiqid-0.2.2/wiqid/data/railSims.rda |only wiqid-0.2.2/wiqid/data/salamanders.rda |only wiqid-0.2.2/wiqid/data/seedbank.rda |only wiqid-0.2.2/wiqid/data/weta.rda |only wiqid-0.2.3/wiqid/DESCRIPTION | 10 +- wiqid-0.2.3/wiqid/MD5 | 97 ++++++++++---------- wiqid-0.2.3/wiqid/NAMESPACE | 11 +- wiqid-0.2.3/wiqid/NEWS | 32 +++++- wiqid-0.2.3/wiqid/R/Bbinomial.R | 45 ++------- wiqid-0.2.3/wiqid/R/Bnormal.R | 8 + wiqid-0.2.3/wiqid/R/Bnormal_2.R | 12 +- wiqid-0.2.3/wiqid/R/BoccSS.R | 11 +- wiqid-0.2.3/wiqid/R/BoccSS0.R | 10 +- wiqid-0.2.3/wiqid/R/Bpoisson.R | 10 +- wiqid-0.2.3/wiqid/R/Bsecr.R | 10 +- wiqid-0.2.3/wiqid/R/BsurvCJS.R | 11 +- wiqid-0.2.3/wiqid/R/Bwiqid_methods.R | 4 wiqid-0.2.3/wiqid/R/TDist.R | 78 ++++++++++++++-- wiqid-0.2.3/wiqid/R/getMCerror.R | 7 - wiqid-0.2.3/wiqid/R/justRunJags.R | 10 +- wiqid-0.2.3/wiqid/R/occ2sps.R | 12 +- wiqid-0.2.3/wiqid/R/plotPost.R | 49 +++++----- wiqid-0.2.3/wiqid/R/plot_Bwiqid_diag_plots.R | 29 ++++- wiqid-0.2.3/wiqid/R/plot_diagPlot.R | 9 + wiqid-0.2.3/wiqid/R/postPriorOverlap.R | 17 ++- wiqid-0.2.3/wiqid/R/secrFit.R |only wiqid-0.2.3/wiqid/data/GrandSkinks.RData |only wiqid-0.2.3/wiqid/data/KanhaTigers.RData |only wiqid-0.2.3/wiqid/data/KillarneyBirds.RData |only wiqid-0.2.3/wiqid/data/MeadowVoles.RData |only wiqid-0.2.3/wiqid/data/Temburong.RData |only wiqid-0.2.3/wiqid/data/dippers.RData |only wiqid-0.2.3/wiqid/data/distTestData.RData |only wiqid-0.2.3/wiqid/data/railSims.RData |only wiqid-0.2.3/wiqid/data/salamanders.RData |only wiqid-0.2.3/wiqid/data/seedbank.RData |only wiqid-0.2.3/wiqid/data/weta.RData |only wiqid-0.2.3/wiqid/inst/tests/testthat/test-BoccSS.R | 10 +- wiqid-0.2.3/wiqid/man/Bbinomial.Rd | 17 ++- wiqid-0.2.3/wiqid/man/Bnormal.Rd | 22 ++-- wiqid-0.2.3/wiqid/man/BoccSS.Rd | 16 +-- wiqid-0.2.3/wiqid/man/Bpoisson.Rd | 17 ++- wiqid-0.2.3/wiqid/man/Bsecr.Rd | 17 ++- wiqid-0.2.3/wiqid/man/GammaDist.Rd | 2 wiqid-0.2.3/wiqid/man/TDist.Rd | 63 +++++++++++- wiqid-0.2.3/wiqid/man/as_Bwiqid.Rd | 4 wiqid-0.2.3/wiqid/man/linkFunctions.Rd | 4 wiqid-0.2.3/wiqid/man/plotDiagnostics.Rd | 19 ++- wiqid-0.2.3/wiqid/man/plotPost.Rd | 14 +- wiqid-0.2.3/wiqid/man/postPriorOverlap.Rd | 12 +- wiqid-0.2.3/wiqid/man/print_Bwiqid.Rd | 2 wiqid-0.2.3/wiqid/man/secrFit.Rd |only wiqid-0.2.3/wiqid/man/survivalCJS.Rd | 8 - wiqid-0.2.3/wiqid/man/wiqid-package.Rd | 3 62 files changed, 452 insertions(+), 260 deletions(-)
Title: Download Weather Data from the Environment and Climate Change
Canada Website
Description: Provides means for downloading historical weather data from
the Environment and Climate Change Canada website
(<http://climate.weather.gc.ca/historical_data/search_historic_data_e.html>).
Data can be downloaded from multiple stations and over large date ranges
and automatically processed into a single dataset. Tools are also provided
to identify stations either by name or proximity to a location.
Author: Steffi LaZerte [aut, cre] (<https://orcid.org/0000-0002-7690-8360>),
Sam Albers [ctb] (<https://orcid.org/0000-0002-9270-7884>),
Nick Brown [ctb] (<https://orcid.org/0000-0002-2719-0671>)
Maintainer: Steffi LaZerte <steffi@steffi.ca>
Diff between weathercan versions 0.3.1 dated 2019-09-29 and 0.3.2 dated 2020-01-08
DESCRIPTION | 15 +- MD5 | 36 ++-- NEWS.md | 7 R/normals.R | 90 +++++++----- R/utils.R | 3 R/weathercan-pkg.R | 6 build/vignette.rds |binary inst/doc/flags.R | 2 inst/doc/flags.html | 4 inst/doc/glossary.R | 4 inst/doc/glossary.html | 4 inst/doc/glossary_normals.R | 8 - inst/doc/glossary_normals.html | 4 inst/doc/interpolate_data.R | 16 +- inst/doc/interpolate_data.html | 288 ++++++++++++++++++--------------------- inst/doc/normals.html | 4 inst/doc/weathercan.html | 4 man/weathercan-package.Rd | 6 tests/testthat/test_08_normals.R | 41 ++++- 19 files changed, 292 insertions(+), 250 deletions(-)
Title: Display Information About Nested Subsets of a Data Frame
Description: A tool for calculating and drawing "variable trees". Variable trees display information about hierarchical subsets of a data frame defined by values of categorical variables.
Author: Nick Barrowman [aut, cre]
Sebastian Gatscha <kona1@gmx.at> [aut] (Shiny interface)
Andrea Leofreddi <a.leofreddi@vleo.net> [cph] (svg-pan-zoom library)
Maintainer: Nick Barrowman <nbarrowman@cheo.on.ca>
Diff between vtree versions 3.0.0 dated 2019-10-14 and 4.0.0 dated 2020-01-08
DESCRIPTION | 15 MD5 | 77 NAMESPACE | 28 NEWS.md | 330 ++- R/VennTable.R | 195 +- R/around.R | 82 R/build.data.frame.R | 120 - R/convertToHTML.R | 78 R/crosstabToCases.R | 88 - R/data.R | 4 R/flowcat.R | 623 +++---- R/grVizToPNG.R | 94 - R/joinflow.R | 48 R/nodeMeanSD.R | 18 R/shiny.R |only R/showflow.R | 90 - R/splitlines.R | 108 - R/summaryNodeFunction.R | 446 ++--- R/svtree.R |only R/tableWithoutSort.R | 34 R/vtree.R | 3715 ++++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/vtree.R | 535 +++--- inst/doc/vtree.Rmd | 3235 +++++++++++++++++++------------------- inst/doc/vtree.html | 2474 +++++++++++++---------------- inst/examples |only inst/www |only man/FakeData.Rd | 2 man/FakeRCT.Rd | 2 man/VennTable.Rd | 19 man/build.data.frame.Rd | 2 man/crosstabToCases.Rd | 4 man/grVizToPNG.Rd | 8 man/init_js.Rd |only man/inlineCssSetup.Rd |only man/renderVtree.Rd |only man/svtree.Rd |only man/use_svgzoom.Rd |only man/vtree-package.Rd |only man/vtree.Rd | 208 +- man/vtreeOutput.Rd |only tests/testthat.R | 8 tests/testthat/test-vtree.R | 443 ++++- vignettes/vtree.Rmd | 3235 +++++++++++++++++++------------------- vignettes/vtreeVignette.css | 410 ++-- 45 files changed, 8579 insertions(+), 8199 deletions(-)
Title: A Statistically Sound 'data.frame' Processor/Conditioner
Description: A 'data.frame' processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner.
'vtreat' prepares variables so that data has fewer exceptional cases, making
it easier to safely use models in production. Common problems 'vtreat' defends
against: 'Inf', 'NA', too many categorical levels, rare categorical levels, and new
categorical levels (levels seen during application, but not during training). Reference:
"'vtreat': a data.frame Processor for Predictive Modeling", Zumel, Mount, 2016, <DOI:10.5281/zenodo.1173313>.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 1.4.8 dated 2019-12-08 and 1.5.0 dated 2020-01-08
DESCRIPTION | 10 ++-- MD5 | 43 +++++++++-------- NAMESPACE | 3 + NEWS.md | 8 +++ R/customCoder.R | 68 +++++++++++++++++----------- R/ft.R | 91 ++++++++++++++++++++++++++++++++++++-- R/mult_class.R | 49 ++++++++++++++------ R/vtreatImpl.R | 24 ++++++++-- inst/doc/MultiClassVtreat.html | 4 - inst/doc/SavingTreamentPlans.html | 4 - inst/doc/VariableImportance.html | 10 ++-- inst/doc/vtreat.html | 10 ++-- inst/doc/vtreatCrossFrames.html | 38 +++++++-------- inst/doc/vtreatGrouping.html | 4 - inst/doc/vtreatOverfit.html | 38 +++++++-------- inst/doc/vtreatRareLevels.html | 4 - inst/doc/vtreatScaleMode.html | 16 +++--- inst/doc/vtreatSignificance.html | 18 +++---- inst/doc/vtreatSplitting.html | 4 - inst/doc/vtreatVariableTypes.html | 42 ++++++++--------- inst/unit_tests/test_ft.R |only man/makeCustomCoderCat.Rd |only man/makeCustomCoderNum.Rd |only man/reexports.Rd | 2 24 files changed, 319 insertions(+), 171 deletions(-)
Title: Graph Probability Distributions with User Supplied Parameters
and Statistics
Description: Graphs the pdf or pmf and highlights what area or probability is
present in user defined locations. Visualize is able to provide lower tail,
bounded, upper tail, and two tail calculations. Supports strict and equal
to inequalities. Also provided on the graph is the mean and variance of
the distribution.
Author: James Balamuta [aut, cph, cre]
(<https://orcid.org/0000-0003-2826-8458>)
Maintainer: James Balamuta <james.balamuta@gmail.com>
Diff between visualize versions 4.3.0 dated 2017-04-27 and 4.4.0 dated 2020-01-08
DESCRIPTION | 20 +- LICENSE | 4 MD5 | 106 ++++++------ NAMESPACE | 56 +++--- NEWS.md | 286 ++++++++++++++++---------------- R/visualize-distributions.R | 180 ++++++++++---------- R/visualize-package.R | 50 ++--- R/visualize.beta.R | 76 ++++---- R/visualize.binom.R | 78 ++++---- R/visualize.cauchy.R | 70 ++++---- R/visualize.chisq.R | 68 +++---- R/visualize.continuous.R | 340 +++++++++++++++++++------------------- R/visualize.discrete.R | 358 ++++++++++++++++++++--------------------- R/visualize.exp.R | 70 ++++---- R/visualize.f.R | 70 ++++---- R/visualize.gamma.R | 76 ++++---- R/visualize.geom.R | 76 ++++---- R/visualize.hyper.R | 80 ++++----- R/visualize.it.R | 172 +++++++++---------- R/visualize.lnorm.R | 72 ++++---- R/visualize.logis.R | 72 ++++---- R/visualize.nbinom.R | 80 ++++----- R/visualize.norm.R | 64 +++---- R/visualize.pois.R | 74 ++++---- R/visualize.t.R | 70 ++++---- R/visualize.unif.R | 66 +++---- R/visualize.wilcox.R | 72 ++++---- README.md | 136 ++++++++++++++- man/figures |only man/visualize-package.Rd | 92 +++++----- man/visualize.beta.Rd | 100 +++++------ man/visualize.binom.Rd | 102 +++++------ man/visualize.cauchy.Rd | 95 +++++----- man/visualize.chisq.Rd | 90 +++++----- man/visualize.continuous.Rd | 100 +++++------ man/visualize.discrete.Rd | 107 ++++++------ man/visualize.distributions.Rd | 200 +++++++++++----------- man/visualize.exp.Rd | 92 +++++----- man/visualize.f.Rd | 94 +++++----- man/visualize.gamma.Rd | 96 +++++----- man/visualize.geom.Rd | 97 +++++------ man/visualize.hyper.Rd | 106 +++++------- man/visualize.it.Rd | 158 ++++++++---------- man/visualize.lnorm.Rd | 97 +++++------ man/visualize.logis.Rd | 97 +++++------ man/visualize.nbinom.Rd | 104 +++++------ man/visualize.norm.Rd | 80 ++++----- man/visualize.pois.Rd | 96 +++++----- man/visualize.t.Rd | 92 +++++----- man/visualize.unif.Rd | 86 ++++----- man/visualize.wilcox.Rd | 96 +++++----- 51 files changed, 2665 insertions(+), 2554 deletions(-)
Title: Uniform Manifold Approximation and Projection
Description: Uniform manifold approximation and projection is a technique
for dimension reduction. The algorithm was described by McInnes and
Healy (2018) in <arXiv:1802.03426>. This package provides an interface
for two implementations. One is written from scratch, including components
for nearest-neighbor search and for embedding. The second implementation
is a wrapper for 'python' package 'umap-learn' (requires separate
installation, see vignette for more details).
Author: Tomasz Konopka [aut, cre]
Maintainer: Tomasz Konopka <tokonopka@gmail.com>
Diff between umap versions 0.2.4.0 dated 2019-12-07 and 0.2.4.1 dated 2020-01-08
DESCRIPTION | 7 +- MD5 | 16 ++--- R/embedding.R | 8 -- build/vignette.rds |binary inst/doc/umap.R | 38 ++++++------- inst/doc/umap.html | 114 +++++++++++++++++++++------------------- inst/doc/umap_learn.R | 18 +++--- inst/doc/umap_learn.html | 28 +++++---- tests/testthat/test_embedding.R | 78 +++++++++++++-------------- 9 files changed, 154 insertions(+), 153 deletions(-)
Title: Clinical Trial Designs in 'rstan'
Description: A collection of clinical trial designs and methods, implemented in
'rstan' and R, including: the Continual Reassessment Method by O'Quigley et
al. (1990) <doi:10.2307/2531628>; EffTox by Thall & Cook (2004)
<doi:10.1111/j.0006-341X.2004.00218.x>; and the Augmented Binary method by
Wason & Seaman (2013) <doi:10.1002/sim.5867>; and more. We provide functions
to aid model-fitting and analysis. The 'rstan' implementations may also
serve as a cookbook to anyone looking to extend or embellish these models.
We hope that this package encourages the use of Bayesian methods in clinical
trials. There is a preponderance of early phase trial designs because this
is where Bayesian methods are used most. If there is a method you would like
implemented, please get in touch.
Author: Kristian Brock [aut, cre] (<https://orcid.org/0000-0002-3921-0166>),
Trustees of Columbia University [cph]
Maintainer: Kristian Brock <kristian.brock@gmail.com>
Diff between trialr versions 0.1.2 dated 2019-06-25 and 0.1.3 dated 2020-01-08
DESCRIPTION | 8 MD5 | 87 ++-- NAMESPACE | 11 NEWS.md | 4 R/CRM.R | 42 -- R/EffTox.R | 91 ---- R/crm_codified_dose_logistic.R |only R/crm_fit.R | 10 R/crm_path_analysis.R | 12 R/crm_process.R | 1 R/eff_at_dose.R |only R/efftox_analysis_to_df.R |only R/efftox_fit.R | 21 - R/efftox_get_tox.R |only R/efftox_path_analysis.R | 15 R/n_at_dose.R |only R/total_weight_at_dose.R |only R/tox_at_dose.R |only R/weights_at_dose.R |only inst/doc/BEBOP.html | 4 inst/doc/CRM-pathways.R | 13 inst/doc/CRM-pathways.Rmd | 23 + inst/doc/CRM-pathways.html | 241 ++++++------ inst/doc/CRM-visualisation.html | 4 inst/doc/CRM.html | 4 inst/doc/EffTox.html | 4 inst/doc/HierarchicalBayesianResponse.html | 6 inst/doc/LevyCaseStudy.R | 25 + inst/doc/LevyCaseStudy.Rmd | 27 + inst/doc/LevyCaseStudy.html | 544 ++++++++++++++-------------- inst/doc/TITE-CRM.html | 4 man/crm_codified_dose_logistic.Rd | 2 man/crm_fit-class.Rd | 7 man/crm_path_analysis.Rd | 12 man/eff_at_dose.Rd |only man/efftox_analysis_to_df.Rd | 2 man/efftox_get_tox.Rd | 2 man/efftox_path_analysis.Rd | 15 man/figures/README-unnamed-chunk-14-1.png |binary man/n_at_dose.Rd |only man/total_weight_at_dose.Rd |only man/tox_at_dose.Rd |only man/weights_at_dose.Rd |only tests/testthat/test_efftox_dtps.R | 3 tests/testthat/test_efftox_parse_outcomes.R | 1 tests/testthat/test_spread_paths.R | 5 tests/testthat/test_stan_crm.R | 131 +++++- tests/testthat/test_stan_efftox.R | 110 ++++- vignettes/CRM-pathways.Rmd | 23 + vignettes/EffTox_cache/html/__packages | 23 - vignettes/LevyCaseStudy.Rmd | 27 + 51 files changed, 858 insertions(+), 706 deletions(-)
Title: Temporal Sensory Data Analysis
Description: Analysis and visualization of data from temporal sensory methods, including for temporal check-all-that-apply (TCATA) and temporal dominance of sensations (TDS).
Author: J.C. Castura [aut, cre, ctb] (<https://orcid.org/0000-0002-1640-833X>)
Maintainer: J.C. Castura <jcastura@compusense.com>
Diff between tempR versions 0.9.9.15 dated 2018-05-29 and 0.9.9.16 dated 2020-01-08
DESCRIPTION | 17 +- MD5 | 64 ++++---- NAMESPACE | 2 R/tcata.R | 59 +++++--- inst/CITATION | 6 man/adjust.brightness.Rd | 48 +++--- man/bootstrap.band.Rd | 72 ++++----- man/convert.tcata.Rd | 56 +++---- man/convert.tcategory.Rd | 62 ++++---- man/count.selections.Rd | 60 ++++---- man/dist.city.block.Rd | 56 +++---- man/fill.gaps.Rd | 68 ++++----- man/get.chance.Rd | 52 +++---- man/get.decluttered.Rd | 97 ++++++------- man/get.differences.Rd | 86 +++++------ man/get.dominance.rates.Rd | 58 +++---- man/get.mat.diff.sign.Rd | 84 +++++------ man/get.significance.Rd | 64 ++++---- man/get.significance.diff.Rd | 104 +++++++------- man/get.smooth.Rd | 78 +++++----- man/get.times.Rd | 62 ++++---- man/lengthwhichis.na.Rd | 42 ++--- man/make.palettes.Rd | 46 +++--- man/plot_pca.trajectories.Rd | 238 ++++++++++++++++---------------- man/pretty_palette.Rd | 40 ++--- man/similarity.tcata.repeatability.Rd | 92 ++++++------ man/similarity.tcata.replication.Rd | 94 ++++++------ man/std.time.Rd | 131 ++++++++--------- man/tcata.diff.plot.Rd | 174 +++++++++++------------ man/tcata.line.plot.Rd | 248 +++++++++++++++++----------------- man/tds.diff.plot.Rd | 151 ++++++++++---------- man/tds.plot.Rd | 130 ++++++++--------- man/tempR.Rd | 19 +- 33 files changed, 1346 insertions(+), 1314 deletions(-)
Title: Collecting Twitter Data
Description: An implementation of calls designed to collect and organize Twitter data via Twitter's REST and stream Application Program Interfaces (API), which can be found at the following URL: <https://developer.twitter.com/en/docs>.
This package has been peer-reviewed by rOpenSci (v. 0.6.9).
Author: Michael W. Kearney [aut, cre] (<https://orcid.org/0000-0002-0730-4694>),
Andrew Heiss [rev] (<https://orcid.org/0000-0002-3948-3914>),
Francois Briatte [rev]
Maintainer: Michael W. Kearney <kearneymw@missouri.edu>
Diff between rtweet versions 0.6.9 dated 2019-12-19 and 0.7.0 dated 2020-01-08
rtweet-0.6.9/rtweet/R/RcppExports.R |only rtweet-0.6.9/rtweet/man/suggested.Rd |only rtweet-0.6.9/rtweet/src |only rtweet-0.6.9/rtweet/tests/testthat/test-access-level.R |only rtweet-0.6.9/rtweet/tests/testthat/test-graph.R |only rtweet-0.6.9/rtweet/tests/testthat/test_suggested_users.R |only rtweet-0.6.9/rtweet/tests/testthat/twitter_tokens |only rtweet-0.7.0/rtweet/DESCRIPTION | 34 - rtweet-0.7.0/rtweet/MD5 | 235 +++++---- rtweet-0.7.0/rtweet/NAMESPACE | 2 rtweet-0.7.0/rtweet/NEWS.md | 11 rtweet-0.7.0/rtweet/R/as_screenname.R | 1 rtweet-0.7.0/rtweet/R/bearer_token.R | 48 +- rtweet-0.7.0/rtweet/R/coords.R | 28 + rtweet-0.7.0/rtweet/R/direct_messages.R | 14 rtweet-0.7.0/rtweet/R/followers.R | 13 rtweet-0.7.0/rtweet/R/friends.R | 62 ++ rtweet-0.7.0/rtweet/R/graph-network.R | 30 + rtweet-0.7.0/rtweet/R/join_rtweet.R | 4 rtweet-0.7.0/rtweet/R/lists_memberships.R | 1 rtweet-0.7.0/rtweet/R/next_cursor.R | 2 rtweet-0.7.0/rtweet/R/post.R | 14 rtweet-0.7.0/rtweet/R/rate_limit.R | 4 rtweet-0.7.0/rtweet/R/retweets.R | 3 rtweet-0.7.0/rtweet/R/rtweet-package.R | 6 rtweet-0.7.0/rtweet/R/save_as_csv.R | 10 rtweet-0.7.0/rtweet/R/search_tweets.R | 10 rtweet-0.7.0/rtweet/R/statuses.R | 1 rtweet-0.7.0/rtweet/R/stream.R | 1 rtweet-0.7.0/rtweet/R/suggested.R | 6 rtweet-0.7.0/rtweet/R/sysdata.rda |binary rtweet-0.7.0/rtweet/R/timeline.R | 10 rtweet-0.7.0/rtweet/R/tokens.R | 12 rtweet-0.7.0/rtweet/R/ts_plot.R | 3 rtweet-0.7.0/rtweet/R/tweets_and_users.R | 13 rtweet-0.7.0/rtweet/R/users.R | 20 rtweet-0.7.0/rtweet/README.md | 155 ++++-- rtweet-0.7.0/rtweet/build/vignette.rds |binary rtweet-0.7.0/rtweet/inst/CITATION | 22 rtweet-0.7.0/rtweet/inst/assets/logo.png |binary rtweet-0.7.0/rtweet/inst/assets/pkgdown.css | 2 rtweet-0.7.0/rtweet/inst/doc/FAQ.R | 12 rtweet-0.7.0/rtweet/inst/doc/FAQ.Rmd | 10 rtweet-0.7.0/rtweet/inst/doc/FAQ.html | 87 +-- rtweet-0.7.0/rtweet/inst/doc/auth.R | 56 +- rtweet-0.7.0/rtweet/inst/doc/auth.Rmd | 119 ++--- rtweet-0.7.0/rtweet/inst/doc/auth.html | 172 ++++--- rtweet-0.7.0/rtweet/inst/doc/intro.R | 36 - rtweet-0.7.0/rtweet/inst/doc/intro.html | 259 +++++----- rtweet-0.7.0/rtweet/inst/doc/stream.R | 21 rtweet-0.7.0/rtweet/inst/doc/stream.Rmd | 10 rtweet-0.7.0/rtweet/inst/doc/stream.html | 333 +++----------- rtweet-0.7.0/rtweet/man/as_screenname.Rd | 9 rtweet-0.7.0/rtweet/man/bearer_token.Rd | 47 + rtweet-0.7.0/rtweet/man/create_token.Rd | 15 rtweet-0.7.0/rtweet/man/direct_messages.Rd | 19 rtweet-0.7.0/rtweet/man/direct_messages_received.Rd | 16 rtweet-0.7.0/rtweet/man/do_call_rbind.Rd | 3 rtweet-0.7.0/rtweet/man/figures/logo.png |binary rtweet-0.7.0/rtweet/man/flatten.Rd | 10 rtweet-0.7.0/rtweet/man/get_collections.Rd | 10 rtweet-0.7.0/rtweet/man/get_favorites.Rd | 25 - rtweet-0.7.0/rtweet/man/get_followers.Rd | 18 rtweet-0.7.0/rtweet/man/get_friends.Rd | 18 rtweet-0.7.0/rtweet/man/get_mentions.Rd | 25 - rtweet-0.7.0/rtweet/man/get_my_timeline.Rd | 25 - rtweet-0.7.0/rtweet/man/get_retweeters.Rd | 6 rtweet-0.7.0/rtweet/man/get_retweets.Rd | 3 rtweet-0.7.0/rtweet/man/get_timeline.Rd | 46 + rtweet-0.7.0/rtweet/man/get_tokens.Rd | 5 rtweet-0.7.0/rtweet/man/get_trends.Rd | 13 rtweet-0.7.0/rtweet/man/invalidate_bearer.Rd | 1 rtweet-0.7.0/rtweet/man/lat_lng.Rd | 3 rtweet-0.7.0/rtweet/man/lists_members.Rd | 35 + rtweet-0.7.0/rtweet/man/lists_statuses.Rd | 41 + rtweet-0.7.0/rtweet/man/lists_subscribers.Rd | 31 - rtweet-0.7.0/rtweet/man/lists_subscriptions.Rd | 12 rtweet-0.7.0/rtweet/man/lists_users.Rd | 9 rtweet-0.7.0/rtweet/man/lookup_coords.Rd | 17 rtweet-0.7.0/rtweet/man/lookup_friendships.Rd | 3 rtweet-0.7.0/rtweet/man/lookup_statuses.Rd | 15 rtweet-0.7.0/rtweet/man/lookup_users.Rd | 10 rtweet-0.7.0/rtweet/man/my_friendships.Rd | 3 rtweet-0.7.0/rtweet/man/next_cursor.Rd | 28 - rtweet-0.7.0/rtweet/man/parse_stream.Rd | 3 rtweet-0.7.0/rtweet/man/post_favorite.Rd | 14 rtweet-0.7.0/rtweet/man/post_follow.Rd | 17 rtweet-0.7.0/rtweet/man/post_friendship.Rd | 6 rtweet-0.7.0/rtweet/man/post_list.Rd | 13 rtweet-0.7.0/rtweet/man/post_tweet.Rd | 18 rtweet-0.7.0/rtweet/man/rate_limit.Rd | 7 rtweet-0.7.0/rtweet/man/read_twitter_csv.Rd | 5 rtweet-0.7.0/rtweet/man/round_time.Rd | 1 rtweet-0.7.0/rtweet/man/rtweet-package.Rd | 10 rtweet-0.7.0/rtweet/man/search_30day.Rd | 12 rtweet-0.7.0/rtweet/man/search_fullarchive.Rd | 12 rtweet-0.7.0/rtweet/man/search_tweets.Rd | 39 + rtweet-0.7.0/rtweet/man/search_users.Rd | 13 rtweet-0.7.0/rtweet/man/stream_tweets.Rd | 14 rtweet-0.7.0/rtweet/man/suggested_users.Rd | 10 rtweet-0.7.0/rtweet/man/trends_available.Rd | 3 rtweet-0.7.0/rtweet/man/tweet_shot.Rd | 6 rtweet-0.7.0/rtweet/man/tweets_data.Rd | 21 rtweet-0.7.0/rtweet/man/tweets_with_users.Rd | 31 - rtweet-0.7.0/rtweet/man/users_data.Rd | 15 rtweet-0.7.0/rtweet/man/write_as_csv.Rd | 18 rtweet-0.7.0/rtweet/tests/testthat/test_aaa.R |only rtweet-0.7.0/rtweet/tests/testthat/test_access_level.R |only rtweet-0.7.0/rtweet/tests/testthat/test_get_favorites.R | 1 rtweet-0.7.0/rtweet/tests/testthat/test_get_followers.R | 20 rtweet-0.7.0/rtweet/tests/testthat/test_get_friends.R | 18 rtweet-0.7.0/rtweet/tests/testthat/test_graph.R |only rtweet-0.7.0/rtweet/tests/testthat/test_lookup_coords.R | 17 rtweet-0.7.0/rtweet/tests/testthat/test_search_tweets.R | 6 rtweet-0.7.0/rtweet/tests/testthat/test_tweet_shot.R | 12 rtweet-0.7.0/rtweet/tests/testthat/test_zzz.R |only rtweet-0.7.0/rtweet/tools/readme/example-tmls.png |binary rtweet-0.7.0/rtweet/vignettes/FAQ.Rmd | 10 rtweet-0.7.0/rtweet/vignettes/auth.Rmd | 119 ++--- rtweet-0.7.0/rtweet/vignettes/files/create-app-1.png |only rtweet-0.7.0/rtweet/vignettes/files/create-app-2.png |only rtweet-0.7.0/rtweet/vignettes/files/create-app-3.png |only rtweet-0.7.0/rtweet/vignettes/files/create-app-4.png |only rtweet-0.7.0/rtweet/vignettes/files/create-app-5.png |only rtweet-0.7.0/rtweet/vignettes/files/create-app-6.png |only rtweet-0.7.0/rtweet/vignettes/files/create-app-7.png |only rtweet-0.7.0/rtweet/vignettes/stream.Rmd | 10 127 files changed, 1688 insertions(+), 1226 deletions(-)
Title: Relational Query Generator for Data Manipulation at Scale
Description: A piped query generator based on Edgar F. Codd's relational
algebra, and on production experience using 'SQL' and 'dplyr' at big data
scale. The design represents an attempt to make 'SQL' more teachable by
denoting composition by a sequential pipeline notation instead of nested
queries or functions. The implementation delivers reliable high
performance data processing on large data systems such as 'Spark',
databases, and 'data.table'. Package features include: data processing trees
or pipelines as observable objects (able to report both columns
produced and columns used), optimized 'SQL' generation as an explicit
user visible table modeling step, plus explicit query reasoning and checking.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rquery versions 1.4.0 dated 2019-12-01 and 1.4.1 dated 2020-01-08
DESCRIPTION | 10 MD5 | 48 ++-- NEWS.md | 7 R/arrow.R | 20 - R/drop_columns.R | 6 R/extend.R | 4 R/order_by.R | 8 R/order_expr.R | 2 build/vignette.rds |binary inst/doc/AssigmentPartitioner.html | 20 - inst/doc/Parameterized_rquery.html | 20 - inst/doc/PipeableSQL.html | 420 +++++++++++++++++------------------- inst/doc/QueryGeneration.html | 26 +- inst/doc/R_mapping.html | 24 -- inst/doc/rquery_intro.html | 36 +-- inst/doc/rquery_many_columns.R |only inst/doc/rquery_many_columns.Rmd |only inst/doc/rquery_many_columns.html |only inst/doc/rquery_substitution.html | 34 +- inst/doc/sql_quoting.html | 30 +- inst/unit_tests/test_drop_columns.R | 15 + man/arrow.Rd | 4 man/drop_columns.Rd | 2 man/order_expr_se.Rd | 2 man/order_rows.Rd | 4 man/orderby.Rd | 4 vignettes/rquery_many_columns.Rmd |only 27 files changed, 379 insertions(+), 367 deletions(-)
Title: Provides 'mio' C++11 Header Files
Description: Provides header files of 'mio', a cross-platform C++11 header-only
library for memory mapped file IO <https://github.com/mandreyel/mio>.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between rmio versions 0.1.2 dated 2019-02-22 and 0.1.3 dated 2020-01-08
DESCRIPTION | 6 MD5 | 22 NAMESPACE | 4 R/rmio-package.R | 4 README.md | 4 inst/COPYRIGHTS | 56 - inst/include/mio/CMakeLists.txt | 27 inst/include/mio/detail/CMakeLists.txt | 13 inst/include/mio/detail/mmap.ipp | 1037 ++++++++++++++++----------------- inst/include/mio/mmap.hpp | 30 inst/include/mio/shared_mmap.hpp | 6 man/rmio-package.Rd | 48 - 12 files changed, 622 insertions(+), 635 deletions(-)
Title: Tools to Accompany the 'psych' Package for Psychological
Research
Description: Support functions, data sets, and vignettes for the 'psych' package. Contains several of the biggest data sets for the 'psych' package as well as one vignette. A few helper functions for file manipulation are included as well. For more information, see the <https://personality-project.org/r> web page.
Author: William Revelle [aut, cre] (<https://orcid.org/0000-0003-4880-9610>)
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psychTools versions 1.9.5.26 dated 2019-05-29 and 1.9.12 dated 2020-01-08
DESCRIPTION | 12 ++-- MD5 | 112 +++++++++++++++++++++++------------------- NAMESPACE | 4 - R/df2latex.R | 7 +- R/read.clipboard.R | 4 + build/vignette.rds |binary data/Damian.rda |only data/Schutz.rda |binary data/USAF.rda |only data/ability.rda |binary data/affect.rda |binary data/bfi.dictionary.rda |binary data/bfi.rda |binary data/blant.rda |binary data/blot.rda |binary data/burt.rda |binary data/cities.rda |binary data/cubits.rda |binary data/cushny.rda |binary data/epi.bfi.rda |binary data/epi.dictionary.rda |binary data/epi.rda |binary data/epiR.rda |binary data/galton.rda |binary data/heights.rda |binary data/holzinger.dictionary.rda |only data/holzinger.raw.rda |only data/holzinger.swineford.rda |only data/income.rda |binary data/iqitems.rda |binary data/msq.rda |binary data/msqR.rda |binary data/neo.rda |binary data/peas.rda |binary data/sai.dictionary.rda |binary data/sai.rda |binary data/spi.dictionary.rda |binary data/spi.keys.rda |binary data/spi.rda |binary data/tai.rda |binary data/vegetables.rda |binary inst/CITATION | 4 - inst/NEWS.Rd | 31 ++++++++++- inst/doc/factor.R |only inst/doc/factor.Rnw |only inst/doc/factor.pdf |only inst/doc/overview.pdf |binary man/ability.Rd | 5 + man/bfi.Rd | 5 + man/cities.Rd | 21 +++---- man/df2latex.Rd | 3 - man/epi.Rd | 17 +----- man/holzinger.swineford.Rd |only man/iqitems.Rd | 2 man/msq.Rd | 2 man/msqR.rd | 2 man/psychTools.Rd | 12 +++- man/read.clipboard.Rd | 10 +++ man/sai.Rd | 13 ++++ man/spengler.Rd |only man/spi.Rd | 2 man/usaf.Rd |only vignettes/factor.Rnw |only 63 files changed, 163 insertions(+), 105 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-20 1.9.12
2019-01-12 1.8.12
2018-10-31 1.8.10
2018-05-06 1.8.4
2018-03-30 1.8.3.3
2017-09-09 1.7.8
2017-05-03 1.7.5
2017-03-22 1.7.3.21
2017-01-08 1.6.12
2016-09-17 1.6.9
2016-06-28 1.6.6
2016-05-12 1.6.4
2015-08-30 1.5.8
2015-07-08 1.5.6
2015-04-27 1.5.4
2015-01-21 1.5.1
2014-08-12 1.4.8.11
2014-08-10 1.4.8
2014-05-14 1.4.5
2014-04-14 1.4.4
2014-03-25 1.4.3
2014-02-04 1.4.2.3
2014-02-03 1.4.2
2014-01-20 1.4.1
2013-12-12 1.3.12
2013-10-14 1.3.10.12
2013-10-07 1.3.10
2013-02-26 1.3.2
2013-01-20 1.2.12
2012-09-07 1.2.8
2012-05-02 1.2.4
2012-02-16 1.2.1
2012-01-02 1.1.12
2011-11-15 1.1.1111
2011-11-02 1.1.11
2011-10-17 1.1.10
2011-06-09 1.0-98
2011-05-15 1.0-97
2011-04-06 1.0-96
2011-03-31 1.0-95
2011-01-09 1.0-94
2010-12-23 1.0-93
2010-09-22 1.0-92
2010-09-15 1.0-91
2010-07-24 1.0-90
2010-06-28 1.0-89
2010-04-27 1.0-88
2010-04-06 1.0-87
2009-12-20 1.0-85
2009-10-26 1.0-83
2009-10-05 1.0-81
2009-09-30 1.0-80
2009-07-30 1.0-78
2009-07-27 1.0-77
2009-07-18 1.0-76
2009-07-01 1.0-75
2009-06-26 1.0-74
2009-06-02 1.0-72
2009-05-25 1.0-70
2009-03-27 1.0-67
2009-02-08 1.0-65
2009-01-25 1.0-63
2009-01-05 1.0-61
2009-01-05 1.0-62
2008-09-10 1.0-58
2008-07-12 1.0-51
2008-03-24 1.0-42
2007-10-11 1.0-33
2007-08-03 1.0-27
2007-06-04 1.0-25
Title: Extract Decennial Census and American Community Survey Data
Description: Download summary files from Census Bureau <https://www2.census.gov/>
and extract data, in particular high resolution data at
block, block group, and tract level, from decennial census and
American Community Survey 1-year and 5-year estimates.
Author: Guanglai Li
Maintainer: Guanglai Li <liguanglai@gmail.com>
Diff between totalcensus versions 0.6.2 dated 2019-09-29 and 0.6.3 dated 2020-01-08
DESCRIPTION | 10 ++--- MD5 | 30 ++++++++------- R/data_acs.R | 28 ++++++++++++++ R/quiet_global_variable_in_cran_check.R | 3 + R/read_decennial.R | 61 +++++++++++++++----------------- R/search_census_and_acs.R | 17 +++++--- data/datalist | 1 data/dict_acs5_table.RData |binary data/lookup_acs5year_2018.RData |only man/convert_fips_to_names.Rd | 8 +++- man/lookup_acs5year_2018.Rd |only man/read_acs1year.Rd | 15 ++++++- man/read_acs5year.Rd | 15 ++++++- man/read_decennial.Rd | 20 ++++++---- man/search_geocomponents.Rd | 3 - man/search_summarylevels.Rd | 3 - man/search_tablecontents.Rd | 3 - 17 files changed, 138 insertions(+), 79 deletions(-)
Title: Autograph R for 'Tensorflow'
Description: Translate R control flow expressions into 'Tensorflow' graphs.
Author: Tomasz Kalinowski [aut, cre]
Maintainer: Tomasz Kalinowski <kalinowskit@gmail.com>
Diff between tfautograph versions 0.1.0 dated 2019-10-09 and 0.2.0 dated 2020-01-08
DESCRIPTION | 8 - MD5 | 47 +++++----- NAMESPACE | 1 R/ctrl-deps.R | 13 -- R/for-dataset.R | 37 ++++--- R/for-tensor.R | 5 - R/if.R | 17 +-- R/loop-common.R | 11 +- R/methods.R | 7 + R/outcome.R | 7 + R/tf-ctrl-flow-wrappers.R | 14 +- R/tf_map.R |only R/undefs.R | 12 +- README.md | 11 +- man/ag_if_vars.Rd | 9 + man/ag_loop_vars.Rd | 13 +- man/ag_while_opts.Rd | 10 +- man/autograph.Rd | 2 man/reexports.Rd | 2 man/sub-subset-.tensorflow.python.ops.tensor_array_ops.TensorArray.Rd | 3 man/tf_assert.Rd | 9 + man/tf_case.Rd | 11 +- man/tf_map.Rd |only man/tf_switch.Rd | 9 + man/view_function_graph.Rd | 12 +- tests/testthat/test-map.R |only 26 files changed, 158 insertions(+), 112 deletions(-)
Title: MLE of a Truncated Normal Distribution with Censored Data
Description: Maximum likelihood estimation (MLE) of parameters assuming an underlying left truncated normal distribution with left censoring described in Williams, J, Kim, H, and Crespi, C. (2019) <arXiv:1911.11221>. Censoring is assumed to occur above the truncation threshold meaning that only censored observations are observed. Additional maximum likelihood estimation procedures are implemented to solve left censored only and left truncated only problems.
Author: Justin Williams [aut, cre]
Maintainer: Justin Williams <williazo@ucla.edu>
Diff between tcensReg versions 0.1.4 dated 2019-12-18 and 0.1.5 dated 2020-01-08
DESCRIPTION | 6 - MD5 | 18 +++-- NEWS |only R/rtnorm.R | 19 +++-- inst/doc/tcensReg.R | 10 +-- inst/doc/tcensReg.Rmd | 13 ++- inst/doc/tcensReg.html | 162 ++++++++++++++++++++++++------------------------- inst/script |only man/rtnorm.Rd | 9 +- vignettes/tcensReg.Rmd | 13 ++- 10 files changed, 135 insertions(+), 115 deletions(-)
Title: Comparing Multiple Survival Functions with Crossing Hazards in R
Description: Contains routines for computing the one-sided/two-sided integrated/maximally selected EL statistics for simultaneous testing, the one-sided/two-sided EL tests for pointwise testing, and an initial test that precedes one-sided testing to exclude the possibility of crossings or alternative orderings among the survival functions.
Author: Hsin-wen Chang [aut, cre] <hwchang@stat.sinica.edu.tw>
Maintainer: Guo-You Lan <jj6020770416jj@gmail.com>
Diff between survELtest versions 1.0.1 dated 2019-02-17 and 2.0.0 dated 2020-01-08
DESCRIPTION | 13 MD5 | 103 ++++-- NAMESPACE | 11 R/a_1.R | 37 +- R/a_1_k.R | 4 R/checkInput_formula_data.R |only R/checkInputs.R |only R/constraints_h.R |only R/division00.R | 12 R/fnc_objective_h.R |only R/gnc_objective_h.R |only R/hazardcross.R |only R/hazardcross._Weibull.R |only R/hepatitis.R | 16 - R/intELtest.R | 112 ++++--- R/jac_constraints_h.R |only R/lambda0.R | 37 +- R/lambda0_k.R | 3 R/neg2ELratio.R | 327 ++------------------ R/neg2ELratio_EL.R |only R/neg2ELratio_bootstrap.R |only R/neg2ELratio_bootstrap_results.R |only R/neg2ELratio_compute_supELtest_n_intELtest.R |only R/neg2ELratio_nocrossings.R |only R/neg2ELratio_t1t2.R |only R/neg_log_likelihood_le_t_eq_h_k.R | 71 ---- R/neg_log_likelihood_le_t_glob_h_k.R | 1 R/neg_log_likelihood_le_t_ineq_h_k.R | 68 ---- R/nocrossings.R | 113 ++++--- R/print.intELtest.R |only R/print.nocrossings.R |only R/print.ptwiseELtest.R |only R/print.supELtest.R |only R/processInput_data.R |only R/processInput_formula.R |only R/processInput_group_order.R |only R/product.R | 12 R/product_mat.R | 16 - R/ptwiseELtest.R | 134 +++++--- R/sigma2_hat.R | 26 - R/sigma2_hat_S1mS2.R | 48 +-- R/summary.intELtest.R |only R/summary.nocrossings.R |only R/summary.ptwiseELtest.R |only R/summary.supELtest.R |only R/supELtest.R | 139 +++++--- R/teststat.R | 412 ++------------------------ R/teststat_bootstrap.R |only R/teststat_bootstrap_results.R |only R/teststat_compute_supELtest_n_intELtest.R |only R/teststat_neg2logR.R |only R/teststat_nocrossings.R |only R/teststat_t1t2.R |only R/theta_hat_j_k.R | 4 R/threearm.R | 2 data/hazardcross.rda |only data/hazardcross_Weibull.rda |only data/threearm.rda |binary man/hazardcross.Rd |only man/hazardcross_Weibull.Rd |only man/hepatitis.Rd | 15 man/intELtest.Rd | 96 +++--- man/nocrossings.Rd | 96 +++--- man/print.intELtest.Rd |only man/print.nocrossings.Rd |only man/print.ptwiseELtest.Rd |only man/print.supELtest.Rd |only man/ptwiseELtest.Rd | 118 +++++-- man/summary.intELtest.Rd |only man/summary.nocrossings.Rd |only man/summary.ptwiseELtest.Rd |only man/summary.supELtest.Rd |only man/supELtest.Rd | 112 ++++--- man/threearm.Rd | 2 74 files changed, 885 insertions(+), 1275 deletions(-)
Title: Create Tessellated Hexagon Maps
Description: Create a hexagon tilegram from spatial polygons. Each polygon is
represented by a hexagon tile, placed as close to it's original centroid
as possible, with a focus on maintaining spatial relationship to a focal
point. Developed to aid visualisation and analysis of spatial distributions
across Australia, which can be challenging due to the concentration of the
population on the coast and wide open interior.
Author: Stephanie Kobakian [aut, cre],
Dianne Cook [aut, ths]
Maintainer: Stephanie Kobakian <stephanie.kobakian@gmail.com>
Diff between sugarbag versions 0.1.1 dated 2019-08-20 and 0.1.2 dated 2020-01-08
DESCRIPTION | 13 ++- MD5 | 64 +++++++++---------- NAMESPACE | 2 NEWS.md | 4 + R/allocate.R | 134 ++++++++++++++++++++++++++++++---------- R/create_centroids.R | 11 ++- R/create_hexmap.R | 9 +- R/fortify_hexagon.R | 1 R/global.R | 7 +- inst/doc/abs-data.R | 2 inst/doc/abs-data.html | 7 -- inst/doc/tasmania.R | 37 +++++------ inst/doc/tasmania.Rmd | 21 +++--- inst/doc/tasmania.html | 36 +++++----- man/allocate.Rd | 120 +++++++++++++++++++---------------- man/capital_cities.Rd | 40 +++++------ man/closest_focal_point.Rd | 54 ++++++++-------- man/create_buffer.Rd | 54 ++++++++-------- man/create_centroids.Rd | 51 ++++++++------- man/create_grid.Rd | 62 +++++++++--------- man/create_hexmap.Rd | 114 ++++++++++++++++++---------------- man/filter_grid_points.Rd | 76 ++++++++++++---------- man/fortify_hexagon.Rd | 81 ++++++++++++------------ man/fortify_sfc.Rd | 42 ++++++------ man/fp19.Rd | 70 ++++++++++---------- man/homeless.Rd | 36 +++++----- man/read_shape.Rd | 62 +++++++++--------- man/reexports.Rd | 30 ++++---- man/sugarbag-package.Rd | 70 ++++++++++---------- man/tas_lga.Rd | 46 ++++++------- man/tas_sa2.Rd | 68 ++++++++++---------- tests/testthat/test-centroids.R | 7 +- vignettes/tasmania.Rmd | 21 +++--- 33 files changed, 788 insertions(+), 664 deletions(-)
Title: Scale Invariant Probabilistic Neural Networks
Description: Scale invariant version of the original PNN proposed by Specht (1990) <doi:10.1016/0893-6080(90)90049-q> with the added functionality of allowing for smoothing along multiple dimensions while accounting for covariances within the data set. It is written in the R statistical programming language. Given a data set with categorical variables, we use this algorithm to estimate the probabilities of a new observation vector belonging to a specific category. This type of neural network provides the benefits of fast training time relative to backpropagation and statistical generalization with only a small set of known observations.
Author: Romin Ebrahimi
Maintainer: Romin Ebrahimi <romin.ebrahimi@utexas.edu>
Diff between spnn versions 1.2 dated 2019-09-12 and 1.2.1 dated 2020-01-08
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 4 ++++ R/cspnn.predict.R | 2 ++ R/spnn.predict.R | 2 ++ build/partial.rdb |binary man/cspnn.learn.Rd | 4 +++- man/cspnn.predict.Rd | 4 +++- man/spnn-package.Rd | 4 +++- 9 files changed, 29 insertions(+), 15 deletions(-)
Title: The Official SolveBio API Client
Description: R language bindings for SolveBio's API.
SolveBio is a biomedical knowledge hub that enables life science
organizations to collect and harmonize the complex, disparate
"multi-omic" data essential for today's R&D and BI needs.
For more information, visit <https://www.solvebio.com>.
Author: David Caplan
Maintainer: David Caplan <dcaplan@solvebio.com>
Diff between solvebio versions 2.7.1 dated 2019-12-16 and 2.7.2 dated 2020-01-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 5 +++++ R/shiny.R | 4 ++-- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Some Movies to Illustrate Concepts in Statistics
Description: Provides movies to help students to understand statistical
concepts. The 'rpanel' package <https://cran.r-project.org/package=rpanel>
is used to create interactive plots that move to illustrate key statistical
ideas and methods. There are movies to: visualise probability distributions
(including user-supplied ones); illustrate sampling distributions of the
sample mean (central limit theorem), the median, the sample maximum
(extremal types theorem) and (the Fisher transformation of the) Pearson
product moment correlation coefficient; examine the influence of an
individual observation in simple linear regression; illustrate key concepts
in statistical hypothesis testing. Also provided are dpqr functions for the
distribution of the Fisher transformation of the correlation coefficient
under sampling from a bivariate normal distribution.
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between smovie versions 1.1.1 dated 2019-11-25 and 1.1.2 dated 2020-01-08
DESCRIPTION | 15 - MD5 | 46 ++-- NAMESPACE | 2 NEWS.md | 6 R/central_limit_theorem.R | 7 R/continuous.R | 8 R/correlation.R | 9 R/extremal_types_theorem.R | 5 R/fisher_pearson.R | 261 +++++++++++----------- R/quantile_central_limit_theorem.R | 7 inst/doc/smovie-vignette.html | 4 man/FPearson.Rd | 153 ++++++------- man/clt.Rd | 326 ++++++++++++++-------------- man/cltq.Rd | 334 +++++++++++++++-------------- man/continuous.Rd | 296 +++++++++++++------------- man/correlation.Rd | 190 ++++++++-------- man/discrete.Rd | 289 +++++++++++++------------ man/ett.Rd | 420 ++++++++++++++++++------------------- man/lev_inf.Rd | 153 ++++++------- man/mean_vs_median.Rd | 227 ++++++++++--------- man/movies.Rd | 80 +++---- man/shypo.Rd | 219 ++++++++++--------- man/smovie.Rd | 149 ++++++------- man/wws.Rd | 366 ++++++++++++++++---------------- 24 files changed, 1858 insertions(+), 1714 deletions(-)
Title: Automatic Calculation of Effects for Piecewise Structural
Equation Models
Description: Provides functionality to automatically calculate direct, indirect,
and total effects from piecewise structural equation models, comprising
lists of fitted models representing structured equations (Lefcheck 2016
<doi:10/f8s8rb>). Confidence intervals are provided via bootstrapping.
Author: Mark Murphy [aut, cre]
Maintainer: Mark Murphy <murphymv@gmail.com>
Diff between semEff versions 0.1.0 dated 2019-11-04 and 0.2.0 dated 2020-01-08
DESCRIPTION | 8 MD5 | 74 +++---- NAMESPACE | 2 NEWS.md | 17 + R/boot_fun.R | 32 +-- R/data.R | 6 R/helper_fun.R | 29 +- R/sem_eff_fun.R | 24 +- R/std_coeff_fun.R | 360 +++++++++++++++++++----------------- README.md | 9 inst/WORDLIST | 12 + man/Object.Type.Rd | 103 +++++----- man/Param.Type.Rd | 74 +++---- man/R2.Rd | 375 +++++++++++++++++++------------------- man/Shipley.Growth.Rd | 70 +++---- man/Shipley.Rd | 70 +++---- man/Shipley.SEM.Boot.Rd | 60 +++--- man/Shipley.SEM.Eff.Rd | 58 ++--- man/Shipley.SEM.Rd | 70 +++---- man/VIF.Rd | 122 ++++++------ man/avgEst.Rd | 184 +++++++++--------- man/bootCI.Rd | 196 +++++++++----------- man/bootEff.Rd | 342 +++++++++++++++++----------------- man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/getData.Rd | 101 +++++----- man/getEff.Rd | 98 +++++----- man/getY.Rd | 335 +++++++++++++++++----------------- man/pSapply.Rd | 113 ++++++----- man/predEff.Rd | 382 ++++++++++++++++++++------------------- man/print.semEff.Rd | 32 +-- man/rMapply.Rd | 98 +++++----- man/sdW.Rd | 48 ++-- man/semEff-package.Rd | 52 ++--- man/semEff.Rd | 291 +++++++++++++++-------------- man/stdCoeff.Rd | 367 +++++++++++++++++++------------------ man/varW.Rd | 96 ++++----- man/xNam.Rd | 102 +++++----- 38 files changed, 2264 insertions(+), 2148 deletions(-)
Title: Construct and Compare scGRN from Single-Cell Transcriptomic Data
Description: A workflow based on machine learning methods to construct and compare single-cell gene regulatory networks (scGRN) using single-cell RNA-seq (scRNA-seq) data collected from different conditions. Uses principal component regression, tensor decomposition, and manifold alignment, to accurately identify even subtly shifted gene expression programs.
Author: Daniel Osorio [aut, cre] (<https://orcid.org/0000-0003-4424-8422>),
Yan Zhong [aut, ctb],
Guanxun Li [aut, ctb],
Jianhua Huang [aut, ctb],
James Cai [aut, ctb, ths] (<https://orcid.org/0000-0002-8081-6725>)
Maintainer: Daniel Osorio <dcosorioh@tamu.edu>
Diff between scTenifoldNet versions 1.0.0 dated 2019-12-15 and 1.1.0 dated 2020-01-08
scTenifoldNet-1.0.0/scTenifoldNet/R/dCoexpression.R |only scTenifoldNet-1.0.0/scTenifoldNet/inst/python/__pycache__ |only scTenifoldNet-1.0.0/scTenifoldNet/man/dCoexpression.Rd |only scTenifoldNet-1.1.0/scTenifoldNet/DESCRIPTION | 10 +++---- scTenifoldNet-1.1.0/scTenifoldNet/MD5 | 13 ++++------ scTenifoldNet-1.1.0/scTenifoldNet/NAMESPACE | 2 - scTenifoldNet-1.1.0/scTenifoldNet/R/dRegulation.R |only scTenifoldNet-1.1.0/scTenifoldNet/R/scTenifoldNet.R | 18 +++++++------- scTenifoldNet-1.1.0/scTenifoldNet/man/dRegulation.Rd |only scTenifoldNet-1.1.0/scTenifoldNet/man/scTenifoldNet.Rd | 12 ++++----- 10 files changed, 27 insertions(+), 28 deletions(-)
Title: A Method to Download Department of Education College Scorecard
Data
Description: A method to download Department of Education College
Scorecard data using the public API
<https://collegescorecard.ed.gov/data/documentation/>. It is based on
the 'dplyr' model of piped commands to select and filter data in a
single chained function call. An API key from the U.S. Department of
Education is required.
Author: Benjamin Skinner [aut, cre] (<https://orcid.org/0000-0002-0337-7415>)
Maintainer: Benjamin Skinner <btskinner@coe.ufl.edu>
Diff between rscorecard versions 0.13.0 dated 2019-10-01 and 0.14.0 dated 2020-01-08
DESCRIPTION | 11 +++-- MD5 | 20 +++++----- NEWS.md | 12 ++++++ R/dictionary.R | 96 ++++++++++++++++++++++++++++++++++---------------- R/get.R | 46 ++++++++++++++++++----- R/sysdata.rda |binary R/utility_functions.R | 48 ++++++++++++++++++------- man/rscorecard.Rd | 1 man/sc_dict.Rd | 26 +++++++++++-- man/sc_filter.Rd | 2 - man/sc_get.Rd | 11 +++++ 11 files changed, 199 insertions(+), 74 deletions(-)
Title: Geographic Profiling Methods for Serial Crime Analysis
Description: An implementation of functions for the analysis of serial crime
incidents. The package implements algorithms for the geographical profiling
of serial incidents in attempt to prioritize the area in which the anchor
point or home base of the perpetrator is located. The geographic profiling
methods in the package are implemented based upon the 'Dragnet' software
by Canter, Coffey, Huntley, and Missen (2000) <doi:10.1023/A:1007551316253>,
the 'CrimeStat' software by Levine (2013)
<https://nij.ojp.gov/topics/articles/crimestat-spatial-statistics-program-analysis-crime-incident-locations>,
and the criminal geographic targeting model outlined in Rossmo (2000, ISBN:978-0849381294)
and Rossmo (1995) <http://summit.sfu.ca/item/6820>.
Author: Jamie Spaulding and Keith Morris
Maintainer: Jamie Spaulding <jspauldi@mix.wvu.edu>
Diff between rgeoprofile versions 0.1.0 dated 2019-11-25 and 0.1.1 dated 2020-01-08
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 2 +- R/cgt_profile.R | 4 ++-- R/lognorm_profile.R | 1 - R/neg_exp_profile.R | 4 ++-- R/norm_profile.R | 1 - R/trun_neg_exp_profile.R | 1 - 8 files changed, 17 insertions(+), 20 deletions(-)
Title: Client for the 'DataCite' API
Description: Client for the web service methods provided
by 'DataCite' (<https://www.datacite.org/>), including functions to interface with
their 'RESTful' search API. The API is backed by 'Elasticsearch', allowing
expressive queries, including faceting.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rdatacite versions 0.4.2 dated 2019-05-07 and 0.5.0 dated 2020-01-08
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Title: Lookup Tables to Generate Poverty Likelihoods and Rates using
the Poverty Probability Index (PPI)
Description: The Poverty Probability Index (PPI) is a poverty measurement tool
for organizations and businesses with a mission to serve the poor. The PPI
is statistically-sound, yet simple to use: the answers to 10 questions about
a household’s characteristics and asset ownership are scored to compute the
likelihood that the household is living below the poverty line – or above by
only a narrow margin. This package contains country-specific lookup data tables
used as reference to determine the poverty likelihood of a household based
on their score from the country-specific PPI questionnaire. These lookup
tables have been extracted from documentation of the PPI found at
<https://www.povertyindex.org> and managed by Innovations for Poverty Action
<https://www.poverty-action.org>.
Author: Ernest Guevarra [aut, cre] (<https://orcid.org/0000-0002-4887-4415>)
Maintainer: Ernest Guevarra <ernestgmd@gmail.com>
Diff between ppitables versions 0.5.1 dated 2019-09-28 and 0.5.2 dated 2020-01-08
DESCRIPTION | 11 ++--- MD5 | 18 ++++---- NEWS.md | 13 ++++++ R/data.R | 34 ++++++++++++++++ R/sysdata.rda |binary README.md | 107 +++++++++++++++++++++++++++------------------------- data/ppiRWA2019.rda |only man/find_table.Rd | 6 +- man/get_table.Rd | 6 +- man/ppiRWA2019.Rd |only man/ppitables.Rd | 2 11 files changed, 129 insertions(+), 68 deletions(-)
Title: Numeric and Visual Comparisons of Heterogeneity in Parametric
Models
Description: Performs statistical tests to compare coefficients and residual
variance across multiple models. Also provides graphical methods for
assessing heterogeneity in coefficients and residuals. Currently supports
linear and generalized linear models, as well as their multi-level and
complex survey-weighted variations from the 'lme4' and 'survey' packages,
respectively. Reference: Li (2015) <https://scholarscompass.vcu.edu/etd/3985/>.
Author: Travis Loux [aut, cre],
Cara Wiskow [aut]
Maintainer: Travis Loux <travis.loux@slu.edu>
Diff between paramhetero versions 0.1.0 dated 2019-04-27 and 0.2.0 dated 2020-01-08
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Title: Optimal Linear Regression
Description: The optimal linear regression olr(), runs all the possible combinations of linear regression
equations. The olr() returns the equation which has the greatest adjusted R-squared term or the greatest R-squared term based
on the user's discretion. Essentially, the olr() returns the best fit equation out of all the possible equations. R-squared increases
with the addition of an explanatory variable whether it is 'significant' or not, thus this was developed to eliminate that conundrum.
Adjusted R-squared is preferred to overcome this phenomenon, but each combination will still produce different results and this will
return the best one. Complimentary functions are included which list all of the equations, all of the equations in ascending order,
a function to give the user a specific model's summary, and the list of adjusted R-squared terms & R-squared terms.
A 'Python' version is available at: <https://pypi.org/project/olr/>.
Author: Mathew Fok
Maintainer: Mathew Fok <mfok@stevens.edu>
Diff between olr versions 1.0 dated 2019-12-22 and 1.1 dated 2020-01-08
DESCRIPTION | 19 +++--- MD5 | 6 +- R/olr_function.R | 154 +++++++++++++++++++++++++++++++++---------------------- man/olr.Rd | 50 ++++++++++------- 4 files changed, 136 insertions(+), 93 deletions(-)
Title: Network Generator for Combinatorial Graph Problems
Description: Methods for the generation of a wide range of network geographies,
e.g., grid networks or clustered networks. Useful for the generation of
benchmarking instances for the investigation of, e.g., Vehicle-Routing-Problems
or Travelling Salesperson Problems.
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between netgen versions 1.3 dated 2016-01-22 and 1.3.2 dated 2020-01-08
netgen-1.3.2/netgen/DESCRIPTION | 16 - netgen-1.3.2/netgen/MD5 | 115 +++++----- netgen-1.3.2/netgen/NAMESPACE | 3 netgen-1.3.2/netgen/NEWS | 15 + netgen-1.3.2/netgen/R/addNodeWeights.R |only netgen-1.3.2/netgen/R/autoplotNetwork.R | 61 ++++- netgen-1.3.2/netgen/R/exportToTSPlibFormat.R | 7 netgen-1.3.2/netgen/R/filterTSPInstances.R | 37 ++- netgen-1.3.2/netgen/R/generateClusteredNetwork.R | 12 - netgen-1.3.2/netgen/R/generateGridNetwork.R | 11 netgen-1.3.2/netgen/R/generateRandomNetwork.R | 8 netgen-1.3.2/netgen/R/getTSPInstancesOverview.R | 13 - netgen-1.3.2/netgen/R/helpers.R | 32 +- netgen-1.3.2/netgen/R/importFromFile.R | 2 netgen-1.3.2/netgen/R/importFromTSPlibFormat.R | 43 +++ netgen-1.3.2/netgen/R/makeNetwork.R | 36 ++- netgen-1.3.2/netgen/R/morphInstances.R | 14 - netgen-1.3.2/netgen/R/pointMatching.R | 88 ++++++- netgen-1.3.2/netgen/R/printNetwork.R | 7 netgen-1.3.2/netgen/R/visualizeMorphing.R | 16 + netgen-1.3.2/netgen/R/visualizePointMatching.R | 74 ++++-- netgen-1.3.2/netgen/R/zzz.R | 1 netgen-1.3.2/netgen/inst/testdata/a280.tsp |only netgen-1.3.2/netgen/inst/testdata/a280.tsp.opt |only netgen-1.3.2/netgen/inst/testdata/a280.tsp.tour |only netgen-1.3.2/netgen/man/addNodeWeights.Rd |only netgen-1.3.2/netgen/man/as.character.Network.Rd | 1 netgen-1.3.2/netgen/man/as.data.frame.Network.Rd | 1 netgen-1.3.2/netgen/man/as.matrix.Network.Rd | 1 netgen-1.3.2/netgen/man/autoplot.Network.Rd | 12 - netgen-1.3.2/netgen/man/dynamise.Rd | 4 netgen-1.3.2/netgen/man/exportToFile.Rd | 1 netgen-1.3.2/netgen/man/exportToTSPlibFormat.Rd | 1 netgen-1.3.2/netgen/man/filterTSPInstances.Rd | 21 + netgen-1.3.2/netgen/man/generateClusteredNetwork.Rd | 10 netgen-1.3.2/netgen/man/generateGridNetwork.Rd | 1 netgen-1.3.2/netgen/man/generateRandomNetwork.Rd | 5 netgen-1.3.2/netgen/man/getDepotCoordinates.Rd | 1 netgen-1.3.2/netgen/man/getNumberOfClusters.Rd | 1 netgen-1.3.2/netgen/man/getNumberOfDepots.Rd | 1 netgen-1.3.2/netgen/man/getNumberOfNodes.Rd | 1 netgen-1.3.2/netgen/man/getOptimalPointMatching.Rd | 23 +- netgen-1.3.2/netgen/man/getPointDistributionStrategies.Rd | 1 netgen-1.3.2/netgen/man/getTSPInstancesOverview.Rd | 6 netgen-1.3.2/netgen/man/getValidEdgeWeightTypes.Rd | 1 netgen-1.3.2/netgen/man/hasDepots.Rd | 1 netgen-1.3.2/netgen/man/importFromFile.Rd | 1 netgen-1.3.2/netgen/man/importFromTSPlibFormat.Rd | 9 netgen-1.3.2/netgen/man/isEuclidean.Rd | 1 netgen-1.3.2/netgen/man/isNetwork.Rd | 1 netgen-1.3.2/netgen/man/makeNetwork.Rd | 16 + netgen-1.3.2/netgen/man/morphInstances.Rd | 10 netgen-1.3.2/netgen/man/rescaleNetwork.Rd | 1 netgen-1.3.2/netgen/man/visualizeMorphing.Rd | 10 netgen-1.3.2/netgen/man/visualizePointMatching.Rd | 21 + netgen-1.3.2/netgen/tests/testthat/test_getOptimalPointMatching.R | 9 netgen-1.3.2/netgen/tests/testthat/test_getTSPInstancesOverview.R | 13 - netgen-1.3.2/netgen/tests/testthat/test_import.R | 15 + netgen-1.3.2/netgen/tests/testthat/test_makeNetwork.R |only netgen-1.3.2/netgen/tests/testthat/test_morphInstances.R | 14 - netgen-1.3.2/netgen/tests/testthat/test_plots.R | 5 netgen-1.3/netgen/man/quoted.Rd |only 62 files changed, 591 insertions(+), 240 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://data.neonscience.org/home>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: National Ecological Observatory Network [aut],
Claire Lunch [cre, ctb],
Christine Laney [ctb],
Nathan Mietkiewicz [ctb],
Eric Sokol [ctb],
Kaelin Cawley [ctb]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 1.3.2 dated 2019-12-03 and 1.3.3 dated 2020-01-08
neonUtilities-1.3.2/neonUtilities/inst/extdata/expected/gp/readme.txt |only neonUtilities-1.3.2/neonUtilities/inst/extdata/expected/gp/validation.csv |only neonUtilities-1.3.2/neonUtilities/inst/extdata/expected/gp/variables.csv |only neonUtilities-1.3.3/neonUtilities/DESCRIPTION | 18 - neonUtilities-1.3.3/neonUtilities/MD5 | 28 - neonUtilities-1.3.3/neonUtilities/R/getReadmePublicationDate.R | 10 neonUtilities-1.3.3/neonUtilities/R/getRecentPublication.R | 12 neonUtilities-1.3.3/neonUtilities/R/readTableNEON.R | 7 neonUtilities-1.3.3/neonUtilities/R/stackByTable.R | 10 neonUtilities-1.3.3/neonUtilities/R/stackDataFilesParallel.R | 39 ++ neonUtilities-1.3.3/neonUtilities/R/sysdata.rda |binary neonUtilities-1.3.3/neonUtilities/R/zipsByProduct.R | 150 ++++++---- neonUtilities-1.3.3/neonUtilities/README.md | 18 + neonUtilities-1.3.3/neonUtilities/inst/extdata/expected/gp/readme_10109.txt |only neonUtilities-1.3.3/neonUtilities/inst/extdata/expected/gp/validation_10109.csv |only neonUtilities-1.3.3/neonUtilities/inst/extdata/expected/gp/variables_10109.csv |only neonUtilities-1.3.3/neonUtilities/man/getReadmePublicationDate.Rd | 4 neonUtilities-1.3.3/neonUtilities/man/stackDataFilesParallel.Rd | 4 18 files changed, 201 insertions(+), 99 deletions(-)
Title: Missing Outcome Data in Health Economic Evaluation
Description: Contains a suite of functions for health economic evaluations with missing outcome data.
The package can fit different types of statistical models under a fully Bayesian approach using the software 'JAGS' (which should be installed locally and which is loaded in 'missingHE' via the 'R' package 'R2jags').
Three classes of models can be fitted under a variety of missing data assumptions: selection models, pattern mixture models and hurdle models.
In addition to model fitting, 'missingHE' provides a set of specialised functions to assess model convergence and fit, and to summarise the statistical and economic results using different types of measures and graphs.
The methods implemented are described in Mason (2018) <doi:10.1002/hec.3793>, Molenberghs (2000) <doi:10.1007/978-1-4419-0300-6_18> and Gabrio (2019) <doi:10.1002/sim.8045>.
Author: Andrea Gabrio [aut, cre]
Maintainer: Andrea Gabrio <ucakgab@ucl.ac.uk>
Diff between missingHE versions 1.2.1 dated 2019-09-21 and 1.3.2 dated 2020-01-08
DESCRIPTION | 8 MD5 | 82 +++---- NAMESPACE | 6 R/data.R | 16 - R/data_read_hurdle.R | 14 - R/data_read_pattern.R | 4 R/data_read_selection.R | 8 R/diagnostic.R | 72 +++--- R/hurdle.R | 12 - R/jagsresults.R | 71 ++++++ R/pattern.R | 12 - R/pic.R | 9 R/ppc.R | 179 +++++++++++++--- R/prior_hurdle.R | 90 ++++++-- R/prior_pattern.R | 315 ++++++++++++++++++++++++++++ R/prior_selection.R | 32 ++ R/run_hurdle.R | 46 +++- R/run_pattern.R | 17 - R/run_selection.R | 17 - R/selection.R | 12 - R/write_hurdle.R | 502 +++++++++++++++++++++++++++++++++++++++++++-- R/write_pattern.R | 335 +++++++++++++++++++++++++++++- R/write_selection.R | 114 +++++++++- data/MenSS.RData |binary man/MenSS.Rd | 16 - man/data_read_hurdle.Rd | 10 man/data_read_pattern.Rd | 4 man/data_read_selection.Rd | 4 man/hurdle.Rd | 3 man/jagsresults.Rd | 71 ++++++ man/pattern.Rd | 3 man/pic.Rd | 9 man/prior_hurdle.Rd | 11 man/prior_pattern.Rd | 3 man/prior_selection.Rd | 11 man/run_hurdle.Rd | 3 man/run_pattern.Rd | 3 man/run_selection.Rd | 3 man/selection.Rd | 3 man/write_hurdle.Rd | 11 man/write_pattern.Rd | 3 man/write_selection.Rd | 11 42 files changed, 1890 insertions(+), 265 deletions(-)
Title: A Toolbox for Working with R Arrays in a Functional Programming
Style
Description: A toolbox for R arrays. Flexibly split, bind, reshape, modify,
subset and name arrays.
Author: Tomasz Kalinowski [aut, cre]
Maintainer: Tomasz Kalinowski <kalinowskit@gmail.com>
Diff between listarrays versions 0.2.0 dated 2019-03-24 and 0.3.0 dated 2020-01-08
DESCRIPTION | 8 MD5 | 70 +++--- NAMESPACE | 96 ++++---- R/bind.R | 416 +++++++++++++++++++------------------- R/dim.R | 276 ++++++++++++------------- R/dim2.R | 229 ++++++++++----------- R/extract.R | 197 ++++++++++-------- R/map.R | 143 ++++++------- R/modify.R | 160 +++++++------- R/onehot.R | 283 ++++++++++++------------- R/reshape.R | 89 ++++---- R/seq_along.R | 72 +++--- R/shuffle.R | 105 ++++----- R/split.R | 447 +++++++++++++++++++++++------------------ R/standardize.R | 76 +++--- R/utils.R | 172 +++++++-------- R/zzz.R | 20 - README.md | 1 man/DIM.Rd | 34 +-- man/array2.Rd | 100 ++++----- man/bind-arrays.Rd | 160 +++++++------- man/drop_dimnames.Rd | 54 ++-- man/expand_dims.Rd | 78 +++---- man/extract_dim.Rd | 104 ++++----- man/map_along_dim.Rd | 114 +++++----- man/modify_along_dim.Rd | 80 +++---- man/ndim.Rd | 28 +- man/onehot.Rd | 157 +++++++------- man/seq_along_dim.Rd | 78 +++---- man/set_as_rows.Rd | 70 +++--- man/set_dim.Rd | 127 ++++++----- man/set_dimnames.Rd | 138 ++++++------ man/shuffle_rows.Rd | 76 +++--- man/split-array.Rd | 207 +++++++++--------- man/t.array.Rd | 46 ++-- tests/testthat/test-dimnames.R | 158 +++++++------- 36 files changed, 2388 insertions(+), 2281 deletions(-)
Title: Language Server Protocol
Description: An implementation of the Language Server Protocol for R. The
Language Server protocol is used by an editor client to integrate
features like auto completion. See
<https://microsoft.github.io/language-server-protocol> for details.
Author: Randy Lai
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between languageserver versions 0.3.2 dated 2019-10-26 and 0.3.3 dated 2020-01-08
languageserver-0.3.2/languageserver/man/content_backward_search.Rd |only languageserver-0.3.2/languageserver/man/style_file.Rd |only languageserver-0.3.2/languageserver/man/workspace_sync.Rd |only languageserver-0.3.2/languageserver/src/document.c |only languageserver-0.3.2/languageserver/src/document.h |only languageserver-0.3.3/languageserver/DESCRIPTION | 13 languageserver-0.3.3/languageserver/MD5 | 136 ++- languageserver-0.3.3/languageserver/NAMESPACE | 2 languageserver-0.3.3/languageserver/NEWS.md | 7 languageserver-0.3.3/languageserver/R/capabilities.R | 4 languageserver-0.3.3/languageserver/R/completion.R | 229 ++++-- languageserver-0.3.3/languageserver/R/definition.R | 208 +----- languageserver-0.3.3/languageserver/R/diagnostics.R | 58 + languageserver-0.3.3/languageserver/R/document.R | 264 ++++--- languageserver-0.3.3/languageserver/R/formatting.R | 104 +-- languageserver-0.3.3/languageserver/R/handlers-general.R | 9 languageserver-0.3.3/languageserver/R/handlers-langfeatures.R | 40 - languageserver-0.3.3/languageserver/R/highlight.R |only languageserver-0.3.3/languageserver/R/hover.R | 143 +++- languageserver-0.3.3/languageserver/R/interfaces.R | 2 languageserver-0.3.3/languageserver/R/languagebase.R | 1 languageserver-0.3.3/languageserver/R/languageclient.R | 58 + languageserver-0.3.3/languageserver/R/languageserver.R | 71 +- languageserver-0.3.3/languageserver/R/log.R | 2 languageserver-0.3.3/languageserver/R/namespace.R | 195 ++++- languageserver-0.3.3/languageserver/R/signature.R | 24 languageserver-0.3.3/languageserver/R/symbol.R |only languageserver-0.3.3/languageserver/R/task.R |only languageserver-0.3.3/languageserver/R/utils.R | 161 ++++ languageserver-0.3.3/languageserver/R/workspace.R | 344 +++------- languageserver-0.3.3/languageserver/README.md | 34 languageserver-0.3.3/languageserver/man/DefinitionCache.Rd | 4 languageserver-0.3.3/languageserver/man/GlobalNameSpace.Rd |only languageserver-0.3.3/languageserver/man/LanguageServer.Rd | 2 languageserver-0.3.3/languageserver/man/Logger.Rd | 2 languageserver-0.3.3/languageserver/man/Message.Rd | 2 languageserver-0.3.3/languageserver/man/Namespace.Rd | 7 languageserver-0.3.3/languageserver/man/Notification.Rd | 2 languageserver-0.3.3/languageserver/man/Request.Rd | 2 languageserver-0.3.3/languageserver/man/Response.Rd | 2 languageserver-0.3.3/languageserver/man/ResponseErrorMessage.Rd | 2 languageserver-0.3.3/languageserver/man/Workspace.Rd | 2 languageserver-0.3.3/languageserver/man/arg_completion.Rd | 3 languageserver-0.3.3/languageserver/man/check_scope.Rd | 2 languageserver-0.3.3/languageserver/man/code_point_from_unit.Rd |only languageserver-0.3.3/languageserver/man/code_point_to_unit.Rd | 6 languageserver-0.3.3/languageserver/man/completion_item_resolve_reply.Rd |only languageserver-0.3.3/languageserver/man/completion_reply.Rd | 2 languageserver-0.3.3/languageserver/man/definition_reply.Rd | 2 languageserver-0.3.3/languageserver/man/diagnose_file.Rd | 2 languageserver-0.3.3/languageserver/man/diagnostics.Rd | 4 languageserver-0.3.3/languageserver/man/document_highlight_reply.Rd |only languageserver-0.3.3/languageserver/man/document_symbol_reply.Rd | 2 languageserver-0.3.3/languageserver/man/enclosed_by_quotes.Rd |only languageserver-0.3.3/languageserver/man/expr_range.Rd |only languageserver-0.3.3/languageserver/man/extract_blocks.Rd |only languageserver-0.3.3/languageserver/man/find_unbalanced_bracket.Rd |only languageserver-0.3.3/languageserver/man/hover_reply.Rd | 2 languageserver-0.3.3/languageserver/man/on_exit.Rd | 2 languageserver-0.3.3/languageserver/man/parse_document.Rd | 2 languageserver-0.3.3/languageserver/man/purl.Rd |only languageserver-0.3.3/languageserver/man/seq_safe.Rd |only languageserver-0.3.3/languageserver/man/signature_reply.Rd | 2 languageserver-0.3.3/languageserver/man/symbol_information.Rd | 4 languageserver-0.3.3/languageserver/man/workspace_symbol_reply.Rd | 2 languageserver-0.3.3/languageserver/src/fsm.c |only languageserver-0.3.3/languageserver/src/fsm.h |only languageserver-0.3.3/languageserver/src/languageserver.c | 10 languageserver-0.3.3/languageserver/src/reader.c | 4 languageserver-0.3.3/languageserver/src/search.c |only languageserver-0.3.3/languageserver/src/search.h |only languageserver-0.3.3/languageserver/src/stack.c |only languageserver-0.3.3/languageserver/src/stack.h |only languageserver-0.3.3/languageserver/tests/testthat/helper-utils.R | 94 ++ languageserver-0.3.3/languageserver/tests/testthat/test-codeunits.R | 3 languageserver-0.3.3/languageserver/tests/testthat/test-completion.R | 77 ++ languageserver-0.3.3/languageserver/tests/testthat/test-definition.R | 14 languageserver-0.3.3/languageserver/tests/testthat/test-hover.R | 20 languageserver-0.3.3/languageserver/tests/testthat/test-langauagecilent.R |only languageserver-0.3.3/languageserver/tests/testthat/test-lintr.R |only languageserver-0.3.3/languageserver/tests/testthat/test-rmarkdown.R |only languageserver-0.3.3/languageserver/tests/testthat/test-search.R |only languageserver-0.3.3/languageserver/tests/testthat/test-signature.R | 6 83 files changed, 1541 insertions(+), 860 deletions(-)
More information about languageserver at CRAN
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Title: Kaya Identity Data for Nations and Regions
Description: Provides data for Kaya identity variables (population, gross
domestic product, primary energy consumption, and energy-related
CO2 emissions) for the world and for individual nations, and
utility functions for looking up data, plotting trends of
Kaya variables, and plotting the fuel mix for a given country
or region. The Kaya identity (Yoichi Kaya and Keiichi Yokobori,
"Environment, Energy, and Economy: Strategies for Sustainability"
(United Nations University Press, 1998) and
<https://en.wikipedia.org/wiki/Kaya_identity>) expresses a nation's
or region's greenhouse gas emissions in terms of its population,
per-capita Gross Domestic Product, the energy intensity of its
economy, and the carbon-intensity of its energy supply.
Author: Jonathan Gilligan [cre, aut] (<https://orcid.org/0000-0003-1375-6686>)
Maintainer: Jonathan Gilligan <jonathan.gilligan@vanderbilt.edu>
Diff between kayadata versions 0.4.2 dated 2019-11-28 and 0.4.3 dated 2020-01-08
DESCRIPTION | 19 MD5 | 66 +- NEWS.md | 12 R/data.R | 17 R/kaya.R | 145 +++-- R/kayadata.R | 30 - R/plot_kaya.R | 157 ++++-- build/vignette.rds |binary data/fuel_mix.rda |binary data/kaya_data.rda |binary inst/doc/kayadata.R |only inst/doc/kayadata.Rmd |only inst/doc/kayadata.html |only inst/doc/policy_analysis.html | 58 +- man/emissions_factors.Rd | 2 man/figures |only man/fuel_mix.Rd | 23 man/generation_capacity.Rd | 10 man/get_fuel_mix.Rd | 30 - man/get_kaya_data.Rd | 71 +- man/get_top_down_trends.Rd | 26 - man/get_top_down_values.Rd | 40 - man/kaya_data.Rd | 38 - man/kayadata-package.Rd | 11 man/lookup_region_code.Rd | 4 man/plot_fuel_mix.Rd | 33 - man/plot_kaya.Rd | 31 + man/project_top_down.Rd | 44 - man/td_trends.Rd | 22 man/td_values.Rd | 28 - tests/figs |only tests/testthat/test_plot_kaya.R |only vignettes/american-political-science-association.csl | 472 +++++++++---------- vignettes/kayadata.Rmd |only 34 files changed, 778 insertions(+), 611 deletions(-)
Title: Balamuta Miscellaneous
Description: Set of common functions used for manipulating colors,
detecting and interacting with 'RStudio', modeling, formatting, determining
users' operating system, feature scaling, and more!
Author: James Balamuta [aut, cre, cph]
(<https://orcid.org/0000-0003-2826-8458>)
Maintainer: James Balamuta <balamut2@illinois.edu>
Diff between jjb versions 0.1.0 dated 2018-10-14 and 0.1.1 dated 2020-01-08
jjb-0.1.0/jjb/man/get_arch.Rd |only jjb-0.1.0/jjb/man/get_graphic_driver.Rd |only jjb-0.1.1/jjb/DESCRIPTION | 12 +++-- jjb-0.1.1/jjb/MD5 | 60 ++++++++++++++--------------- jjb-0.1.1/jjb/NAMESPACE | 4 - jjb-0.1.1/jjb/NEWS.md | 10 +++- jjb-0.1.1/jjb/R/colors.R | 16 +++++-- jjb-0.1.1/jjb/R/feature-scaling.R | 19 +++++++-- jjb-0.1.1/jjb/R/formatting.R | 22 ++++++++-- jjb-0.1.1/jjb/R/ints.R | 12 +++-- jjb-0.1.1/jjb/R/is_os.R | 48 ++++++++++++++--------- jjb-0.1.1/jjb/R/jjb-package.R | 2 jjb-0.1.1/jjb/R/mat.R | 28 +++++++++---- jjb-0.1.1/jjb/R/misc.R | 38 ++++++++++++------ jjb-0.1.1/jjb/R/modeling.R | 17 +++++--- jjb-0.1.1/jjb/R/order.R | 5 +- jjb-0.1.1/jjb/R/strs.R | 9 ++-- jjb-0.1.1/jjb/R/utilities.R | 34 ++++++++++++---- jjb-0.1.1/jjb/R/weather.R | 29 ++++++++++---- jjb-0.1.1/jjb/inst/CITATION | 6 +- jjb-0.1.1/jjb/man/char_at.Rd | 4 - jjb-0.1.1/jjb/man/circle_matrix.Rd | 3 - jjb-0.1.1/jjb/man/convert_cols.Rd | 2 jjb-0.1.1/jjb/man/external_graphs.Rd | 6 ++ jjb-0.1.1/jjb/man/is_rstudio.Rd | 2 jjb-0.1.1/jjb/man/is_whole.Rd | 2 jjb-0.1.1/jjb/man/jjb-package.Rd | 10 ++++ jjb-0.1.1/jjb/man/lagged.Rd | 7 ++- jjb-0.1.1/jjb/man/mkdir.Rd | 6 ++ jjb-0.1.1/jjb/man/pad_number.Rd | 2 jjb-0.1.1/jjb/man/system_arch.Rd |only jjb-0.1.1/jjb/man/system_graphic_driver.Rd |only jjb-0.1.1/jjb/man/tr.Rd | 2 33 files changed, 274 insertions(+), 143 deletions(-)
More information about diversityForest at CRAN
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Title: Fit a Penalized Continuation Ratio Model for Predicting an
Ordinal Response
Description: Provides a function for fitting a penalized constrained continuation ratio model using the glmpath algorithm and methods for extracting coefficient estimates, predicted class, class probabilities, and plots.
Author: Kellie J. Archer
Maintainer: Kellie J. Archer <archer.43@osu.edu>
Diff between glmpathcr versions 1.0.7 dated 2018-06-30 and 1.0.8 dated 2020-01-08
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/fitted.glmpathcr.R | 4 ++-- R/glmpathcr.R | 7 +++++-- R/predict.glmpathcr.R | 4 ++-- R/summary.glmpathcr.R | 8 ++++---- build/partial.rdb |binary build/vignette.rds |binary data/diabetes.rda |binary inst/NEWS.Rd | 7 +++++++ inst/doc/glmpathcr.pdf |binary 11 files changed, 34 insertions(+), 24 deletions(-)
Title: Fit a Penalized Constrained Continuation Ratio Model for
Predicting an Ordinal Response
Description: Penalized methods are useful for fitting over-parameterized models. This package includes functions for restructuring an ordinal
response dataset for fitting continuation ratio models for datasets where the number of covariates exceeds the sample size or when
there is collinearity among the covariates. The glmnet fitting algorithm is used to fit the continuation ratio model after data restructuring.
Author: Kellie J. Archer
Maintainer: Kellie J. Archer <archer.43@osu.edu>
Diff between glmnetcr versions 1.0.4 dated 2018-06-04 and 1.0.5 dated 2020-01-08
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/glmnetcr.R | 19 +++++++++++-------- R/predict.glmnetcr.R | 8 ++++---- build/partial.rdb |binary build/vignette.rds |binary data/diabetes.rda |binary inst/NEWS.Rd | 6 ++++++ inst/doc/glmnetcr.pdf |binary man/glmnetcr.Rd | 17 ++++++++++++----- man/plot.glmnetcr.Rd | 7 +++---- 11 files changed, 50 insertions(+), 35 deletions(-)
Title: Plot Multiple Sequence Alignment using 'ggplot2'
Description: Supports visualizing multiple sequence alignment of DNA and protein sequences using 'ggplot2'. It supports a number of colour schemes, including Chemistry, Clustal, Shapely, Taylor and Zappo. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as aligning a phylogenetic tree produced by 'ggtree' with multiple sequence alignment.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>),
Lang Zhou [aut],
Huina Huang [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggmsa versions 0.0.1 dated 2019-10-07 and 0.0.2 dated 2020-01-08
ggmsa-0.0.1/ggmsa/man/msa_data.Rd |only ggmsa-0.0.2/ggmsa/DESCRIPTION | 14 ++-- ggmsa-0.0.2/ggmsa/MD5 | 25 +++++-- ggmsa-0.0.2/ggmsa/NAMESPACE | 5 + ggmsa-0.0.2/ggmsa/NEWS.md |only ggmsa-0.0.2/ggmsa/R/geom_msa.R | 11 ++- ggmsa-0.0.2/ggmsa/R/ggmsa.R | 10 +-- ggmsa-0.0.2/ggmsa/R/msa_data.R | 68 +++++++++++++++------ ggmsa-0.0.2/ggmsa/R/prepare_fasta.R |only ggmsa-0.0.2/ggmsa/build |only ggmsa-0.0.2/ggmsa/inst/doc |only ggmsa-0.0.2/ggmsa/inst/extdata/LeaderRepeat_All.fa |only ggmsa-0.0.2/ggmsa/man/geom_msa.Rd | 8 +- ggmsa-0.0.2/ggmsa/man/ggmsa.Rd | 12 ++- ggmsa-0.0.2/ggmsa/man/tidy_msa.Rd |only ggmsa-0.0.2/ggmsa/vignettes |only 16 files changed, 107 insertions(+), 46 deletions(-)
Title: Easily Scrape and Process AFL Data
Description: An easy package for scraping and processing Australia Rules Football (AFL)
data. 'fitzRoy' provides a range of functions for accessing publicly available data
from 'AFL Tables' <https://afltables.com>, 'Footy Wire' <https://www.footywire.com> and
'The Squiggle' <https://squiggle.com.au>. Further functions allow for easy processing,
cleaning and transformation of this data into formats that can be used for analysis.
Author: James Day [cre, aut],
Robert Nguyen [aut],
Matthew Erbs [ctb],
Oscar Lane [aut],
Jason Zivkovic [ctb]
Maintainer: James Day <jamesthomasday@gmail.com>
Diff between fitzRoy versions 0.2.0 dated 2019-11-30 and 0.3.0 dated 2020-01-08
DESCRIPTION | 17 +- MD5 | 58 +++--- NAMESPACE | 2 NEWS.md | 9 + R/afltables_basic.R | 37 ++++ R/afltables_player.R | 4 R/footywire-calcs.R | 122 +++++++++----- R/return_ladder.R |only R/womens_stats.R | 2 README.md | 19 +- inst/doc/elo-ratings-example.R | 141 ++++++++-------- inst/doc/elo-ratings-example.Rmd | 27 +-- inst/doc/elo-ratings-example.html | 126 +-------------- inst/doc/mens-stats.R | 99 ++++++----- inst/doc/mens-stats.Rmd | 45 ++++- inst/doc/mens-stats.html | 170 ++------------------ inst/doc/womens-stats.R | 56 +++--- inst/doc/womens-stats.Rmd | 35 ++-- inst/doc/womens-stats.html | 277 +-------------------------------- man/calculate_round.Rd | 2 man/fitzRoy-package.Rd | 1 man/get_aflw_cookie.Rd | 2 man/get_footywire_betting_odds.Rd | 6 man/get_squiggle_data.Rd | 6 man/replace_venues.Rd |only man/return_ladder.Rd |only tests/testthat/test-afltables_player.R | 8 tests/testthat/test-footywire.R | 115 +++++++++++-- tests/testthat/test-return_ladder.R |only vignettes/elo-ratings-example.Rmd | 27 +-- vignettes/mens-stats.Rmd | 45 ++++- vignettes/womens-stats.Rmd | 35 ++-- 32 files changed, 671 insertions(+), 822 deletions(-)
Title: Rename and Encode Data Frames Using External Crosswalk Files
Description: A pair of functions for renaming and encoding data frames
using external crosswalk files. It is especially useful when
constructing master data sets from multiple smaller data
sets that do not name or encode variables consistently
across files. Based on similar commands in 'Stata'.
Author: Benjamin Skinner [aut, cre] (<https://orcid.org/0000-0002-0337-7415>)
Maintainer: Benjamin Skinner <btskinner@coe.ufl.edu>
Diff between crosswalkr versions 0.2.5 dated 2019-10-23 and 0.2.6 dated 2020-01-08
DESCRIPTION | 8 +-- MD5 | 31 +++++++++----- NEWS.md | 5 ++ R/encodefrom.R | 16 ++++--- R/renamefrom.R | 4 - R/utility_functions.R | 73 ++++++++++++++++++++++++++++++++--- build/vignette.rds |binary inst/doc/collapse.R |only inst/doc/collapse.Rmd |only inst/doc/collapse.html |only inst/doc/crosswalkr.R | 20 ++++----- inst/doc/crosswalkr.html | 71 +++++++++++++++++++++++----------- man/crosswalkr.Rd | 1 man/encodefrom.Rd | 32 ++++++++++++--- man/renamefrom.Rd | 32 ++++++++++++--- tests/testthat/test-check-dups.R | 8 +++ tests/testthat/test-check-nums.R |only tests/testthat/testdata/cw_dup_2.csv |only tests/testthat/testdata/cw_dup_3.csv |only vignettes/collapse.Rmd |only 20 files changed, 225 insertions(+), 76 deletions(-)
Title: Discrete Response Regression for High-Dimensional Data
Description: Provides a function for fitting Poisson and negative binomial regression models when the number of parameters exceeds the sample size, using the the generalized monotone incremental forward stagewise method.
Author: Kellie Archer [aut, cre]
Maintainer: Kellie Archer <archer.43@osu.edu>
Diff between countgmifs versions 0.0.1 dated 2018-07-10 and 0.0.2 dated 2020-01-08
DESCRIPTION | 6 +++--- MD5 | 14 ++++++++------ R/countgmifs.R | 16 ++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/NEWS.Rd |only inst/doc/countgmifs.R | 1 - inst/doc/countgmifs.pdf |binary 9 files changed, 19 insertions(+), 18 deletions(-)
Title: Do a Git Style Diff of the Rows Between Two Dataframes with
Similar Structure
Description: Compares two dataframes which have the same column
structure to show the rows that have changed. Also gives a git style diff format
to quickly see what has changed in addition to summary statistics.
Author: Alex Joseph [aut, cre]
Maintainer: Alex Joseph <alexsanjoseph@gmail.com>
Diff between compareDF versions 1.8.0 dated 2019-06-02 and 2.0.0 dated 2020-01-08
DESCRIPTION | 16 ++-- MD5 | 19 +++-- NAMESPACE | 1 NEWS.md | 46 +++++++----- R/fnsComparison.R | 129 ++++-------------------------------- R/fnsOutputs.R |only README.md | 80 ++++++++++++++-------- man/compare_df.Rd | 18 ----- man/create_output_table.Rd |only man/view_html.Rd | 2 tests/testthat/test-fnsComparison.R | 87 ------------------------ tests/testthat/test-fnsOutputs.R |only 12 files changed, 120 insertions(+), 278 deletions(-)
Title: Covariate Balance Tables and Plots
Description: Generate balance tables and plots for covariates of groups preprocessed through matching, weighting or subclassification, for example, using propensity scores. Includes integration with 'MatchIt', 'twang', 'Matching', 'optmatch', 'CBPS', 'ebal', 'WeightIt', and 'designmatch' for assessing balance on the output of their preprocessing functions. Users can also specify data for balance assessment not generated through the above packages. Also included are methods for assessing balance in clustered or multiply imputed data sets or data sets with longitudinal treatments.
Author: Noah Greifer [aut, cre] (<https://orcid.org/0000-0003-3067-7154>)
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between cobalt versions 3.9.0 dated 2019-10-06 and 4.0.0 dated 2020-01-08
cobalt-3.9.0/cobalt/inst/doc/cobalt_A2_cluster_imp.R |only cobalt-3.9.0/cobalt/inst/doc/cobalt_A2_cluster_imp.Rmd |only cobalt-3.9.0/cobalt/inst/doc/cobalt_A2_cluster_imp.html |only cobalt-3.9.0/cobalt/vignettes/cobalt_A2_cluster_imp.Rmd |only cobalt-4.0.0/cobalt/DESCRIPTION | 21 cobalt-4.0.0/cobalt/MD5 | 130 cobalt-4.0.0/cobalt/NAMESPACE | 12 cobalt-4.0.0/cobalt/NEWS.md | 82 cobalt-4.0.0/cobalt/R/SHARED.R | 346 cobalt-4.0.0/cobalt/R/bal.plot.R | 509 - cobalt-4.0.0/cobalt/R/bal.sum.R | 305 cobalt-4.0.0/cobalt/R/bal.tab.R | 136 cobalt-4.0.0/cobalt/R/base.bal.tab.R | 1627 +-- cobalt-4.0.0/cobalt/R/functions_for_processing.R | 2186 ++-- cobalt-4.0.0/cobalt/R/get.w.R | 41 cobalt-4.0.0/cobalt/R/internal_utilities.R | 10 cobalt-4.0.0/cobalt/R/love.plot.R | 687 - cobalt-4.0.0/cobalt/R/print.bal.tab.R | 1125 -- cobalt-4.0.0/cobalt/R/utilities.R | 355 cobalt-4.0.0/cobalt/R/x2base.R | 4505 ++++------ cobalt-4.0.0/cobalt/README.md | 4 cobalt-4.0.0/cobalt/build/partial.rdb |binary cobalt-4.0.0/cobalt/build/vignette.rds |binary cobalt-4.0.0/cobalt/inst/WORDLIST |only cobalt-4.0.0/cobalt/inst/doc/cobalt_A0_basic_use.R | 62 cobalt-4.0.0/cobalt/inst/doc/cobalt_A0_basic_use.Rmd | 40 cobalt-4.0.0/cobalt/inst/doc/cobalt_A0_basic_use.html | 232 cobalt-4.0.0/cobalt/inst/doc/cobalt_A1_other_packages.R | 78 cobalt-4.0.0/cobalt/inst/doc/cobalt_A1_other_packages.Rmd | 37 cobalt-4.0.0/cobalt/inst/doc/cobalt_A1_other_packages.html | 87 cobalt-4.0.0/cobalt/inst/doc/cobalt_A2_segmented_data.R |only cobalt-4.0.0/cobalt/inst/doc/cobalt_A2_segmented_data.Rmd |only cobalt-4.0.0/cobalt/inst/doc/cobalt_A2_segmented_data.html |only cobalt-4.0.0/cobalt/inst/doc/cobalt_A3_longitudinal_treat.R | 20 cobalt-4.0.0/cobalt/inst/doc/cobalt_A3_longitudinal_treat.Rmd | 6 cobalt-4.0.0/cobalt/inst/doc/cobalt_A3_longitudinal_treat.html | 35 cobalt-4.0.0/cobalt/inst/doc/cobalt_A4_love.plot.R | 34 cobalt-4.0.0/cobalt/inst/doc/cobalt_A4_love.plot.Rmd | 20 cobalt-4.0.0/cobalt/inst/doc/cobalt_A4_love.plot.html | 141 cobalt-4.0.0/cobalt/inst/figures/README-unnamed-chunk-3-1.png |binary cobalt-4.0.0/cobalt/inst/figures/README-unnamed-chunk-3-2.png |binary cobalt-4.0.0/cobalt/inst/figures/README-unnamed-chunk-4-1.png |binary cobalt-4.0.0/cobalt/man/bal.plot.Rd | 61 cobalt-4.0.0/cobalt/man/bal.tab.CBPS.Rd | 16 cobalt-4.0.0/cobalt/man/bal.tab.Match.Rd | 8 cobalt-4.0.0/cobalt/man/bal.tab.Rd | 12 cobalt-4.0.0/cobalt/man/bal.tab.default.Rd | 6 cobalt-4.0.0/cobalt/man/bal.tab.df.formula.Rd | 10 cobalt-4.0.0/cobalt/man/bal.tab.df.formula.list.Rd | 14 cobalt-4.0.0/cobalt/man/bal.tab.matchit.Rd | 16 cobalt-4.0.0/cobalt/man/bal.tab.mimids.Rd |only cobalt-4.0.0/cobalt/man/bal.tab.ps.Rd | 29 cobalt-4.0.0/cobalt/man/bal.tab.weightit.Rd | 24 cobalt-4.0.0/cobalt/man/balance.summary.Rd | 75 cobalt-4.0.0/cobalt/man/class-bal.tab.cluster.Rd | 2 cobalt-4.0.0/cobalt/man/class-bal.tab.imp.Rd | 6 cobalt-4.0.0/cobalt/man/class-bal.tab.msm.Rd | 2 cobalt-4.0.0/cobalt/man/class-bal.tab.multi.Rd | 14 cobalt-4.0.0/cobalt/man/class-bal.tab.subclass.Rd | 15 cobalt-4.0.0/cobalt/man/cobalt-package.Rd | 2 cobalt-4.0.0/cobalt/man/display_options.Rd | 6 cobalt-4.0.0/cobalt/man/get.w.Rd | 8 cobalt-4.0.0/cobalt/man/love.plot.Rd | 24 cobalt-4.0.0/cobalt/man/print.bal.tab.Rd | 26 cobalt-4.0.0/cobalt/man/splitfactor.Rd | 47 cobalt-4.0.0/cobalt/man/var.names.Rd | 2 cobalt-4.0.0/cobalt/vignettes/cobalt_A0_basic_use.Rmd | 40 cobalt-4.0.0/cobalt/vignettes/cobalt_A1_other_packages.Rmd | 37 cobalt-4.0.0/cobalt/vignettes/cobalt_A2_segmented_data.Rmd |only cobalt-4.0.0/cobalt/vignettes/cobalt_A3_longitudinal_treat.Rmd | 6 cobalt-4.0.0/cobalt/vignettes/cobalt_A4_love.plot.Rmd | 20 71 files changed, 6419 insertions(+), 6982 deletions(-)
Title: Exploring Genomic Relations for Enhanced Interpretation Through
Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR by Fang et al. (2016) <doi:10.1186/s13073-016-0384-y> is to provide a data interpretation system necessary to do "big data" science. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes, SNPs or genomic regions, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks, TF binding sites and genomic segments) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between XGR versions 1.1.6 dated 2019-07-12 and 1.1.7 dated 2020-01-08
DESCRIPTION | 11 MD5 | 451 ++++++++++++++++++++-------------------- NAMESPACE | 11 R/ClassMethod-XGR.r | 130 +++++++++++ R/xCircos.r | 11 R/xColormap.r | 14 + R/xDefineEQTL.r | 55 ++-- R/xDefineGenomicAnno.r | 5 R/xDefineHIC.r | 15 - R/xDefineNet.r | 21 - R/xDefineOntology.r | 9 R/xEnrichChord.r | 9 R/xEnrichForest.r | 10 R/xEnricherGenes.r | 11 R/xEnricherGenesAdv.r | 5 R/xEnricherSNPs.r | 9 R/xGGnetwork.r | 27 +- R/xGGraph.r | 2 R/xGR.r | 5 R/xGR2GeneScores.r | 9 R/xGR2nGenes.r | 11 R/xGR2xGeneAnno.r | 15 - R/xGR2xGeneAnnoAdv.r | 15 - R/xGR2xGeneScores.r | 7 R/xGR2xGenes.r | 32 +- R/xGRsampling.r | 5 R/xGRscores.r | 5 R/xGRviaGeneAnno.r | 13 - R/xGRviaGeneAnnoAdv.r | 5 R/xGRviaGenomicAnno.r | 17 - R/xGRviaGenomicAnnoAdv.r | 19 - R/xGeneID2Symbol.r | 7 R/xGraphML2AA.r | 17 - R/xLayout.r | 167 ++++++++++++++ R/xLiftOver.r | 5 R/xMarkNet.r |only R/xObjSize.r | 4 R/xRDataLoader.r | 257 ++++++++++++++-------- R/xSNP2GeneScores.r | 7 R/xSNP2cGenes.r | 9 R/xSNP2eGenes.r | 7 R/xSNP2nGenes.r | 15 - R/xSNPlocations.r | 11 R/xSNPscores.r | 7 R/xSocialiserGenes.r | 11 R/xSocialiserSNPs.r | 9 R/xSubneterGR.r | 64 ++++- R/xSubneterGenes.r | 15 - R/xSubneterGenesAdv.r |only R/xSubneterGenesMST.r |only R/xSubneterSNPs.r | 61 +++-- R/xSymbol2GeneID.r | 7 data/Haploid_regulators.RData |binary data/ImmunoBase.RData |binary data/JKscience_TS2A.RData |binary inst/EG.html |only inst/GS.html |only inst/NEWS | 32 ++ inst/eTerm.html | 15 + inst/iSubg.html |only inst/xAddCoords.html | 11 inst/xAuxEmbed.html | 7 inst/xCircos.html | 31 ++ inst/xColormap.html | 37 ++- inst/xCombineNet.html | 10 inst/xConverter.html | 8 inst/xCtree.html | 20 + inst/xDAGanno.html | 9 inst/xDAGpropagate.html | 11 inst/xDAGsim.html | 12 - inst/xDefineEQTL.html | 108 ++++++--- inst/xDefineGenomicAnno.html | 49 ++-- inst/xDefineHIC.html | 27 +- inst/xDefineNet.html | 40 ++- inst/xDefineOntology.html | 60 +++-- inst/xEnrichBarplot.html | 18 + inst/xEnrichChord.html | 16 + inst/xEnrichCompare.html | 16 + inst/xEnrichCtree.html | 27 +- inst/xEnrichD3.html | 12 - inst/xEnrichDAGplot.html | 33 ++ inst/xEnrichDAGplotAdv.html | 27 +- inst/xEnrichDotplot.html | 17 + inst/xEnrichForest.html | 21 + inst/xEnrichGGraph.html | 20 + inst/xEnrichHeatmap.html | 11 inst/xEnrichLadder.html | 23 +- inst/xEnrichMatrix.html | 28 +- inst/xEnrichNetplot.html | 35 ++- inst/xEnrichRadial.html | 22 + inst/xEnrichTreemap.html | 33 ++ inst/xEnrichViewer.html | 11 inst/xEnricher.html | 27 +- inst/xEnricherGenes.html | 38 ++- inst/xEnricherGenesAdv.html | 39 ++- inst/xEnricherSNPs.html | 36 ++- inst/xEnricherYours.html | 20 + inst/xGGnetwork.html | 63 +++-- inst/xGGraph.html | 26 +- inst/xGR.html | 18 + inst/xGR2GeneScores.html | 23 +- inst/xGR2nGenes.html | 27 +- inst/xGR2xGeneAnno.html | 51 +++- inst/xGR2xGeneAnnoAdv.html | 50 +++- inst/xGR2xGeneScores.html | 26 +- inst/xGR2xGenes.html | 38 ++- inst/xGRsampling.html | 19 - inst/xGRscores.html | 12 - inst/xGRviaGeneAnno.html | 37 ++- inst/xGRviaGeneAnnoAdv.html | 42 ++- inst/xGRviaGenomicAnno.html | 27 +- inst/xGRviaGenomicAnnoAdv.html | 32 ++ inst/xGeneID2Symbol.html | 15 + inst/xGraphML.html | 34 ++- inst/xGraphML2AA.html | 58 +++-- inst/xHeatmap.html | 34 ++- inst/xHeatmapAdv.html | 53 +++- inst/xLayout.html | 49 +++- inst/xLiftOver.html | 21 + inst/xMEabf.html | 9 inst/xMarkNet.html |only inst/xOBOcode.html | 45 +++ inst/xObjSize.html | 8 inst/xPieplot.html | 14 - inst/xRDataLoader.html | 51 +++- inst/xReport.html | 12 - inst/xSNP2GeneScores.html | 33 ++ inst/xSNP2cGenes.html | 22 + inst/xSNP2eGenes.html | 17 + inst/xSNP2nGenes.html | 19 + inst/xSNPlocations.html | 19 + inst/xSNPscores.html | 19 + inst/xSocialiser.html | 19 + inst/xSocialiserDAGplot.html | 32 ++ inst/xSocialiserDAGplotAdv.html | 32 ++ inst/xSocialiserGenes.html | 27 +- inst/xSocialiserNetplot.html | 31 ++ inst/xSocialiserSNPs.html | 29 +- inst/xSubneterGR.html | 97 ++++++-- inst/xSubneterGenes.html | 53 +++- inst/xSubneterGenesAdv.html |only inst/xSubneterGenesMST.html |only inst/xSubneterSNPs.html | 85 +++++-- inst/xSymbol2GeneID.html | 17 + inst/xVisNet.html | 30 +- man/EG.Rd |only man/GS.Rd |only man/eTerm.Rd | 15 + man/iSubg.Rd |only man/xAddCoords.Rd | 11 man/xAuxEmbed.Rd | 7 man/xCircos.Rd | 29 +- man/xColormap.Rd | 37 ++- man/xCombineNet.Rd | 10 man/xConverter.Rd | 8 man/xCtree.Rd | 20 + man/xDAGanno.Rd | 9 man/xDAGpropagate.Rd | 11 man/xDAGsim.Rd | 12 - man/xDefineEQTL.Rd | 102 +++++---- man/xDefineGenomicAnno.Rd | 47 ++-- man/xDefineHIC.Rd | 25 +- man/xDefineNet.Rd | 38 ++- man/xDefineOntology.Rd | 58 +++-- man/xEnrichBarplot.Rd | 18 + man/xEnrichChord.Rd | 16 + man/xEnrichCompare.Rd | 16 + man/xEnrichCtree.Rd | 27 +- man/xEnrichD3.Rd | 12 - man/xEnrichDAGplot.Rd | 33 ++ man/xEnrichDAGplotAdv.Rd | 27 +- man/xEnrichDotplot.Rd | 17 + man/xEnrichForest.Rd | 21 + man/xEnrichGGraph.Rd | 20 + man/xEnrichHeatmap.Rd | 11 man/xEnrichLadder.Rd | 23 +- man/xEnrichMatrix.Rd | 28 +- man/xEnrichNetplot.Rd | 35 ++- man/xEnrichRadial.Rd | 22 + man/xEnrichTreemap.Rd | 33 ++ man/xEnrichViewer.Rd | 11 man/xEnricher.Rd | 29 +- man/xEnricherGenes.Rd | 38 ++- man/xEnricherGenesAdv.Rd | 37 ++- man/xEnricherSNPs.Rd | 36 ++- man/xEnricherYours.Rd | 22 + man/xGGnetwork.Rd | 69 ++++-- man/xGGraph.Rd | 26 +- man/xGR.Rd | 16 + man/xGR2GeneScores.Rd | 21 + man/xGR2nGenes.Rd | 25 +- man/xGR2xGeneAnno.Rd | 51 +++- man/xGR2xGeneAnnoAdv.Rd | 48 +++- man/xGR2xGeneScores.Rd | 24 +- man/xGR2xGenes.Rd | 36 ++- man/xGRsampling.Rd | 17 - man/xGRscores.Rd | 10 man/xGRviaGeneAnno.Rd | 37 ++- man/xGRviaGeneAnnoAdv.Rd | 40 ++- man/xGRviaGenomicAnno.Rd | 27 +- man/xGRviaGenomicAnnoAdv.Rd | 32 ++ man/xGeneID2Symbol.Rd | 13 - man/xGraphML.Rd | 34 ++- man/xGraphML2AA.Rd | 55 +++- man/xHeatmap.Rd | 34 ++- man/xHeatmapAdv.Rd | 53 +++- man/xLayout.Rd | 47 +++- man/xLiftOver.Rd | 19 + man/xMEabf.Rd | 11 man/xMarkNet.Rd |only man/xOBOcode.Rd | 47 +++- man/xObjSize.Rd | 8 man/xPieplot.Rd | 14 - man/xRDataLoader.Rd | 49 +++- man/xReport.Rd | 12 - man/xSNP2GeneScores.Rd | 31 +- man/xSNP2cGenes.Rd | 20 + man/xSNP2eGenes.Rd | 15 + man/xSNP2nGenes.Rd | 17 + man/xSNPlocations.Rd | 17 + man/xSNPscores.Rd | 17 + man/xSocialiser.Rd | 21 + man/xSocialiserDAGplot.Rd | 32 ++ man/xSocialiserDAGplotAdv.Rd | 32 ++ man/xSocialiserGenes.Rd | 27 +- man/xSocialiserNetplot.Rd | 31 ++ man/xSocialiserSNPs.Rd | 29 +- man/xSubneterGR.Rd | 95 ++++++-- man/xSubneterGenes.Rd | 55 +++- man/xSubneterGenesAdv.Rd |only man/xSubneterGenesMST.Rd |only man/xSubneterSNPs.Rd | 83 +++++-- man/xSymbol2GeneID.Rd | 15 + man/xVisNet.Rd | 30 +- 234 files changed, 4611 insertions(+), 1938 deletions(-)
Title: Stepwise Regression Analysis
Description: Stepwise regression analysis for variable selection can be used to get the best candidate final regression model with the forward selection, backward elimination and bidirectional elimination approaches. Best subset selection fit a separate least squares regression for each possible combination of all predictors. Both the above two procedures in this package can use weighted data to get best regression model in univariate regression and multivariate regression analysis(Alsubaihi, A. A., (2002) <doi:10.18637/jss.v007.i12>). Besides, continuous variables nested within class effect is also considered in both two procedures. A widely used selection criteria are available which includes Akaike information criterion(Darlington, R. B. (1968) <doi:10.1037/h0025471>, Judge, G. G. (1985) <doi:10.2307/1391738>), corrected Akaike information criterion(Hurvich, C. M., and Tsai, C. (1989) <doi:10.1093/biomet/76.2.297>), Bayesian information criterion(Sawa, T. (1978) <doi:10.2307/1913828>, Judge, G. G. (1985) <doi:10.2307/1391738>), Mallows Cp statistic(Mallows, C. L. (1973) <doi:10.1080/00401706.1995.10484370>, Hocking, R. R. (1976) <doi:10.2307/2529336>), Hannan and Quinn information criterion(Hannan, E. J. and Quinn, B. G. (1979) <doi:10.1111/j.2517-6161.1979.tb01072.x>, Mcquarrie, A. D. R. and Tsai, C. L. (1998) <doi:10.1142/3573>), corrected Hannan and Quinn information criterion(Mcquarrie, A. D. R. and Tsai, C. L. (1998) <doi:10.1142/3573>), Schwarz criterion(Schwarz, G. (1978) <doi:10.1214/aos/1176344136>, Judge, G. G. (1985) <doi:10.2307/1391738>), adjusted R-square statistic(Darlington, R. B. (1968) <doi:10.1037/h0025471>, Judge, G. G. (1985) <doi:10.2307/1391738>) and significance levels(Mckeon, J. J. (1974) <doi:10.1093/biomet/61.2.381>, Harold Hotelling. (1992) <doi:10.1007/978-1-4612-0919-5_4>, Pillai, K. C. S. (2006) <doi:10.1002/0471667196.ess1965.pub2>), where multicollinearity can be detected with checking tolerance value.
Author: Junhui Li,Xiaohuan Lu,Kun Cheng,Wenxin Liu
Maintainer: Junhui Li <junhuili@cau.edu.cn>
Diff between StepReg versions 1.3.3 dated 2019-11-25 and 1.3.4 dated 2020-01-08
DESCRIPTION | 10 +++--- MD5 | 8 ++--- R/bestsubset.R | 8 ++--- R/stepwise.R | 73 ++++++++++++++++++++++++++++++++++++++----------- man/StepReg-package.Rd | 6 ++-- 5 files changed, 74 insertions(+), 31 deletions(-)
Title: Statistical Significance of the Markowitz Portfolio
Description: A collection of tools for analyzing significance of
Markowitz portfolios.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between MarkowitzR versions 1.0.1 dated 2018-05-26 and 1.0.2 dated 2020-01-08
ChangeLog | 4 +++ DESCRIPTION | 22 ++++++++---------- MD5 | 34 +++++++++++++++------------- NAMESPACE | 1 R/MarkowitzR.r | 11 ++++++--- R/portinf.r | 2 - R/utils.r | 2 - R/vcov.r | 10 ++++---- build/vignette.rds |binary inst/doc/AsymptoticMarkowitz.R |only inst/doc/AsymptoticMarkowitz.pdf |binary inst/doc/MarkowitzR.R |only inst/doc/MarkowitzR.pdf |binary man/MarkowitzR.Rd | 5 +--- man/NEWS.Rd | 7 +++++ man/itheta_vcov.Rd | 4 +-- man/theta_vcov.Rd | 4 +-- tests/testthat.R | 4 +-- tests/testthat/test-basic.r | 46 +++++++++++++++++++++++---------------- 19 files changed, 90 insertions(+), 66 deletions(-)
Title: Isolation-Based Outlier Detection
Description: Fast and multi-threaded implementation of
isolation forest (Liu, Ting, Zhou (2008) <doi:10.1109/ICDM.2008.17>),
extended isolation forest (Hariri, Kind, Brunner (2018) <arXiv:1811.02141>),
SCiForest (Liu, Ting, Zhou (2010) <doi:10.1007/978-3-642-15883-4_18>),
and fair-cut forest (Cortes (2019) <arXiv:1911.06646>),
for isolation-based outlier detection, clustered outlier detection, distance or similarity
approximation (Cortes (2019) <arXiv:1910.12362>),
and imputation of missing values (Cortes (2019) <arXiv:1911.06646>),
based on random or guided decision tree splitting. Provides simple heuristics for fitting the model to
categorical columns and handling missing data, and offers options for varying between random and guided
splits, and for using different splitting criteria.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between isotree versions 0.1.5 dated 2019-12-18 and 0.1.8 dated 2020-01-08
isotree-0.1.5/isotree/man/add_isolation_tree.Rd |only isotree-0.1.8/isotree/DESCRIPTION | 10 +- isotree-0.1.8/isotree/LICENSE | 2 isotree-0.1.8/isotree/MD5 | 22 +++--- isotree-0.1.8/isotree/NAMESPACE | 2 isotree-0.1.8/isotree/R/isoforest.R | 64 +++++++++++-------- isotree-0.1.8/isotree/man/add.isolation.tree.Rd |only isotree-0.1.8/isotree/man/isolation.forest.Rd | 62 +++++++++++------- isotree-0.1.8/isotree/man/unpack.isolation.forest.Rd | 4 - isotree-0.1.8/isotree/src/dist.cpp | 2 isotree-0.1.8/isotree/src/fit_model.cpp | 19 +++-- isotree-0.1.8/isotree/src/predict.cpp | 2 isotree-0.1.8/isotree/src/utils.cpp | 8 +- 13 files changed, 118 insertions(+), 79 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.5.3 dated 2019-12-20 and 1.5.4 dated 2020-01-08
DESCRIPTION | 8 +-- MD5 | 14 +++-- NAMESPACE | 3 - R/RcppExports.R | 4 + R/gamma_statistic.R |only man/gamma_statistic.Rd |only src/RcppExports.cpp | 16 ++++++ src/STMathExpression.cpp | 22 ++++++--- src/phylogenetics_cpp_routines.cpp | 90 ++++++++++++++++++++++++++++++++++++- 9 files changed, 138 insertions(+), 19 deletions(-)
Title: Process Biogas Data and Predict Biogas Production
Description: High- and low-level functions for processing biogas data and predicting biogas production. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas quantity can be converted between volume, mass, and moles. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated using volumetric, manometric, gravimetric, or gas density methods for any number of bottles. With cumulative methane production data and data on bottle contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Biogas quantity and composition can be predicted from substrate composition and additional, optional data. Lastly, inoculum and substrate mass can be determined for planning BMP experiments.
Author: Sasha D. Hafner [aut, cre],
Charlotte Rennuit [aut],
Camilla Justesen [aut],
Nanna Lojborg [aut],
Jacob Mortensen [aut],
Sergi Astals [ctb],
Konrad Koch [ctb],
Soeren Weinrich [ctb],
Jin Mi Triolo [ctb],
Ali Heidarzadeh Vazifehkhoran [ctb]
Maintainer: Sasha D. Hafner <sasha.hafner@eng.au.dk>
Diff between biogas versions 1.10.3 dated 2018-05-16 and 1.23.2 dated 2020-01-08
ChangeLog | 132 ++++++++++++ DESCRIPTION | 18 + MD5 | 108 ++++++---- NAMESPACE | 3 NEWS | 56 +++++ R/GDComp.R |only R/calcBgGD.R |only R/calcBgMan.R |only R/calcBgVol.R |only R/checkArgClassValue.R | 2 R/cumBg.R | 333 ++++++++++++++++++------------- R/cumBgDataPrep.R |only R/gasDens.R |only R/interp.R | 10 R/mass2vol.R | 191 ++++++++--------- R/massLoss.R |only R/planBMP.R | 5 R/rbindf.R | 20 - R/summBg.R | 223 ++++++++++++++++++-- README.md | 10 build/vignette.rds |binary data/UQGDBiogas.rda |only data/UQGDSetup.rda |only data/comp.rda |binary data/comp2.rda |binary data/feedSetup.rda |only data/feedVol.rda |only data/mass.rda |binary data/massw.rda |binary data/s3compl.rda |binary data/s3compw.rda |binary data/s3lcombo.rda |binary data/s3voll.rda |binary data/s3volw.rda |binary data/setup.rda |binary data/setup2.rda |binary data/sludgeTwoBiogas.rda |only data/sludgeTwoSetup.rda |only data/strawComp.rda |binary data/strawMass.rda |binary data/strawPressure.rda |binary data/strawSetup.rda |binary data/vol.rda |binary data/vol2.rda |binary inst/doc/biogas_quick_start.pdf |binary inst/doc/calcBgMan_function.R |only inst/doc/calcBgMan_function.Rnw |only inst/doc/calcBgMan_function.pdf |only inst/doc/calcBgVol_function.R |only inst/doc/calcBgVol_function.Rnw |only inst/doc/calcBgVol_function.pdf |only inst/doc/predBg_function.R | 2 inst/doc/predBg_function.pdf |binary man/UQGDBiogas.Rd |only man/UQGDSetup.Rd |only man/calcBgGD.Rd |only man/calcBgMan.Rd |only man/calcBgVol.Rd |only man/cumBg.Rd | 33 ++- man/feedSetup.Rd |only man/feedVol.Rd |only man/interp.Rd | 2 man/mass2vol.Rd | 4 man/planBMP.Rd | 6 man/sludgeTwoBiogas.Rd |only man/sludgeTwoSetup.Rd |only man/summBg.Rd | 46 +++- tests/testthat/test_HighLevelFunctions.R | 25 +- vignettes/calcBgMan_function.Rnw |only vignettes/calcBgVol_function.Rnw |only 70 files changed, 890 insertions(+), 339 deletions(-)
Title: Bayesian Aggregate Treatment Effects
Description: Running and comparing meta-analyses of data with hierarchical
Bayesian models in Stan, including convenience functions for formatting
data, plotting and pooling measures specific to meta-analysis.
Author: Witold Wiecek [cre, aut],
Rachael Meager [aut],
Brice Green [ctb] (extra features for LOO CV and visuals),
Trustees of Columbia University [cph] (tools/make_cc.R)
Maintainer: Witold Wiecek <witold.wiecek@gmail.com>
Diff between baggr versions 0.2.0 dated 2019-10-29 and 0.3.0 dated 2020-01-08
DESCRIPTION | 14 +- MD5 | 109 ++++++++++++---------- NAMESPACE | 17 +++ NEWS.md | 19 +++ R/aaa.R | 3 R/auto_prior.R | 40 ++++++-- R/baggr.R | 40 +++++++- R/baggr_compare.R | 16 ++- R/baggr_plot.R | 39 ++++++-- R/check_cols.R | 25 +++-- R/convert_inputs.R | 117 +++++++++++++++--------- R/detect_input_type.R | 14 +- R/forest_plot.R |only R/group_effects.R | 24 +++- R/loocv.R | 115 +++++++++++++++++++++-- R/mint.R | 30 ++++-- R/names.R | 8 + R/plot.R | 80 ++++++++++++++++ R/pooling_metrics.R | 120 +++++++++++++++++++----- R/prepare_ma.R | 116 ++++++++++++++++++----- R/print_baggr.R | 90 ++++++++++++++---- R/prior_dist.R | 6 + R/trt_effects.R | 74 ++++++++++++--- build/vignette.rds |binary inst/doc/baggr.R | 67 +++++++++---- inst/doc/baggr.Rmd | 171 ++++++++++++++++++++++++++--------- inst/doc/baggr.html | 204 ++++++++++++++++++++++++++++++------------ inst/doc/baggr_binary.R |only inst/doc/baggr_binary.Rmd |only inst/doc/baggr_binary.html |only man/baggr.Rd | 7 + man/baggr_plot.Rd | 16 ++- man/baggr_theme_set.Rd |only man/convert_inputs.Rd | 2 man/effect_draw.Rd | 6 + man/effect_plot.Rd | 15 ++- man/forest_plot.Rd |only man/group_effects.Rd | 13 +- man/is.baggr_cv.Rd |only man/loo_compare.Rd |only man/loocv.Rd | 12 +- man/mint.Rd |only man/pooling.Rd | 73 +++++++++++++-- man/prepare_ma.Rd | 33 +++++- man/prepare_prior.Rd |only man/print.baggr.Rd | 10 +- man/print.baggr_cv.Rd |only man/print.compare_baggr_cv.Rd |only man/priors.Rd | 6 + man/treatment_effect.Rd | 15 ++- src/stan_files/full.stan | 4 src/stan_files/logit.stan |only tests/testthat/Rplots.pdf |binary tests/testthat/test_binary.R |only tests/testthat/test_full.R | 13 ++ tests/testthat/test_helpers.R | 39 +++++++- tests/testthat/test_loo.R | 16 +++ tests/testthat/test_mutau.R | 13 +- tests/testthat/test_prior.R | 29 +++++ tests/testthat/test_rubin.R | 74 +++++++-------- vignettes/baggr.Rmd | 171 ++++++++++++++++++++++++++--------- vignettes/baggr.bib | 96 ++++++++++++++++--- vignettes/baggr_binary.Rmd |only 63 files changed, 1718 insertions(+), 503 deletions(-)
Title: Computation of the WHO Child Growth Standards
Description: Provides WHO Child Growth Standards (z-scores) with
confidence intervals and standard errors around the
prevalence estimates, taking into account complex sample designs.
More information on the methods is
available online:
<http://www.who.int/childgrowth/standards/en/>.
Author: Dirk Schumacher [aut, cre],
Elaine Borghi [ctb],
Jonathan Polonsky [ctb]
Maintainer: Dirk Schumacher <mail@dirk-schumacher.net>
Diff between anthro versions 0.9.1 dated 2019-03-23 and 0.9.2 dated 2020-01-08
DESCRIPTION | 10 MD5 | 59 +- NEWS.md | 12 R/anthro.R | 8 R/assertions.R | 45 + R/prevalence.R | 350 +++++++------- R/utils.R | 46 + R/z-score-arm-circumference-for-age.R | 13 R/z-score-bmi-for-age.R | 13 R/z-score-head-circumference-for-age.R | 15 R/z-score-helper.R | 103 ++-- R/z-score-length-for-age.R | 15 R/z-score-subscapular-skinfold-for-age.R | 13 R/z-score-triceps-skinfold-for-age.R | 13 R/z-score-weight-for-age.R | 15 R/z-score-weight-for-lenhei.R | 200 ++++---- R/z-score.R | 86 ++- README.md |only man/anthro.Rd | 1 man/anthro_prevalence.Rd | 31 - man/anthro_zscores.Rd | 29 - tests/testthat/test-age-groups.R | 8 tests/testthat/test-prevalence.R | 35 - tests/testthat/test-utils.R | 11 tests/testthat/test-zscore-arm-circumference-for-age.R | 2 tests/testthat/test-zscore-bmi-for-age.R | 15 tests/testthat/test-zscore-head-circumference-for-age.R | 2 tests/testthat/test-zscore-subscapular-skinfold-for-age.R | 2 tests/testthat/test-zscore-weight-for-age.R | 19 tests/testthat/test-zscore-weight-for-lenhei.R | 2 tests/testthat/test-zscores.R | 121 +++- 31 files changed, 753 insertions(+), 541 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, univariate and multivariate, with optional kernel term and
sampling techniques.
Author: Alencar Xavier, William Muir, Kyle Kocak, Shizhong Xu, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 1.6.5 dated 2019-06-05 and 1.6.6 dated 2020-01-08
DESCRIPTION | 9 - MD5 | 16 +- R/RcppExports.R | 282 ++++++++++++++++++++++++++-------------------------- inst/CITATION | 19 +-- man/bWGR.Rd | 5 man/mix.Rd | 3 man/mvr.Rd | 1 src/RcppExports.cpp | 41 ++++--- src/wgr20190605.cpp | 256 ++++++++++++++++++++++++++++++++--------------- 9 files changed, 372 insertions(+), 260 deletions(-)
Title: Classification Based on Association Rules
Description: Provides a function to build an association rule-based classifier for data frames, and to classify incoming data frames using such a classifier.
Author: Ian Johnson [aut, cre, cph],
Michael Hahsler [aut, cph],
Tyler Giallanza [ctb]
Maintainer: Ian Johnson <ianjjohnson@icloud.com>
Diff between arulesCBA versions 1.1.5 dated 2019-11-12 and 1.1.6 dated 2020-01-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/doc/arulesCBA.pdf |binary tests/testthat/test-RCAR.R | 3 ++- 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Converts Human gene symbols to entrez IDs
Description: Queries multiple resources authors HGNC (2019) <https://www.genenames.org>, authors limma (2015) <doi:10.1093/nar/gkv007>
to find the correspondence between evolving nomenclature of human gene symbols, aliases, previous symbols or synonyms with
stable, curated gene entrezID from NCBI database. This allows fast, accurate and up-to-date correspondence
between human gene expression datasets from various date and platform (e.g: gene symbol: BRCA1 - ID: 672).
Author: Raphael Bonnet [aut, cre] (Université Côte d’Azur),
Jean-François Peyron [aut] (Inserm)
Maintainer: Raphael Bonnet <raphael.bonnet@univ-cotedazur.fr>
Diff between aliases2entrez versions 0.0.6 dated 2019-10-06 and 0.1.0 dated 2020-01-08
DESCRIPTION | 8 ++-- MD5 | 8 ++-- NEWS | 3 + R/convert_symbols.R | 85 ++++++++++++++++++++++++++++++++++------------------ R/update_symbols.R | 1 5 files changed, 69 insertions(+), 36 deletions(-)
More information about aliases2entrez at CRAN
Permanent link
Title: Estimating Absolute Protein Quantities from Label-Free LC-MS/MS
Proteomics Data
Description: Determination of absolute protein quantities is necessary for multiple applications, such as mechanistic modeling of biological systems. Quantitative liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics can measure relative protein abundance on a system-wide scale. To estimate absolute quantitative information using these relative abundance measurements requires additional information such as heavy-labeled references of known concentration. Multiple methods have been using different references and strategies; some are easily available whereas others require more effort on the users end. Hence, we believe the field might benefit from making some of these methods available under an automated framework, which also facilitates validation of the chosen strategy. We have implemented the most commonly used absolute label-free protein abundance estimation methods for LC-MS/MS modes quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, we used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation. Our open-source software is written in the statistical programming language R and validated and demonstrated on a synthetic sample.
Author: George Rosenberger, Hannes Roest, Christina Ludwig, Ruedi Aebersold, Lars Malmstroem
Maintainer: George Rosenberger <gr2578@cumc.columbia.edu>
Diff between aLFQ versions 1.3.5 dated 2019-04-30 and 1.3.6 dated 2020-01-08
DESCRIPTION | 10 +++---- MD5 | 14 +++++----- NAMESPACE | 2 - R/ALF.R | 14 +++++----- R/ProteinInference.R | 53 ++------------------------------------- man/ALF.Rd | 11 +------- man/ProteinInference.Rd | 18 +++---------- tests/Examples/aLFQ-Ex.Rout.save | 8 ++--- 8 files changed, 33 insertions(+), 97 deletions(-)
Title: Higher Criticism Test of Two Frequency Counts Tables
Description: Higher Criticism (HC) test between two frequency tables. Test is based on an adaptation of the Tukey-Donoho-Jin HC statistic to testing frequency tables described in Kipnis (2019) <arXiv:1911.01208>.
Author: Alon Kipnis <kipnisal@stanford.edu>
Maintainer: Alon Kipnis <kipnisal@stanford.edu>
Diff between TableHC versions 0.1.1 dated 2019-11-06 and 0.1.2 dated 2020-01-08
TableHC-0.1.1/TableHC/man/tables.HC.Rd |only TableHC-0.1.1/TableHC/man/tables.pval.Rd |only TableHC-0.1.2/TableHC/DESCRIPTION | 9 + TableHC-0.1.2/TableHC/MD5 | 26 ++--- TableHC-0.1.2/TableHC/NAMESPACE | 4 TableHC-0.1.2/TableHC/NEWS.md | 2 TableHC-0.1.2/TableHC/R/TableHC.R | 120 +++++++++++++++--------- TableHC-0.1.2/TableHC/README.md | 10 +- TableHC-0.1.2/TableHC/inst/doc/my-vignette.Rmd | 53 +++++++--- TableHC-0.1.2/TableHC/inst/doc/my-vignette.html | 54 +++++++--- TableHC-0.1.2/TableHC/man/HC.vals.Rd | 39 +++++-- TableHC-0.1.2/TableHC/man/two.sample.HC.Rd |only TableHC-0.1.2/TableHC/man/two.sample.pvals.Rd |only TableHC-0.1.2/TableHC/tests/testthat.R | 1 TableHC-0.1.2/TableHC/tests/testthat/testthat.R | 38 ++++--- TableHC-0.1.2/TableHC/vignettes/my-vignette.Rmd | 53 +++++++--- 16 files changed, 262 insertions(+), 147 deletions(-)
Title: Exact Bayesian Model Selection Methods for the Sparse Normal
Sequence Model
Description: Contains fast functions to calculate the exact Bayes posterior
for the Sparse Normal Sequence Model, which implement the algorithms described in
Van Erven and Szabo (2018) <arXiv:1810.10883>. For general hierarchical priors,
sample sizes up to 10,000 are feasible within half an hour on a standard laptop.
For beta-binomial spike-and-slab priors, a faster algorithm is provided, which
can handle sample sizes of 100,000 in half an hour. In the implementation,
special care has been taken to assure numerical stability of the methods even for
such large sample sizes.
Author: Steven de Rooij [cre, aut],
Tim van Erven [aut],
Botond Szabo [aut]
Maintainer: Steven de Rooij <steven.de.rooij@gmail.com>
Diff between SequenceSpikeSlab versions 0.1 dated 2019-12-13 and 0.1.1 dated 2020-01-08
DESCRIPTION | 6 MD5 | 13 NEWS |only build/vignette.rds |binary inst/doc/SequenceSpikeSlab-vignette.Rmd | 2 inst/doc/SequenceSpikeSlab-vignette.html | 634 ++++++++++++++----------------- src/SequenceSpikeSlab.cpp | 2 vignettes/SequenceSpikeSlab-vignette.Rmd | 2 8 files changed, 301 insertions(+), 358 deletions(-)
More information about SequenceSpikeSlab at CRAN
Permanent link
Title: Robust Tail Dependence Estimation
Description: Robust tail dependence estimation for bivariate models. This package is based on two papers by the authors:'Robust and bias-corrected estimation of the coefficient of tail dependence' and 'Robust and bias-corrected estimation of probabilities of extreme failure sets'. This work was supported by a research grant (VKR023480) from VILLUM FONDEN and an international project for scientific cooperation (PICS-6416).
Author: Christophe Dutang [aut, cre], Armelle Guillou [ctb], Yuri Goegebeur [ctb]
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between RTDE versions 0.2-0 dated 2015-07-20 and 0.2-1 dated 2020-01-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 10 +++++----- R/data-fit-probRTDE.R | 2 +- R/fitRTDE.R | 6 +++--- inst/CITATION | 2 +- inst/NEWS | 5 +++++ 7 files changed, 25 insertions(+), 20 deletions(-)
Title: R Interface to 'Bloomberg Data License'
Description: R interface to access prices and market data with the
'Bloomberg Data License' service from
<https://www.bloomberg.com/professional/product/data-license/>.
As a prerequisite, a valid Data License from 'Bloomberg' is needed
together with the corresponding SFTP credentials and whitelisting
of the IP from which accessing the service.
This software and its author are in no way affiliated,
endorsed, or approved by 'Bloomberg' or any of its affiliates.
'Bloomberg' is a registered trademark.
Author: Emanuele Guidotti [aut, cre] (<https://orcid.org/0000-0002-8961-6623>)
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>
Diff between RblDataLicense versions 0.2.1 dated 2019-09-07 and 0.2.2 dated 2020-01-08
DESCRIPTION | 20 ++++++++++++-------- MD5 | 10 ++++++++-- NEWS.md |only README.md | 18 +++++++++++------- build |only inst |only vignettes |only 7 files changed, 31 insertions(+), 17 deletions(-)
More information about RblDataLicense at CRAN
Permanent link
Title: An Analysis Toolbox for Hermitian Positive Definite Matrices
Description: An implementation of data analysis tools for samples of symmetric or
Hermitian positive definite matrices, such as collections of covariance matrices
or spectral density matrices. The tools in this package can be used to perform: (i)
intrinsic wavelet transforms for curves (1D) or surfaces (2D) of Hermitian positive
definite matrices with applications to dimension reduction, denoising and clustering in the
space of Hermitian positive definite matrices; and (ii) exploratory data analysis and inference
for samples of positive definite matrices by means of intrinsic data depth functions and
rank-based hypothesis tests in the space of Hermitian positive definite matrices.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between pdSpecEst versions 1.2.3 dated 2018-10-06 and 1.2.4 dated 2020-01-08
DESCRIPTION | 11 MD5 | 66 - NEWS.md | 11 R/benchmark.R | 20 R/cluster.R | 38 - R/depth.R | 24 R/estimation.R | 36 - R/examples.R | 209 +++--- R/invwavtrans.R | 36 - R/meandist.R | 14 R/polynomial.R | 2 R/ranktests.R | 10 R/wavtrans.R | 37 - README.md | 34 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 47 - inst/doc/depth_ranktests.Rmd | 4 inst/doc/depth_ranktests.html | 478 +++++++------- inst/doc/wavelet_est_clust.Rmd | 5 inst/doc/wavelet_est_clust.html | 200 +++-- man/H.coeff.Rd | 12 man/InvWavTransf1D.Rd | 8 man/WavTransf1D.Rd | 10 man/pdCART.Rd | 6 man/pdMean.Rd | 6 man/pdSpecClust1D.Rd | 8 man/pdSpecClust2D.Rd | 8 man/pdSpecEst1D.Rd | 4 man/rExamples1D.Rd | 27 src/mean_fun.cpp | 1363 ++++++++++++++++++++-------------------- tests/testthat/test-geometry.R | 2 vignettes/depth_ranktests.Rmd | 4 vignettes/wavelet_est_clust.Rmd | 5 34 files changed, 1435 insertions(+), 1310 deletions(-)
Title: Owen Q-Function
Description: Evaluates the Owen Q-function for an integer value of the degrees of freedom, by applying Owen's algorithm (1965) <doi:10.1093/biomet/52.3-4.437>.
It is useful for the calculation of the power of equivalence tests.
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between OwenQ versions 1.0.1 dated 2019-08-30 and 1.0.3 dated 2020-01-08
DESCRIPTION | 10 MD5 | 76 - NAMESPACE | 38 NEWS.md | 12 R/OwenQ.R | 250 +++--- R/OwenT.R | 52 - R/Student.R | 96 +- R/internal.R | 6 R/pOwen.R | 508 ++++++------ R/psbt.R | 272 +++--- R/specialOwen2.R | 80 +- README.md | 12 build/vignette.rds |binary inst/doc/OwenQ.R | 20 inst/doc/OwenQ.Rmd | 582 +++++++------- inst/doc/OwenQ.html | 169 ++-- inst/doc/Validation.R | 50 - inst/doc/Validation.Rmd | 1458 ++++++++++++++++++------------------- inst/doc/Validation.html | 483 ++++++------ man/OwenQ1.Rd | 84 +- man/OwenQ2.Rd | 84 +- man/OwenT.Rd | 64 - man/powen.Rd | 148 +-- man/psbt.Rd | 128 +-- man/ptOwen.Rd | 74 - man/spowen2.Rd | 68 - src/Owen.cpp | 223 ++--- tests/testthat.R | 8 tests/testthat/test-OwenQ1_algo1.R | 190 ++-- tests/testthat/test-OwenQ1_algo2.R | 190 ++-- tests/testthat/test-OwenQ2_algo1.R | 152 +-- tests/testthat/test-OwenQ2_algo2.R | 152 +-- tests/testthat/test-OwenT.R | 186 ++-- tests/testthat/test-pOwen_algo1.R | 818 ++++++++++---------- tests/testthat/test-pOwen_algo2.R | 818 ++++++++++---------- tests/testthat/test-ptOwen.R | 50 - tests/testthat/test-spowen2.R | 32 vignettes/OwenQ.Rmd | 582 +++++++------- vignettes/Validation.Rmd | 1458 ++++++++++++++++++------------------- 39 files changed, 4820 insertions(+), 4863 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.4.7.1 dated 2019-11-20 and 0.4.8 dated 2020-01-08
DESCRIPTION | 10 MD5 | 95 ++--- NAMESPACE | 1 R/ARMA_optim.R | 8 R/Boost.R | 135 ++++--- R/Causation.R | 4 R/Co_PM_dep.R | 20 - R/Dependence.R | 4 R/Dependence_base.R | 117 ++---- R/Internal_Functions.R | 19 - R/Multivariate_Regression.R | 84 +++- R/NNS_Distance.R | 34 +- R/NNS_VAR.R | 30 - R/Normalization.R | 22 - R/Partial_Moments.R | 23 - R/Partition_Map.R | 289 +++++++---------- R/Regression.R | 132 +++++-- R/Stack.R | 92 +++-- R/dy_dx.R | 20 - R/gvload.R | 1 README.md |only build/vignette.rds |binary inst/doc/NNSvignette_Classification.R | 35 +- inst/doc/NNSvignette_Classification.Rmd | 35 +- inst/doc/NNSvignette_Classification.html | 155 ++++++--- inst/doc/NNSvignette_Clustering_and_Regression.R | 44 +- inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 56 ++- inst/doc/NNSvignette_Clustering_and_Regression.html | 322 ++++++++++--------- inst/doc/NNSvignette_Correlation_and_Dependence.R | 24 - inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 12 inst/doc/NNSvignette_Correlation_and_Dependence.html | 230 +++++++------ inst/doc/NNSvignette_Forecasting.R | 27 - inst/doc/NNSvignette_Forecasting.Rmd | 8 inst/doc/NNSvignette_Forecasting.html | 149 +++++--- inst/doc/NNSvignette_Partial_Moments.R | 20 - inst/doc/NNSvignette_Partial_Moments.html | 149 +++++--- man/NNS.ARMA.optim.Rd | 4 man/NNS.VAR.Rd | 2 man/NNS.boost.Rd | 24 - man/NNS.distance.Rd | 2 man/NNS.part.Rd | 4 man/NNS.reg.Rd | 6 man/NNS.stack.Rd | 22 - man/PM.matrix.Rd | 10 man/dy.dx.Rd | 10 vignettes/NNSvignette_Classification.Rmd | 35 +- vignettes/NNSvignette_Clustering_and_Regression.Rmd | 56 ++- vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 12 vignettes/NNSvignette_Forecasting.Rmd | 8 49 files changed, 1517 insertions(+), 1084 deletions(-)
Title: Decision Trees with Structural Equation Models Fit in 'Mplus'
Description: Uses recursive partitioning to create homogeneous subgroups based on structural equation models
fit in 'Mplus', a stand-alone program developed by Muthen and Muthen.
Author: Sarfaraz Serang [aut,cre],
Ross Jacobucci [aut,cre],
Kevin J. Grimm [ctb],
Gabriela Stegmann [ctb],
Andreas M. Brandmaier [ctb]
Maintainer: Sarfaraz Serang <sarfaraz.serang@usu.edu>
Diff between MplusTrees versions 0.0.1 dated 2019-07-19 and 0.1.1 dated 2020-01-08
DESCRIPTION | 6 +- MD5 | 13 ++++- NAMESPACE | 2 R/MplusTrees.R | 120 +++++++++++++++++++++++++++++++++++------------------- R/cpcalc.R |only R/foldcombiner.R |only R/foldmaker.R |only R/indicator.R |only R/leafgrouper.R |only man/MplusTrees.Rd | 30 ++++++++++++- 10 files changed, 120 insertions(+), 51 deletions(-)
Title: Probabilistic Supervised Learning for 'mlr3'
Description: Provides extensions for probabilistic supervised
learning for 'mlr3'. This includes extending the regression task to
probabilistic and interval regression, adding a survival task, and
other specialized models, predictions, and measures.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>),
Franz Kiraly [aut],
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Andreas Bender [ctb] (<https://orcid.org/0000-0001-5628-8611>)
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>
Diff between mlr3proba versions 0.1.0 dated 2019-12-22 and 0.1.1 dated 2020-01-08
DESCRIPTION | 15 - MD5 | 195 +++++++-------- NAMESPACE | 4 NEWS.md | 9 R/LearnerSurvBlackboost.R | 19 - R/LearnerSurvCVGlmnet.R | 11 R/LearnerSurvCoxPH.R | 5 R/LearnerSurvFlexible.R | 6 R/LearnerSurvGBM.R | 26 -- R/LearnerSurvGamboost.R | 31 -- R/LearnerSurvGlmboost.R | 15 - R/LearnerSurvGlmnet.R | 11 R/LearnerSurvKaplan.R | 5 R/LearnerSurvMboost.R | 33 -- R/LearnerSurvNelson.R | 14 - R/LearnerSurvParametric.R | 5 R/LearnerSurvPenalized.R | 7 R/LearnerSurvRandomForestSRC.R | 8 R/LearnerSurvRanger.R | 12 R/LearnerSurvRpart.R | 9 R/LearnerSurvSVM.R | 15 - R/MeasureSurvBeggC.R | 4 R/MeasureSurvChamblessAUC.R | 6 R/MeasureSurvGonenHellersC.R | 4 R/MeasureSurvGraf.R | 19 - R/MeasureSurvGrafSE.R | 5 R/MeasureSurvHarrellC.R | 4 R/MeasureSurvHungAUC.R | 4 R/MeasureSurvIntLogloss.R | 14 - R/MeasureSurvIntLoglossSE.R | 5 R/MeasureSurvIntegrated.R | 26 +- R/MeasureSurvNagelkR2.R | 4 R/MeasureSurvOQuigleyR2.R | 4 R/MeasureSurvSongAUC.R | 4 R/MeasureSurvSongTNR.R | 4 R/MeasureSurvSongTPR.R | 4 R/MeasureSurvUnoAUC.R | 4 R/MeasureSurvUnoC.R | 9 R/MeasureSurvUnoTNR.R | 4 R/MeasureSurvUnoTPR.R | 4 R/MeasureSurvXuR2.R | 4 R/TaskSurv.R | 10 R/integrated_scores.R | 14 - R/weighted_survival_score.R | 10 R/zzz.R | 1 README.md | 125 +++++---- build/partial.rdb |binary inst/doc/survival.R | 17 - inst/doc/survival.Rmd | 17 - inst/doc/survival.html | 91 +++---- inst/references.bib |only man/LearnerSurvBlackboost.Rd | 17 - man/LearnerSurvCVGlmnet.Rd | 12 man/LearnerSurvCoxPH.Rd | 5 man/LearnerSurvFlexible.Rd | 6 man/LearnerSurvGBM.Rd | 26 -- man/LearnerSurvGamboost.Rd | 23 - man/LearnerSurvGlmboost.Rd | 15 - man/LearnerSurvGlmnet.Rd | 12 man/LearnerSurvKaplan.Rd | 5 man/LearnerSurvMboost.Rd | 33 -- man/LearnerSurvNelson.Rd | 14 - man/LearnerSurvParametric.Rd | 5 man/LearnerSurvPenalized.Rd | 3 man/LearnerSurvRandomForestSRC.Rd | 8 man/LearnerSurvRanger.Rd | 10 man/LearnerSurvRpart.Rd | 5 man/LearnerSurvSVM.Rd | 15 - man/MeasureSurvBeggC.Rd | 4 man/MeasureSurvChamblessAUC.Rd | 4 man/MeasureSurvGonenC.Rd | 4 man/MeasureSurvGraf.Rd | 12 man/MeasureSurvGrafSE.Rd | 5 man/MeasureSurvHarrellC.Rd | 4 man/MeasureSurvHungAUC.Rd | 4 man/MeasureSurvIntLogloss.Rd | 7 man/MeasureSurvIntLoglossSE.Rd | 5 man/MeasureSurvNagelkR2.Rd | 4 man/MeasureSurvOQuigleyR2.Rd | 4 man/MeasureSurvSongAUC.Rd | 4 man/MeasureSurvSongTNR.Rd | 4 man/MeasureSurvSongTPR.Rd | 4 man/MeasureSurvUnoAUC.Rd | 4 man/MeasureSurvUnoC.Rd | 12 man/MeasureSurvUnoTNR.Rd | 4 man/MeasureSurvUnoTPR.Rd | 4 man/MeasureSurvXuR2.Rd | 4 man/TaskSurv.Rd | 8 tests/testthat/test_PredictionSurv.R | 14 - tests/testthat/test_mlr_learners_surv_blackboost.R | 6 tests/testthat/test_mlr_learners_surv_coxph.R | 1 tests/testthat/test_mlr_learners_surv_cvglmnet.R | 5 tests/testthat/test_mlr_learners_surv_glmnet.R | 5 tests/testthat/test_mlr_learners_surv_svm.R | 3 tests/testthat/test_mlr_measures.R | 5 tests/testthat/test_mlr_measures_MeasureSurvIntegrated.R | 3 tests/testthat/test_pipeop_crankcompositor.R | 9 tests/testthat/test_pipeop_distrcompositor.R | 11 vignettes/survival.Rmd | 17 - 99 files changed, 528 insertions(+), 746 deletions(-)
Title: Inferential Statistics
Description: Computation of various confidence intervals (Altman et al. (2000), ISBN:978-0-727-91375-3; Hedderich and Sachs (2018), ISBN:978-3-662-56657-2) including bootstrapped versions (Davison and Hinkley (1997), ISBN:978-0-511-80284-3) as well as Hsu (Hedderich and Sachs (2018), ISBN:978-3-662-56657-2), permutation (Janssen (1997), <doi:10.1016/S0167-7152(97)00043-6>), bootstrap (Davison and Hinkley (1997), ISBN:978-0-511-80284-3) and multiple imputation (Barnard and Rubin (1999), <doi:10.1093/biomet/86.4.948>) t-test. Graphical visualization by volcano plots.
Author: Matthias Kohl [aut, cre] (<https://orcid.org/0000-0001-9514-8910>)
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKinfer versions 0.3 dated 2019-12-02 and 0.4 dated 2020-01-08
DESCRIPTION | 12 - MD5 | 28 +-- NAMESPACE | 11 - NEWS | 6 R/boot.t.test.R | 2 R/imputeSD.R | 5 R/volcano.R |only build/vignette.rds |binary inst/doc/MKinfer.R | 60 ++++--- inst/doc/MKinfer.Rmd | 28 +++ inst/doc/MKinfer.html | 396 +++++++++++++++++++++++++----------------------- man/0MKinfer-package.Rd | 7 man/cvCI.Rd | 4 man/hsu.t.test.Rd | 8 man/volcano.Rd |only vignettes/MKinfer.Rmd | 28 +++ 16 files changed, 357 insertions(+), 238 deletions(-)
Title: Multivariate Functional Principal Component Analysis for Data
Observed on Different Dimensional Domains
Description: Calculate a multivariate functional principal component analysis
for data observed on different dimensional domains. The estimation algorithm
relies on univariate basis expansions for each element of the multivariate
functional data (Happ & Greven, 2018) <doi:10.1080/01621459.2016.1273115>. Multivariate and univariate functional data objects are
represented by S4 classes for this type of data implemented in the package
'funData'. For more details on the general concepts of both packages and a case study, see Happ (2018) <arXiv:1707.02129>.
Author: Clara Happ-Kurz [aut, cre] (<https://orcid.org/0000-0003-4737-3835>)
Maintainer: Clara Happ-Kurz <clara.happ@stat.uni-muenchen.de>
Diff between MFPCA versions 1.3-2 dated 2019-03-20 and 1.3-4 dated 2020-01-08
DESCRIPTION | 16 ++++++++-------- MD5 | 20 ++++++++++---------- NEWS.md | 12 ++++++++++++ R/MFPCA_calculation.R | 6 +++--- R/univPCA.R | 4 ++-- README.md | 4 ++-- build/partial.rdb |binary configure | 18 +++++++++--------- configure.ac | 2 +- inst/CITATION | 2 +- tests/testthat/test_fftw.R | 16 ++++++++-------- 11 files changed, 56 insertions(+), 44 deletions(-)
Title: Clustering and Visualizing Distance Matrices
Description: Defines the classes used to explore, cluster and
visualize distance matrices, especially those arising from binary data.
Author: Kevin R. Coombes, Caitlin E. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Mercator versions 0.9.5 dated 2019-08-29 and 0.9.6 dated 2020-01-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + NEWS | 16 ++++++++++++++-- R/04-vis.R | 6 +++++- inst/doc/mercator.html | 4 ++-- 6 files changed, 31 insertions(+), 14 deletions(-)
Title: Evidential Clustering
Description: Various clustering algorithms that produce a credal partition,
i.e., a set of Dempster-Shafer mass functions representing the membership of objects
to clusters. The mass functions quantify the cluster-membership uncertainty of the objects.
The algorithms are: Evidential c-Means (ECM), Relational Evidential c-Means (RECM),
Constrained Evidential c-Means (CECM), EVCLUS, EK-NNclus and bootclus.
Author: Thierry Denoeux
Maintainer: Thierry Denoeux <tdenoeux@utc.fr>
Diff between evclust versions 1.0.3 dated 2016-09-04 and 1.1.0 dated 2020-01-08
evclust-1.0.3/evclust/R/plaus_dist.R |only evclust-1.1.0/evclust/DESCRIPTION | 16 - evclust-1.1.0/evclust/MD5 | 64 +++--- evclust-1.1.0/evclust/NAMESPACE | 5 evclust-1.1.0/evclust/NEWS |only evclust-1.1.0/evclust/R/bootclus.R |only evclust-1.1.0/evclust/R/build_matrices.R |only evclust-1.1.0/evclust/R/createR.R |only evclust-1.1.0/evclust/R/kevclus.R | 3 evclust-1.1.0/evclust/R/mass_from_P_new.R |only evclust-1.1.0/evclust/R/pairwise_mass.R |only evclust-1.1.0/evclust/R/summary.credpart.R | 3 evclust-1.1.0/evclust/build/vignette.rds |binary evclust-1.1.0/evclust/inst/doc/Introduction.R | 61 ++++-- evclust-1.1.0/evclust/inst/doc/Introduction.Rmd | 44 ++++ evclust-1.1.0/evclust/inst/doc/Introduction.html | 221 ++++++++++++++--------- evclust-1.1.0/evclust/man/EkNNclus.Rd | 10 - evclust-1.1.0/evclust/man/bootclus.Rd |only evclust-1.1.0/evclust/man/butterfly.Rd | 1 evclust-1.1.0/evclust/man/cecm.Rd | 30 ++- evclust-1.1.0/evclust/man/createD.Rd | 1 evclust-1.1.0/evclust/man/createPairs.Rd | 1 evclust-1.1.0/evclust/man/create_MLCL.Rd | 1 evclust-1.1.0/evclust/man/ecm.Rd | 24 +- evclust-1.1.0/evclust/man/evclust.Rd | 2 evclust-1.1.0/evclust/man/extractMass.Rd | 15 + evclust-1.1.0/evclust/man/fourclass.Rd | 1 evclust-1.1.0/evclust/man/kevclus.Rd | 48 +++- evclust-1.1.0/evclust/man/knn_dist.Rd | 7 evclust-1.1.0/evclust/man/makeF.Rd | 1 evclust-1.1.0/evclust/man/plot.credpart.Rd | 17 + evclust-1.1.0/evclust/man/protein.Rd | 1 evclust-1.1.0/evclust/man/recm.Rd | 25 +- evclust-1.1.0/evclust/man/s2.Rd | 1 evclust-1.1.0/evclust/man/summary.credpart.Rd | 4 evclust-1.1.0/evclust/vignettes/Introduction.Rmd | 44 ++++ evclust-1.1.0/evclust/vignettes/tdenoeux.bib | 9 37 files changed, 443 insertions(+), 217 deletions(-)
Title: Visualise Twitter Interactions
Description: Allows building an edge table from data frame of tweets,
also provides function to build nodes and another create a temporal graph.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between graphTweets versions 0.5.2 dated 2019-07-10 and 0.5.3 dated 2020-01-08
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- NEWS.md | 4 ++++ man/edges_from_text.Rd | 9 +++++++-- man/graphTweets.Rd | 1 - 5 files changed, 23 insertions(+), 15 deletions(-)
Title: Computation of Generalized Nash Equilibria
Description: Provide functions to compute standard and generalized Nash Equilibria.
Optimization methods are available nonsmooth reformulation, fixed-point formulation,
minimization problem and constrained-equation reformulation.
See e.g. Kanzow and Facchinei (2010), <doi:10.1007/s10479-009-0653-x>.
Author: Christophe Dutang
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between GNE versions 0.99-2 dated 2018-08-09 and 0.99-3 dated 2020-01-08
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 9 +++++---- R/solv-GNE.R | 8 ++++---- R/solv-SE.R | 12 ++++++------ R/solv-ceq.R | 18 +++++++++--------- R/solv-eq.R | 2 +- R/solv-fpeq.R | 6 +++--- R/solv-minpb.R | 14 +++++++------- R/solv-nseq.R | 18 +++++++++--------- R/util-eval-list-test.R | 2 +- build/vignette.rds |binary inst/NEWS | 5 +++++ inst/doc/GNE-howto.pdf |binary man/GNE.Rd | 2 +- tests/sensi-analysis-duopoly.R | 11 +++++++---- 16 files changed, 77 insertions(+), 68 deletions(-)
Title: Perform the Joint Graphical Lasso and Selects Tuning Parameters
Description: Can be used to simultaneously estimate networks (Gaussian Graphical Models) in data from different groups or classes via Joint Graphical Lasso. Tuning parameters are selected via information criteria (AIC / BIC / extended BIC) or cross validation.
Author: Giulio Costantini, Nils Kappelmann, Sacha Epskamp
Maintainer: Giulio Costantini <giulio.costantini@unimib.it>
Diff between EstimateGroupNetwork versions 0.1.2 dated 2017-03-20 and 0.2.2 dated 2020-01-08
DESCRIPTION | 12 ++++++------ MD5 | 19 ++++++++++++++----- NAMESPACE | 5 ++++- NEWS.md |only R/BootTable.R |only R/EstimateGroupNetwork.R | 6 +++--- R/GroupBootPlot.R |only R/GroupNetworkBoot.R |only R/MyJGL.R | 32 +++++++++++++++++++++++++++++++- R/globals.R |only inst |only man/BootTable.Rd |only man/EstimateGroupNetwork.Rd | 7 ++++--- man/GroupBootPlot.Rd |only man/GroupNetworkBoot.Rd |only 15 files changed, 62 insertions(+), 19 deletions(-)
More information about EstimateGroupNetwork at CRAN
Permanent link
Title: A Class for Working with Time Series Based on 'data.table' and
'R6' with Largely Optional Reference Semantics
Description: Basic time series functionalities such as listing of missing
values, application of arbitrary aggregation as well as rolling window
functions and automatic detection of periodicity. As it is mainly based on
'data.table', it is fast and - in combination with the 'R6' package - offers
reference semantics. In addition to its native R6 interface, it provides an
S3 interface inclusive an S3 wrapper method generator for those who prefer
the latter.
Author: Gerold Hepp [aut, cre]
Maintainer: Gerold Hepp <ghepp@iwag.tuwien.ac.at>
Diff between DTSg versions 0.2.1 dated 2019-10-20 and 0.3.0 dated 2020-01-08
DESCRIPTION | 11 LICENSE | 2 MD5 | 88 +++---- NAMESPACE | 7 NEWS.md | 12 - R/ClassDTSg.R | 296 ++++++++++++++++--------- R/S3WrapperGenerator.R | 20 - R/Swrappers.R | 65 +++-- R/aaa.R | 5 R/assertives.R | 26 +- R/data.R | 3 R/funby.R | 34 +- R/funinterpolate.R | 24 +- R/rollback.R | 4 build/vignette.rds |binary inst/doc/a_basicUsage.R | 39 +-- inst/doc/a_basicUsage.Rmd | 9 inst/doc/a_basicUsage.html | 31 +- inst/doc/b_advancedUsage.R | 24 +- inst/doc/b_advancedUsage.Rmd | 12 - inst/doc/b_advancedUsage.html | 27 +- man/DTSg.Rd | 353 +++++++++++++++---------------- man/S3WrapperGenerator.Rd | 76 +++--- man/TALFs.Rd | 272 +++++++++++------------ man/aggregate.DTSg.Rd | 215 +++++++++--------- man/alter.DTSg.Rd | 122 +++++----- man/clone.DTSg.Rd | 92 ++++---- man/colapply.DTSg.Rd | 139 ++++++------ man/cols.DTSg.Rd | 82 +++---- man/flow.Rd | 39 +-- man/interpolateLinear.Rd | 104 ++++----- man/merge.DTSg.Rd | 90 +++---- man/nas.DTSg.Rd | 96 ++++---- man/plot.DTSg.Rd | 133 ++++++----- man/refresh.DTSg.Rd | 76 +++--- man/rollapply.DTSg.Rd | 185 ++++++++-------- man/rollback.Rd | 86 +++---- man/summary.DTSg.Rd | 80 +++---- man/values.DTSg.Rd | 132 ++++++----- tests/testthat/helper_funby.R | 46 ++-- tests/testthat/test_DTSg.R | 159 ++++++++++--- tests/testthat/test_S3WrapperGenerator.R |only tests/testthat/test_assertives.R |only tests/testthat/test_rollback.R | 22 + vignettes/a_basicUsage.Rmd | 9 vignettes/b_advancedUsage.Rmd | 12 - 46 files changed, 1823 insertions(+), 1536 deletions(-)
Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data
analysis, drake rebuilds intermediate data objects when their
dependencies change, and it skips work when the results are already up
to date. Not every execution starts from scratch, there is native
support for parallel and distributed computing, and completed projects
have tangible evidence that they are reproducible. Extensive
documentation, from beginner-friendly tutorials to practical examples
and more, is available at the reference website
<https://docs.ropensci.org/drake/> and the online manual
<https://books.ropensci.org/drake/>.
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Alex Axthelm [ctb],
Jasper Clarkberg [ctb],
Kirill Müller [ctb],
Ben Bond-Lamberty [ctb] (<https://orcid.org/0000-0001-9525-4633>),
Tristan Mahr [ctb] (<https://orcid.org/0000-0002-8890-5116>),
Miles McBain [ctb] (<https://orcid.org/0000-0003-2865-2548>),
Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>),
Ellis Hughes [ctb],
Matthew Mark Strasiotto [ctb],
Ben Marwick [rev],
Peter Slaughter [rev],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between drake versions 7.8.0 dated 2019-12-02 and 7.9.0 dated 2020-01-08
drake-7.8.0/drake/R/create_drake_layout.R |only drake-7.8.0/drake/tests/testthat/test-analysis.R |only drake-7.8.0/drake/tests/testthat/test-build.R |only drake-7.8.0/drake/tests/testthat/test-cache.R |only drake-7.8.0/drake/tests/testthat/test-checks.R |only drake-7.8.0/drake/tests/testthat/test-clustermq.R |only drake-7.8.0/drake/tests/testthat/test-code_to_function.R |only drake-7.8.0/drake/tests/testthat/test-commands.R |only drake-7.8.0/drake/tests/testthat/test-console.R |only drake-7.8.0/drake/tests/testthat/test-decorated-storr.R |only drake-7.8.0/drake/tests/testthat/test-deprecate.R |only drake-7.8.0/drake/tests/testthat/test-dsl.R |only drake-7.8.0/drake/tests/testthat/test-dynamic.R |only drake-7.8.0/drake/tests/testthat/test-examples.R |only drake-7.8.0/drake/tests/testthat/test-files.R |only drake-7.8.0/drake/tests/testthat/test-flow.R |only drake-7.8.0/drake/tests/testthat/test-future.R |only drake-7.8.0/drake/tests/testthat/test-graph.R |only drake-7.8.0/drake/tests/testthat/test-hash-tables.R |only drake-7.8.0/drake/tests/testthat/test-history.R |only drake-7.8.0/drake/tests/testthat/test-hpc.R |only drake-7.8.0/drake/tests/testthat/test-imports.R |only drake-7.8.0/drake/tests/testthat/test-interactive.R |only drake-7.8.0/drake/tests/testthat/test-keras.R |only drake-7.8.0/drake/tests/testthat/test-lazy.R |only drake-7.8.0/drake/tests/testthat/test-lock.R |only drake-7.8.0/drake/tests/testthat/test-memory.R |only drake-7.8.0/drake/tests/testthat/test-meta.R |only drake-7.8.0/drake/tests/testthat/test-missed.R |only drake-7.8.0/drake/tests/testthat/test-plans.R |only drake-7.8.0/drake/tests/testthat/test-prework.R |only drake-7.8.0/drake/tests/testthat/test-queue.R |only drake-7.8.0/drake/tests/testthat/test-recovery.R |only drake-7.8.0/drake/tests/testthat/test-retry.R |only drake-7.8.0/drake/tests/testthat/test-rng.R |only drake-7.8.0/drake/tests/testthat/test-rstudio.R |only drake-7.8.0/drake/tests/testthat/test-testing.R |only drake-7.8.0/drake/tests/testthat/test-time.R |only drake-7.8.0/drake/tests/testthat/test-triggers.R |only drake-7.8.0/drake/tests/testthat/test-utils.R |only drake-7.8.0/drake/tests/testthat/test-visuals.R |only drake-7.9.0/drake/DESCRIPTION | 15 drake-7.9.0/drake/MD5 | 237 ++++++----- drake-7.9.0/drake/NAMESPACE | 12 drake-7.9.0/drake/NEWS.md | 50 ++ drake-7.9.0/drake/R/analyze_code.R | 75 ++- drake-7.9.0/drake/R/backend_clustermq.R | 52 ++ drake-7.9.0/drake/R/backend_future.R | 35 + drake-7.9.0/drake/R/build_times.R | 87 +--- drake-7.9.0/drake/R/cache.R | 135 +++++- drake-7.9.0/drake/R/clean.R | 28 - drake-7.9.0/drake/R/create_drake_graph.R | 14 drake-7.9.0/drake/R/create_drake_spec.R |only drake-7.9.0/drake/R/decorate_storr.R | 156 ++++++- drake-7.9.0/drake/R/deprecated.R | 28 + drake-7.9.0/drake/R/deps.R | 31 - drake-7.9.0/drake/R/drake_build.R | 6 drake-7.9.0/drake/R/drake_config.R | 159 ++++++- drake-7.9.0/drake/R/drake_graph_info.R | 26 - drake-7.9.0/drake/R/drake_history.R | 2 drake-7.9.0/drake/R/drake_meta_.R | 152 ++++--- drake-7.9.0/drake/R/drake_plan.R | 39 + drake-7.9.0/drake/R/drake_plan_helpers.R | 49 +- drake-7.9.0/drake/R/dynamic.R | 259 +++++-------- drake-7.9.0/drake/R/expose_imports.R | 105 +---- drake-7.9.0/drake/R/handle_triggers.R | 47 +- drake-7.9.0/drake/R/hpc.R | 60 +-- drake-7.9.0/drake/R/local_build.R | 44 +- drake-7.9.0/drake/R/make.R | 92 ++-- drake-7.9.0/drake/R/manage_memory.R | 142 ++++--- drake-7.9.0/drake/R/outdated.R | 37 + drake-7.9.0/drake/R/package.R | 24 - drake-7.9.0/drake/R/predict_runtime.R | 6 drake-7.9.0/drake/R/process_imports.R | 10 drake-7.9.0/drake/R/r_make.R | 8 drake-7.9.0/drake/R/rstudio.R | 2 drake-7.9.0/drake/R/store_outputs.R | 53 +- drake-7.9.0/drake/R/transform_plan.R | 33 + drake-7.9.0/drake/R/use_drake.R | 26 - 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Title: Dirichlet Process Weibull Mixture Model for Survival Data
Description: Use Dirichlet process Weibull mixture model and dependent Dirichlet process Weibull mixture model for survival data with and without competing risks. Dirichlet process Weibull mixture model is used for data without covariates and dependent Dirichlet process model is used for regression data. The package is designed to handle exact/right-censored/ interval-censored observations without competing risks and exact/right-censored observations for data with competing risks. Inside each cluster of Dirichlet process, we assume a multiplicative effect of covariates as in Cox model and Fine and Gray model. For wrapper of the DPdensity function from the R package DPpackage (already archived by CRAN) that uses the Low Information Omnibus prior, please check (<https://github.com/mjmartens/DPdensity-wrapper-with-LIO-prior>).
Author: Yushu Shi
Maintainer: Yushu Shi <shiyushu2006@gmail.com>
Diff between DPWeibull versions 1.4 dated 2019-11-14 and 1.5 dated 2020-01-08
DESCRIPTION | 12 MD5 | 26 - R/RcppExports.R | 7 R/compdpm.R | 158 ++++----- R/compreg.R | 188 +++++------ R/dpm.R | 116 +++---- R/plot.R | 644 ++++++++++++++++++++-------------------- R/pred.R | 5 R/reg.R | 22 - data/deterioration.rda |only man/deterioration.Rd |only man/dpweib.Rd | 784 +++++++++++++++++++++++++------------------------ src/noreg.cpp | 15 src/reg.cpp | 23 - src/reggilks.cpp | 31 + 15 files changed, 1032 insertions(+), 999 deletions(-)
Title: Interface to 'the CAVD DataSpace'
Description: Provides a convenient API interface to access immunological data
within 'the CAVD DataSpace'(<https://dataspace.cavd.org>), a data sharing
and discovery tool that facilitates exploration of HIV immunological data
from pre-clinical and clinical HIV vaccine studies.
Author: Ju Yeong Kim [aut, cre, cph],
Sean Hughes [rev] (Sean reviewed the package for ropensci, see
<https://github.com/ropensci/software-review/issues/261>),
Jason Taylor [aut],
Helen Miller [aut]
Maintainer: Ju Yeong Kim <jkim2345@fredhutch.org>
Diff between DataSpaceR versions 0.7.2 dated 2019-08-21 and 0.7.3 dated 2020-01-08
DataSpaceR-0.7.2/DataSpaceR/inst/doc/Accessing_Monoconal_Antibody_Data.R |only DataSpaceR-0.7.2/DataSpaceR/inst/doc/Accessing_Monoconal_Antibody_Data.Rmd |only DataSpaceR-0.7.2/DataSpaceR/inst/doc/Accessing_Monoconal_Antibody_Data.html |only DataSpaceR-0.7.2/DataSpaceR/inst/doc/Intro_to_DataSpaceR.R |only DataSpaceR-0.7.2/DataSpaceR/inst/doc/Intro_to_DataSpaceR.Rmd |only DataSpaceR-0.7.2/DataSpaceR/inst/doc/Intro_to_DataSpaceR.html |only DataSpaceR-0.7.2/DataSpaceR/vignettes/Accessing_Monoconal_Antibody_Data.Rmd |only DataSpaceR-0.7.2/DataSpaceR/vignettes/Intro_to_DataSpaceR.Rmd |only DataSpaceR-0.7.3/DataSpaceR/DESCRIPTION | 17 DataSpaceR-0.7.3/DataSpaceR/MD5 | 55 - DataSpaceR-0.7.3/DataSpaceR/NAMESPACE | 2 DataSpaceR-0.7.3/DataSpaceR/NEWS.md | 5 DataSpaceR-0.7.3/DataSpaceR/R/DataSpaceConnection.R | 8 DataSpaceR-0.7.3/DataSpaceR/R/DataSpaceStudy.R | 349 ++++++++-- DataSpaceR-0.7.3/DataSpaceR/R/helpers.R | 12 DataSpaceR-0.7.3/DataSpaceR/R/netrc.R | 2 DataSpaceR-0.7.3/DataSpaceR/README.md | 78 +- DataSpaceR-0.7.3/DataSpaceR/build/vignette.rds |binary DataSpaceR-0.7.3/DataSpaceR/inst/doc/DataSpaceR.R |only DataSpaceR-0.7.3/DataSpaceR/inst/doc/DataSpaceR.Rmd |only DataSpaceR-0.7.3/DataSpaceR/inst/doc/DataSpaceR.html |only DataSpaceR-0.7.3/DataSpaceR/inst/doc/Monoconal_Antibody_Data.R |only DataSpaceR-0.7.3/DataSpaceR/inst/doc/Monoconal_Antibody_Data.Rmd |only DataSpaceR-0.7.3/DataSpaceR/inst/doc/Monoconal_Antibody_Data.html |only DataSpaceR-0.7.3/DataSpaceR/inst/doc/Non_Integrated_Datasets.R |only DataSpaceR-0.7.3/DataSpaceR/inst/doc/Non_Integrated_Datasets.Rmd |only DataSpaceR-0.7.3/DataSpaceR/inst/doc/Non_Integrated_Datasets.html |only DataSpaceR-0.7.3/DataSpaceR/man/DataSpaceConnection.Rd | 106 ++- DataSpaceR-0.7.3/DataSpaceR/man/DataSpaceMab.Rd | 56 + DataSpaceR-0.7.3/DataSpaceR/man/DataSpaceStudy.Rd | 119 +++ DataSpaceR-0.7.3/DataSpaceR/man/checkNetrc.Rd | 3 DataSpaceR-0.7.3/DataSpaceR/man/connectDS.Rd | 3 DataSpaceR-0.7.3/DataSpaceR/man/writeNetrc.Rd | 11 DataSpaceR-0.7.3/DataSpaceR/tests/testthat/helper.R |only DataSpaceR-0.7.3/DataSpaceR/tests/testthat/test-connection.R | 6 DataSpaceR-0.7.3/DataSpaceR/tests/testthat/test-study.R | 104 ++ DataSpaceR-0.7.3/DataSpaceR/vignettes/DataSpaceR.Rmd |only DataSpaceR-0.7.3/DataSpaceR/vignettes/Monoconal_Antibody_Data.Rmd |only DataSpaceR-0.7.3/DataSpaceR/vignettes/Non_Integrated_Datasets.Rmd |only 39 files changed, 752 insertions(+), 184 deletions(-)
Title: The Entire Transcript from the Office in Tidy Format
Description: The complete scripts from the American version of
the Office television show in tibble format. Use this package to
analyze and have fun with text from the best series of all time.
Author: Brad Lindblad [aut, cre],
Lucas Graybuck [ctb]
Maintainer: Brad Lindblad <bradley.lindblad@gmail.com>
Diff between schrute versions 0.1.0 dated 2019-12-15 and 0.1.1 dated 2020-01-08
DESCRIPTION | 25 +++++++++++-------- MD5 | 19 +++++++------- NEWS.md | 8 ++++-- R/data-theoffice.R | 4 ++- README.md | 40 ++++++++++++++++-------------- build/vignette.rds |binary data/theoffice.rda |binary inst/CITATION |only inst/doc/theoffice.html | 62 ++++++++++++++++++++++++++++++------------------ man/figures/logo.png |binary man/theoffice.Rd | 4 ++- 11 files changed, 98 insertions(+), 64 deletions(-)
Title: Copula-Based Estimation and Statistical Process Control for
Serially Correlated Time Series
Description: Estimation and statistical process control are performed under
copula-based time-series models.
Available are statistical methods in Long and Emura (2014 JCSA),
Emura et al. (2017 Commun Stat-Simul) <DOI:10.1080/03610918.2015.1073303>,
Huang and Emura (2019 Commun Stat-Simul) <DOI:10.1080/03610918.2019.1602647> and Huang, Chen and Emura (2019-, in revision).
Author: Takeshi Emura, Xinwei Huang, Weiru Chen, Ting-Hsuan Long
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between Copula.Markov versions 2.5 dated 2019-11-29 and 2.6 dated 2020-01-08
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ R/Clayton.Markov.GOF.R | 10 +++++----- R/Clayton.Markov.MLE.R | 6 +++--- R/Clayton.Markov.MLE.binom.R | 4 ++-- R/Clayton.Markov2.MLE.R | 7 ++++--- R/Joe.Markov.MLE.R | 6 +++--- man/Clayton.Markov.DATA.Rd | 2 +- man/Clayton.Markov.MLE.Rd | 4 ++-- man/Clayton.Markov.MLE.binom.Rd | 4 ++-- man/Clayton.Markov2.MLE.Rd | 4 ++-- man/Copula.Markov-package.Rd | 4 ++-- man/Joe.Markov.MLE.Rd | 4 ++-- 13 files changed, 45 insertions(+), 44 deletions(-)
Title: Spatial Absorbing Markov Chains
Description: An implementation of the framework described in "Toward a unified
framework for connectivity that disentangles movement and mortality in space
and time" by Fletcher et al. (2019) <doi:10.1111/ele.13333>.
Incorporates both resistance and absorption with spatial absorbing Markov
chains (SAMC) to provide several short-term and long-term predictions for
metrics related to connectivity in landscapes.
Author: Andrew Marx [aut, cre, cph] (<https://orcid.org/0000-0002-7456-1631>),
Robert Fletcher [ctb] (<https://orcid.org/0000-0003-1717-5707>),
Miguel Acevedo [ctb] (<https://orcid.org/0000-0002-8289-1497>),
Jorge Sefair [ctb] (<https://orcid.org/0000-0002-5887-8938>),
Chao Wang [ctb] (<https://orcid.org/0000-0003-2706-5122>)
Maintainer: Andrew Marx <andrewjmarx@ufl.edu>
Diff between samc versions 1.0.3 dated 2019-08-21 and 1.0.4 dated 2020-01-08
DESCRIPTION | 16 ++++++------ MD5 | 48 +++++++++++++++++++------------------- NEWS.md | 6 ++++ inst/doc/overview.R | 7 ++++- inst/doc/overview.Rmd | 7 ++++- inst/doc/overview.html | 4 +-- inst/doc/performance.html | 4 +-- inst/doc/troubleshooting.html | 4 +-- inst/doc/tutorial-animations.R | 5 +++ inst/doc/tutorial-animations.Rmd | 5 +++ inst/doc/tutorial-animations.html | 6 ++-- inst/doc/tutorial-basic.R | 7 ++++- inst/doc/tutorial-basic.Rmd | 7 ++++- inst/doc/tutorial-basic.html | 6 ++-- inst/doc/tutorial-ggplot.R | 5 +++ inst/doc/tutorial-ggplot.Rmd | 5 +++ inst/doc/tutorial-ggplot.html | 8 +++--- inst/doc/tutorial-temporal.R | 5 +++ inst/doc/tutorial-temporal.Rmd | 5 +++ inst/doc/tutorial-temporal.html | 4 +-- vignettes/overview.Rmd | 7 ++++- vignettes/tutorial-animations.Rmd | 5 +++ vignettes/tutorial-basic.Rmd | 7 ++++- vignettes/tutorial-ggplot.Rmd | 5 +++ vignettes/tutorial-temporal.Rmd | 5 +++ 25 files changed, 137 insertions(+), 56 deletions(-)
Title: API to Melbourne Pedestrian Data
Description: Provides API to Melbourne pedestrian data in tidy
data form.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>)
Maintainer: Earo Wang <earo.wang@gmail.com>
Diff between rwalkr versions 0.5.0 dated 2019-11-18 and 0.5.1 dated 2020-01-08
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/soda.R | 3 ++- README.md | 20 ++++++++++---------- man/figure/plot-1.png |binary man/melb_walk.Rd | 3 +-- man/melb_walk_fast.Rd | 3 +-- 9 files changed, 31 insertions(+), 27 deletions(-)
Title: Candidate Gene Prioritization for Non-Communicable Diseases
Based on Functional Information
Description: In gene sequencing methods, the topological features of protein-protein interaction (PPI) networks are
often used, such as ToppNet <https://toppgene.cchmc.org>. In this study, a candidate gene prioritization method
was proposed for non-communicable diseases considering disease risks transferred between genes in weighted disease
PPI networks with weights for nodes and edges based on functional information.
Author: Erqiang Hu [aut, cre]
Maintainer: Erqiang Hu <13766876214@163.com>
Diff between prioGene versions 0.99.0 dated 2019-08-30 and 1.0.0 dated 2020-01-08
prioGene-0.99.0/prioGene/data/GO_human.rda |only prioGene-0.99.0/prioGene/data/Q.rda |only prioGene-0.99.0/prioGene/inst/WORDLIST |only prioGene-0.99.0/prioGene/man/GO_human.Rd |only prioGene-0.99.0/prioGene/man/Q.Rd |only prioGene-0.99.0/prioGene/tests/spelling.R |only prioGene-0.99.0/prioGene/vignettes/my-vignete.R |only prioGene-0.99.0/prioGene/vignettes/my-vignete.html |only prioGene-1.0.0/prioGene/DESCRIPTION | 26 - prioGene-1.0.0/prioGene/MD5 | 67 +- prioGene-1.0.0/prioGene/NAMESPACE | 5 prioGene-1.0.0/prioGene/R/data.R | 38 - prioGene-1.0.0/prioGene/R/deal_GO.R | 94 ++- prioGene-1.0.0/prioGene/R/prioritization.R | 34 - prioGene-1.0.0/prioGene/R/weight.R | 10 prioGene-1.0.0/prioGene/README.md | 111 +--- prioGene-1.0.0/prioGene/build/vignette.rds |binary prioGene-1.0.0/prioGene/data/datalist |only prioGene-1.0.0/prioGene/data/metabolic_net.rda |only prioGene-1.0.0/prioGene/inst/doc/my-vignete.R |only prioGene-1.0.0/prioGene/inst/doc/my-vignete.Rmd |only prioGene-1.0.0/prioGene/inst/doc/my-vignete.html |only prioGene-1.0.0/prioGene/inst/doc/prioGene.R | 80 --- prioGene-1.0.0/prioGene/inst/doc/prioGene.Rmd | 138 ----- prioGene-1.0.0/prioGene/inst/doc/prioGene.html | 545 ++++++++++++++------- prioGene-1.0.0/prioGene/man/edge_weight.Rd | 2 prioGene-1.0.0/prioGene/man/genes_mat.Rd | 2 prioGene-1.0.0/prioGene/man/get_Q.Rd | 10 prioGene-1.0.0/prioGene/man/get_R.Rd | 15 prioGene-1.0.0/prioGene/man/get_W.Rd | 3 prioGene-1.0.0/prioGene/man/get_edge_weight.Rd | 6 prioGene-1.0.0/prioGene/man/get_gene_mat.Rd | 10 prioGene-1.0.0/prioGene/man/get_neighbor.Rd | 3 prioGene-1.0.0/prioGene/man/get_term_mat.Rd | 10 prioGene-1.0.0/prioGene/man/metabolic_net.Rd |only prioGene-1.0.0/prioGene/man/net.Rd | 2 prioGene-1.0.0/prioGene/man/net_disease.Rd | 2 prioGene-1.0.0/prioGene/man/net_disease_term.Rd | 2 prioGene-1.0.0/prioGene/man/node_weight.Rd | 2 prioGene-1.0.0/prioGene/man/terms_mat.Rd | 2 prioGene-1.0.0/prioGene/vignettes/my-vignete.Rmd |only prioGene-1.0.0/prioGene/vignettes/prioGene.Rmd | 138 ----- 42 files changed, 626 insertions(+), 731 deletions(-)
Title: Fetch Data from 'National Stock Exchange (India)'
Description: Fetch data related to stocks, index, futures & options from the
'NSE (National Stock Exchange, India)'. This package is community maintained
and is not officially supported by 'NSE'. The accuracy of data is only as
correct as provided on <https://www.nseindia.com>.
Author: Lokesh Kumar [aut],
Aravind Hebbali [aut, cre],
Lionel Pinto [ctb]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between nse2r versions 0.1.0 dated 2019-12-16 and 0.1.1 dated 2020-01-08
DESCRIPTION | 6 MD5 | 18 +- NEWS.md | 4 R/nse-advance-decline.R | 2 R/nse-fo.R | 4 R/nse-index.R | 4 R/nse-preopen.R | 4 R/nse-stock.R | 12 - R/nse-utils.R | 22 --- README.md | 332 +++++++++++++++++++++++------------------------- 10 files changed, 194 insertions(+), 214 deletions(-)
Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI'
Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws'
<https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between noctua versions 1.4.0 dated 2019-12-19 and 1.5.0 dated 2020-01-08
noctua-1.4.0/noctua/tests/testthat/test-datatransfer.R |only noctua-1.5.0/noctua/DESCRIPTION | 17 +- noctua-1.5.0/noctua/MD5 | 69 +++++---- noctua-1.5.0/noctua/NAMESPACE | 3 noctua-1.5.0/noctua/NEWS.md | 44 ++++-- noctua-1.5.0/noctua/R/Connection.R | 65 ++++++++ noctua-1.5.0/noctua/R/DataTypes.R | 73 ++++++---- noctua-1.5.0/noctua/R/Driver.R | 4 noctua-1.5.0/noctua/R/File_Parser.R |only noctua-1.5.0/noctua/R/Options.R |only noctua-1.5.0/noctua/R/Result.R | 21 +- noctua-1.5.0/noctua/R/Table.R | 4 noctua-1.5.0/noctua/R/View.R |only noctua-1.5.0/noctua/R/utils.R | 47 +----- noctua-1.5.0/noctua/inst |only noctua-1.5.0/noctua/man/AthenaWriteTables.Rd | 61 ++++++-- noctua-1.5.0/noctua/man/Query.Rd | 11 - noctua-1.5.0/noctua/man/assume_role.Rd | 11 + noctua-1.5.0/noctua/man/dbConnect-AthenaDriver-method.Rd | 25 ++- noctua-1.5.0/noctua/man/dbDisconnect.Rd | 2 noctua-1.5.0/noctua/man/dbExistsTable.Rd | 2 noctua-1.5.0/noctua/man/dbFetch.Rd | 2 noctua-1.5.0/noctua/man/dbGetPartition.Rd | 2 noctua-1.5.0/noctua/man/dbGetQuery.Rd | 5 noctua-1.5.0/noctua/man/dbGetTables.Rd |only noctua-1.5.0/noctua/man/dbListFields.Rd | 2 noctua-1.5.0/noctua/man/dbListTables.Rd | 8 - noctua-1.5.0/noctua/man/dbQuote.Rd | 2 noctua-1.5.0/noctua/man/dbRemoveTable.Rd | 5 noctua-1.5.0/noctua/man/dbShow.Rd | 2 noctua-1.5.0/noctua/man/db_copy_to.Rd | 18 +- noctua-1.5.0/noctua/man/db_save_query.Rd | 11 + noctua-1.5.0/noctua/man/noctua_options.Rd |only noctua-1.5.0/noctua/man/session_token.Rd | 11 + noctua-1.5.0/noctua/man/sqlCreateTable.Rd | 21 +- noctua-1.5.0/noctua/man/sqlData.Rd | 10 - noctua-1.5.0/noctua/man/work_group.Rd | 26 ++- noctua-1.5.0/noctua/tests/testthat/test-datatransfer-datatable.R |only noctua-1.5.0/noctua/tests/testthat/test-datatransfer-vroom.R |only 39 files changed, 378 insertions(+), 206 deletions(-)