Title: Maximum Approximate Bernstein/Beta Likelihood Estimation
Description: Fit data from a continuous population with a smooth density on finite interval by an approximate Bernstein polynomial model which is a mixture of certain beta distributions and find maximum approximate Bernstein likelihood estimator of the unknown coefficients. Consequently, maximum likelihood estimates of the unknown density, distribution functions, and more can be obtained. If the support of the density is not the unit interval then transformation can be applied. This is an implementation of the methods proposed by the author of this package published in the Journal of Nonparametric Statistics: Guan (2016) <doi:10.1080/10485252.2016.1163349> and Guan (2017) <doi:10.1080/10485252.2017.1374384>. For data with covariates, under some semiparametric regression models such as Cox proportional hazards model and the accelerated failure time model, the baseline survival function can be estimated smoothly based on general interval censored data.
Author: Zhong Guan [aut, cre]
Maintainer: Zhong Guan <zguan@iusb.edu>
Diff between mable versions 3.1.0 dated 2022-06-07 and 3.1.1 dated 2022-06-23
DESCRIPTION | 12 +- MD5 | 45 ++++---- R/Vaal-Flow.r | 5 R/cosmesis-data.r |only R/mable-aft-model.r | 2 R/mable-multivar.r | 275 ++++++++++++++++++++++++++++----------------------- R/mable-ph-model.r | 2 R/mable.r | 26 ++-- data/cosmesis.rda |only inst/doc/mable.R | 4 inst/doc/mable.Rmd | 7 - inst/doc/mable.pdf |binary man/Vaal.Flow.Rd | 5 man/cosmesis.Rd |only man/mable.Rd | 2 man/mable.aft.Rd | 1 man/mable.ctrl.Rd | 6 - man/mable.ic.Rd | 2 man/mable.mvar.Rd | 9 + man/maple.aft.Rd | 1 man/optimable.Rd | 2 man/summary.mable.Rd | 11 -- src/mable.c | 185 +++++++++++++++++++++++----------- src/mable_init.c | 4 vignettes/mable.Rmd | 7 - 25 files changed, 358 insertions(+), 255 deletions(-)
Title: High-Dimensional Screening for Semiparametric Longitudinal
Regression
Description: Implements variable screening techniques for ultra-high
dimensional regression settings. Techniques for independent (iid) data,
varying-coefficient models, and longitudinal data are implemented. The package
currently contains three screen functions: screenIID(), screenLD() and screenVCM(),
and six methods for simulating dataset: simulateDCSIS(), simulateLD, simulateMVSIS(),
simulateMVSISNY(), simulateSIRS() and simulateVCM(). The package is based on the work of
Li-Ping ZHU, Lexin LI, Runze LI, and Li-Xing ZHU (2011) <DOI:10.1198/jasa.2011.tm10563>,
Runze LI, Wei ZHONG, & Liping ZHU (2012) <DOI:10.1080/01621459.2012.695654>,
Jingyuan LIU, Runze LI, & Rongling WU (2014) <DOI:10.1080/01621459.2013.850086>
Hengjian CUI, Runze LI, & Wei ZHONG (2015) <DOI:10.1080/01621459.2014.920256>, and
Wanghuan CHU, Runze LI and Matthew REIMHERR (2016) <DOI:10.1214/16-AOAS912>.
Author: Runze Li [aut],
Liying Huang [aut],
John Dziak [aut, cre]
Maintainer: John Dziak <dziakj1@gmail.com>
Diff between VariableScreening versions 0.2.0 dated 2018-08-09 and 0.2.1 dated 2022-06-23
DESCRIPTION | 24 +++++------- MD5 | 38 +++++++++---------- R/screenIID.R | 26 ++++++------- R/screenLD.R | 95 ++++++++++++++++++++++++++----------------------- R/screenVCM.R | 41 +++++++++++++-------- R/simulateDCSIS.r | 29 +++++++++----- R/simulateLD.R | 36 ++++++++---------- R/simulateMVSIS.R | 8 +--- R/simulateMVSISNY.R | 4 +- R/simulateSIRS.r | 27 +++++++++---- R/simulateVCM.R | 39 ++++++++++---------- man/screenIID.Rd | 26 +++++-------- man/screenLD.Rd | 64 ++++++++++++++++++++++----------- man/screenVCM.Rd | 43 +++++++++++++--------- man/simulateDCSIS.Rd | 10 +---- man/simulateLD.Rd | 44 ++++++++++++---------- man/simulateMVSIS.Rd | 8 +--- man/simulateMVSISNY.Rd | 5 +- man/simulateSIRS.Rd | 15 +++++-- man/simulateVCM.Rd | 18 +++++---- 20 files changed, 329 insertions(+), 271 deletions(-)
More information about VariableScreening at CRAN
Permanent link
Title: Bayesian Mortality Modelling with 'Stan'
Description: Implementation of popular mortality models using the 'rstan'
package, which provides the R interface to the 'Stan' C++ library for
Bayesian estimation. The package supports well-known models proposed in the
actuarial and demographic literature including the Lee-Carter (1992)
<doi:10.1080/01621459.1992.10475265> and the Cairns-Blake-Dowd (2006)
<doi:10.1111/j.1539-6975.2006.00195.x> models. By a simple call, the user
inputs deaths and exposures and the package outputs the MCMC simulations for
each parameter, the log likelihoods and predictions. Moreover, the package
includes tools for model selection and Bayesian model averaging by leave
future-out validation.
Author: Karim Barigou [aut, cre] ,
Pierre-Olivier Goffard [aut]
Maintainer: Karim Barigou <karim290492@gmail.com>
Diff between StanMoMo versions 1.0.0 dated 2021-10-07 and 1.1.0 dated 2022-06-23
StanMoMo-1.0.0/StanMoMo/R/load_HMD_data.R |only StanMoMo-1.0.0/StanMoMo/man/load_HMD_data.Rd |only StanMoMo-1.1.0/StanMoMo/DESCRIPTION | 6 StanMoMo-1.1.0/StanMoMo/MD5 | 16 - StanMoMo-1.1.0/StanMoMo/NAMESPACE | 1 StanMoMo-1.1.0/StanMoMo/NEWS.md | 11 StanMoMo-1.1.0/StanMoMo/README.md | 130 ++++++----- StanMoMo-1.1.0/StanMoMo/inst/doc/StanMoMo.Rmd | 277 ++++++++++++------------- StanMoMo-1.1.0/StanMoMo/inst/doc/StanMoMo.html | 14 - StanMoMo-1.1.0/StanMoMo/vignettes/StanMoMo.Rmd | 277 ++++++++++++------------- 10 files changed, 372 insertions(+), 360 deletions(-)
Title: Statistics Norway's Miscellaneous Tools
Description: Functions used by other packages from Statistics Norway are gathered. General data manipulation functions, and functions for hierarchical computations are included (Langsrud, 2020) <doi:10.13140/RG.2.2.27313.61283>. The hierarchy specification functions are useful within statistical disclosure control.
Author: Oyvind Langsrud [aut, cre],
Daniel Lupp [aut],
Bjoern-Helge Mevik [ctb]
Maintainer: Oyvind Langsrud <oyl@ssb.no>
Diff between SSBtools versions 1.3.0 dated 2022-04-01 and 1.3.3 dated 2022-06-23
DESCRIPTION | 12 ++++++------ MD5 | 24 +++++++++++++----------- NAMESPACE | 4 ++++ R/AutoHierarchies.R | 17 +++++++++++++++++ R/DummyDuplicated.R | 2 +- R/Extend0.R | 15 ++++++++++++--- R/Extend0rnd1.R |only R/GaussSuppression.R | 13 ++++++++++++- R/LSfitNonNeg.R | 2 +- R/ModelMatrix.R | 2 +- man/Extend0.Rd | 3 +++ man/Extend0rnd1.Rd |only man/GaussSuppression.Rd | 3 +++ man/Hierarchy2Formula.Rd | 18 ++++++++++++++++++ 14 files changed, 91 insertions(+), 24 deletions(-)
Title: Scalable Joint Species Distribution Modeling
Description: A scalable method to estimate joint Species Distribution Models (jSDMs) for big community datasets based on a Monte Carlo approximation of the joint likelihood. The numerical approximation is based on 'PyTorch' and 'reticulate', and can be run on CPUs and GPUs alike. The method is described in Pichler & Hartig (2021) <doi:10.1111/2041-210X.13687>. The package contains various extensions, including support for different response families, ability to account for spatial autocorrelation, and deep neural networks instead of the linear predictor in jSDMs.
Author: Maximilian Pichler [aut, cre] ,
Florian Hartig [aut] ,
Wang Cai [ctb]
Maintainer: Maximilian Pichler <maximilian.pichler@biologie.uni-regensburg.de>
Diff between sjSDM versions 1.0.1 dated 2022-03-11 and 1.0.2 dated 2022-06-23
DESCRIPTION | 10 MD5 | 46 - NEWS.md | 10 R/Rsquared.R | 4 R/installation_help.R | 8 R/plot.R | 37 - R/sjSDM.R | 36 - README.md | 4 build/sjSDM.pdf |binary build/vignette.rds |binary inst/doc/Dependencies.Rmd | 8 inst/doc/Dependencies.html | 284 ++++++++++-- inst/doc/sjSDM.html | 284 ++++++++++-- inst/python/sjSDM_py/__pycache__/__init__.cpython-37.pyc |binary inst/python/sjSDM_py/__pycache__/dist_mvp.cpython-37.pyc |binary inst/python/sjSDM_py/__pycache__/model_sjSDM.cpython-37.pyc |binary inst/python/sjSDM_py/__pycache__/optimizer.cpython-37.pyc |binary inst/python/sjSDM_py/__pycache__/utils_fa.cpython-37.pyc |binary man/Rsquared.Rd | 4 man/installation_help.Rd | 8 man/plot.sjSDM.Rd | 2 man/plotsjSDMcoef.Rd | 3 man/sjSDM.Rd | 38 - vignettes/Dependencies.Rmd | 8 24 files changed, 631 insertions(+), 163 deletions(-)
Title: Multiphase Optimization Strategy
Description: Provides functions similar to the 'SAS' macros previously provided
to accompany Collins, Dziak, and Li (2009) <DOI:10.1037/a0015826>
and Dziak, Nahum-Shani, and Collins (2012) <DOI:10.1037/a0026972>, papers
which outline practical benefits and challenges of factorial
and fractional factorial experiments for scientists interested
in developing biological and/or behavioral interventions, especially
in the context of the multiphase optimization strategy
(see Collins, Kugler & Gwadz 2016) <DOI:10.1007/s10461-015-1145-4>. The package
currently contains three functions. First, RelativeCosts1() draws a graph
of the relative cost of complete and reduced factorial designs versus
other alternatives. Second, RandomAssignmentGenerator() returns a dataframe
which contains a list of random numbers that can be used to conveniently
assign participants to conditions in an experiment with
many conditions. Third, FactorialPowerPlan() estimates the power, detectable effect
size, or required sample size of a factorial or fractional factorial
experiment, for main effects or interactions, given several possible choices
of effect size metric, and allowing pretests and clustering.
Author: Linda Collins [aut],
Liying Huang [aut],
John Dziak [aut, cre]
Maintainer: John Dziak <dziakj1@gmail.com>
Diff between MOST versions 0.1.0 dated 2017-11-09 and 0.1.2 dated 2022-06-23
DESCRIPTION | 24 ++++++++++++------------ MD5 | 8 ++++---- man/FactorialPowerPlan.Rd | 28 +++++++++++++++++++++------- man/RandomAssignmentGenerator.Rd | 1 - man/RelativeCosts1.Rd | 11 +++++++---- 5 files changed, 44 insertions(+), 28 deletions(-)
Title: Visualization and Tools for Ichimoku Kinko Hyo Strategies
Description: An implementation of 'Ichimoku Kinko Hyo', also commonly known as
'cloud charts'. Static and interactive visualizations with tools for
creating, backtesting and development of quantitative 'ichimoku' strategies.
As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement
on candlestick charting, originating from Japan and now in widespread use in
technical analysis worldwide. Translating as 'one-glance equilibrium chart',
it allows the price action and market structure of financial securities to
be determined 'at-a-glance'. Incorporates an interface with the OANDA
fxTrade API <https://developer.oanda.com/> for retrieving historical and
live streaming price data for major currencies, metals, commodities,
government bonds and stock indices.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between ichimoku versions 1.3.1 dated 2022-05-23 and 1.3.2 dated 2022-06-23
DESCRIPTION | 23 ++++++++------ MD5 | 72 ++++++++++++++++++++++----------------------- NEWS.md | 9 +++++ R/archive.R | 16 ++++++++++ R/data.R | 16 ++++++++++ R/ichimoku-package.R | 20 +++++++++++- R/ichimoku.R | 16 ++++++++++ R/iplot.R | 16 ++++++++++ R/methods.R | 16 ++++++++++ R/mltools.R | 16 ++++++++++ R/oanda.R | 22 +++++++++++-- R/plot.R | 28 +++++++++++++---- R/strat.R | 16 ++++++++++ R/switch.R | 16 ++++++++++ R/sysdata.rda |binary R/utils.R | 16 ++++++++++ README.md | 8 ++++- inst/doc/reference.R | 2 - inst/doc/reference.Rmd | 4 +- inst/doc/reference.html | 6 +-- inst/doc/strategies.Rmd | 2 - inst/doc/strategies.html | 2 - inst/doc/utilities.Rmd | 2 - inst/doc/utilities.html | 2 - inst/doc/xoanda.Rmd | 6 +-- inst/doc/xoanda.html | 8 +++-- man/autoplot.ichimoku.Rd | 6 +-- man/ichimoku-package.Rd | 4 +- man/oanda_chart.Rd | 6 +-- man/oanda_studio.Rd | 2 - man/plot.ichimoku.Rd | 10 +++--- src/shikokuchuo.c | 41 ++++++++++++++++++------- tests/testthat/test-plot.R | 6 +-- vignettes/reference.Rmd | 4 +- vignettes/strategies.Rmd | 2 - vignettes/utilities.Rmd | 2 - vignettes/xoanda.Rmd | 6 +-- 37 files changed, 339 insertions(+), 110 deletions(-)
Title: Dendrochronology Program Library in R
Description: Perform tree-ring analyses such as detrending, chronology
building, and cross dating. Read and write standard file formats
used in dendrochronology.
Author: Andy Bunn [aut, cph, cre, trl],
Mikko Korpela [aut, cph, trl],
Franco Biondi [aut, cph],
Filipe Campelo [aut, cph],
Pierre Merian [aut, cph],
Fares Qeadan [aut, cph],
Christian Zang [aut, cph],
Allan Buras [ctb],
Alice Cecile [ctb],
Manfred Mudelsee [...truncated...]
Maintainer: Andy Bunn <bunna@wwu.edu>
Diff between dplR versions 1.7.3 dated 2022-06-10 and 1.7.4 dated 2022-06-23
ChangeLog | 13 +++++++++++++ DESCRIPTION | 28 ++++++++++++++-------------- MD5 | 18 ++++++++++-------- NAMESPACE | 5 ++++- R/chron.ci.R |only R/detrend.series.R | 19 +++++++++++++++---- R/zzz.R | 2 ++ TODO | 2 ++ man/chron.ars.Rd | 40 ++++++++-------------------------------- man/chron.ci.Rd |only man/detrend.series.Rd | 6 +++++- 11 files changed, 73 insertions(+), 60 deletions(-)
Title: Bayesian Analysis to Compare Models using Resampling Statistics
Description: Bayesian analysis used here to answer the question: "when
looking at resampling results, are the differences between models
'real'?" To answer this, a model can be created were the performance
statistic is the resampling statistics (e.g. accuracy or RMSE). These
values are explained by the model types. In doing this, we can get
parameter estimates for each model's affect on performance and make
statistical (and practical) comparisons between models. The methods
included here are similar to Benavoli et al (2017)
<https://jmlr.org/papers/v18/16-305.html>.
Author: Max Kuhn [aut, cre] ,
RStudio [cph, fnd]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between tidyposterior versions 0.1.0 dated 2021-03-25 and 1.0.0 dated 2022-06-23
tidyposterior-0.1.0/tidyposterior/inst/doc/Different_Bayesian_Models.Rmd |only tidyposterior-0.1.0/tidyposterior/inst/doc/Different_Bayesian_Models.html |only tidyposterior-0.1.0/tidyposterior/inst/doc/Getting_Started.Rmd |only tidyposterior-0.1.0/tidyposterior/inst/doc/Getting_Started.html |only tidyposterior-0.1.0/tidyposterior/vignettes/Different_Bayesian_Models.Rmd |only tidyposterior-0.1.0/tidyposterior/vignettes/Getting_Started.Rmd |only tidyposterior-1.0.0/tidyposterior/DESCRIPTION | 47 +- tidyposterior-1.0.0/tidyposterior/MD5 | 56 +-- tidyposterior-1.0.0/tidyposterior/NAMESPACE | 10 tidyposterior-1.0.0/tidyposterior/NEWS.md | 6 tidyposterior-1.0.0/tidyposterior/R/0_imports.R | 16 - tidyposterior-1.0.0/tidyposterior/R/contrasts.R | 65 ++-- tidyposterior-1.0.0/tidyposterior/R/dplyr-compat.R | 1 tidyposterior-1.0.0/tidyposterior/R/misc.R | 15 tidyposterior-1.0.0/tidyposterior/R/perf_mod.R | 140 +++++--- tidyposterior-1.0.0/tidyposterior/R/posterior_diff-compat.R | 2 tidyposterior-1.0.0/tidyposterior/R/posteriors-compat.R | 2 tidyposterior-1.0.0/tidyposterior/R/posteriors.R | 23 - tidyposterior-1.0.0/tidyposterior/R/reexports.R | 1 tidyposterior-1.0.0/tidyposterior/R/transformations.R | 27 + tidyposterior-1.0.0/tidyposterior/R/zzz.R | 1 tidyposterior-1.0.0/tidyposterior/build/vignette.rds |binary tidyposterior-1.0.0/tidyposterior/inst/doc/tidyposterior.Rmd |only tidyposterior-1.0.0/tidyposterior/inst/doc/tidyposterior.html |only tidyposterior-1.0.0/tidyposterior/man/autoplot.posterior_diff.Rd | 1 tidyposterior-1.0.0/tidyposterior/man/figures/logo.png |only tidyposterior-1.0.0/tidyposterior/man/perf_mod.Rd | 66 ++-- tidyposterior-1.0.0/tidyposterior/man/tidyposterior-package.Rd |only tidyposterior-1.0.0/tidyposterior/man/transformations.Rd | 1 tidyposterior-1.0.0/tidyposterior/tests/testthat/_snaps |only tidyposterior-1.0.0/tidyposterior/tests/testthat/test_contrast.R | 19 - tidyposterior-1.0.0/tidyposterior/tests/testthat/test_dplyr_new.R | 13 tidyposterior-1.0.0/tidyposterior/tests/testthat/test_perf_mod.R | 158 +++++----- tidyposterior-1.0.0/tidyposterior/tests/testthat/test_tidy.R | 15 tidyposterior-1.0.0/tidyposterior/vignettes/tidyposterior.Rmd |only 35 files changed, 382 insertions(+), 303 deletions(-)
Title: Raven Hydrological Modelling Framework R Support and Analysis
Description: Utilities for processing input and output files associated with the Raven Hydrological Modelling Framework. Includes various plotting functions, model diagnostics, reading output files into extensible time series format, and support for writing Raven input files.
The 'RavenR' package is also archived at Chlumsky et al. (2020) <doi:10.5281/zenodo.4248183>.
The Raven Hydrologic Modelling Framework method can be referenced with Craig et al. (2020) <doi:10.1016/j.envsoft.2020.104728>.
Author: Robert Chlumsky [cre, aut] ,
James Craig [ctb, aut] ,
Leland Scantlebury [ctb, aut],
Simon Lin [ctb, aut],
Sarah Grass [ctb, aut],
Genevieve Brown [ctb, aut],
Rezgar Arabzadeh [ctb, aut]
Maintainer: Robert Chlumsky <rchlumsk@uwaterloo.ca>
Diff between RavenR versions 2.1.8 dated 2022-06-11 and 2.1.9 dated 2022-06-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/doc/Introduction_to_RavenR.R | 6 +++++- inst/doc/Introduction_to_RavenR.Rmd | 6 +++++- inst/doc/Introduction_to_RavenR.html | 14 +++++++++----- vignettes/Introduction_to_RavenR.Rmd | 6 +++++- 6 files changed, 33 insertions(+), 17 deletions(-)
Title: Create Data with Identical Statistics
Description: Creates data with identical statistics (metamers) using an iterative
algorithm proposed by Matejka & Fitzmaurice (2017) <DOI:10.1145/3025453.3025912>.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>
Diff between metamer versions 0.2.0 dated 2019-09-18 and 0.3.0 dated 2022-06-23
metamer-0.2.0/metamer/R/metamer-list-class.R |only metamer-0.2.0/metamer/R/set-functions.R |only metamer-0.2.0/metamer/man/metamerize.Rd |only metamer-0.2.0/metamer/man/set_minimize.Rd |only metamer-0.2.0/metamer/man/trim.Rd |only metamer-0.3.0/metamer/DESCRIPTION | 13 metamer-0.3.0/metamer/MD5 | 56 +- metamer-0.3.0/metamer/NAMESPACE | 23 - metamer-0.3.0/metamer/NEWS.md | 20 metamer-0.3.0/metamer/R/draw-data.R | 3 metamer-0.3.0/metamer/R/functionals.R |only metamer-0.3.0/metamer/R/metamer-class.R |only metamer-0.3.0/metamer/R/metamer-package.R | 4 metamer-0.3.0/metamer/R/metamerize.R | 211 ++-------- metamer-0.3.0/metamer/R/methods.R | 19 metamer-0.3.0/metamer/R/stop-conditions.R |only metamer-0.3.0/metamer/R/utilities.R | 83 +++ metamer-0.3.0/metamer/README.md | 114 ++--- metamer-0.3.0/metamer/build |only metamer-0.3.0/metamer/man/delayed_with.Rd | 14 metamer-0.3.0/metamer/man/densify.Rd | 12 metamer-0.3.0/metamer/man/draw_data.Rd | 12 metamer-0.3.0/metamer/man/figures/README-unnamed-chunk-1-1.png |binary metamer-0.3.0/metamer/man/figures/README-unnamed-chunk-5-1.png |binary metamer-0.3.0/metamer/man/figures/README-unnamed-chunk-6-1.gif |binary metamer-0.3.0/metamer/man/figures/README-unnamed-chunk-8-1.gif |binary metamer-0.3.0/metamer/man/mean_dist_to.Rd | 17 metamer-0.3.0/metamer/man/mean_dist_to_sf.Rd |only metamer-0.3.0/metamer/man/mean_self_proximity.Rd | 11 metamer-0.3.0/metamer/man/metamer-package.Rd | 10 metamer-0.3.0/metamer/man/metamerise.Rd |only metamer-0.3.0/metamer/man/moments_n.Rd | 12 metamer-0.3.0/metamer/man/rounding.Rd |only metamer-0.3.0/metamer/man/set_params.Rd |only metamer-0.3.0/metamer/man/stop_conditions.Rd |only metamer-0.3.0/metamer/tests/testthat/test-metamerize.R | 65 --- 36 files changed, 337 insertions(+), 362 deletions(-)
Title: Geographic Tools for Studying Gerrymandering
Description: A compilation of tools to complete common tasks for studying gerrymandering. This focuses on the geographic tool side of common problems, such as linking different levels of spatial units or estimating how to break up units. Functions exist for creating redistricting-focused data for the US.
Author: Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <christopherkenny@fas.harvard.edu>
Diff between geomander versions 2.0.3 dated 2022-03-06 and 2.1.0 dated 2022-06-23
DESCRIPTION | 16 - MD5 | 31 +- NAMESPACE | 8 NEWS.md | 5 R/alarm.R | 33 +- R/baf_to_vtd.R |only R/center.R | 51 ++++ R/contiguity.R | 45 +++ R/geomander-package.R | 2 R/regionalize.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/Merging_Election_Data.html | 295 ++++++++++++++++++++++-- inst/doc/Redistricting_School_Districts.html | 319 +++++++++++++++++++++++---- man/baf_to_vtd.Rd |only man/check_contiguity.Rd | 38 ++- man/geos_circle_center.Rd |only man/get_alarm.Rd | 9 man/st_circle_center.Rd |only 19 files changed, 738 insertions(+), 114 deletions(-)
Title: Weighted and Standard Elo Rates
Description: Estimates the standard and weighted Elo (WElo, Angelini et al., 2022 <doi:10.1016/j.ejor.2021.04.011>) rates. The current version provides Elo and WElo rates for tennis, according to different systems of weights (games or sets) and scale factors (constant, proportional to the number of matches, with more weight on Grand Slam matches or matches played on a specific surface). Moreover, the package gives the possibility of estimating the (bootstrap) standard errors for the rates. Finally, the package includes betting functions that automatically select the matches on which place a bet.
Author: Vincenzo Candila [aut, cre]
Maintainer: Vincenzo Candila <candilav@gmail.com>
Diff between welo versions 0.1.1 dated 2021-10-12 and 0.1.2 dated 2022-06-23
DESCRIPTION | 15 +- MD5 | 22 ++-- NAMESPACE | 11 ++ NEWS.md | 6 + R/functions.R | 260 +++++++++++++++++++++++++++++++++++++++++++++----- build/partial.rdb |binary inst/CITATION | 2 inst/REFERENCES.bib | 6 - man/betting.Rd | 10 - man/random_betting.Rd | 23 +--- man/tennis_data.Rd |only man/welo_plot.Rd |only man/welofit.Rd | 4 13 files changed, 293 insertions(+), 66 deletions(-)
Title: Universal Storage Engine for Sparse and Dense Multidimensional
Arrays
Description: The universal storage engine 'TileDB' introduces a
powerful on-disk format for multi-dimensional arrays. It supports
dense and sparse arrays, dataframes and key-values stores, cloud
storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression,
encryption and checksum filters, uses a fully multi-threaded
implementation, supports parallel I/O, data versioning ('time
travel'), metadata and groups. It is implemented as an embeddable
cross-platform C++ library with APIs from several languages, and
integrations.
Author: TileDB, Inc. [aut, cph],
Dirk Eddelbuettel [cre]
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>
Diff between tiledb versions 0.13.0 dated 2022-05-16 and 0.14.0 dated 2022-06-23
DESCRIPTION | 8 MD5 | 54 NAMESPACE | 5 NEWS.md | 35 R/Array.R | 22 R/DataFrame.R | 2 R/Query.R | 9 R/QueryCondition.R | 27 R/RcppExports.R | 4 R/TileDBArray.R | 5 R/batchedQuery.R |only README.md | 5 configure | 4807 ++++++++++++++++++++++++++-------- configure.ac | 8 inst/tinytest/test_attr.R | 36 inst/tinytest/test_filter.R | 4 inst/tinytest/test_query.R | 3 inst/tinytest/test_querycondition.R | 67 inst/tinytest/test_tiledbarray.R | 31 man/completedBatched.Rd |only man/createBatched.Rd |only man/fetchBatched.Rd |only man/statusBatched.Rd |only man/tiledb_array_is_open.Rd |only man/tiledb_query_condition_combine.Rd | 5 src/RcppExports.cpp | 12 src/batched.cpp |only src/libtiledb.cpp | 245 - src/libtiledb.h | 2 src/nullable.cpp | 17 tools/m4 |only tools/tiledbVersion.txt | 4 32 files changed, 4197 insertions(+), 1220 deletions(-)
Title: Functions to Work with NCBI Accessions and Taxonomy
Description: Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment.
Author: Scott Sherrill-Mix [aut, cre]
Maintainer: Scott Sherrill-Mix <shescott@upenn.edu>
Diff between taxonomizr versions 0.8.0 dated 2021-05-06 and 0.9.2 dated 2022-06-23
DESCRIPTION | 13 +- MD5 | 48 +++++----- NAMESPACE | 2 R/taxa.R | 176 +++++++++++++++++++++++++++++++++++---- README.md | 160 ++++++++++++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/usage.R | 18 ++++ inst/doc/usage.Rmd | 129 +++++++++++++++++++++++++++- inst/doc/usage.html | 198 +++++++++++++++++++++++++++++++++++--------- man/accessionToTaxa.Rd | 2 man/getAccession2taxid.Rd | 2 man/getNamesAndNodes.Rd | 2 man/getRawTaxonomy.Rd | 4 man/makeNewick.Rd | 21 ++++ man/normalizeTaxa.Rd |only man/prepareDatabase.Rd | 13 ++ man/read.accession2taxid.Rd | 5 - man/read.names.Rd | 2 man/read.names.sql.Rd | 2 man/read.nodes.Rd | 2 man/read.nodes.sql.Rd | 2 man/taxonomizr-package.Rd | 2 man/topoSort.Rd |only src/taxaTrim.c | 26 ++++- tests/testthat/test_taxa.R | 122 ++++++++++++++++++++++----- vignettes/usage.Rmd | 129 +++++++++++++++++++++++++++- 26 files changed, 939 insertions(+), 141 deletions(-)
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams [aut, cre],
Michael Collyer [aut],
Antigoni Kaliontzopoulou [aut],
Erica Baken [aut]
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 4.0.3 dated 2022-03-02 and 4.0.4 dated 2022-06-23
DESCRIPTION | 8 MD5 | 58 ++-- NAMESPACE | 4 NEWS.md | 14 + R/combine.subsets.R | 5 R/compare.ZVrel.R |only R/geomorph.utils.r | 37 ++ R/gpagen.r | 2 R/integration.Vrel.r |only R/modularity.test.r | 6 R/morphol.disparity.r | 26 - R/plotRefToTarget.r | 24 - R/procD.lm.r | 3 R/procD.pgls.r | 25 + R/shape.predictor.r | 6 R/shared.support.code.R | 8 build/vignette.rds |binary inst/CITATION | 6 inst/doc/geomorph.PCA.html | 383 ++++++++++++++++++++++++---- inst/doc/geomorph.assistance.html | 506 ++++++++++++++++++++++++++++++++------ inst/doc/geomorph.digitize3D.html | 310 +++++++++++++++++++++-- inst/doc/geomorph.functions.html | 336 +++++++++++++++++++++---- man/combine.subsets.Rd | 4 man/compare.ZVrel.Rd |only man/gpagen.Rd | 2 man/integration.Vrel.Rd |only man/modularity.test.Rd | 6 man/morphol.disparity.Rd | 26 - man/plotRefToTarget.Rd | 20 - man/print.compare.ZVrel.Rd |only man/procD.pgls.Rd | 14 + man/shape.predictor.Rd | 6 man/summary.compare.ZVrel.Rd |only 33 files changed, 1556 insertions(+), 289 deletions(-)
More information about shinyCohortBuilder at CRAN
Permanent link
Title: Libraries, Data Dictionaries, and a Data Step for R
Description: Contains a set of functions to create data libraries,
generate data dictionaries, and simulate a data step.
The libname() function will load a directory of data into
a library in one line of code. The dictionary() function
will generate data dictionaries for individual
data frames or an entire library. And the datestep() function
will perform row-by-row data processing.
Author: David J. Bosak
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between libr versions 1.2.2 dated 2021-11-22 and 1.2.3 dated 2022-06-23
DESCRIPTION | 8 MD5 | 89 ++++---- NAMESPACE | 1 NEWS.md | 9 R/datastep.R | 48 ++++ R/dictionary.R | 12 - R/libname.R | 248 +++++++++++++++++++++- R/utilities.R | 9 README.md | 7 build/vignette.rds |binary inst/doc/libr-basics.Rmd | 2 inst/doc/libr-basics.html | 241 +++++++++++++++++++++- inst/doc/libr-datastep.html | 278 ++++++++++++++++++++++++- inst/doc/libr-disclaimer.html | 203 ++++++++++++++++++ inst/doc/libr-eq.html | 217 +++++++++++++++++++- inst/doc/libr-example1.html | 215 +++++++++++++++++++ inst/doc/libr-example2.html | 200 ++++++++++++++++++ inst/doc/libr-faq.R | 3 inst/doc/libr-faq.Rmd | 16 - inst/doc/libr-faq.html | 320 ++++++++++++++++++++++++++--- inst/doc/libr-management.html | 207 ++++++++++++++++++- inst/doc/libr.html | 367 ++++++++++++++++++++++++++++++---- man/datastep.Rd | 14 + man/is.lib.Rd | 1 man/lib_add.Rd | 1 man/lib_copy.Rd | 3 man/lib_delete.Rd | 1 man/lib_export.Rd |only man/lib_info.Rd | 1 man/lib_load.Rd | 1 man/lib_path.Rd | 1 man/lib_remove.Rd | 1 man/lib_replace.Rd | 1 man/lib_size.Rd | 1 man/lib_sync.Rd | 1 man/lib_unload.Rd | 1 man/lib_write.Rd | 1 man/libname.Rd | 8 man/print.lib.Rd | 1 tests/testthat/data/demo_studya.rdata |only tests/testthat/data/demo_studyb.rdata |only tests/testthat/test-datastep.R | 55 +++++ tests/testthat/test-dictionary.R | 17 + tests/testthat/test-libname.R | 60 +++++ tests/testthat/test-specs.R | 7 vignettes/libr-basics.Rmd | 2 vignettes/libr-faq.Rmd | 16 - 47 files changed, 2678 insertions(+), 217 deletions(-)
Title: Small-Sample Adjustments for Wald Tests Using Sandwich
Estimators
Description: Tests coefficients with sandwich estimator of variance and with small samples. Regression types supported are gee, linear regression, and conditional logistic regression.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between saws versions 0.9-6.2 dated 2019-12-16 and 0.9-7.0 dated 2022-06-23
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 5 +++++ R/geeUOmega.R | 17 ++++++++++++++--- R/print.saws.R | 8 +++++--- man/print.saws.Rd | 5 ++++- man/saws-package.Rd | 4 ++-- man/saws.Rd | 3 ++- 8 files changed, 43 insertions(+), 21 deletions(-)
Title: Spatial Analysis of Vectra Immunoflourescent Data
Description: Visualization and analysis of Vectra Immunoflourescent
data. Options for calculating both the univariate and bivariate Ripley's K
are included. Calculations are performed using a permutation-based
approach presented by Wilson et al. <doi:10.1101/2021.04.27.21256104>.
Author: Jordan Creed [aut],
Ram Thapa [aut],
Christopher Wilson [aut],
Alex Soupir [aut],
Oscar Ospina [aut],
Brooke Fridley [cph],
Fridley Lab [cre]
Maintainer: Fridley Lab <fridley.lab@moffitt.org>
Diff between spatialTIME versions 1.2.0 dated 2021-09-11 and 1.2.1 dated 2022-06-23
DESCRIPTION | 16 MD5 | 20 - R/plot_immunoflo.R | 2 R/ripleys_k.R | 8 R/subset_mif.R | 7 R/utils-helpers.R | 8 build/vignette.rds |binary inst/doc/intro.R | 11 inst/doc/intro.Rmd | 12 inst/doc/intro.html | 878 ++++++++++++++++++++++++++++++++++++---------------- vignettes/intro.Rmd | 12 11 files changed, 666 insertions(+), 308 deletions(-)
Title: A Set of Common Tools for Seasonal to Decadal Verification
Description: The advanced version of package 's2dverification'. It is
intended for 'seasonal to decadal' (s2d) climate forecast verification, but
it can also be used in other kinds of forecasts or general climate analysis.
This package is specially designed for the comparison between the experimental
and observational datasets. The functionality of the included functions covers
from data retrieval, data post-processing, skill scores against observation,
to visualization. Compared to 's2dverification', 's2dv' is more compatible
with the package 'startR', able to use multiple cores for computation and
handle multi-dimensional arrays with a higher flexibility.
Author: BSC-CNS [aut, cph],
An-Chi Ho [aut, cre],
Nuria Perez-Zanon [aut],
Roberto Bilbao [ctb],
Josep Cos [ctb],
Carlos Delgado [ctb],
Llorenc Lledo [ctb],
Andrea Manrique [ctb],
Deborah Verfaillie [ctb]
Maintainer: An-Chi Ho <an.ho@bsc.es>
Diff between s2dv versions 1.1.0 dated 2021-12-17 and 1.2.0 dated 2022-06-23
DESCRIPTION | 15 - MD5 | 90 +++++---- NAMESPACE | 5 NEWS.md | 15 + R/ACC.R | 413 +++++++++++++++++++++++++------------------- R/AMV.R | 4 R/CDORemap.R | 68 ++++--- R/Clim.R | 317 +++++++++++++++++++++------------ R/Cluster.R | 58 +++--- R/ColorBar.R | 4 R/DiffCorr.R |only R/EOF.R | 2 R/Eno.R | 2 R/GMST.R | 4 R/GSAT.R | 4 R/Histo2Hindcast.R | 2 R/Load.R | 34 +-- R/MeanDims.R | 13 - R/Persistence.R | 6 R/PlotACC.R | 4 R/PlotEquiMap.R | 161 +++++++++++------ R/PlotLayout.R | 15 + R/RPS.R |only R/RPSS.R |only R/RandomWalkTest.R | 4 R/Regression.R | 2 R/ResidualCorr.R |only R/SPOD.R | 4 R/TPI.R | 6 R/Utils.R | 16 - data/sampleDepthData.RData |binary data/sampleMap.RData |binary data/sampleTimeSeries.RData |binary man/ACC.Rd | 71 ++++--- man/CDORemap.Rd | 41 +++- man/Clim.Rd | 29 +-- man/Cluster.Rd | 3 man/DiffCorr.Rd |only man/MeanDims.Rd | 7 man/PlotACC.Rd | 4 man/PlotEquiMap.Rd | 23 ++ man/PlotLayout.Rd | 15 + man/RPS.Rd |only man/RPSS.Rd |only man/RandomWalkTest.Rd | 4 man/ResidualCorr.Rd |only man/s2dv-package.Rd | 11 - man/sampleDepthData.Rd | 6 man/sampleMap.Rd | 6 man/sampleTimeSeries.Rd | 6 50 files changed, 924 insertions(+), 570 deletions(-)
Title: Quantification of Asymmetric Dependence
Description: A copula-based measure for quantifying asymmetry in dependence and associations. Documentation and theory about 'qad' is provided
by the paper by Junker, Griessenberger & Trutschnig (2021, <doi:10.1016/j.csda.2020.107058>), and the paper by Trutschnig (2011, <doi:10.1016/j.jmaa.2011.06.013>).
Author: Florian Griessenberger [aut, cre],
Robert R. Junker [aut],
Valentin Petzel [aut],
Wolfgang Trutschnig [aut]
Maintainer: Florian Griessenberger <florian.griessenberger@sbg.ac.at>
Diff between qad versions 1.0.1 dated 2021-12-02 and 1.0.2 dated 2022-06-23
DESCRIPTION | 7 +- MD5 | 56 ++++++++++------ NAMESPACE | 2 R/data.R |only R/emp_c_copula.R | 3 R/plots.R | 68 +++++++++++++++----- R/predict_qad.R | 15 ++-- R/qad.R | 30 ++++++-- build/partial.rdb |only build/vignette.rds |binary data |only inst/doc/qad-vignette.R | 2 inst/doc/qad-vignette.Rmd | 4 - inst/doc/qad-vignette.html | 7 +- man/PlantDiversity.Rd |only man/heatmap.qad.Rd | 14 ++-- man/pairwise.qad.Rd | 7 +- man/predict.qad.Rd | 11 +-- man/qad.Rd | 6 - tests/testthat/test-D1.R | 3 tests/testthat/test-ECBC.R | 2 tests/testthat/test-predict.R | 2 tests/testthat/test-qad.R | 16 +++- tests/testthat/test-utilityfunctions.R | 2 vignettes/man/figures/README-example1-1.pdf |only vignettes/man/figures/README-example2-1.pdf |only vignettes/man/figures/README-plot1-1.pdf |only vignettes/man/figures/README-plotforecast-1.pdf |only vignettes/man/figures/README-plotforecast-2.pdf |only vignettes/man/figures/README-unnamed-chunk-13-1.pdf |only vignettes/man/figures/README-unnamed-chunk-4-1.pdf |only vignettes/man/figures/README-unnamed-chunk-5-1.pdf |only vignettes/man/figures/README-unnamed-chunk-6-1.pdf |only vignettes/man/figures/README-unnamed-chunk-6-2.pdf |only vignettes/man/figures/README-unnamed-chunk-7-1.pdf |only vignettes/man/figures/README-unnamed-chunk-7-2.pdf |only vignettes/qad-vignette.Rmd | 4 - 37 files changed, 176 insertions(+), 85 deletions(-)
Title: Make Static HTML Documentation for a Package
Description: Generate an attractive and useful website from a source
package. 'pkgdown' converts your documentation, vignettes, 'README',
and more to 'HTML' making it easy to share information about your
package online.
Author: Hadley Wickham [aut, cre] ,
Jay Hesselberth [aut] ,
Maelle Salmon [aut] ,
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between pkgdown versions 2.0.4 dated 2022-06-10 and 2.0.5 dated 2022-06-23
DESCRIPTION | 6 +- MD5 | 62 +++++++++++++------------- NEWS.md | 19 +++++++ R/build-articles.R | 13 +++-- R/build-home-authors.R | 2 R/build-home-community.R | 9 +++ R/build-reference.R | 7 -- R/deploy-site.R | 2 R/repo.R | 4 - R/topics-external.R | 9 ++- R/topics.R | 7 -- R/utils.R | 18 ------- build/pkgdown.pdf |binary man/build_articles.Rd | 7 ++ man/build_reference.Rd | 5 -- tests/testthat/_snaps/build-home-community.md | 3 - tests/testthat/_snaps/check.md | 2 tests/testthat/_snaps/topics-external.md | 14 ++++- tests/testthat/_snaps/topics.md | 6 ++ tests/testthat/assets/reference/DESCRIPTION | 2 tests/testthat/assets/reference/R/funs.R | 2 tests/testthat/assets/reference/man/a.Rd | 1 tests/testthat/assets/reference/man/b.Rd | 1 tests/testthat/test-build-home-citation.R | 12 +++++ tests/testthat/test-build-home-community.R | 3 - tests/testthat/test-build-reference.R | 5 ++ tests/testthat/test-repo.R | 9 +-- tests/testthat/test-topics-external.R | 4 + tests/testthat/test-topics.R | 29 +++++++++++- tests/testthat/test-tweak-page.R | 2 tests/testthat/test-tweak-reference.R | 4 - tests/testthat/test-tweak-tags.R | 2 32 files changed, 175 insertions(+), 96 deletions(-)
Title: Analysis and Visualization of Archaeological Count Data
Description: An easy way to examine archaeological count data. This
package provides several tests and measures of diversity:
heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.),
richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and
similarity (Brainerd-Robinson, etc.). The package make it easy to
visualize count data and statistical thresholds: rank vs abundance
plots, heatmaps, Ford (1962) and Bertin (1977) diagrams.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Matthew Peeples [ctb] ,
Ben Marwick [ctb] ,
Anne Philippe [ctb] ,
Jean-Baptiste Fourvel [ctb]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tabula versions 1.6.1 dated 2021-05-25 and 1.7.0 dated 2022-06-23
tabula-1.6.1/tabula/R/permute.R |only tabula-1.6.1/tabula/R/refine_ca.R |only tabula-1.6.1/tabula/R/seriate_average.R |only tabula-1.6.1/tabula/R/seriate_rank.R |only tabula-1.6.1/tabula/R/test_diversity.R |only tabula-1.6.1/tabula/inst/doc/seriation.R |only tabula-1.6.1/tabula/inst/doc/seriation.Rmd |only tabula-1.6.1/tabula/inst/doc/seriation.html |only tabula-1.6.1/tabula/inst/examples/ex-plot_line.R |only tabula-1.6.1/tabula/inst/examples/ex-refine.R |only tabula-1.6.1/tabula/inst/examples/ex-seriation.R |only tabula-1.6.1/tabula/man/PermutationOrder-class.Rd |only tabula-1.6.1/tabula/man/RefineCA-class.Rd |only tabula-1.6.1/tabula/man/figures/README-permute-incidence-1.png |only tabula-1.6.1/tabula/man/figures/README-permute-incidence-2.png |only tabula-1.6.1/tabula/man/heterogeneity-index.Rd |only tabula-1.6.1/tabula/man/plot_matrix.Rd |only tabula-1.6.1/tabula/man/richness-index.Rd |only tabula-1.6.1/tabula/man/seriation.Rd |only tabula-1.6.1/tabula/man/similarity-method.Rd |only tabula-1.6.1/tabula/man/turnover-index.Rd |only tabula-1.6.1/tabula/tests/figs |only tabula-1.6.1/tabula/tests/testthat/test-seriation.R |only tabula-1.6.1/tabula/vignettes/seriation.Rmd |only tabula-1.7.0/tabula/DESCRIPTION | 65 tabula-1.7.0/tabula/MD5 | 240 +- tabula-1.7.0/tabula/NAMESPACE | 77 tabula-1.7.0/tabula/NEWS.md | 44 tabula-1.7.0/tabula/R/AllClasses.R | 100 tabula-1.7.0/tabula/R/AllGenerics.R | 1052 +++++---- tabula-1.7.0/tabula/R/coerce.R | 2 tabula-1.7.0/tabula/R/deprecate.R | 550 ++++ tabula-1.7.0/tabula/R/index_diversity.R | 281 +- tabula-1.7.0/tabula/R/index_heterogeneity.R | 462 +--- tabula-1.7.0/tabula/R/index_rarefaction.R | 134 - tabula-1.7.0/tabula/R/index_richness.R | 547 ++-- tabula-1.7.0/tabula/R/index_similarity.R | 453 ++- tabula-1.7.0/tabula/R/index_test.R |only tabula-1.7.0/tabula/R/index_turnover.R | 265 +- tabula-1.7.0/tabula/R/mutators.R | 38 tabula-1.7.0/tabula/R/plot_bertin.R | 16 tabula-1.7.0/tabula/R/plot_diversity.R | 158 - tabula-1.7.0/tabula/R/plot_ford.R | 43 tabula-1.7.0/tabula/R/plot_heatmap.R | 85 tabula-1.7.0/tabula/R/plot_rank.R | 12 tabula-1.7.0/tabula/R/plot_spot.R | 160 - tabula-1.7.0/tabula/R/reexport.R | 44 tabula-1.7.0/tabula/R/show.R | 43 tabula-1.7.0/tabula/R/statistics.R | 158 - tabula-1.7.0/tabula/R/subset.R | 58 tabula-1.7.0/tabula/R/tabula-package.R | 9 tabula-1.7.0/tabula/README.md | 230 -- tabula-1.7.0/tabula/build/partial.rdb |binary tabula-1.7.0/tabula/build/vignette.rds |binary tabula-1.7.0/tabula/inst/doc/bibliography.Rmd | 1 tabula-1.7.0/tabula/inst/doc/bibliography.html | 478 +++- tabula-1.7.0/tabula/inst/doc/diversity.R | 67 tabula-1.7.0/tabula/inst/doc/diversity.Rmd | 71 tabula-1.7.0/tabula/inst/doc/diversity.html | 1136 ++++++---- tabula-1.7.0/tabula/inst/examples/ex-diversity.R | 17 tabula-1.7.0/tabula/inst/examples/ex-diversity_old.R | 28 tabula-1.7.0/tabula/inst/examples/ex-independance.R | 10 tabula-1.7.0/tabula/inst/examples/ex-occurrence.R | 5 tabula-1.7.0/tabula/inst/examples/ex-plot_bar.R | 11 tabula-1.7.0/tabula/inst/examples/ex-plot_diversity.R | 11 tabula-1.7.0/tabula/inst/examples/ex-plot_matrix.R | 10 tabula-1.7.0/tabula/inst/examples/ex-plot_rank.R | 5 tabula-1.7.0/tabula/inst/examples/ex-plot_spot.R | 7 tabula-1.7.0/tabula/inst/examples/ex-resample.R |only tabula-1.7.0/tabula/inst/examples/ex-richness.R | 18 tabula-1.7.0/tabula/inst/examples/ex-similarity.R | 18 tabula-1.7.0/tabula/inst/examples/ex-test.R | 3 tabula-1.7.0/tabula/inst/examples/ex-turnover.R | 12 tabula-1.7.0/tabula/man/DiversityIndex.Rd | 20 tabula-1.7.0/tabula/man/deprecate.Rd |only tabula-1.7.0/tabula/man/figures/README-plot-occ-1.png |binary tabula-1.7.0/tabula/man/figures/README-sample-size-1.png |binary tabula-1.7.0/tabula/man/figures/README-sample-size-2.png |binary tabula-1.7.0/tabula/man/figures/README-similarity-brainerd-1.png |binary tabula-1.7.0/tabula/man/heterogeneity.Rd |only tabula-1.7.0/tabula/man/independance.Rd | 34 tabula-1.7.0/tabula/man/mutator.Rd | 17 tabula-1.7.0/tabula/man/occurrence.Rd |only tabula-1.7.0/tabula/man/plot_bar.Rd | 32 tabula-1.7.0/tabula/man/plot_diversity.Rd | 51 tabula-1.7.0/tabula/man/plot_heatmap.Rd |only tabula-1.7.0/tabula/man/plot_line.Rd | 18 tabula-1.7.0/tabula/man/plot_spot.Rd | 70 tabula-1.7.0/tabula/man/rarefaction.Rd |only tabula-1.7.0/tabula/man/reexports.Rd | 19 tabula-1.7.0/tabula/man/resample.Rd |only tabula-1.7.0/tabula/man/richness.Rd |only tabula-1.7.0/tabula/man/similarity.Rd |only tabula-1.7.0/tabula/man/simulate.Rd |only tabula-1.7.0/tabula/man/stats_bootstrap.Rd | 2 tabula-1.7.0/tabula/man/stats_jackknife.Rd | 2 tabula-1.7.0/tabula/man/subset.Rd | 12 tabula-1.7.0/tabula/man/tabula-package.Rd | 20 tabula-1.7.0/tabula/man/test_diversity.Rd | 12 tabula-1.7.0/tabula/man/turnover.Rd |only tabula-1.7.0/tabula/tests/testthat/_snaps/diversity |only tabula-1.7.0/tabula/tests/testthat/_snaps/diversity.md | 108 tabula-1.7.0/tabula/tests/testthat/_snaps/plots |only tabula-1.7.0/tabula/tests/testthat/_snaps/rarefaction.md |only tabula-1.7.0/tabula/tests/testthat/_snaps/richness |only tabula-1.7.0/tabula/tests/testthat/_snaps/richness.md | 138 + tabula-1.7.0/tabula/tests/testthat/_snaps/similarity |only tabula-1.7.0/tabula/tests/testthat/_snaps/similarity.md |only tabula-1.7.0/tabula/tests/testthat/_snaps/statistics.md |only tabula-1.7.0/tabula/tests/testthat/test-classes.R | 20 tabula-1.7.0/tabula/tests/testthat/test-diversity.R | 121 - tabula-1.7.0/tabula/tests/testthat/test-plots.R | 87 tabula-1.7.0/tabula/tests/testthat/test-rarefaction.R | 18 tabula-1.7.0/tabula/tests/testthat/test-richness.R | 137 - tabula-1.7.0/tabula/tests/testthat/test-similarity.R | 97 tabula-1.7.0/tabula/tests/testthat/test-statistics.R | 9 tabula-1.7.0/tabula/tests/testthat/test-turnover.R | 59 tabula-1.7.0/tabula/vignettes/bibliography.Rmd | 1 tabula-1.7.0/tabula/vignettes/bibliography.bib | 1129 ++++----- tabula-1.7.0/tabula/vignettes/diversity.Rmd | 71 120 files changed, 5243 insertions(+), 4295 deletions(-)
Title: Model Wrappers for Rule-Based Models
Description: Bindings for additional models for use with the 'parsnip'
package. Models include prediction rule ensembles (Friedman and
Popescu, 2008) <doi:10.1214/07-AOAS148>, C5.0 rules (Quinlan, 1992
ISBN: 1558602380), and Cubist (Kuhn and Johnson, 2013)
<doi:10.1007/978-1-4614-6849-3>.
Author: Emil Hvitfeldt [aut, cre] ,
Max Kuhn [aut] ,
RStudio [cph, fnd]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between rules versions 0.2.0 dated 2022-03-14 and 1.0.0 dated 2022-06-23
rules-0.2.0/rules/man/cubist_and_rulefit.Rd |only rules-0.2.0/rules/man/mtry_prop.Rd |only rules-0.2.0/rules/tests/testthat/test-helpers.R |only rules-1.0.0/rules/DESCRIPTION | 33 - rules-1.0.0/rules/MD5 | 60 - rules-1.0.0/rules/NAMESPACE | 4 rules-1.0.0/rules/NEWS.md | 16 rules-1.0.0/rules/R/0_imports.R | 14 rules-1.0.0/rules/R/C5_rules.R | 126 +--- rules-1.0.0/rules/R/C5_rules_data.R | 2 rules-1.0.0/rules/R/cubist_rules.R | 42 - rules-1.0.0/rules/R/cubist_rules_data.R | 1 rules-1.0.0/rules/R/rule_fit.R | 153 +++- rules-1.0.0/rules/R/rule_fit_data.R | 18 rules-1.0.0/rules/R/tidy_C5.0.R |only rules-1.0.0/rules/R/tidy_cubist.R | 71 +- rules-1.0.0/rules/R/tidy_xrf.R | 17 rules-1.0.0/rules/R/zzz.R | 1 rules-1.0.0/rules/README.md | 8 rules-1.0.0/rules/build |only rules-1.0.0/rules/inst/WORDLIST | 2 rules-1.0.0/rules/man/multi_predict.Rd | 30 rules-1.0.0/rules/man/reexports.Rd | 3 rules-1.0.0/rules/man/rules-internal.Rd | 7 rules-1.0.0/rules/man/rules-package.Rd |only rules-1.0.0/rules/man/tidy.cubist.Rd | 284 +++++++-- rules-1.0.0/rules/tests/spelling.R | 9 rules-1.0.0/rules/tests/testthat.R | 6 rules-1.0.0/rules/tests/testthat/_snaps |only rules-1.0.0/rules/tests/testthat/helpers.R |only rules-1.0.0/rules/tests/testthat/test-c5.R | 258 ++++++-- rules-1.0.0/rules/tests/testthat/test-cubist.R | 346 +++++++---- rules-1.0.0/rules/tests/testthat/test-rule-fit-binomial.R | 109 +-- rules-1.0.0/rules/tests/testthat/test-rule-fit-multinomial.R | 91 +- rules-1.0.0/rules/tests/testthat/test-rule-fit-regression.R | 128 +++- 35 files changed, 1254 insertions(+), 585 deletions(-)
Title: Interface to the 'Pharmpy' 'Pharmacometrics' Library
Description: Interface to the 'Pharmpy' 'pharmacometrics' library. The 'Reticulate' package is used to interface Python from R.
Author: Rikard Nordgren [aut, cre, cph],
Stella Belin [aut, cph],
Mats O. Karlsson [sad],
Andrew C. Hooker [sad],
Sebastian Ueckert [sad] ,
Simon Carter [rev],
Simon Buatois [rev],
Joao A. Abrantes [rev],
F. Hoffmann-La Roche Ltd. [fnd]
Maintainer: Rikard Nordgren <rikard.nordgren@farmaci.uu.se>
Diff between pharmr versions 0.33.1 dated 2021-10-15 and 0.73.1 dated 2022-06-23
pharmr-0.33.1/pharmr/man/set_lag_time.Rd |only pharmr-0.33.1/pharmr/man/update_source.Rd |only pharmr-0.73.1/pharmr/DESCRIPTION | 16 pharmr-0.73.1/pharmr/MD5 | 202 pharmr-0.73.1/pharmr/NAMESPACE | 111 pharmr-0.73.1/pharmr/R/check_pharmpy.R | 7 pharmr-0.73.1/pharmr/R/functions_wrapper.R | 3213 +++++++++- pharmr-0.73.1/pharmr/R/install.R | 30 pharmr-0.73.1/pharmr/R/printing.R |only pharmr-0.73.1/pharmr/R/utils.R | 12 pharmr-0.73.1/pharmr/README.md | 85 pharmr-0.73.1/pharmr/man/add_allometry.Rd |only pharmr-0.73.1/pharmr/man/add_covariance_step.Rd |only pharmr-0.73.1/pharmr/man/add_covariate_effect.Rd | 2 pharmr-0.73.1/pharmr/man/add_estimation_step.Rd | 26 pharmr-0.73.1/pharmr/man/add_iiv.Rd | 7 pharmr-0.73.1/pharmr/man/add_iov.Rd | 15 pharmr-0.73.1/pharmr/man/add_lag_time.Rd |only pharmr-0.73.1/pharmr/man/add_pk_iiv.Rd |only pharmr-0.73.1/pharmr/man/add_population_parameter.Rd |only pharmr-0.73.1/pharmr/man/add_time_after_dose.Rd |only pharmr-0.73.1/pharmr/man/append_estimation_step_options.Rd | 18 pharmr-0.73.1/pharmr/man/bump_model_number.Rd |only pharmr-0.73.1/pharmr/man/calculate_aic.Rd |only pharmr-0.73.1/pharmr/man/calculate_bic.Rd |only pharmr-0.73.1/pharmr/man/calculate_corr_from_cov.Rd |only pharmr-0.73.1/pharmr/man/calculate_corr_from_inf.Rd |only pharmr-0.73.1/pharmr/man/calculate_cov_from_corrse.Rd |only pharmr-0.73.1/pharmr/man/calculate_cov_from_inf.Rd |only pharmr-0.73.1/pharmr/man/calculate_epsilon_gradient_expression.Rd |only pharmr-0.73.1/pharmr/man/calculate_eta_gradient_expression.Rd |only pharmr-0.73.1/pharmr/man/calculate_inf_from_corrse.Rd |only pharmr-0.73.1/pharmr/man/calculate_inf_from_cov.Rd |only pharmr-0.73.1/pharmr/man/calculate_parameters_from_ucp.Rd |only pharmr-0.73.1/pharmr/man/calculate_se_from_cov.Rd |only pharmr-0.73.1/pharmr/man/calculate_se_from_inf.Rd |only pharmr-0.73.1/pharmr/man/calculate_ucp_scale.Rd |only pharmr-0.73.1/pharmr/man/check_dataset.Rd |only pharmr-0.73.1/pharmr/man/check_high_correlations.Rd |only pharmr-0.73.1/pharmr/man/check_parameters_near_bounds.Rd |only pharmr-0.73.1/pharmr/man/check_pharmpy.Rd | 22 pharmr-0.73.1/pharmr/man/cleanup_model.Rd |only pharmr-0.73.1/pharmr/man/convert_model.Rd | 4 pharmr-0.73.1/pharmr/man/create_report.Rd |only pharmr-0.73.1/pharmr/man/create_results.Rd | 2 pharmr-0.73.1/pharmr/man/create_rng.Rd | 2 pharmr-0.73.1/pharmr/man/create_symbol.Rd |only pharmr-0.73.1/pharmr/man/drop_columns.Rd |only pharmr-0.73.1/pharmr/man/drop_dropped_columns.Rd |only pharmr-0.73.1/pharmr/man/evaluate_epsilon_gradient.Rd |only pharmr-0.73.1/pharmr/man/evaluate_eta_gradient.Rd |only pharmr-0.73.1/pharmr/man/evaluate_individual_prediction.Rd |only pharmr-0.73.1/pharmr/man/evaluate_population_prediction.Rd |only pharmr-0.73.1/pharmr/man/evaluate_weighted_residuals.Rd |only pharmr-0.73.1/pharmr/man/expand_additional_doses.Rd |only pharmr-0.73.1/pharmr/man/find_clearance_parameters.Rd |only pharmr-0.73.1/pharmr/man/find_volume_parameters.Rd |only pharmr-0.73.1/pharmr/man/fit.Rd | 4 pharmr-0.73.1/pharmr/man/fix_or_unfix_parameters.Rd |only pharmr-0.73.1/pharmr/man/fix_parameters.Rd | 2 pharmr-0.73.1/pharmr/man/fix_parameters_to.Rd | 10 pharmr-0.73.1/pharmr/man/generate_model_code.Rd |only pharmr-0.73.1/pharmr/man/get_baselines.Rd |only pharmr-0.73.1/pharmr/man/get_bioavailability.Rd |only pharmr-0.73.1/pharmr/man/get_concentration_parameters_from_data.Rd |only pharmr-0.73.1/pharmr/man/get_config_path.Rd |only pharmr-0.73.1/pharmr/man/get_covariate_baselines.Rd |only pharmr-0.73.1/pharmr/man/get_doseid.Rd |only pharmr-0.73.1/pharmr/man/get_doses.Rd |only pharmr-0.73.1/pharmr/man/get_ids.Rd |only pharmr-0.73.1/pharmr/man/get_individual_parameters.Rd |only pharmr-0.73.1/pharmr/man/get_individual_prediction_expression.Rd |only pharmr-0.73.1/pharmr/man/get_lag_times.Rd |only pharmr-0.73.1/pharmr/man/get_mdv.Rd |only pharmr-0.73.1/pharmr/man/get_observation_expression.Rd |only pharmr-0.73.1/pharmr/man/get_observations.Rd | 4 pharmr-0.73.1/pharmr/man/get_omegas.Rd |only pharmr-0.73.1/pharmr/man/get_pk_parameters.Rd |only pharmr-0.73.1/pharmr/man/get_population_prediction_expression.Rd |only pharmr-0.73.1/pharmr/man/get_sigmas.Rd |only pharmr-0.73.1/pharmr/man/get_thetas.Rd |only pharmr-0.73.1/pharmr/man/get_unit_of.Rd |only pharmr-0.73.1/pharmr/man/greekify_model.Rd |only pharmr-0.73.1/pharmr/man/has_first_order_elimination.Rd |only pharmr-0.73.1/pharmr/man/has_michaelis_menten_elimination.Rd |only pharmr-0.73.1/pharmr/man/has_mixed_mm_fo_elimination.Rd |only pharmr-0.73.1/pharmr/man/has_random_effect.Rd |only pharmr-0.73.1/pharmr/man/has_zero_order_elimination.Rd |only pharmr-0.73.1/pharmr/man/install_pharmpy.Rd | 2 pharmr-0.73.1/pharmr/man/install_pharmpy_devel.Rd |only pharmr-0.73.1/pharmr/man/list_time_varying_covariates.Rd |only pharmr-0.73.1/pharmr/man/load_example_model.Rd | 2 pharmr-0.73.1/pharmr/man/make_declarative.Rd |only pharmr-0.73.1/pharmr/man/mu_reference_model.Rd |only pharmr-0.73.1/pharmr/man/omit_data.Rd |only pharmr-0.73.1/pharmr/man/predict_influential_individuals.Rd | 4 pharmr-0.73.1/pharmr/man/predict_influential_outliers.Rd | 10 pharmr-0.73.1/pharmr/man/predict_outliers.Rd | 4 pharmr-0.73.1/pharmr/man/print_fit_summary.Rd |only pharmr-0.73.1/pharmr/man/print_model_code.Rd |only pharmr-0.73.1/pharmr/man/print_pharmpy_version.Rd |only pharmr-0.73.1/pharmr/man/rank_models.Rd |only pharmr-0.73.1/pharmr/man/read_dataset_from_datainfo.Rd |only pharmr-0.73.1/pharmr/man/read_model_from_string.Rd | 10 pharmr-0.73.1/pharmr/man/read_results.Rd | 2 pharmr-0.73.1/pharmr/man/remove_covariance_step.Rd |only pharmr-0.73.1/pharmr/man/remove_estimation_step.Rd | 14 pharmr-0.73.1/pharmr/man/remove_iiv.Rd | 2 pharmr-0.73.1/pharmr/man/remove_iov.Rd | 9 pharmr-0.73.1/pharmr/man/remove_lag_time.Rd | 2 pharmr-0.73.1/pharmr/man/remove_loq_data.Rd |only pharmr-0.73.1/pharmr/man/remove_unused_parameters_and_rvs.Rd |only pharmr-0.73.1/pharmr/man/rename_symbols.Rd |only pharmr-0.73.1/pharmr/man/resample_data.Rd |only pharmr-0.73.1/pharmr/man/retrieve_models.Rd |only pharmr-0.73.1/pharmr/man/run_allometry.Rd |only pharmr-0.73.1/pharmr/man/run_amd.Rd |only pharmr-0.73.1/pharmr/man/run_covsearch.Rd |only pharmr-0.73.1/pharmr/man/run_iivsearch.Rd |only pharmr-0.73.1/pharmr/man/run_iovsearch.Rd |only pharmr-0.73.1/pharmr/man/run_modelsearch.Rd |only pharmr-0.73.1/pharmr/man/run_resmod.Rd |only pharmr-0.73.1/pharmr/man/run_tool.Rd | 2 pharmr-0.73.1/pharmr/man/set_bolus_absorption.Rd | 2 pharmr-0.73.1/pharmr/man/set_dtbs_error_model.Rd | 4 pharmr-0.73.1/pharmr/man/set_estimation_step.Rd | 19 pharmr-0.73.1/pharmr/man/set_evaluation_step.Rd |only pharmr-0.73.1/pharmr/man/set_initial_estimates.Rd | 4 pharmr-0.73.1/pharmr/man/set_lower_bounds.Rd |only pharmr-0.73.1/pharmr/man/set_ode_solver.Rd | 30 pharmr-0.73.1/pharmr/man/set_power_on_ruv.Rd | 12 pharmr-0.73.1/pharmr/man/set_proportional_error_model.Rd | 8 pharmr-0.73.1/pharmr/man/set_seq_zo_fo_absorption.Rd | 3 pharmr-0.73.1/pharmr/man/set_time_varying_error_model.Rd |only pharmr-0.73.1/pharmr/man/set_transit_compartments.Rd | 6 pharmr-0.73.1/pharmr/man/set_upper_bounds.Rd |only pharmr-0.73.1/pharmr/man/simplify_expression.Rd |only pharmr-0.73.1/pharmr/man/solve_ode_system.Rd |only pharmr-0.73.1/pharmr/man/summarize_errors.Rd |only pharmr-0.73.1/pharmr/man/summarize_individuals.Rd |only pharmr-0.73.1/pharmr/man/summarize_individuals_count_table.Rd |only pharmr-0.73.1/pharmr/man/summarize_modelfit_results.Rd | 14 pharmr-0.73.1/pharmr/man/transform_etas_boxcox.Rd | 2 pharmr-0.73.1/pharmr/man/transform_etas_john_draper.Rd | 2 pharmr-0.73.1/pharmr/man/transform_etas_tdist.Rd | 2 pharmr-0.73.1/pharmr/man/translate_nmtran_time.Rd |only pharmr-0.73.1/pharmr/man/unconstrain_parameters.Rd |only pharmr-0.73.1/pharmr/man/undrop_columns.Rd |only pharmr-0.73.1/pharmr/man/unfix_parameters.Rd | 4 pharmr-0.73.1/pharmr/man/unfix_parameters_to.Rd | 20 pharmr-0.73.1/pharmr/man/update_inits.Rd | 14 pharmr-0.73.1/pharmr/man/write_csv.Rd |only pharmr-0.73.1/pharmr/man/write_results.Rd |only pharmr-0.73.1/pharmr/tests/testthat/test-transform.R | 5 154 files changed, 3633 insertions(+), 375 deletions(-)
Title: Limited-memory BFGS Optimization
Description: A wrapper built around the libLBFGS optimization library by Naoaki Okazaki. The lbfgs package implements both the Limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) and the Orthant-Wise Quasi-Newton Limited-Memory (OWL-QN) optimization algorithms. The L-BFGS algorithm solves the problem of minimizing an objective, given its gradient, by iteratively computing approximations of the inverse Hessian matrix. The OWL-QN algorithm finds the optimum of an objective plus the L1-norm of the problem's parameters. The package offers a fast and memory-efficient implementation of these optimization routines, which is particularly suited for high-dimensional problems.
Author: Antonio Coppola [aut, cre, cph],
Brandon Stewart [aut, cph],
Naoaki Okazaki [aut, cph],
David Ardia [ctb, cph],
Dirk Eddelbuettel [ctb, cph],
Katharine Mullen [ctb, cph],
Jorge Nocedal [ctb, cph]
Maintainer: Antonio Coppola <acoppola@stanford.edu>
Diff between lbfgs versions 1.2.1.1 dated 2022-05-23 and 1.2.1.2 dated 2022-06-23
lbfgs-1.2.1.1/lbfgs/README.md |only lbfgs-1.2.1.2/lbfgs/DESCRIPTION | 12 ++++++------ lbfgs-1.2.1.2/lbfgs/MD5 | 12 ++++++------ lbfgs-1.2.1.2/lbfgs/NAMESPACE | 2 +- lbfgs-1.2.1.2/lbfgs/inst/doc/Vignette.Rnw | 22 +++++++++++----------- lbfgs-1.2.1.2/lbfgs/inst/doc/Vignette.pdf |binary lbfgs-1.2.1.2/lbfgs/src/RegisterDynamicSymbol.c |only lbfgs-1.2.1.2/lbfgs/vignettes/Vignette.Rnw | 22 +++++++++++----------- 8 files changed, 35 insertions(+), 35 deletions(-)
Title: Model Wrappers for Discriminant Analysis
Description: Bindings for additional classification models for use with
the 'parsnip' package. Models include flavors of discriminant
analysis, such as linear (Fisher (1936)
<doi:10.1111/j.1469-1809.1936.tb02137.x>), regularized (Friedman
(1989) <doi:10.1080/01621459.1989.10478752>), and flexible (Hastie,
Tibshirani, and Buja (1994) <doi:10.1080/01621459.1994.10476866>), as
well as naive Bayes classifiers (Hand and Yu (2007)
<doi:10.1111/j.1751-5823.2001.tb00465.x>).
Author: Emil Hvitfeldt [aut, cre] ,
Max Kuhn [aut] ,
RStudio [cph, fnd]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between discrim versions 0.2.0 dated 2022-03-09 and 1.0.0 dated 2022-06-23
DESCRIPTION | 44 ++++---- MD5 | 60 ++++++------ NEWS.md | 4 R/data.R | 7 - R/discrim_flexible_data.R | 3 R/discrim_linear_data.R | 8 - R/discrim_quad_data.R | 4 R/discrim_regularized_data.R | 1 R/helpers.R | 12 +- R/naive_Bayes_data.R | 1 R/parameters.R | 1 inst/WORDLIST | 2 man/discrim-package.Rd | 28 ++++- man/figures/README-example-1.png |binary man/parabolic.Rd | 4 tests/spelling.R | 9 + tests/testthat/_snaps |only tests/testthat/helper-objects.R | 5 - tests/testthat/test-flexible.R | 50 ++++++---- tests/testthat/test-linear-fda.R | 54 ++++++---- tests/testthat/test-linear-lda.R | 69 ++++++------- tests/testthat/test-linear-sda.R | 37 +++---- tests/testthat/test-linear-sparsediscrim.R | 134 ++++++++++++++------------- tests/testthat/test-naive-Bayes.R | 54 ++++------ tests/testthat/test-naive-Bayes_naivebayes.R | 66 ++++++------- tests/testthat/test-parameters.R | 4 tests/testthat/test-quad-qda.R | 43 +++----- tests/testthat/test-quad-sparsediscrim.R | 118 +++++++++++++---------- tests/testthat/test-rda.R | 54 ++++------ 29 files changed, 447 insertions(+), 429 deletions(-)
Title: Adherence to Medications
Description: Computation of adherence to medications from Electronic Health care
Data and visualization of individual medication histories and adherence
patterns. The package implements a set of S3 classes and
functions consistent with current adherence guidelines and definitions.
It allows the computation of different measures of
adherence (as defined in the literature, but also several original ones),
their publication-quality plotting,
the estimation of event duration and time to initiation,
the interactive exploration of patient medication history and
the real-time estimation of adherence given various parameter settings.
It scales from very small datasets stored in flat CSV files to very large
databases and from single-thread processing on mid-range consumer
laptops to parallel processing on large heterogeneous computing clusters.
It exposes a standardized interface allowing it to be used from other
programming languages and platforms, such as Python.
Author: Dan Dediu [aut, cre],
Alexandra Dima [aut],
Samuel Allemann [aut]
Maintainer: Dan Dediu <ddediu@gmail.com>
Diff between AdhereR versions 0.7.0 dated 2021-09-18 and 0.8.0 dated 2022-06-23
DESCRIPTION | 12 MD5 | 130 NAMESPACE | 159 R/adherer.R |19609 +++++------ R/call-adherer-external.R | 1273 R/matching_function.R | 4680 +- R/plotting.R | 2900 - R/polypharmacy.R | 1945 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 74 inst/doc/AdhereR-overview.R | 995 inst/doc/AdhereR-overview.Rmd | 2347 - inst/doc/AdhereR-overview.html | 5491 +-- inst/doc/adherer_with_databases.pdf.asis | 10 inst/doc/calling-AdhereR-from-python3.R | 10 inst/doc/calling-AdhereR-from-python3.Rmd | 2946 - inst/doc/calling-AdhereR-from-python3.html | 7106 ++- inst/html-templates/css-template.css | 66 inst/html-templates/html-template.html | 266 inst/html-templates/javascript-template.js | 2048 - inst/specialVignettes/adherer_with_databases.Rmd | 1900 - inst/specialVignettes/apa.csl | 1550 inst/specialVignettes/bibliography.bibtex | 28 inst/wrappers/python3/ReadMe.md |only inst/wrappers/python3/adherer.py | 7067 ++- inst/wrappers/python3/jupyter_notebook_python3_py2.ipynb |only inst/wrappers/python3/jupyter_notebook_python3_wrapper.ipynb |only man/CMA0.Rd | 477 man/CMA1.Rd | 612 man/CMA2.Rd | 604 man/CMA5.Rd | 595 man/CMA6.Rd | 595 man/CMA7.Rd | 603 man/CMA8.Rd | 623 man/CMA9.Rd | 607 man/CMA_per_episode.Rd | 712 man/CMA_polypharmacy.Rd | 5 man/CMA_sliding_window.Rd | 659 man/callAdhereR.Rd | 92 man/compute.event.int.gaps.Rd | 397 man/compute.treatment.episodes.Rd | 437 man/compute_event_durations.Rd | 522 man/cover_special_periods.Rd | 264 man/durcomp.dispensing.Rd | 78 man/durcomp.hospitalisation.Rd | 62 man/durcomp.prescribing.Rd | 90 man/get.event.plotting.area.Rd | 56 man/get.legend.plotting.area.Rd | 60 man/get.plotted.events.Rd | 154 man/get.plotted.partial.cmas.Rd | 84 man/getCMA.Rd | 118 man/getCallerWrapperLocation.Rd | 56 man/getEventsToEpisodesMapping.Rd |only man/getEventsToSlidingWindowsMapping.Rd |only man/getInnerEventInfo.Rd |only man/last.plot.get.info.Rd | 156 man/map.event.coords.to.plot.Rd | 164 man/med.events.Rd | 88 man/plot.CMA0.Rd | 629 man/plot.CMA1.Rd | 696 man/plot.CMA_per_episode.Rd | 1047 man/plot_interactive_cma.Rd | 78 man/print.CMA0.Rd | 244 man/prune_event_durations.Rd | 210 man/time_to_initiation.Rd | 194 vignettes/AdhereR-overview.Rmd | 2347 - vignettes/adherer_with_databases.pdf.asis | 10 vignettes/calling-AdhereR-from-python3.Rmd | 2946 - 69 files changed, 42694 insertions(+), 37289 deletions(-)
Title: Create Flexible Forest Plot
Description: Create forest plot based on the layout of the data. Confidence interval in multiple columns by groups can be done easily. Editing plot, inserting/adding text, applying theme to the plot and much more.
Author: Alimu Dayimu [aut, cre]
Maintainer: Alimu Dayimu <ad938@cam.ac.uk>
Diff between forestploter versions 0.1.5 dated 2022-05-07 and 0.1.6 dated 2022-06-23
DESCRIPTION | 8 MD5 | 41 ++--- NEWS.md | 81 +++++----- R/check_errors.r | 9 + R/forest.R | 38 ++++ R/helper.R | 10 - R/make-xaixs.R | 14 - R/theme.R | 19 ++ inst/doc/forestploter-intro.html | 14 - man/check_errors.Rd | 7 man/forest.Rd | 7 man/forest_theme.Rd | 15 + man/make_xaxis.Rd | 12 + tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/forest/edit-plot-with-theme.svg | 6 tests/testthat/_snaps/forest/multiple-columns-and-multi-parameters.svg | 8 tests/testthat/_snaps/forest/multiple-columns.svg | 20 +- tests/testthat/_snaps/forest/simple-forest-plot-with-theme.svg | 6 tests/testthat/_snaps/forest/simple-forest-plot.svg | 8 tests/testthat/_snaps/forest/summary-ci.svg |only tests/testthat/test-forest.R | 52 ++++++ tests/testthat/test-theme.R | 4 22 files changed, 265 insertions(+), 114 deletions(-)
Title: Analyse Citation Data from Google Scholar
Description: Provides functions to extract citation data from Google
Scholar. Convenience functions are also provided for comparing
multiple scholars and predicting future h-index values.
Author: Guangchuang Yu [aut, cre] ,
James Keirstead [aut],
Gregory Jefferis [aut] ,
Gordon Getzinger [ctb],
Jorge Cimentada [ctb],
Max Czapanskiy [ctb],
Dominique Makowski [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between scholar versions 0.2.2 dated 2021-07-13 and 0.2.3 dated 2022-06-23
scholar-0.2.2/scholar/man/get_impactfactor.Rd |only scholar-0.2.3/scholar/DESCRIPTION | 26 +-- scholar-0.2.3/scholar/MD5 | 45 ++--- scholar-0.2.3/scholar/NAMESPACE | 3 scholar-0.2.3/scholar/NEWS.md | 9 + scholar-0.2.3/scholar/R/data.R | 12 - scholar-0.2.3/scholar/R/format_publications.R |only scholar-0.2.3/scholar/R/getCompleteAuthors.R | 2 scholar-0.2.3/scholar/R/predict.r | 3 scholar-0.2.3/scholar/R/publications.r | 69 ++++---- scholar-0.2.3/scholar/R/scholar-package.r | 4 scholar-0.2.3/scholar/R/scholar.r | 68 +++++--- scholar-0.2.3/scholar/R/sysdata.rda |binary scholar-0.2.3/scholar/build/partial.rdb |binary scholar-0.2.3/scholar/build/vignette.rds |binary scholar-0.2.3/scholar/inst/WORDLIST |only scholar-0.2.3/scholar/inst/doc/scholar.html | 167 ++++++++++++-------- scholar-0.2.3/scholar/man/format_authors.Rd | 2 scholar-0.2.3/scholar/man/format_publications.Rd |only scholar-0.2.3/scholar/man/get_journalrank.Rd | 2 scholar-0.2.3/scholar/man/get_profile.Rd | 20 +- scholar-0.2.3/scholar/man/get_publications.Rd | 6 scholar-0.2.3/scholar/man/predict_h_index.Rd | 3 scholar-0.2.3/scholar/man/scholar-package.Rd | 6 scholar-0.2.3/scholar/tests/spelling.R |only scholar-0.2.3/scholar/tests/testthat/test-scholar.R | 2 26 files changed, 273 insertions(+), 176 deletions(-)
Title: GORpipe Tool for R
Description: R library for executing GOR queries using local GORpipe.
Author: Genuity Science [cph],
Andri Stefansson [aut, cre],
Edvald Gislason [ctb]
Maintainer: Andri Stefansson <andri@genuitysci.com>
Diff between gorpiper versions 1.0.0 dated 2022-05-09 and 1.0.1 dated 2022-06-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/package.R | 27 ++++++++++----------------- man/gorpiper.Rd | 23 ++++++++--------------- 5 files changed, 30 insertions(+), 40 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-02 0.2
2013-09-17 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-18 0.1.5
2012-06-14 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-24 1.1.0
2011-09-02 1.0.8
2010-08-11 1.0.6
2005-06-22 1.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-05-23 0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-18 0.4.2
2017-04-20 0.2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-25 1.0
Title: Non-Trivial Balance of Centrifuge Rotors
Description: Find the numbers of test tubes that can be balanced in centrifuge
rotors and show various ways to load them. Refer to Pham (2020)
<doi:10.31224/osf.io/4xs38> for more information on package functionality.
Author: Duy Nghia Pham [aut, cre]
Maintainer: Duy Nghia Pham <nghiapham@yandex.com>
Diff between centrifugeR versions 0.1.5 dated 2020-09-23 and 0.1.6 dated 2022-06-23
DESCRIPTION | 20 +++++++++----------- MD5 | 30 +++++++++++++++++++----------- NAMESPACE | 15 +++++++++++++++ R/centrifugeR-package.R | 43 +++++++++++++++++++++---------------------- R/p2c.R |only R/pie2.R |only R/rotor.R |only R/rotorCheck.R | 7 ++----- R/rotorEqual.R | 7 ++----- R/rotorVerify.R | 28 ++-------------------------- R/zzz.R | 6 ++++-- build |only inst/CITATION | 2 +- man/centrifugeR-package.Rd | 37 +++++++++++++++++-------------------- man/figures |only man/p2c.Rd |only man/pie2.Rd |only man/rotor.Rd |only man/rotorCheck.Rd | 5 ----- man/rotorEqual.Rd | 5 ----- 20 files changed, 92 insertions(+), 113 deletions(-)
Title: Computes Value at Risk and Expected Shortfall for over 100
Parametric Distributions
Description: Computes Value at risk and expected shortfall, two most popular measures of financial risk, for over one hundred parametric distributions, including all commonly known distributions. Also computed are the corresponding probability density function and cumulative distribution function.
Author: Saralees Nadarajah, Stephen Chan and Emmanuel Afuecheta
Maintainer: Saralees Nadarajah <Saralees.Nadarajah@manchester.ac.uk>
Diff between VaRES versions 1.0 dated 2013-08-27 and 1.0.1 dated 2022-06-23
DESCRIPTION | 11 +++++------ MD5 | 4 ++-- NAMESPACE | 7 +++++++ 3 files changed, 14 insertions(+), 8 deletions(-)
Title: Rock Fabric and Strain Analysis Tools
Description: Provides functions to complete three-dimensional rock fabric and strain analyses following the Rf Phi, Fry, and normalized Fry methods. Also allows for plotting of results and interactive 3D visualization functionality.
Author: Jeffrey R. Webber
Maintainer: Jeffrey R. Webber <jwebber@geo.umass.edu>
Diff between RockFab versions 1.2 dated 2014-01-14 and 1.2.1 dated 2022-06-23
RockFab-1.2.1/RockFab/DESCRIPTION | 8 ++++---- RockFab-1.2.1/RockFab/MD5 | 5 ++--- RockFab-1.2.1/RockFab/NAMESPACE | 6 ++++++ RockFab-1.2/RockFab/R/RockFab-internal.R |only 4 files changed, 12 insertions(+), 7 deletions(-)
Title: Positive Definite Sparse Covariance Estimators
Description: Compute and tune some positive definite and sparse covariance
estimators.
Author: Adam J. Rothman
Maintainer: Adam J. Rothman <arothman@umn.edu>
Diff between PDSCE versions 1.2 dated 2013-06-13 and 1.2.1 dated 2022-06-23
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NAMESPACE | 2 ++ 3 files changed, 10 insertions(+), 8 deletions(-)
Title: Order-Restricted Information Criterion-Based Clustering
Algorithm
Description: A user-friendly R-based software package for
gene clustering. Clusters are given by genes matched to
prespecified profiles across various ordered treatment groups.
It is particularly useful for analyzing data obtained from
short time-course or dose-response microarray experiments.
Author: Tianqing Liu, Nan Lin, Ningzhong Shi and Baoxue Zhang
Maintainer: Tianqing Liu <tianqingliu@gmail.com>
Diff between ORIClust versions 1.0-1 dated 2009-11-09 and 1.0-2 dated 2022-06-23
DESCRIPTION | 12 +++++++----- MD5 |only NAMESPACE |only data/Breast.rda |binary 4 files changed, 7 insertions(+), 5 deletions(-)
Title: Nozzle Reports
Description: The Nozzle package provides an API to generate HTML
reports with dynamic user interface elements based on
JavaScript and CSS (Cascading Style Sheets). Nozzle was
designed to facilitate summarization and rapid browsing of
complex results in data analysis pipelines where multiple
analyses are performed frequently on big data sets. The package
can be applied to any project where user-friendly reports need
to be created.
Author: Nils Gehlenborg <nils@hms.harvard.edu>
Maintainer: Nils Gehlenborg <nils@hms.harvard.edu>
Diff between Nozzle.R1 versions 1.1-1 dated 2013-05-15 and 1.1-1.1 dated 2022-06-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NAMESPACE | 2 ++ 3 files changed, 7 insertions(+), 5 deletions(-)
Title: Non-Negative Matrix Factorization
Description: Non-negative Matrix Factorization.
Author: Suhai Liu
Maintainer: Suhai (Timothy) Liu <tim.liu@alumni.duke.edu>
Diff between NMFN versions 2.0 dated 2011-01-05 and 2.0.1 dated 2022-06-23
DESCRIPTION | 11 ++++++----- MD5 |only NAMESPACE |only man/NMFN-package.Rd | 5 ++++- 4 files changed, 10 insertions(+), 6 deletions(-)
Title: Generalised Odds Ratios
Description: Calculates Agresti's generalized odds ratios.
For a randomly selected pair of observations
from two groups, calculates the odds that
the second group will have a higher scoring outcome
than that of the first group.
Package provides hypothesis testing for if this odds
ratio is significantly different to 1 (equal chance).
Author: Hannah Johns [aut, cre]
Maintainer: Hannah Johns <htjohns@gmail.com>
Diff between genodds versions 1.1.0 dated 2021-11-20 and 1.1.2 dated 2022-06-23
DESCRIPTION | 16 - MD5 | 24 +- NAMESPACE | 14 - NEWS.md | 7 R/data.R | 44 +-- R/genodds.R | 172 ++++++++++++--- R/genodds.power.R | 478 +++++++++++++++++++++--------------------- README.md | 83 +++---- man/alteplase.Rd | 64 ++--- man/genodds.Rd | 295 ++++++++++++++----------- man/genodds.power.Rd | 156 ++++++------- tests/testthat.R | 8 tests/testthat/test-genodds.R | 378 ++++++++++++++++----------------- 13 files changed, 948 insertions(+), 791 deletions(-)
Title: An Interface to the Dash Ecosystem for Authoring Reactive Web
Applications
Description: A framework for building analytical web applications, Dash offers a pleasant and productive development experience. No JavaScript required.
Author: Chris Parmer [aut],
Ryan Patrick Kyle [aut] ,
Carson Sievert [aut] ,
Hammad Khan [aut, cre] ,
Plotly Technologies [cph]
Maintainer: Hammad Khan <hammadkhan@plotly.com>
Diff between dash versions 0.9.3 dated 2021-11-07 and 0.9.4 dated 2022-06-23
DESCRIPTION | 6 MD5 | 10 - R/dash.R | 2 man/dash-package.Rd | 1 tests/manual/package_namespace.R |only tests/testthat/test-attributes.R | 257 +++++++++++++++++++++++++++++++++++++++ tests/testthat/test-routes.R |only 7 files changed, 267 insertions(+), 9 deletions(-)
Title: Efficient Branch and Bound Variable Selection for GLMs using
'RcppArmadillo'
Description: Performs efficient and scalable glm best
subset selection using a novel implementation of a branch and bound algorithm.
To speed up the model fitting process, a range of optimization
methods are implemented in 'RcppArmadillo'. Parallel computation
is available using 'OpenMP'.
Author: Jacob Seedorff [aut, cre]
Maintainer: Jacob Seedorff <jwseedorff@uiowa.edu>
Diff between BranchGLM versions 1.1.1 dated 2022-06-13 and 1.1.2 dated 2022-06-23
DESCRIPTION | 8 +- MD5 | 14 ++-- R/BranchGLM.R | 32 +++++------ R/VariableSelection.R | 10 +++ inst/doc/BranchGLM-Vignette.html | 110 +++++++++++++++++++-------------------- src/BranchGLMHelpers.cpp | 99 +++++++++++++++-------------------- src/CrossProducts.cpp |only src/CrossProducts.h |only src/ParBranchGLMHelpers.cpp | 25 ++------ 9 files changed, 142 insertions(+), 156 deletions(-)