Title: Utilities for Working with Air Quality Monitoring Data
Description: Utilities for working with air quality monitoring data
with a focus on small particulates (PM2.5) generated by wildfire
smoke. Functions are provided for downloading available data from
the United States 'EPA' <https://www.epa.gov/outdoor-air-quality-data> and
it's 'AirNow' air quality site <https://www.airnow.gov>.
Additional sources of PM2.5 data made accessible by the package include:
'AIRSIS' (password protected) <https://www.oceaneering.com/data-management/>
and 'WRCC' <https://wrcc.dri.edu/cgi-bin/smoke.pl>.
Data compilations are provided by 'PWFSL'
<https://www.fs.fed.us/pnw/pwfsl/>.
Author: Jonathan Callahan [aut, cre],
Rohan Aras [aut],
Zach Dingels [aut],
Jon Hagg [aut],
Jimin Kim [aut],
Hans Martin [aut],
Helen Miller [aut],
Spencer Pease [aut],
Rex Thompson [aut],
Alice Yang [aut]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between PWFSLSmoke versions 1.2.4 dated 2019-05-01 and 1.2.100 dated 2019-07-18
PWFSLSmoke-1.2.100/PWFSLSmoke/DESCRIPTION | 16 - PWFSLSmoke-1.2.100/PWFSLSmoke/MD5 | 98 +++++----- PWFSLSmoke-1.2.100/PWFSLSmoke/NAMESPACE | 9 PWFSLSmoke-1.2.100/PWFSLSmoke/R/PWFSLSmoke-deprecated.R | 60 ++++-- PWFSLSmoke-1.2.100/PWFSLSmoke/R/PWFSLSmoke.R | 5 PWFSLSmoke-1.2.100/PWFSLSmoke/R/airnow_createDataDataframes.R | 63 ++++-- PWFSLSmoke-1.2.100/PWFSLSmoke/R/airnow_createMetaDataframes.R | 7 PWFSLSmoke-1.2.100/PWFSLSmoke/R/airnow_createMonitorObjects.R | 4 PWFSLSmoke-1.2.100/PWFSLSmoke/R/airnow_downloadHourlyData.R | 53 +++-- PWFSLSmoke-1.2.100/PWFSLSmoke/R/airnow_downloadParseData.R | 4 PWFSLSmoke-1.2.100/PWFSLSmoke/R/monitor_getCurrentStatus.R | 43 +--- PWFSLSmoke-1.2.100/PWFSLSmoke/R/monitor_stamenmap.R | 2 PWFSLSmoke-1.2.100/PWFSLSmoke/R/monitor_staticmap.R |only PWFSLSmoke-1.2.100/PWFSLSmoke/R/staticmap_getEsrimapBrick.R |only PWFSLSmoke-1.2.100/PWFSLSmoke/R/staticmap_getRasterBrick.R |only PWFSLSmoke-1.2.100/PWFSLSmoke/R/staticmap_getStamenmapBrick.R | 44 +--- PWFSLSmoke-1.2.100/PWFSLSmoke/R/timeInfo.R | 31 +-- PWFSLSmoke-1.2.100/PWFSLSmoke/R/wrcc_EBAMQualityControl.R | 2 PWFSLSmoke-1.2.100/PWFSLSmoke/R/wrcc_createMonitorObject.R | 22 +- PWFSLSmoke-1.2.100/PWFSLSmoke/R/wrcc_createRawDataframe.R | 10 - PWFSLSmoke-1.2.100/PWFSLSmoke/R/wrcc_downloadData.R | 24 -- PWFSLSmoke-1.2.100/PWFSLSmoke/R/wrcc_identifyMonitorType.R | 66 ++++++ PWFSLSmoke-1.2.100/PWFSLSmoke/R/wrcc_parseData.R | 4 PWFSLSmoke-1.2.100/PWFSLSmoke/R/wrcc_qualityControl.R | 2 PWFSLSmoke-1.2.100/PWFSLSmoke/data/WRCC.RData |binary PWFSLSmoke-1.2.100/PWFSLSmoke/inst/doc/Data_Model.html | 7 PWFSLSmoke-1.2.100/PWFSLSmoke/inst/doc/Maps_and_Timeseries_Plots.R | 25 ++ PWFSLSmoke-1.2.100/PWFSLSmoke/inst/doc/Maps_and_Timeseries_Plots.Rmd | 52 ++++- PWFSLSmoke-1.2.100/PWFSLSmoke/inst/doc/Maps_and_Timeseries_Plots.html | 60 +++--- PWFSLSmoke-1.2.100/PWFSLSmoke/inst/doc/NowCast.html | 7 PWFSLSmoke-1.2.100/PWFSLSmoke/inst/doc/PWFSLSmoke.Rmd | 2 PWFSLSmoke-1.2.100/PWFSLSmoke/inst/doc/PWFSLSmoke.html | 17 + PWFSLSmoke-1.2.100/PWFSLSmoke/man/PWFSLSmoke-deprecated.Rd | 14 + PWFSLSmoke-1.2.100/PWFSLSmoke/man/WRCC.Rd | 5 PWFSLSmoke-1.2.100/PWFSLSmoke/man/airnow_createDataDataframes.Rd | 28 +- PWFSLSmoke-1.2.100/PWFSLSmoke/man/airnow_createMonitorObjects.Rd | 2 PWFSLSmoke-1.2.100/PWFSLSmoke/man/airnow_downloadHourlyData.Rd | 21 +- PWFSLSmoke-1.2.100/PWFSLSmoke/man/monitor_getCurrentStatus.Rd | 43 +--- PWFSLSmoke-1.2.100/PWFSLSmoke/man/monitor_staticmap.Rd |only PWFSLSmoke-1.2.100/PWFSLSmoke/man/staticmap_getEsrimapBrick.Rd |only PWFSLSmoke-1.2.100/PWFSLSmoke/man/staticmap_getRasterBrick.Rd |only PWFSLSmoke-1.2.100/PWFSLSmoke/man/staticmap_getStamenmapBrick.Rd | 21 +- PWFSLSmoke-1.2.100/PWFSLSmoke/man/timeInfo.Rd | 5 PWFSLSmoke-1.2.100/PWFSLSmoke/man/wrcc_createRawDataframe.Rd | 6 PWFSLSmoke-1.2.100/PWFSLSmoke/man/wrcc_downloadData.Rd | 4 PWFSLSmoke-1.2.100/PWFSLSmoke/man/wrcc_identifyMonitorType.Rd | 2 PWFSLSmoke-1.2.100/PWFSLSmoke/man/wrcc_parseData.Rd | 2 PWFSLSmoke-1.2.100/PWFSLSmoke/tests/testthat/test-timeinfo.R | 22 ++ PWFSLSmoke-1.2.100/PWFSLSmoke/vignettes/Maps_and_Timeseries_Plots.Rmd | 52 ++++- PWFSLSmoke-1.2.100/PWFSLSmoke/vignettes/PWFSLSmoke.Rmd | 2 PWFSLSmoke-1.2.4/PWFSLSmoke/R/esriMap_getMap.R |only PWFSLSmoke-1.2.4/PWFSLSmoke/R/esriMap_plotOnStaticMap.R |only PWFSLSmoke-1.2.4/PWFSLSmoke/R/monitor_esriMap.R |only PWFSLSmoke-1.2.4/PWFSLSmoke/man/esriMap_getMap.Rd |only PWFSLSmoke-1.2.4/PWFSLSmoke/man/esriMap_plotOnStaticMap.Rd |only PWFSLSmoke-1.2.4/PWFSLSmoke/man/monitor_esriMap.Rd |only 56 files changed, 604 insertions(+), 364 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut],
Gur Yaari [aut],
Namita Gupta [aut],
Jason Vander Heiden [aut, cre],
Ang Cui [ctb],
Susanna Marquez [ctb],
Julian Zhou [ctb],
Nima Nouri [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between shazam versions 0.1.11 dated 2019-01-28 and 0.2.0 dated 2019-07-18
DESCRIPTION | 14 - MD5 | 45 ++-- NAMESPACE | 21 - NEWS.md | 31 ++ R/Baseline.R | 8 R/Core.R | 3 R/DistToNearest.R | 352 +++++++++++++++++++++++-------- R/MutationProfiling.R | 403 ++++++++++++++++++------------------ R/Shazam.R | 26 +- R/Shmulate.R | 48 +++- R/TargetingModels.R | 280 +++++++++++++------------ build/vignette.rds |binary inst/doc/Baseline-Vignette.pdf |binary inst/doc/DistToNearest-Vignette.pdf |binary inst/doc/Mutation-Vignette.pdf |binary inst/doc/Shmulate-Vignette.pdf |binary inst/doc/Targeting-Vignette.pdf |binary man/calcBaseline.Rd | 2 man/consensusSequence.Rd |only man/distToNearest.Rd | 116 +++++++--- man/groupBaseline.Rd | 4 man/shazam.Rd | 3 man/shmulateSeq.Rd | 9 man/shmulateTree.Rd | 9 24 files changed, 844 insertions(+), 530 deletions(-)
Title: Tidyverse-Friendly Introductory Linear Regression
Description: Datasets and wrapper functions for tidyverse-friendly introductory linear regression, used in ModernDive: An Introduction to Statistical and Data Sciences via R available at <http://moderndive.com/> and DataCamp's Modeling with Data in the Tidyverse available at <https://www.datacamp.com/courses/modeling-with-data-in-the-tidyverse>.
Author: Albert Y. Kim [cre],
Chester Ismay [aut],
Andrew Bray [ctb],
Delaney Moran [ctb]
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>
Diff between moderndive versions 0.2.0 dated 2018-07-06 and 0.3.0 dated 2019-07-18
moderndive-0.2.0/moderndive/R/bowl_samples.R |only moderndive-0.2.0/moderndive/R/evals.R |only moderndive-0.2.0/moderndive/R/house_prices.R |only moderndive-0.2.0/moderndive/R/mythbusters_yawn.R |only moderndive-0.2.0/moderndive/R/pennies_sample.R |only moderndive-0.2.0/moderndive/R/tactile_prop_red.R |only moderndive-0.3.0/moderndive/DESCRIPTION | 23 moderndive-0.3.0/moderndive/MD5 | 74 ++- moderndive-0.3.0/moderndive/NAMESPACE | 5 moderndive-0.3.0/moderndive/NEWS.md | 34 + moderndive-0.3.0/moderndive/R/bowl.R | 76 +++ moderndive-0.3.0/moderndive/R/datasets.R |only moderndive-0.3.0/moderndive/R/ggplot_parallel_slopes.R |only moderndive-0.3.0/moderndive/R/moderndive.R | 2 moderndive-0.3.0/moderndive/R/pennies.R | 86 +++ moderndive-0.3.0/moderndive/R/regression_functions.R | 233 ++++++---- moderndive-0.3.0/moderndive/build |only moderndive-0.3.0/moderndive/data/DD_vs_SB.rda |only moderndive-0.3.0/moderndive/data/MA_schools.rda |only moderndive-0.3.0/moderndive/data/bowl_sample_1.rda |only moderndive-0.3.0/moderndive/data/evals.rda |binary moderndive-0.3.0/moderndive/data/house_prices.rda |binary moderndive-0.3.0/moderndive/data/movies_sample.rda |only moderndive-0.3.0/moderndive/data/orig_pennies_sample.rda |only moderndive-0.3.0/moderndive/data/pennies_resamples.rda |only moderndive-0.3.0/moderndive/data/pennies_sample.rda |binary moderndive-0.3.0/moderndive/data/promotions.rda |only moderndive-0.3.0/moderndive/data/promotions_shuffled.rda |only moderndive-0.3.0/moderndive/inst |only moderndive-0.3.0/moderndive/man/DD_vs_SB.Rd |only moderndive-0.3.0/moderndive/man/MA_schools.Rd |only moderndive-0.3.0/moderndive/man/bowl_sample_1.Rd |only moderndive-0.3.0/moderndive/man/bowl_samples.Rd | 7 moderndive-0.3.0/moderndive/man/evals.Rd | 13 moderndive-0.3.0/moderndive/man/get_regression_points.Rd | 23 moderndive-0.3.0/moderndive/man/gg_parallel_slopes.Rd |only moderndive-0.3.0/moderndive/man/house_prices.Rd | 2 moderndive-0.3.0/moderndive/man/moderndive.Rd | 2 moderndive-0.3.0/moderndive/man/movies_sample.Rd |only moderndive-0.3.0/moderndive/man/mythbusters_yawn.Rd | 2 moderndive-0.3.0/moderndive/man/orig_pennies_sample.Rd |only moderndive-0.3.0/moderndive/man/pennies_resamples.Rd |only moderndive-0.3.0/moderndive/man/pennies_sample.Rd | 43 - moderndive-0.3.0/moderndive/man/promotions.Rd |only moderndive-0.3.0/moderndive/man/promotions_shuffled.Rd |only moderndive-0.3.0/moderndive/man/tactile_prop_red.Rd | 5 moderndive-0.3.0/moderndive/tests/testthat/test-get_regression_functions.R | 112 ++-- moderndive-0.3.0/moderndive/tests/testthat/test_gg_parallel_slopes.R |only moderndive-0.3.0/moderndive/vignettes |only 49 files changed, 529 insertions(+), 213 deletions(-)
Title: Clustering with Matrix Gaussian and Matrix Transformation
Mixture Models
Description: Provides matrix Gaussian mixture models, matrix transformation mixture models and their model-based clustering results. The parsimonious models of the mean matrices and variance covariance matrices are implemented with a total of 196 variations.
Author: Xuwen Zhu [aut, cre],
Volodymyr Melnykov [aut],
Shuchismita Sarkar [ctb],
Michael Hutt [ctb, cph],
Stephen Moshier [ctb, cph],
Rouben Rostamian [ctb, cph],
Carl Edward Rasmussen [ctb, cph],
Dianne Cook [ctb, cph]
Maintainer: Xuwen Zhu <xuwen.zhu@louisville.edu>
Diff between MatTransMix versions 0.1.4 dated 2019-07-18 and 0.1.5 dated 2019-07-18
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 4 ++++ R/libMatTransFull.R | 2 +- src/libFull.c | 7 +++++-- 5 files changed, 17 insertions(+), 10 deletions(-)
Title: Set Operations for Many Sets
Description: Set operations for many sets. The base functions for set operations
in R can be used for only two sets. This package uses 'purr' to find the
union, intersection and difference of three or more sets. This package also
provides functions for pairwise set operations among several sets. Further,
based on 'ggplot2' and 'ggforce', a Venn diagram can be drawn for two or
three sets. For bigger data sets, a clustered heatmap showing presence/absence
of the elements of the sets can be drawn based on the 'pheatmap' package.
Finally, enrichment test can be applied to two sets whether an overlap is
statistically significant or not.
Author: Turgut Yigit Akyol [aut, cre]
Maintainer: Turgut Yigit Akyol <tyakyol@gmail.com>
Diff between RVenn versions 1.0.0 dated 2019-05-08 and 1.1.0 dated 2019-07-18
RVenn-1.0.0/RVenn/R/package-RVenn.R |only RVenn-1.0.0/RVenn/man/construct.Rd |only RVenn-1.1.0/RVenn/DESCRIPTION | 28 +- RVenn-1.1.0/RVenn/MD5 | 48 ++-- RVenn-1.1.0/RVenn/NAMESPACE | 7 RVenn-1.1.0/RVenn/R/Construct.R | 33 --- RVenn-1.1.0/RVenn/R/Heatmap.R |only RVenn-1.1.0/RVenn/R/Pairs.R |only RVenn-1.1.0/RVenn/R/RVenn.R |only RVenn-1.1.0/RVenn/R/SetOperations.R | 2 RVenn-1.1.0/RVenn/inst/doc/vignette.R | 20 + RVenn-1.1.0/RVenn/inst/doc/vignette.Rmd | 61 +++++ RVenn-1.1.0/RVenn/inst/doc/vignette.html | 187 +++++++++++++----- RVenn-1.1.0/RVenn/man/RVenn.Rd | 16 + RVenn-1.1.0/RVenn/man/Venn.Rd |only RVenn-1.1.0/RVenn/man/discern.Rd | 18 + RVenn-1.1.0/RVenn/man/discern_pairs.Rd |only RVenn-1.1.0/RVenn/man/enrichment_test.Rd | 29 +- RVenn-1.1.0/RVenn/man/ggvenn.Rd | 16 - RVenn-1.1.0/RVenn/man/overlap.Rd | 10 RVenn-1.1.0/RVenn/man/overlap_pairs.Rd |only RVenn-1.1.0/RVenn/man/setmap.Rd |only RVenn-1.1.0/RVenn/man/unite.Rd | 10 RVenn-1.1.0/RVenn/man/unite_pairs.Rd |only RVenn-1.1.0/RVenn/tests/testthat/test_construct.R | 18 - RVenn-1.1.0/RVenn/tests/testthat/test_enrichment.R | 8 RVenn-1.1.0/RVenn/tests/testthat/test_ggvenn.R | 10 RVenn-1.1.0/RVenn/tests/testthat/test_pairs.R |only RVenn-1.1.0/RVenn/tests/testthat/test_setmap.R |only RVenn-1.1.0/RVenn/tests/testthat/test_setoperations.R | 24 +- RVenn-1.1.0/RVenn/vignettes/vignette.Rmd | 61 +++++ 31 files changed, 412 insertions(+), 194 deletions(-)
Title: Trace Plots, Density Plots and Chain Comparisons for MCMC
Samples
Description: Provides a function for examining posterior MCMC samples
from a single chain using trace plots and density plots, and from
multiple chains by comparing posterior medians and credible intervals
from each chain. These plotting functions have a variety of options,
such as figure sizes, legends, parameters to plot, and saving plots to file.
Functions interface with the NIMBLE software package, see
de Valpine, Turek, Paciorek, Anderson-Bergman, Temple Lang and Bodik (2017)
<doi:10.1080/10618600.2016.1172487>.
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between basicMCMCplots versions 0.2.1 dated 2019-07-07 and 0.2.2 dated 2019-07-18
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/plots.R | 7 +++++-- man/chainsPlot.Rd | 6 ++++-- 4 files changed, 15 insertions(+), 10 deletions(-)
More information about basicMCMCplots at CRAN
Permanent link
Title: Produce Charts that you See on the Fingertips Website
Description: Use Fingertips charts to recreate the visualisations
that are displayed on the Fingertips website (<http://fingertips.phe.org.uk/>).
Author: Sebastian Fox [aut, cre]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>
Diff between fingertipscharts versions 0.0.6 dated 2019-05-13 and 0.0.8 dated 2019-07-18
DESCRIPTION | 6 MD5 | 78 +- NEWS.md | 8 R/theme.R | 98 -- build/vignette.rds |binary inst/doc/quick_charts.R | 2 inst/doc/quick_charts.Rmd | 2 inst/doc/quick_charts.html | 28 tests/figs/area-profiles-example/area-profiles-example.svg | 216 ++--- tests/figs/area-profiles/differing-dps-area-profiles.svg | 192 ++--- tests/figs/area-profiles/domains-included-area-profiles.svg | 256 +++--- tests/figs/area-profiles/full-area-all-dividers-profiles.svg | 192 ++--- tests/figs/area-profiles/full-area-profiles.svg | 192 ++--- tests/figs/area-profiles/full-with-factor-area-profiles.svg | 172 ++-- tests/figs/area-profiles/no-dt-area-profiles.svg | 92 +- tests/figs/box-plots-example/box-plot-example.svg | 302 ++++---- tests/figs/box-plots/box-plots.svg | 146 +-- tests/figs/compare-areas/asc-compare-areas.svg | 198 ++--- tests/figs/compare-areas/desc-compare-areas.svg | 198 ++--- tests/figs/compare-areas/desc-no-fill-compare-areas-displaying-values.svg | 194 ++--- tests/figs/compare-areas/desc-no-fill-compare-areas.svg | 170 ++-- tests/figs/compare-areas/no-top-areas-asc-compare-areas.svg | 198 ++--- tests/figs/compare-areas/no-top-areas-desc-compare-areas.svg | 198 ++--- tests/figs/compare-indicators-example/compare-indicators-example.svg | 336 ++++----- tests/figs/compare-indicators/compare-indicators-high-r2.svg | 262 +++---- tests/figs/compare-indicators/compare-indicators-highlight.svg | 260 +++---- tests/figs/compare-indicators/compare-indicators-no-highlight.svg | 260 +++---- tests/figs/map-example/map-example.svg | 366 +++++----- tests/figs/map/map-p1.svg | 366 +++++----- tests/figs/map/map.svg | 366 +++++----- tests/figs/overview/overview-no-top-areas.svg | 358 ++++----- tests/figs/overview/overview-top-areas.svg | 358 ++++----- tests/figs/population-example/population-example.svg | 170 ++-- tests/figs/population/full-pop-pyramid.svg | 162 ++-- tests/figs/population/no-comparator-pop-pyramid.svg | 154 ++-- tests/figs/population/one-comparator-pop-pyramid.svg | 158 ++-- tests/figs/trends-example/trends-example.svg | 186 ++--- tests/figs/trends/with-fill-trends.svg | 138 +-- tests/figs/trends/without-fill-trends.svg | 138 +-- vignettes/quick_charts.Rmd | 2 40 files changed, 3576 insertions(+), 3602 deletions(-)
More information about fingertipscharts at CRAN
Permanent link
Title: Efficient Jonckheere-Terpstra Test Statistics for Robust Machine
Learning and Genome-Wide Association Studies
Description: This 'Rcpp'-based package implements highly efficient functions for the calculation of the Jonckheere-Terpstra statistic. It can be used for a variety of applications, including feature selection in machine learning problems, or to conduct genome-wide association studies (GWAS) with multiple quantitative phenotypes. The code leverages 'OpenMP' directives for multi-core computing to reduce overall processing time.
Author: Jiaxing Lin, Alexander Sibley, Ivo Shterev, and Kouros Owzar
Maintainer: Jiaxing Lin <jiaxing.lin@duke.edu>
Diff between fastJT versions 1.0.4 dated 2017-08-14 and 1.0.5 dated 2019-07-18
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NEWS | 5 +++++ build/vignette.rds |binary inst/CITATION |only inst/doc/fastJT.Rnw | 2 +- inst/doc/fastJT.pdf |binary man/fastJT-package.Rd | 4 ++-- vignettes/fastJT.Rnw | 2 +- 9 files changed, 21 insertions(+), 15 deletions(-)
Title: Import, Manipulate and Explore the Results of an 'Antares'
Simulation
Description: Import, manipulate and explore results generated by 'Antares', a
powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems
(more information about 'Antares' here : <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). You can see the results of several ANTARES studies here : <http://bpnumerique.rte-france.com/>.
Author: Veronique Bachelier [aut, cre],
Jalal-Edine ZAWAM [aut],
Frederic Breant [aut],
Victor Perrier [aut],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
RTE [cph]
Maintainer: Veronique Bachelier <veronique.bachelier@rte-france.com>
Diff between antaresRead versions 2.2.3 dated 2019-02-13 and 2.2.4 dated 2019-07-18
DESCRIPTION | 18 MD5 | 23 NEWS | 5 R/importInput.R | 29 R/setSimulationPath.R | 2 build/vignette.rds |binary inst/doc/antares.html | 377 +++ inst/doc/antaresH5.html | 2669 +++++++++++++++++++++++++++- inst/testdata/antares-test-study-v7.tar.gz |only tests/testthat/helper_init.R | 234 +- tests/testthat/test-RemoveInputColumn.R | 7 tests/testthat/test-readAntares_districts.R | 5 tests/testthat/test-setup.R | 2 13 files changed, 3067 insertions(+), 304 deletions(-)
Title: Edit an 'Antares' Simulation
Description: Edit an 'Antares' simulation before running it : create new areas, links, thermal
clusters or binding constraints or edit existing ones. Update 'Antares' general & optimization settings.
'Antares' is an open source power system generator, more information available here : <https://antares-simulator.org/>.
Author: Veronique Bachelier [aut, cre],
Frederic Breant [aut],
Victor Perrier [aut],
Baptiste Seguinot [ctb],
Benoit Thieurmel [ctb],
Titouan Robert [ctb],
Jalal-Edine Zawam [ctb],
Etienne Sanchez [ctb],
RTE [cph]
Maintainer: Veronique Bachelier <veronique.bachelier@rte-france.com>
Diff between antaresEditObject versions 0.1.6 dated 2019-05-13 and 0.1.7 dated 2019-07-18
DESCRIPTION | 14 +- MD5 | 12 +- NEWS.md | 6 + R/createBindingConstraint.R | 12 +- R/createLink.R | 18 ++- R/createPSP.R | 207 ++++++++++++++++++++++++++++++++++---------- man/createLink.Rd | 18 ++- 7 files changed, 205 insertions(+), 82 deletions(-)
More information about antaresEditObject at CRAN
Permanent link
Title: Mass Spectrometry Tools
Description: Common mass spectrometry tools described in John Roboz (2013) <doi:10.1201/b15436>. It allows checking element
isotopes, calculating (isotope labelled) exact monoisitopic mass, m/z values and mass accuracy, and inspecting possible contaminant mass peaks,
examining possible adducts in electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI)
ion sources.
Author: Yonghui Dong
Maintainer: Yonghui Dong <yonghui.dong@gmail.com>
Diff between MSbox versions 1.2.0 dated 2019-02-24 and 1.2.1 dated 2019-07-18
MSbox-1.2.0/MSbox/R/get_formula.R |only MSbox-1.2.0/MSbox/man/formula.Rd |only MSbox-1.2.1/MSbox/DESCRIPTION | 10 +++++----- MSbox-1.2.1/MSbox/MD5 | 14 +++++++------- MSbox-1.2.1/MSbox/NAMESPACE | 2 +- MSbox-1.2.1/MSbox/R/describe.R |only MSbox-1.2.1/MSbox/R/sysdata.rda |binary MSbox-1.2.1/MSbox/R/what.R | 30 ++++++++++++++++++------------ MSbox-1.2.1/MSbox/README.md | 34 +++++++++++++++++++++++++++------- MSbox-1.2.1/MSbox/man/describe.Rd |only 10 files changed, 58 insertions(+), 32 deletions(-)
Title: Generalized Mortality Estimator
Description: Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Author: Daniel Dalthorp [aut, cre],
Juniper Simonis [aut],
Lisa Madsen [aut],
Manuela Huso [aut],
Paul Rabie [aut],
Jeffrey Mintz [aut],
Robert Wolpert [aut],
Jared Studyvin [aut],
Franzi Korner-Nievergelt [aut]
Maintainer: Daniel Dalthorp <ddalthorp@usgs.gov>
Diff between GenEst versions 1.2.4 dated 2019-04-12 and 1.3.0 dated 2019-07-18
DESCRIPTION | 8 - MD5 | 65 +++++----- NAMESPACE | 8 + R/GenEst.R | 3 R/app_download_functions.R | 229 ++++++++++++++++++++++++++++++++++- R/app_panels.R | 20 ++- R/app_server.R | 18 +- R/app_table_functions.R | 24 ++- R/app_ui.R | 1 R/app_update_input.R | 8 - R/app_update_output.R | 69 +++++----- R/app_update_rv.R | 15 +- R/app_utilities.R | 12 + R/app_widgets.R | 48 ++++--- R/detection_probability_functions.R | 84 ++++++++++++ R/dwp_functions.R |only R/mortality_functions.R | 48 +++++-- R/splits_figure_functions.R | 16 ++ build/vignette.rds |binary inst/doc/GenEstGUI.html | 4 inst/doc/command-line-example.html | 118 +++++++++--------- inst/doc/solar-examples.html | 30 ++-- inst/doc/wind-examples.html | 234 ++++++++++++++++++------------------ man/CO_DWP.Rd |only man/DWPbyCarcass.Rd | 2 man/cpmCPCellPlot.Rd | 2 man/downloadCPmod.Rd |only man/downloadMres.Rd |only man/downloadSEmod.Rd |only man/dwpm.Rd |only man/estM.Rd | 15 +- man/estg.Rd | 10 + man/modelInputWidget.Rd | 2 man/plot.splitSummary.Rd | 6 man/rdwp.Rd |only man/update_output.Rd | 4 man/widgetMaker.Rd | 2 37 files changed, 754 insertions(+), 351 deletions(-)
Title: Statistical Learning on Sparse Matrices
Description: Implements many algorithms for statistical learning on
sparse matrices - matrix factorizations, matrix completion,
elastic net regressions, factorization machines.
Also 'rsparse' enhances 'Matrix' package by providing methods for
multithreaded <sparse, dense> matrix products and native slicing of
the sparse matrices in Compressed Sparse Row (CSR) format.
List of the algorithms for regression problems:
1) Elastic Net regression via Follow The Proximally-Regularized Leader (FTRL)
Stochastic Gradient Descent (SGD), as per McMahan et al(, <doi:10.1145/2487575.2488200>)
2) Factorization Machines via SGD, as per Rendle (2010, <doi:10.1109/ICDM.2010.127>)
List of algorithms for matrix factorization and matrix completion:
1) Weighted Regularized Matrix Factorization (WRMF) via Alternating Least
Squares (ALS) - paper by Hu, Koren, Volinsky (2008, <doi:10.1109/ICDM.2008.22>)
2) Maximum-Margin Matrix Factorization via ALS, paper by Rennie, Srebro
(2005, <doi:10.1145/1102351.1102441>)
3) Fast Truncated Singular Value Decomposition (SVD), Soft-Thresholded SVD,
Soft-Impute matrix completion via ALS - paper by Hastie, Mazumder
et al. (2014, <arXiv:1410.2596>)
4) Linear-Flow matrix factorization, from 'Practical linear models for
large-scale one-class collaborative filtering' by Sedhain, Bui, Kawale et al
(2016, ISBN:978-1-57735-770-4)
5) GlobalVectors (GloVe) matrix factorization via SGD, paper by Pennington,
Socher, Manning (2014, <https://www.aclweb.org/anthology/D14-1162>)
Package is reasonably fast and memory efficient - it allows to work with large
datasets - millions of rows and millions of columns. This is particularly useful
for practitioners working on recommender systems.
Author: Dmitriy Selivanov [aut, cre, cph]
(<https://orcid.org/0000-0001-5413-1506>),
Drew Schmidt [ctb] (configure script for BLAS, LAPACK detection),
Wei-Chen Chen [ctb] (configure script and work on linking to float
package)
Maintainer: Dmitriy Selivanov <selivanov.dmitriy@gmail.com>
Diff between rsparse versions 0.3.3.1 dated 2019-04-14 and 0.3.3.2 dated 2019-07-18
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 9 +++++++-- R/metrics.R | 4 ++-- R/model_FactorizationMachine.R | 4 +--- R/utils.R | 6 ++++++ R/zzz.R | 26 +++++++++++++++++++++++++- README.md | 4 ++-- configure | 25 +++++++++---------------- configure.ac | 12 ++++++++---- man/metrics.Rd | 4 ++-- 11 files changed, 76 insertions(+), 46 deletions(-)
Title: Control Charts with Guaranteed In-Control Performance and
Cautious Parameters Learning
Description: Design and use of control charts for detecting mean changes
based on a delayed updating of the in-control parameter estimates.
See Capizzi and Masarotto (2019) <doi:10.1080/00224065.2019.1640096> for the
description of the method.
Author: Giovanna Capizzi and Guido Masarotto
Maintainer: Giovanna Capizzi <giovanna.capizzi@unipd.it>
Diff between CautiousLearning versions 1.0 dated 2019-07-15 and 1.0.1 dated 2019-07-18
DESCRIPTION | 6 ++-- MD5 | 7 ++--- NEWS |only R/init.R | 1 src/cautious.cpp | 76 +++++++++++++++++++++++++++++++------------------------ 5 files changed, 52 insertions(+), 38 deletions(-)
More information about CautiousLearning at CRAN
Permanent link
More information about wyz.code.offensiveProgramming at CRAN
Permanent link
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 1.4.2 dated 2019-07-01 and 1.4.3 dated 2019-07-18
DESCRIPTION | 12 ++++----- MD5 | 33 +++++++++++++------------ NEWS.md | 5 +++ R/customCoder.R | 19 +++++++------- README.md | 2 - inst/doc/MultiClassVtreat.html | 4 +-- inst/doc/SavingTreamentPlans.html | 4 +-- inst/doc/VariableImportance.html | 10 +++---- inst/doc/vtreat.html | 32 ++++++++++++------------- 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_consts_rejected.R |only 18 files changed, 145 insertions(+), 140 deletions(-)
Title: Distance Measures for Time Series Data
Description: A set of commonly used distance measures and some additional functions which, although initially not designed for this purpose, can be used to measure the dissimilarity between time series. These measures can be used to perform clustering, classification or other data mining tasks which require the definition of a distance measure between time series.
Author: Usue Mori [aut, cre],
Alexander Mendiburu [aut],
Jose A. Lozano [aut],
Duarte Folgado [ctb]
Maintainer: Usue Mori <usue.mori@ehu.eus>
Diff between TSdist versions 3.5 dated 2019-03-14 and 3.6 dated 2019-07-18
DESCRIPTION | 16 +-- MD5 | 17 +-- NAMESPACE | 2 R/database_distances.R | 2 R/tam_distance.R |only R/ts_distances.R | 5 inst/tests/test.tam.R |only man/TAMDistance.Rd |only man/TSDatabaseDistances.Rd | 237 ++++++++++++++++++++++----------------------- man/TSDistances.Rd | 236 ++++++++++++++++++++++---------------------- src/EDR.c | 2 11 files changed, 264 insertions(+), 253 deletions(-)
Title: Create and (Interactively) Modify Nested Hierarchies
Description: Provides functionality to generate, (interactively) modify (by adding, removing and renaming nodes) and convert nested hierarchies between different formats.
These tree like structures can be used to define for example complex hierarchical tables used for statistical disclosure control.
Author: Bernhard Meindl [aut, cre]
Maintainer: Bernhard Meindl <Bernhard.Meindl@statistik.gv.at>
Diff between sdcHierarchies versions 0.18 dated 2019-04-23 and 0.18.1 dated 2019-07-18
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 5 +++++ build/vignette.rds |binary inst/app/global.R | 19 ++++++++++--------- inst/doc/usage.html | 10 +++++++--- tests/testthat/test_hier_grid.R | 1 - 7 files changed, 32 insertions(+), 23 deletions(-)
More information about sdcHierarchies at CRAN
Permanent link
Title: Spatial Association Between Regionalizations
Description: Calculates a degree of spatial association between regionalizations
or categorical maps using the information-theoretical V-measure
(Nowosad and Stepinski (2018) <doi:10.1080/13658816.2018.1511794>). It also
offers an R implementation of the MapCurve method
(Hargrove et al. (2006) <doi:10.1007/s10109-006-0025-x>).
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Tomasz Stepinski [aut],
Space Informatics Lab [cph]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between sabre versions 0.2.1 dated 2018-09-17 and 0.3.1 dated 2019-07-18
DESCRIPTION | 10 ++-- MD5 | 51 +++++++++++++------------ NAMESPACE | 7 +++ R/data.R | 34 +++++++++++++--- R/mapcurves_calc.R | 44 ++++++++++++++++++++- R/vmeasure_calc.R | 63 +++++++++++++++++++++++++++++-- README.md | 10 ++-- build/vignette.rds |binary data/partitions1.rda |only data/partitions2.rda |only inst/CITATION | 8 +-- inst/doc/sabre.R | 4 - inst/doc/sabre.Rmd | 6 +- inst/doc/sabre.html | 57 +++++++++++++++++++--------- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-2-2.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-6-2.png |binary man/mapcurves_calc.Rd | 17 +++++--- man/partitions1.Rd |only man/partitions2.Rd |only man/regions1.Rd | 7 +-- man/regions2.Rd | 7 +-- man/vmeasure_calc.Rd | 18 ++++++-- tests/testthat.R | 1 tests/testthat/test-eco-us.R | 6 +- tests/testthat/test-fig1.R | 4 - tests/testthat/test-raster.R |only vignettes/sabre.Rmd | 6 +- 29 files changed, 265 insertions(+), 95 deletions(-)
Title: Using KEEL in R Code
Description: 'KEEL' is a popular Java software for a large number of different knowledge data discovery tasks.
This package takes the advantages of 'KEEL' and R, allowing to use 'KEEL' algorithms in simple R code.
The implemented R code layer between R and 'KEEL' makes easy both using 'KEEL' algorithms in R as implementing new algorithms for 'RKEEL' in a very simple way.
It includes more than 100 algorithms for classification, regression, preprocess, association rules and imbalance learning, which allows a more complete experimentation process.
For more information about KEEL, see <http://www.keel.es/>.
Author: Jose M. Moyano [aut, cre],
Luciano Sanchez [aut],
Oliver Sanchez [ctb],
Jesus Alcala-Fernandez [ctb]
Maintainer: Jose M. Moyano <jmoyano@uco.es>
Diff between RKEEL versions 1.2.7 dated 2019-01-18 and 1.3.1 dated 2019-07-18
DESCRIPTION | 8 - MD5 | 16 +- R/ClassificationAlgorithm.R | 6 - R/KeelAlgorithm.R | 3 man/C45-C.Rd | 72 ++++++------- man/CART-C.Rd | 12 +- man/FPgrowth-A.Rd | 230 +++++++++++++++++++++--------------------- man/FuzzyApriori-A.Rd | 232 +++++++++++++++++++++---------------------- man/writeDatFromDataframe.Rd | 4 9 files changed, 292 insertions(+), 291 deletions(-)
Title: Randomization Tests
Description: A collection of randomization tests, data sets and examples. The current version focuses on three testing problems and their implementation in empirical work. First, it facilitates the empirical researcher to test for particular hypotheses, such as comparisons of means, medians, and variances from k populations using robust permutation tests, which asymptotic validity holds under very weak assumptions, while retaining the exact rejection probability in finite samples when the underlying distributions are identical. Second, the description and implementation of a permutation test for testing the continuity assumption of the baseline covariates in the sharp regression discontinuity design (RDD) as in Canay and Kamat (2017) <https://goo.gl/UZFqt7>. More specifically, it allows the user to select a set of covariates and test the aforementioned hypothesis using a permutation test based on the Cramer-von Miss test statistic. Graphical inspection of the empirical CDF and histograms for the variables of interest is also supported in the package. Third, it provides the practitioner with an effortless implementation of a permutation test based on the martingale decomposition of the empirical process for the goodness-of-fit testing problem with an estimated nuisance parameter. An application of this testing problem is the one of testing for heterogeneous treatment effects in a randomized control trial.
Author: Mauricio Olivares-Gonzalez [aut, cre],
Ignacio Sarmiento-Barbieri [aut]
Maintainer: Mauricio Olivares-Gonzalez <maurice.olivares@gmail.com>
Diff between RATest versions 0.1.5 dated 2019-07-12 and 0.1.6 dated 2019-07-18
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++++------- NAMESPACE | 3 +++ R/PT.Khmaladze.fit.R | 2 +- R/group.action.R |only R/summary.PT.Khmaladze.fit.R | 24 ++++++++++++++++++++---- R/summary.RPT.R | 20 ++++++++++++++++++++ inst/doc/RDperm.pdf |binary man/PT.Khmaladze.fit.Rd | 4 ++-- man/group.action.Rd |only man/summary.PT.Khmaladze.fit.Rd |only man/summary.RPT.Rd |only 12 files changed, 62 insertions(+), 19 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources ('rpart', 'RWeka', 'PMML') yielding objects that share
functionality for print()/plot()/predict() methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree()) and model-based
recursive partitioning (mob()) from the 'party' package are provided based
on the new infrastructure. A description of this package was published
by Hothorn and Zeileis (2015) <http://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>),
Heidi Seibold [ctb] (<https://orcid.org/0000-0002-8960-9642>),
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.2-4 dated 2019-05-17 and 1.2-5 dated 2019-07-18
DESCRIPTION | 8 ++-- MD5 | 20 +++++------ R/ctree.R | 4 ++ R/extree.R | 2 + build/vignette.rds |binary inst/NEWS.Rd | 10 +++++ inst/doc/constparty.pdf |binary inst/doc/ctree.pdf |binary inst/doc/mob.pdf |binary inst/doc/partykit.pdf |binary tests/regtest-party.Rout.save | 76 +++++++++++++++++++++--------------------- 11 files changed, 68 insertions(+), 52 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 Mérian [aut, cph],
Fares Qeadan [aut, cph],
Christian Zang [aut, cph],
Allan Buras [ctb],
Jacob Cecile [ctb],
Manfred Mudelsee [ctb],
Michael Schulz [ctb]
Maintainer: Andy Bunn <andy.bunn@wwu.edu>
Diff between dplR versions 1.6.9 dated 2018-11-05 and 1.7.0 dated 2019-07-18
dplR-1.6.9/dplR/inst/doc/00_INDEX |only dplR-1.6.9/dplR/inst/doc/build-math-dplR.R |only dplR-1.6.9/dplR/inst/doc/math-dplR.R |only dplR-1.6.9/dplR/inst/doc/math-dplR.Rnw.txt |only dplR-1.6.9/dplR/inst/doc/math-dplR.bib |only dplR-1.6.9/dplR/inst/doc/math-dplR.pdf |only dplR-1.6.9/dplR/man/plotRings.Rd |only dplR-1.7.0/dplR/ChangeLog | 61 +++ dplR-1.7.0/dplR/DESCRIPTION | 21 - dplR-1.7.0/dplR/MD5 | 55 +- dplR-1.7.0/dplR/NAMESPACE | 5 dplR-1.7.0/dplR/R/ccf.series.rwl.R | 22 + dplR-1.7.0/dplR/R/corr.rwl.seg.R | 509 ++++++++++----------------- dplR-1.7.0/dplR/R/insert.ring.R | 18 dplR-1.7.0/dplR/R/plot.crs.R |only dplR-1.7.0/dplR/R/plotRings.R | 240 ------------ dplR-1.7.0/dplR/R/redfit.R | 2 dplR-1.7.0/dplR/R/series.rwl.plot.R | 24 + dplR-1.7.0/dplR/R/xskel.ccf.plot.R | 31 + dplR-1.7.0/dplR/README.md |only dplR-1.7.0/dplR/build/vignette.rds |binary dplR-1.7.0/dplR/inst/doc/chron-dplR.pdf |binary dplR-1.7.0/dplR/inst/doc/intro-dplR.pdf |binary dplR-1.7.0/dplR/inst/doc/timeseries-dplR.pdf |binary dplR-1.7.0/dplR/inst/doc/xdate-dplR.R | 2 dplR-1.7.0/dplR/inst/doc/xdate-dplR.pdf |binary dplR-1.7.0/dplR/man/ccf.series.rwl.Rd | 17 dplR-1.7.0/dplR/man/corr.rwl.seg.Rd | 14 dplR-1.7.0/dplR/man/dplR-defunct.Rd |only dplR-1.7.0/dplR/man/insert.ring.Rd | 57 ++- dplR-1.7.0/dplR/man/plot.crs.Rd |only dplR-1.7.0/dplR/man/xskel.ccf.plot.Rd | 19 - dplR-1.7.0/dplR/vignettes/intro-dplR.Rnw | 2 dplR-1.7.0/dplR/vignettes/xdate-dplR.Rnw | 30 - 34 files changed, 484 insertions(+), 645 deletions(-)
Title: Connecting to Various Database Platforms
Description: An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server',
'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', 'Google BigQuery', and 'SQLite'). Also includes support for
fetching data as 'ffdf' objects. Uses 'Java Database Connectivity' ('JDBC') to connect to databases (except SQLite).
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Observational Health Data Science and Informatics [cph],
Microsoft Inc. [cph] (SQL Server JDBC driver),
PostgreSQL Global Development Group [cph] (PostgreSQL JDBC driver),
Oracle Inc. [cph] (Oracle JDBC driver),
Amazon Inc. [cph] (RedShift JDBC driver)
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between DatabaseConnector versions 2.3.0 dated 2019-02-21 and 2.4.1 dated 2019-07-18
DESCRIPTION | 9 MD5 | 54 NEWS.md | 30 R/Compression.R | 2 R/Connect.R | 11 R/DBI.R | 2 R/DatabaseConnector.R | 2 R/InsertTable.R | 47 R/Sql.R | 90 README.md | 6 build/DatabaseConnector.pdf | 8876 ++++------ build/vignette.rds |binary inst/doc/UsingDatabaseConnector.Rmd | 6 inst/doc/UsingDatabaseConnector.pdf |binary inst/java/DatabaseConnector.jar |binary java/org/ohdsi/databaseConnector/Authentication.java |only java/org/ohdsi/databaseConnector/BatchedInsert.java | 15 java/org/ohdsi/databaseConnector/BatchedQuery.java | 15 man/connect.Rd | 5 man/createConnectionDetails.Rd | 5 man/createZipFile.Rd | 4 man/dbWriteTable-DatabaseConnectorConnection-character-data.frame-method.Rd | 2 man/executeSql.Rd | 8 man/jdbcDrivers.Rd | 2 man/renderTranslateExecuteSql.Rd | 8 tests/testthat/test-bulkUpload.R |only tests/testthat/test-insertTable.R | 183 tests/testthat/test-sendUpdates.R | 136 vignettes/UsingDatabaseConnector.Rmd | 6 29 files changed, 4767 insertions(+), 4757 deletions(-)
More information about DatabaseConnector at CRAN
Permanent link
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
Author: Jason Vander Heiden [aut, cre],
Namita Gupta [aut],
Susanna Marquez [ctb],
Daniel Gadala-Maria [ctb],
Ruoyi Jiang [ctb],
Nima Nouri [ctb],
Kenneth Hoehn [ctb],
Julian Zhou [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between alakazam versions 0.2.11 dated 2018-09-14 and 0.3.0 dated 2019-07-18
alakazam-0.2.11/alakazam/man/DiversityTest-class.Rd |only alakazam-0.3.0/alakazam/DESCRIPTION | 26 alakazam-0.3.0/alakazam/MD5 | 89 - alakazam-0.3.0/alakazam/NAMESPACE | 39 alakazam-0.3.0/alakazam/NEWS.md | 41 alakazam-0.3.0/alakazam/R/Alakazam.R | 41 alakazam-0.3.0/alakazam/R/Classes.R | 175 -- alakazam-0.3.0/alakazam/R/Core.R | 2 alakazam-0.3.0/alakazam/R/Deprecated.R |only alakazam-0.3.0/alakazam/R/Diversity.R | 1240 ++++++++------- alakazam-0.3.0/alakazam/R/Gene.R | 917 +++++++++-- alakazam-0.3.0/alakazam/R/Lineage.R | 409 ++++ alakazam-0.3.0/alakazam/R/Sequence.R | 15 alakazam-0.3.0/alakazam/R/Topology.R | 39 alakazam-0.3.0/alakazam/build/vignette.rds |binary alakazam-0.3.0/alakazam/inst/doc/AminoAcids-Vignette.pdf |binary alakazam-0.3.0/alakazam/inst/doc/Diversity-Vignette.R | 51 alakazam-0.3.0/alakazam/inst/doc/Diversity-Vignette.Rmd | 76 alakazam-0.3.0/alakazam/inst/doc/Diversity-Vignette.pdf |binary alakazam-0.3.0/alakazam/inst/doc/GeneUsage-Vignette.Rmd | 5 alakazam-0.3.0/alakazam/inst/doc/GeneUsage-Vignette.pdf |binary alakazam-0.3.0/alakazam/inst/doc/Lineage-Vignette.R | 29 alakazam-0.3.0/alakazam/inst/doc/Lineage-Vignette.Rmd | 51 alakazam-0.3.0/alakazam/inst/doc/Lineage-Vignette.pdf |binary alakazam-0.3.0/alakazam/inst/doc/Topology-Vignette.pdf |binary alakazam-0.3.0/alakazam/man/AbundanceCurve-class.Rd | 14 alakazam-0.3.0/alakazam/man/DiversityCurve-class.Rd | 29 alakazam-0.3.0/alakazam/man/alakazam.Rd | 8 alakazam-0.3.0/alakazam/man/alphaDiversity.Rd |only alakazam-0.3.0/alakazam/man/calcCoverage.Rd | 2 alakazam-0.3.0/alakazam/man/calcDiversity.Rd | 2 alakazam-0.3.0/alakazam/man/combineIgphyml.Rd |only alakazam-0.3.0/alakazam/man/countClones.Rd | 2 alakazam-0.3.0/alakazam/man/countGenes.Rd | 4 alakazam-0.3.0/alakazam/man/estimateAbundance.Rd | 46 alakazam-0.3.0/alakazam/man/graphToPhylo.Rd |only alakazam-0.3.0/alakazam/man/groupGenes.Rd | 89 - alakazam-0.3.0/alakazam/man/nonsquareDist.Rd | 9 alakazam-0.3.0/alakazam/man/phyloToGraph.Rd |only alakazam-0.3.0/alakazam/man/plotAbundanceCurve.Rd | 2 alakazam-0.3.0/alakazam/man/plotDiversityCurve.Rd | 10 alakazam-0.3.0/alakazam/man/plotDiversityTest.Rd | 29 alakazam-0.3.0/alakazam/man/rarefyDiversity.Rd | 10 alakazam-0.3.0/alakazam/man/readIgphyml.Rd |only alakazam-0.3.0/alakazam/man/testDiversity.Rd | 18 alakazam-0.3.0/alakazam/src/RcppDistance.cpp | 38 alakazam-0.3.0/alakazam/vignettes/Diversity-Vignette.Rmd | 76 alakazam-0.3.0/alakazam/vignettes/GeneUsage-Vignette.Rmd | 5 alakazam-0.3.0/alakazam/vignettes/Lineage-Vignette.Rmd | 51 49 files changed, 2601 insertions(+), 1088 deletions(-)
Title: Optimal Bayesian Experimental Design using the ACE Algorithm
Description: Optimal Bayesian experimental design using the approximate coordinate exchange (ACE) algorithm.
Author: Antony M. Overstall, David C. Woods & Maria Adamou
Maintainer: Antony M. Overstall <A.M.Overstall@soton.ac.uk>
Diff between acebayes versions 1.6.0 dated 2018-12-19 and 1.7 dated 2019-07-18
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/acebayes.R | 27 +++++++++++++++++++++++++-- R/sysdata.rda |binary build/vignette.rds |binary inst/doc/acebayes.pdf |binary man/acebayes-package.Rd | 16 ++++++++-------- man/aceglm.Rd | 31 +++++++++++++++---------------- man/overstallwoods.Rd | 8 ++++---- man/utilities.Rd | 4 ++-- 10 files changed, 67 insertions(+), 45 deletions(-)
Title: Truncated Maximum Likelihood Fit and Robust Accelerated Failure
Time Regression for Gaussian and Log-Weibull Case
Description: R functions for the computation of the truncated maximum
likelihood and the robust accelerated failure time regression
for gaussian and log-Weibull case.
Author: Alfio Marazzi <Alfio.Marazzi@unisante.ch>, Jean-Luc Muralti
Maintainer: A. Randriamiharisoa <exelami@gmail.com>
Diff between RobustAFT versions 1.4-3 dated 2018-06-25 and 1.4-4 dated 2019-07-18
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- src/init.c | 10 +++++----- src/robaft.f | 14 +++++++------- src/tmlest.f | 8 ++++---- 5 files changed, 26 insertions(+), 26 deletions(-)
Title: Implementation of the Horseshoe Prior
Description: Contains functions for applying the horseshoe prior to high-
dimensional linear regression, yielding the posterior mean and credible
intervals, amongst other things. The key parameter tau can be equipped with
a prior or estimated via maximum marginal likelihood estimation (MMLE).
The main function, horseshoe, is for linear regression. In addition, there
are functions specifically for the sparse normal means problem, allowing
for faster computation of for example the posterior mean and posterior
variance. Finally, there is a function available to perform variable
selection, using either a form of thresholding, or credible intervals.
Author: Stephanie van der Pas [cre, aut],
James Scott [aut],
Antik Chakraborty [aut],
Anirban Bhattacharya [aut]
Maintainer: Stephanie van der Pas <svdpas@math.leidenuniv.nl>
Diff between horseshoe versions 0.1.0 dated 2016-11-08 and 0.2.0 dated 2019-07-18
DESCRIPTION | 11 ++++++----- MD5 | 39 ++++++++++++++++++++++----------------- NEWS.md | 5 +++++ R/HS_MMLE.R | 10 +++++++--- R/HS_normal_means.R | 10 +++++++--- R/HS_post_mean.R | 4 ++-- R/HS_post_var.R | 4 ++-- R/HS_var_select.R | 10 +++++++--- R/horseshoe.R | 9 +++++---- build |only inst |only man/Basic.integrand.Rd | 1 - man/Basic.y.Rd | 1 - man/Basic.y.vec.Rd | 1 - man/HS.MMLE.Rd | 11 +++++++---- man/HS.normal.means.Rd | 17 ++++++++++------- man/HS.post.mean.Rd | 5 ++--- man/HS.post.var.Rd | 5 ++--- man/HS.var.select.Rd | 11 +++++++---- man/horseshoe.Rd | 10 +++++----- vignettes |only 21 files changed, 96 insertions(+), 68 deletions(-)
Title: Key and Secret Management in 'Azure'
Description: Manage keys, certificates, secrets, and storage accounts in Microsoft's 'Key Vault' service: <https://azure.microsoft.com/services/key-vault>. Provides facilities to store and retrieve secrets, use keys to encrypt, decrypt, sign and verify data, and manage certificates. Integrates with the 'AzureAuth' package to enable authentication with a certificate, and with the 'openssl' package for importing and exporting cryptographic objects. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureKeyVault versions 1.0.0 dated 2019-05-14 and 1.0.1 dated 2019-07-18
DESCRIPTION | 13 ++++---- MD5 | 32 +++++++++++---------- NEWS.md |only R/add_methods.R | 4 +- R/az_vault.R | 12 ++++---- R/certificates.R | 6 ++-- R/keys.R | 8 ++--- R/object_props.R | 4 +- R/secrets.R | 6 ++-- R/storage_accounts.R | 8 ++--- R/stored_key.R | 4 +- R/utils.R | 60 +++++++++++++++++++++++++--------------- R/vault_endpoint.R | 10 ++++-- README.md | 10 ++++-- inst/doc/intro.Rmd | 2 - inst/doc/intro.html | 2 - tests/testthat/test06_chartok.R |only vignettes/intro.Rmd | 2 - 18 files changed, 105 insertions(+), 78 deletions(-)
Title: Variable Selection Using Random Forests
Description: Three steps variable selection procedure based on random forests.
Initially developed to handle high dimensional data (for which number of
variables largely exceeds number of observations), the package is very
versatile and can treat most dimensions of data, for regression and
supervised classification problems. First step is dedicated to eliminate
irrelevant variables from the dataset. Second step aims to select all
variables related to the response for interpretation purpose. Third step
refines the selection by eliminating redundancy in the set of variables
selected by the second step, for prediction purpose.
Genuer, R. Poggi, J.-M. and Tuleau-Malot, C. (2015)
<https://journal.r-project.org/archive/2015-2/genuer-poggi-tuleaumalot.pdf>.
Author: Robin Genuer [aut, cre],
Jean-Michel Poggi [aut],
Christine Tuleau-Malot [aut]
Maintainer: Robin Genuer <Robin.Genuer@u-bordeaux.fr>
Diff between VSURF versions 1.0.4 dated 2018-04-10 and 1.1.0 dated 2019-07-18
DESCRIPTION | 17 - MD5 | 36 +- NAMESPACE | 2 NEWS | 16 - R/PM10.R | 7 R/VSURF.R | 307 ++++++++++--------- R/VSURF_interp.R | 480 ++++++++++++++++++++----------- R/VSURF_pred.R | 280 ++++++++++++------ R/VSURF_thres.R | 403 +++++++++++++++----------- man/PM10.Rd | 7 man/VSURF.Rd | 213 +++++++------ man/VSURF_interp.Rd | 119 ++++--- man/VSURF_pred.Rd | 111 ++++--- man/VSURF_thres.Rd | 135 ++++---- man/plot.VSURF.Rd | 5 tests/testthat/case_win32_test_iris.R | 6 tests/testthat/case_win32b_test_orange.R | 6 tests/testthat/test_iris.R | 43 +- tests/testthat/test_orange.R | 51 ++- 19 files changed, 1360 insertions(+), 884 deletions(-)
Title: Collecting Social Media Data and Generating Networks for
Analysis
Description: A suite of tools for collecting and constructing networks from social media data.
Provides easy-to-use functions for collecting data across popular platforms (Twitter, YouTube
and Reddit) and generating different types of networks for analysis.
Author: Timothy Graham, Robert Ackland, Chung-hong Chan, Bryan Gertzel
Maintainer: Bryan Gertzel <bryan.gertzel@anu.edu.au>
Diff between vosonSML versions 0.26.3 dated 2019-02-22 and 0.27.2 dated 2019-07-18
vosonSML-0.26.3/vosonSML/R/AddUserData.twitter.R |only vosonSML-0.26.3/vosonSML/R/SaveCredential.R |only vosonSML-0.26.3/vosonSML/man/figures |only vosonSML-0.26.3/vosonSML/man/vosonSML-colon-colon-AddUserData.twitter.Rd |only vosonSML-0.26.3/vosonSML/man/vosonSML-colon-colon-SaveCredential.Rd |only vosonSML-0.27.2/vosonSML/DESCRIPTION | 9 vosonSML-0.27.2/vosonSML/MD5 | 49 ++-- vosonSML-0.27.2/vosonSML/NAMESPACE | 8 vosonSML-0.27.2/vosonSML/NEWS.md | 52 ++++ vosonSML-0.27.2/vosonSML/R/AddTwitterUserData.R |only vosonSML-0.27.2/vosonSML/R/Authenticate.R | 8 vosonSML-0.27.2/vosonSML/R/Authenticate.twitter.R | 76 +++---- vosonSML-0.27.2/vosonSML/R/Collect.R | 14 + vosonSML-0.27.2/vosonSML/R/Collect.reddit.R | 22 -- vosonSML-0.27.2/vosonSML/R/Collect.twitter.R | 15 + vosonSML-0.27.2/vosonSML/R/Collect.youtube.R | 2 vosonSML-0.27.2/vosonSML/R/Create.actor.reddit.R | 81 +++++-- vosonSML-0.27.2/vosonSML/R/Create.actor.twitter.R | 2 vosonSML-0.27.2/vosonSML/R/Create.semantic.twitter.R | 108 ++++++---- vosonSML-0.27.2/vosonSML/R/ImportData.R | 24 +- vosonSML-0.27.2/vosonSML/R/Utils.R | 61 ++++- vosonSML-0.27.2/vosonSML/R/vosonSML-package.R | 7 vosonSML-0.27.2/vosonSML/README.md | 83 +++++-- vosonSML-0.27.2/vosonSML/man/Authenticate.Rd | 8 vosonSML-0.27.2/vosonSML/man/Authenticate.twitter.Rd | 30 +- vosonSML-0.27.2/vosonSML/man/Create.actor.twitter.Rd | 2 vosonSML-0.27.2/vosonSML/man/vosonSML-colon-colon-AddTwitterUserData.Rd |only vosonSML-0.27.2/vosonSML/man/vosonSML-colon-colon-ImportData.Rd | 13 - vosonSML-0.27.2/vosonSML/man/vosonSML-package.Rd | 3 29 files changed, 441 insertions(+), 236 deletions(-)
Title: Thematic Map Tools
Description: Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.
Author: Martijn Tennekes [aut, cre]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmaptools versions 2.0-1 dated 2018-08-07 and 2.0-2 dated 2019-07-18
DESCRIPTION | 14 ++++---- MD5 | 72 ++++++++++++++++++++++--------------------- NEWS | 7 ++++ R/aggregate_map.R | 5 ++- R/append_data.R | 6 +++ R/geocode_OSM.R | 24 ++++++++------ R/get_proj4_code.R | 40 +++++++++++++++--------- R/line_functions.R | 4 +- R/pkg.R | 15 ++++++++- R/raster_functions.R |only R/read_osm.R | 7 +--- R/read_shape.R | 15 ++++++--- R/sample_dots.R | 9 +++-- R/sbind.R | 4 +- R/set_projection.R | 73 -------------------------------------------- R/smooth_map.R | 25 ++++++++++++--- R/smooth_raster_cover.R | 5 +-- R/to_raster.R | 19 +++++++++-- R/xxx_raster.R | 34 ++++++++++++++++++-- R/xxx_scales.R | 42 +++++++++++++++++++------ man/aggregate_map.Rd | 2 - man/append_data.Rd | 2 - man/double_line.Rd | 2 - man/points_to_raster.Rd | 4 +- man/poly_to_raster.Rd | 2 - man/read_GPX.Rd | 4 +- man/read_osm.Rd | 4 +- man/read_shape.Rd | 2 - man/rev_geocode_OSM.Rd | 6 +-- man/sample_dots.Rd | 2 - man/sbind.Rd | 2 - man/set_projection.Rd | 4 +- man/simplify_shape.Rd | 4 +- man/smooth_map.Rd | 16 +++++---- man/smooth_raster_cover.Rd | 2 - man/tmaptools-deprecated.Rd |only man/tmaptools-package.Rd | 8 +--- man/write_shape.Rd | 2 - 38 files changed, 276 insertions(+), 212 deletions(-)
Title: Thematic Maps
Description: Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.
Author: Martijn Tennekes [aut, cre],
Joel Gombin [ctb],
Sebastian Jeworutzki [ctb],
Kent Russell [ctb],
Richard Zijdeman [ctb],
John Clouse [ctb],
Robin Lovelace [ctb],
Jakub Nowosad [ctb],
Jannes Muenchow [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmap versions 2.2 dated 2019-01-05 and 2.3 dated 2019-07-18
DESCRIPTION | 13 - MD5 | 124 ++++++++-------- NAMESPACE | 10 + NEWS | 10 + R/cellplot.R | 4 R/gridplot.R | 6 R/meta_plot.R | 6 R/meta_plot_items.R | 14 + R/num2pal.R | 29 +++ R/pkg.R | 6 R/plot_map.R | 2 R/plot_misc_functions.R | 81 +++++++++- R/prearrange_element_order.R | 18 +- R/preprocess_facet_layout.R | 23 ++- R/preprocess_gt.R | 8 - R/preprocess_shapes.R | 60 ++++++- R/print_tmap.R | 110 +++++++++----- R/process_aes.R | 9 - R/process_color_aes.R | 10 + R/process_facet_layout.R | 83 ++++++---- R/process_gps.R | 50 +++--- R/process_layers.R | 7 R/process_legend_format.R | 6 R/process_meta.R | 24 +-- R/process_tiles.R | 24 ++- R/process_tm.R | 8 - R/shiny.R |only R/tm_add_legend.R | 4 R/tm_layers.R | 106 ++++++++++---- R/tm_layout.R | 28 +-- R/tm_misc_elements.R | 76 +++++++--- R/tmap_animation.R | 13 + R/tmap_arrange.R | 18 +- R/tmap_options.R | 14 + R/tmap_save.R | 68 +++++---- R/view_tmap.R | 317 +++++++++++++++++++++++++++--------------- R/xxx_raster.R | 23 ++- R/xxx_scales.R | 45 ++++- build/vignette.rds |binary inst/doc/tmap-JSS-code.html | 3 inst/doc/tmap-changes-v2.html | 9 - inst/doc/tmap-getstarted.html | 19 +- inst/tips.txt | 2 man/axis_labels.Rd | 4 man/renderTmap.Rd |only man/tm_add_legend.Rd | 4 man/tm_compass.Rd | 8 - man/tm_grid.Rd | 55 ++++++- man/tm_iso.Rd | 2 man/tm_layout.Rd | 40 ++--- man/tm_lines.Rd | 13 + man/tm_polygons.Rd | 15 + man/tm_raster.Rd | 29 +++ man/tm_scale_bar.Rd | 8 - man/tm_sf.Rd | 5 man/tm_symbols.Rd | 25 ++- man/tm_text.Rd | 13 + man/tm_tiles.Rd | 10 - man/tmap-package.Rd | 12 - man/tmap_animation.Rd | 7 man/tmap_arrange.Rd | 10 - man/tmap_leaflet.Rd | 7 man/tmap_options.Rd | 8 - man/tmap_save.Rd | 14 - 64 files changed, 1200 insertions(+), 579 deletions(-)
Title: Resampled Data Frames
Description: Create data frames with virtual groups that can be used with
'dplyr' to efficiently compute resampled statistics, generate the data for
hypothetical outcome plots, and fit multiple models on resampled variations
of the original data.
Author: Davis Vaughan [aut, cre]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between strapgod versions 0.0.2 dated 2019-05-16 and 0.0.3 dated 2019-07-18
DESCRIPTION | 8 MD5 | 12 - NEWS.md | 8 build/vignette.rds |binary inst/doc/dplyr-support.html | 355 ++++++++++++++++----------------- inst/doc/virtual-bootstraps.html | 65 +++--- tests/testthat/test-dplyr-group-funs.R | 6 7 files changed, 235 insertions(+), 219 deletions(-)
Title: Build Binary Classification Models in One Integrated Offering
Description: Provides a toolkit for building predictive models in one integrated offering. Contains infrastructure functionalities such as data exploration and preparation, missing values treatment, outliers treatment, variable derivation, variable selection, dimensionality reduction, grid search for hyperparameters, data mining and visualization, model evaluation, strategy analysis etc. 'creditmodel' is designed to make the development of binary classification models (machine learning based models as well as credit scorecard) simpler and faster.
The references including:
1.Anderson, R. (2007). The credit scoring toolkit: Theory and practice for retail credit risk management and decision automation.
2.Find, S. (2012, ISBN13: 9780230347762). Credit scoring, response modelling and insurance rating:A practical guide to forecasting consumer behaviour.
Author: Dongping Fan [aut, cre]
Maintainer: Dongping Fan <fdp@pku.edu.cn>
Diff between creditmodel versions 1.1.0 dated 2019-05-18 and 1.1.1 dated 2019-07-18
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NEWS.md | 12 +++++++++--- R/data_process_tools.R | 27 ++++++++++++++++++--------- R/data_transformation.R | 1 - inst/doc/demo.html | 2 +- man/get_names.Rd | 3 ++- vignettes/Untitled.md |only 8 files changed, 41 insertions(+), 25 deletions(-)
Title: Adjust Srt File to Get Better Experience when Watching Movie
Description: Srt file is a common subtitle format for videos, it contains subtitle and when the subtitle showed.
This package is for align time of srt file, and also change color, style and position of subtitle in videos,
the srt file will be read as a vector into R, and can be write into srt file after modified using this package.
Author: Jim Chen [aut, cre]
Maintainer: Jim Chen <jim71183@gmail.com>
Diff between SRTtools versions 1.1.0 dated 2019-07-02 and 1.2.0 dated 2019-07-18
SRTtools-1.1.0/SRTtools/README.md |only SRTtools-1.2.0/SRTtools/DESCRIPTION | 6 ++--- SRTtools-1.2.0/SRTtools/MD5 | 10 ++++----- SRTtools-1.2.0/SRTtools/NAMESPACE | 1 SRTtools-1.2.0/SRTtools/NEWS | 7 +++++- SRTtools-1.2.0/SRTtools/R/main.R | 31 ++++++++++++++++++++++++++++++ SRTtools-1.2.0/SRTtools/man/srt.remove.Rd |only 7 files changed, 46 insertions(+), 9 deletions(-)
Title: Longitudinal Regression Trees and Forests
Description: Builds regression trees and random forests for longitudinal or functional data using a spline projection method. Implements and extends the work of Yu and Lambert (1999) <doi:10.1080/10618600.1999.10474847>. This method allows trees and forests to be built while considering either level and shape or only shape of response trajectories.
Author: Anna Neufeld [aut, cre],
Brianna Heggeseth [aut, ths]
Maintainer: Anna Neufeld <aneufeld@uw.edu>
Diff between splinetree versions 0.1.1 dated 2019-01-07 and 0.2.0 dated 2019-07-18
splinetree-0.1.1/splinetree/vignettes/Forest-intro.Rmd |only splinetree-0.2.0/splinetree/DESCRIPTION | 8 splinetree-0.2.0/splinetree/MD5 | 97 ++- splinetree-0.2.0/splinetree/NEWS.md | 17 splinetree-0.2.0/splinetree/R/forest_evaluation.R | 23 splinetree-0.2.0/splinetree/R/forest_helpers.R | 6 splinetree-0.2.0/splinetree/R/forest_prediction.R | 12 splinetree-0.2.0/splinetree/R/other_useful_fns.R | 8 splinetree-0.2.0/splinetree/R/plotting.R | 43 - splinetree-0.2.0/splinetree/R/splineForest.R | 59 +- splinetree-0.2.0/splinetree/R/splineTree.R | 31 - splinetree-0.2.0/splinetree/R/tree_evaluation.R | 14 splinetree-0.2.0/splinetree/R/tree_print.R | 12 splinetree-0.2.0/splinetree/README.md | 5 splinetree-0.2.0/splinetree/build/vignette.rds |binary splinetree-0.2.0/splinetree/data/datalist |only splinetree-0.2.0/splinetree/data/forest.rda |binary splinetree-0.2.0/splinetree/data/tree.rda |binary splinetree-0.2.0/splinetree/inst/doc/Forest-Intro.html | 365 ++++++++++----- splinetree-0.2.0/splinetree/inst/doc/Long-Intro.html | 284 ++++++++--- splinetree-0.2.0/splinetree/inst/doc/Tree-Intro.html | 228 +++++++-- splinetree-0.2.0/splinetree/man/avSize.Rd | 2 splinetree-0.2.0/splinetree/man/forest.Rd | 2 splinetree-0.2.0/splinetree/man/getNodeData.Rd | 2 splinetree-0.2.0/splinetree/man/nodePlot.Rd | 2 splinetree-0.2.0/splinetree/man/plotNode.Rd | 4 splinetree-0.2.0/splinetree/man/predictCoeffs.Rd | 4 splinetree-0.2.0/splinetree/man/predictCoeffsForest.Rd | 6 splinetree-0.2.0/splinetree/man/predictY.Rd | 4 splinetree-0.2.0/splinetree/man/predictYForest.Rd | 6 splinetree-0.2.0/splinetree/man/predict_y_training.Rd | 2 splinetree-0.2.0/splinetree/man/projectedR2.Rd | 2 splinetree-0.2.0/splinetree/man/projectedR2Forest.Rd | 13 splinetree-0.2.0/splinetree/man/pruneForest.Rd | 4 splinetree-0.2.0/splinetree/man/spaghettiPlot.Rd | 2 splinetree-0.2.0/splinetree/man/splineForest.Rd | 21 splinetree-0.2.0/splinetree/man/splineTree.Rd | 8 splinetree-0.2.0/splinetree/man/splineTreePlot.Rd | 6 splinetree-0.2.0/splinetree/man/stPlot.Rd | 4 splinetree-0.2.0/splinetree/man/stPrint.Rd | 4 splinetree-0.2.0/splinetree/man/terminalNodeSummary.Rd | 2 splinetree-0.2.0/splinetree/man/treeSimilarity.Rd | 4 splinetree-0.2.0/splinetree/man/treeSize.Rd | 2 splinetree-0.2.0/splinetree/man/treeSummary.Rd | 4 splinetree-0.2.0/splinetree/man/yR2.Rd | 2 splinetree-0.2.0/splinetree/man/yR2Forest.Rd | 8 splinetree-0.2.0/splinetree/tests/testthat/test_forest.R | 2 splinetree-0.2.0/splinetree/vignettes/Forest-Intro.Rmd |only splinetree-0.2.0/splinetree/vignettes/Long-Intro.Rmd | 18 splinetree-0.2.0/splinetree/vignettes/Tree-Intro.Rmd | 8 splinetree-0.2.0/splinetree/vignettes/thesis.bib | 11 51 files changed, 921 insertions(+), 450 deletions(-)
Title: Simulation of in Silico Multi-Omic Networks
Description: A tool for the simulation of gene expression profiles for in silico regulatory networks. The package generates gene regulatory networks, which include protein-coding and noncoding genes linked via different types of regulation: regulation of transcription, translation, RNA or protein decay, and post-translational modifications. The effect of genetic mutations on the system behaviour is accounted for via the simulation of genetically different in silico individuals. The ploidy of the system is not restricted to the usual haploid or diploid situations, but is defined by the user. A choice of stochastic simulation algorithms allow us to simulate the expression profiles (RNA and if applicable protein abundance) of the genes in the in silico system for the different in silico individuals. A tutorial explaining how to use the package is available at <https://oliviaab.github.io/sismonr/>. Manuscript in preparation; see also Angelin-Bonnet O., Biggs P.J. and Vignes M. (2018) <doi:10.1109/BIBM.2018.8621131>.
Author: Olivia Angelin-Bonnet [aut, cre]
(<https://orcid.org/0000-0002-7708-2919>),
Patrick Biggs [aut] (<https://orcid.org/0000-0002-0285-4101>),
Matthieu Vignes [aut] (<https://orcid.org/0000-0001-8929-2975>),
John M. Chambers [ctb]
Maintainer: Olivia Angelin-Bonnet <olivia.angelinbonnet@gmail.com>
Diff between sismonr versions 1.1.3 dated 2019-07-15 and 1.1.4 dated 2019-07-18
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 3 +++ inst/doc/sismonr_vignette.html | 4 ++-- tests/testthat/test-in_silico_population.R | 10 +++++++--- tests/testthat/test-in_silico_system.R | 10 +++++++--- tests/testthat/test-julia_evaluators.R | 10 +++++++--- tests/testthat/test-stochastic_simulation.R | 10 +++++++--- 8 files changed, 43 insertions(+), 24 deletions(-)
Title: Record Everything that Happens in a 'Shiny' Application
Description: Track and record the use of applications and the user's interactions with 'Shiny' inputs.
Allow to save inputs clicked, output generated and eventually errors.
Author: Fanny Meyer [aut],
Victor Perrier [aut, cre],
Silex Technologies [fnd] (https://www.silex-ip.com),
iamkun [cph] (dayjs library),
Mozilla [cph] (localForage library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between shinylogs versions 0.1.5 dated 2019-05-09 and 0.1.6 dated 2019-07-18
DESCRIPTION | 6 - MD5 | 26 +++-- NAMESPACE | 2 NEWS.md | 7 + R/read.R | 3 R/storage.R | 8 + R/tracking.R | 155 ++++++++++++++++++++++---------- README.md | 30 +++++- inst/assets/js/shinylogs-localForage.js | 28 +++-- man/figures |only man/store_null.Rd | 8 + man/track_usage.Rd | 5 - man/use_tracking.Rd |only 13 files changed, 201 insertions(+), 77 deletions(-)
Title: A Semi-Supervised Category Identification and Assignment Tool
Description: An automatic cell type detection and assignment algorithm for single cell RNA-Seq and Cytof/FACS data. 'SCINA' is capable of assigning cell type identities to a pool of cells profiled by scRNA-Seq or Cytof/FACS data with prior knowledge of markers, such as genes and protein symbols that are highly or lowly expressed in each category. See Zhang Z, et al (2019) <doi:10.3390/genes10070531> for more details.
Author: Ze Zhang
Maintainer: Ze Zhang <Ze.Zhang@utsouthwestern.edu>
Diff between SCINA versions 1.1.0 dated 2019-04-29 and 1.2.0 dated 2019-07-18
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- man/SCINA.Rd | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: R Functions for Robust Statistics
Description: Locations problems, M-estimates of coefficients and scale
in linear regression, Weights for bounded influence regression,
Covariance matrix of the coefficient estimates, Asymptotic
relative efficiency of regression M-estimates, Robust testing
in linear models, High breakdown point regression, M-estimates
of covariance matrices, M-estimates for discrete generalized
linear models.
Author: Alfio Marazzi <Alfio.Marazzi@unisante.ch>
Maintainer: A. Randriamiharisoa <exelami@gmail.com>
Diff between robeth versions 2.7-4 dated 2018-08-24 and 2.7-5 dated 2019-07-18
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- src/init.c | 28 ++++++++++++++-------------- src/robeth.f | 6 +++--- 4 files changed, 26 insertions(+), 26 deletions(-)
Title: Xsimd C++ Header-Only Library Files
Description: This header-only library provides modern, portable C++ wrappers for SIMD
intrinsics and parallelized, optimized math implementations (SSE, AVX, NEON, AVX512).
By placing this library in this package, we offer an efficient distribution system for
Xsimd <https://github.com/QuantStack/xsimd> for R packages using CRAN.
Author: Marc A. Suchard [aut, cre],
Andrew J. Holbrook [aut],
Observational Health Data Sciences and Informatics [cph],
Johan Mabille [cph, ctb] (author and copyright holder of Xsimd library
under a BSD-3 license),
Sylvain Corlay [cph, ctb] (author and copyright holder of Xsimd library
under a BSD-3 license),
Alexander J. Lee [cph, ctb] (author and copyright holder of
FeatureDetector library under a CC0 1.0 license)
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between RcppXsimd versions 7.1.3 dated 2019-05-24 and 7.1.4 dated 2019-07-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/include/xsimd/types/xsimd_avx512_int8.hpp | 2 ++ inst/include/xsimd/types/xsimd_avx_int8.hpp | 6 ++++-- inst/include/xsimd/types/xsimd_sse_int8.hpp | 2 ++ 6 files changed, 21 insertions(+), 11 deletions(-)
Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving,
viewing, visualizing, summarizing, transforming, and combining data. It also
contains functionality to generate reproducible reports of the analyses
conducted in the application.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.data versions 0.9.9 dated 2019-03-04 and 1.0.0 dated 2019-07-18
DESCRIPTION | 14 +++---- MD5 | 40 ++++++++++----------- NEWS.md | 6 +++ R/explore.R | 3 + R/radiant.R | 4 +- R/transform.R | 35 +++++++++++++++++++ R/visualize.R | 6 +-- inst/app/global.R | 17 +++++++++ inst/app/radiant.R | 2 - inst/app/tools/app/report_r.R | 13 ++++--- inst/app/tools/app/report_rmd.R | 12 +++--- inst/app/tools/data/explore_ui.R | 2 - inst/app/tools/data/pivotr_ui.R | 2 - inst/app/tools/data/transform_ui.R | 68 ++++++++++++++++++++++++++++++------- inst/app/tools/data/visualize_ui.R | 2 - inst/app/tools/help/transform.Rmd | 3 + inst/app/tools/help/transform.md | 3 + inst/app/www/js/run_return.js | 2 - man/iterms.Rd | 2 - man/pfun.Rd | 2 - tests/testthat/test_funs.R | 38 +++++++++++++++++--- 21 files changed, 209 insertions(+), 67 deletions(-)
Title: Quantification of Asymmetric Dependence
Description: A copula-based measure for quantifying asymmetry in dependence and associations.
Author: Florian Griessenberger, Robert R. Junker, Wolfgang Trutschnig
Maintainer: Florian Griessenberger <Florian.Griessenberger@sbg.ac.at>
Diff between qad versions 0.1.0 dated 2018-12-23 and 0.1.1 dated 2019-07-18
DESCRIPTION | 13 ++-- MD5 | 26 ++++---- NAMESPACE | 2 R/emp_c_copula.R | 47 +++++++-------- R/plots.R | 157 +++++++++++++++++++++++++++++----------------------- R/qad.R | 27 ++++++-- man/emp_c_copula.Rd | 4 - man/figures |only man/heatmap.qad.Rd | 11 ++- man/pairwise.qad.Rd | 6 + man/plot.qad.Rd | 7 +- man/plot_density.Rd | 7 +- man/qad-package.Rd |only man/qad.Rd | 9 ++ 14 files changed, 188 insertions(+), 128 deletions(-)
Title: Execute and Control System Processes
Description: Tools to run system processes in the background.
It can check if a background process is running; wait on a background
process to finish; get the exit status of finished processes; kill
background processes. It can read the standard output and error of
the processes, using non-blocking connections. 'processx' can poll
a process for standard output or error, with a timeout. It can also
poll several processes at once.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>),
Winston Chang [aut],
RStudio [cph, fnd],
Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between processx versions 3.4.0 dated 2019-07-03 and 3.4.1 dated 2019-07-18
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/run.R | 4 ++-- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Creating Pretty Documents from R Markdown
Description: Creating tiny yet beautiful documents and vignettes from R
Markdown. The package provides the 'html_pretty' output format as an
alternative to the 'html_document' and 'html_vignette' engines that
convert R Markdown into HTML pages. Various themes and syntax highlight
styles are supported.
Author: Yixuan Qiu [aut, cre],
Jason Long [ctb] (the Cayman, Tactile and Architect themes),
Renyuan Zou [ctb] (the Leonids theme),
Michael Rose [ctb] (the HPSTR theme),
JJ Allaire [ctb] (pandoc template for rmarkdown),
Hadley Wickham [ctb] (the html_vignette() function),
Yihui Xie [ctb] (the html_vignette() function),
Steve Matteson [ctb] (the Open Sans fonts),
Emily Eisenberg [ctb] (the KaTeX library),
Sophie Alpert [ctb] (the KaTeX library)
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between prettydoc versions 0.2.1 dated 2018-01-16 and 0.3.0 dated 2019-07-18
DESCRIPTION | 20 MD5 | 85 +- R/html_pretty.R | 45 + README.md | 66 +- build/vignette.rds |binary inst/AUTHORS | 5 inst/NEWS.Rd | 10 inst/doc/architect.Rmd | 38 + inst/doc/architect.html | 280 ++++++--- inst/doc/cayman.Rmd | 38 + inst/doc/cayman.html | 289 ++++++--- inst/doc/hpstr.Rmd | 38 + inst/doc/hpstr.html | 289 ++++++--- inst/doc/leonids.Rmd | 38 + inst/doc/leonids.html | 293 ++++++---- inst/doc/tactile.Rmd | 38 + inst/doc/tactile.html | 293 ++++++---- inst/resources/css/highlight/github.css | 18 inst/resources/css/highlight/vignette.css | 24 inst/resources/css/katex |only inst/resources/fonts/KaTeX_AMS-Regular.woff |only inst/resources/fonts/KaTeX_Caligraphic-Bold.woff |only inst/resources/fonts/KaTeX_Caligraphic-Regular.woff |only inst/resources/fonts/KaTeX_Fraktur-Bold.woff |only inst/resources/fonts/KaTeX_Fraktur-Regular.woff |only inst/resources/fonts/KaTeX_Main-Bold.woff |only inst/resources/fonts/KaTeX_Main-BoldItalic.woff |only inst/resources/fonts/KaTeX_Main-Italic.woff |only inst/resources/fonts/KaTeX_Main-Regular.woff |only inst/resources/fonts/KaTeX_Math-BoldItalic.woff |only inst/resources/fonts/KaTeX_Math-Italic.woff |only inst/resources/fonts/KaTeX_SansSerif-Bold.woff |only inst/resources/fonts/KaTeX_SansSerif-Italic.woff |only inst/resources/fonts/KaTeX_SansSerif-Regular.woff |only inst/resources/fonts/KaTeX_Script-Regular.woff |only inst/resources/fonts/KaTeX_Size1-Regular.woff |only inst/resources/fonts/KaTeX_Size2-Regular.woff |only inst/resources/fonts/KaTeX_Size3-Regular.woff |only inst/resources/fonts/KaTeX_Size4-Regular.woff |only inst/resources/fonts/KaTeX_Typewriter-Regular.woff |only inst/resources/js |only inst/resources/templates/architect.html | 278 ++++++--- inst/resources/templates/cayman.html | 278 ++++++--- inst/resources/templates/hpstr.html | 278 ++++++--- inst/resources/templates/leonids.html | 278 ++++++--- inst/resources/templates/tactile.html | 278 ++++++--- inst/rmarkdown/templates/html_pretty_document/skeleton/skeleton.Rmd | 6 inst/rmarkdown/templates/html_pretty_vignette/skeleton/skeleton.Rmd | 4 man/html_pretty.Rd | 16 vignettes/architect.Rmd | 38 + vignettes/cayman.Rmd | 38 + vignettes/hpstr.Rmd | 38 + vignettes/leonids.Rmd | 38 + vignettes/tactile.Rmd | 38 + 54 files changed, 2476 insertions(+), 1037 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between openssl versions 1.4 dated 2019-05-31 and 1.4.1 dated 2019-07-18
DESCRIPTION | 6 ++--- MD5 | 42 ++++++++++++++++++------------------ NEWS | 4 +++ R/cert.R | 6 +++-- R/keygen.R | 1 R/list.R | 4 +-- R/write.R | 4 +-- build/vignette.rds |binary inst/doc/bignum.html | 28 ++++++++++++------------ inst/doc/crypto_hashing.html | 8 +++--- inst/doc/keys.html | 42 ++++++++++++++++++------------------ inst/doc/secure_rng.html | 18 +++++++-------- man/keygen.Rd | 1 src/cert.c | 7 +++--- src/compatibility.c | 12 ++++++++++ src/compatibility.h | 7 +++++- src/rsa.c | 2 + src/write.c | 40 ++++++++++++++++++++++++++++------ tests/testthat/test_keys_dsa.R | 7 ++++++ tests/testthat/test_keys_ecdsa.R | 7 ++++++ tests/testthat/test_keys_ecdsa384.R | 7 ++++++ tests/testthat/test_keys_ecdsa521.R | 7 ++++++ 22 files changed, 171 insertions(+), 89 deletions(-)
Title: Minimum Energy Designs
Description: This is a method (MinED) for mining probability distributions using deterministic sampling which is proposed by Joseph, Wang, Gu, Lv, and Tuo (2018). The MinED samples can be used for approximating the target distribution. They can be generated from a density function that is known only up to a proportionality constant and thus, it might find applications in Bayesian computation. Moreover, the MinED samples are generated with much fewer evaluations of the density function compared to random sampling-based methods such as MCMC and therefore, this method will be especially useful when the unnormalized posterior is expensive or time consuming to evaluate.
Author: Dianpeng Wang and V. Roshan Joseph
Maintainer: Dianpeng Wang <wdp@bit.edu.cn>
Diff between mined versions 1.0-1 dated 2018-12-16 and 1.0-2 dated 2019-07-18
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/RcppExports.R | 4 ++-- man/mined-package.Rd | 2 +- man/mined.Rd | 12 ++++++++---- src/CreateMED.cpp | 14 ++++++++++++-- src/RcppExports.cpp | 9 +++++---- 7 files changed, 38 insertions(+), 23 deletions(-)
Title: Tools to Read, Analyze and Visualize Metadynamics HILLS Files
from 'Plumed'
Description: Metadynamics is a state of the art biomolecular simulation technique.
'Plumed' Tribello, G.A. et al. (2014) <doi:10.1016/j.cpc.2013.09.018> program makes
it possible to perform metadynamics using various simulation codes. The results of
metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package
'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package.
It uses a fast algorithm by Hosek, P. and Spiwok, V. (2016) <doi:10.1016/j.cpc.2015.08.037>
to calculate a free energy surface from hills. Minima can be located and plotted on
the free energy surface. Transition states can be analyzed by Nudged Elastic Band
method by Henkelman, G. and Jonsson, H. (2000) <doi:10.1063/1.1323224>. Free energy
surfaces, minima and transition paths can be plotted to produce publication quality
images.
Author: Vojtech Spiwok [aut, cre] (<https://orcid.org/0000-0001-8108-2033>)
Maintainer: Vojtech Spiwok <spiwokv@vscht.cz>
Diff between metadynminer versions 0.1.4 dated 2019-03-13 and 0.1.5 dated 2019-07-18
DESCRIPTION | 9 - MD5 | 36 +++-- NAMESPACE | 7 + R/minimaandpaths.R | 68 ++++++++- R/readingandfes.R | 295 +++++++++++++++++++++++++++++-------------- README.md | 1 man/feprof.Rd | 17 -- man/feprof.minima.Rd |only man/fes.Rd | 11 - man/fes.hillsfile.Rd |only man/fes2.Rd | 11 - man/fes2.hillsfile.Rd |only man/fesminima.Rd | 10 - man/fesminima.fes.Rd |only man/oneminimum.Rd | 13 - man/oneminimum.fes.Rd |only man/plotheights.Rd | 11 - man/plotheights.hillsfile.Rd |only man/read.plumed.Rd |only src/mm.cpp | 42 +++--- tests |only 21 files changed, 349 insertions(+), 182 deletions(-)
Title: Tools for Parsing, Manipulating, and Graphing Taxonomic
Abundance Data
Description: A set of tools for parsing, manipulating, and graphing data
classified by a hierarchy (e.g. a taxonomy).
Author: Zachary Foster [aut, cre],
Niklaus Grunwald [ths],
Rob Gilmore [ctb]
Maintainer: Zachary Foster <zacharyfoster1989@gmail.com>
Diff between metacoder versions 0.3.2 dated 2019-04-08 and 0.3.3 dated 2019-07-18
DESCRIPTION | 13 -- MD5 | 56 ++++---- NEWS.md | 5 R/as_phyloseq.R | 7 + R/calculations.R | 49 ++++--- R/heat_tree.R | 2 R/heat_tree_matrix.R | 57 ++++++-- R/option_parsers.R | 6 R/startup.R | 14 +- inst/doc/introduction.html | 184 ++++++++++++++++++++++++++++- man/calc_group_mean.Rd | 2 man/calc_group_median.Rd | 2 man/calc_group_rsd.Rd | 2 man/calc_group_stat.Rd | 2 man/calc_n_samples.Rd | 2 man/calc_obs_props.Rd | 2 man/calc_prop_samples.Rd | 4 man/calc_taxon_abund.Rd | 2 man/compare_groups.Rd | 11 + man/counts_to_presence.Rd | 2 man/get_taxmap_cols.Rd | 2 man/get_taxmap_data.Rd | 2 man/get_taxmap_other_cols.Rd | 2 man/heat_tree.Rd | 2 man/heat_tree_matrix.Rd | 2 man/ncbi_taxon_sample.Rd | 27 ++-- man/rarefy_obs.Rd | 2 man/zero_low_counts.Rd | 2 tests/testthat/test--parsers_and_writers.R | 2 29 files changed, 352 insertions(+), 115 deletions(-)
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 0.1.3 dated 2018-12-03 and 0.2.0 dated 2019-07-18
DESCRIPTION | 14 +- MD5 | 35 +++-- NAMESPACE | 3 NEWS.md |only R/initializeLogging.R | 70 +++------- R/pylogger.R | 263 ++++++++++++++++++++++------------------- R/utils-pipe.R |only R/utils-time.R |only build/vignette.rds |binary inst/doc/cache-management.html | 34 ++++- inst/doc/error-handling.Rmd | 4 inst/doc/error-handling.html | 71 +++++++---- inst/doc/logging.Rmd | 4 inst/doc/logging.html | 97 +++++++++------ man/dateRange.Rd |only man/initializeLogging.Rd | 31 ---- man/logger.setLevel.Rd | 10 - man/logger.setup.Rd | 52 ++++---- man/pipe.Rd |only vignettes/error-handling.Rmd | 4 vignettes/logging.Rmd | 4 21 files changed, 388 insertions(+), 308 deletions(-)
More information about MazamaCoreUtils at CRAN
Permanent link
Title: Clustering with Matrix Gaussian and Matrix Transformation
Mixture Models
Description: Provides matrix Gaussian mixture models, matrix transformation mixture models and their model-based clustering results. The parsimonious models of the mean matrices and variance covariance matrices are implemented with a total of 196 variations.
Author: Xuwen Zhu [aut, cre],
Volodymyr Melnykov [aut],
Shuchismita Sarkar [ctb],
Michael Hutt [ctb, cph],
Stephen Moshier [ctb, cph],
Rouben Rostamian [ctb, cph],
Carl Edward Rasmussen [ctb, cph],
Dianne Cook [ctb, cph]
Maintainer: Xuwen Zhu <xuwen.zhu@louisville.edu>
Diff between MatTransMix versions 0.1.2 dated 2019-06-18 and 0.1.4 dated 2019-07-18
DESCRIPTION | 8 - MD5 | 20 ++-- NEWS | 8 + R/libMatTransFull.R | 51 ++++++++++- demo/EMalgorithm1.R | 6 - demo/EMalgorithm2.R | 6 - man/MatTrans.EM.Rd | 7 - src/MatTransMix.h | 10 +- src/crosen1.c | 29 +++--- src/crosen2.c | 26 ++--- src/libFull.c | 226 ++++++++++++++-------------------------------------- 11 files changed, 168 insertions(+), 229 deletions(-)
More information about matrixStrucTest at CRAN
Permanent link
Title: Joint Frailty-Copula Models for Tumour Progression and Death in
Meta-Analysis
Description: Perform likelihood estimation and dynamic prediction under
joint frailty-copula models for tumour progression and death in meta-analysis.
A penalized likelihood method is employed for estimating model parameters, where the baseline hazard functions are modeled by smoothing splines.
The methods are applicable for meta-analytic data combining several studies.
The methods can analyze data having information on both terminal event time (e.g., time-to-death) and non-terminal event time (e.g., time-to-tumour progression).
See Emura et al. (2017) <doi:10.1177/0962280215604510> for likelihood estimation, and
Emura et al. (2018) <doi:10.1177/0962280216688032> for dynamic prediction.
Survival data from ovarian cancer patients are also available.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 3.3 dated 2019-06-12 and 3.4 dated 2019-07-18
DESCRIPTION | 8 ++++---- MD5 | 6 ++++-- R/jointCox.Weibull.reg.R |only man/joint.Cox-package.Rd | 4 ++-- man/jointCox.Weibull.reg.Rd |only 5 files changed, 10 insertions(+), 8 deletions(-)
Title: Fit Text Inside a Box in 'ggplot2'
Description: Provides 'ggplot2' geoms to fit text into a box by growing, shrinking
or wrapping the text.
Author: David Wilkins [aut, cre]
Maintainer: David Wilkins <david@wilkox.org>
Diff between ggfittext versions 0.8.0 dated 2019-06-23 and 0.8.1 dated 2019-07-18
DESCRIPTION | 11 +++--- MD5 | 48 ++++++++++++++++++++---------- NEWS.md | 10 ++++++ R/geom_fit_text.R | 5 +++ build/vignette.rds |binary inst/WORDLIST |only inst/doc/introduction-to-ggfittext.html | 10 ++++-- man/figures/README-hero-1.png |binary man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary tests/figs |only tests/spelling.R |only tests/testthat/test-geom_bar_text.R |only tests/testthat/test-geom_fit_text.R | 13 ++++++++ tests/testthat/test_plots.R |only 22 files changed, 73 insertions(+), 24 deletions(-)
Title: Mediation Analysis for Generalized Linear Models Using the
Difference Method
Description: Causal mediation analysis for a single exposure/treatment and a
single mediator, both allowed to be either continuous or binary. The package
implements the difference method and provide point and interval estimates as
well as testing for the natural direct and indirect effects and the mediation
proportion. Nevo, Xiao and Spiegelman (2019) <doi:10.1515/ijb-2017-0006>.
Author: Daniel Nevo [aut, cre]
Maintainer: Daniel Nevo <danielnevo@gmail.com>
Diff between GEEmediate versions 1.1.1 dated 2017-05-12 and 1.1.3 dated 2019-07-18
DESCRIPTION | 13 +-- MD5 | 9 +- R/DupliData.R | 35 ++++++-- R/Methods.R | 211 +++++++++++++++++++++++++++--------------------------- README.md |only man/GEEmediate.Rd | 157 +++++++++++++++++++--------------------- 6 files changed, 224 insertions(+), 201 deletions(-)
Title: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from
Functional MRI of the Brain ('FMRIB')
Description: Wrapper functions that interface with 'FSL'
<http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>, a powerful and commonly-used 'neuroimaging'
software, using system commands. The goal is to be able to interface with 'FSL'
completely in R, where you pass R objects of class 'nifti', implemented by
package 'oro.nifti', and the function executes an 'FSL' command and returns an R
object of class 'nifti' if desired.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between fslr versions 2.22.0 dated 2018-11-19 and 2.23.0 dated 2019-07-18
DESCRIPTION | 8 +- MD5 | 29 +++++---- NAMESPACE | 3 NEWS.md | 4 + R/face_removal_mask.R |only R/flirt_apply.R | 2 R/fslhd.R | 6 + R/fslview.R | 9 ++ R/mni_fname.R | 14 ++++ build/vignette.rds |binary inst/doc/dti_data.html | 146 ++++++++++++++++++++++++++++------------------- inst/doc/fslr.html | 37 +++++++++-- inst/extdata |only man/face_removal_mask.Rd |only man/fslview.help.Rd | 9 ++ man/mni_fname.Rd | 3 16 files changed, 182 insertions(+), 88 deletions(-)
Title: Wrapper Functions for 'Freesurfer'
Description: Wrapper functions that interface with 'Freesurfer'
<https://surfer.nmr.mgh.harvard.edu/>, a powerful and
commonly-used 'neuroimaging'
software, using system commands. The goal is to be able to interface with
'Freesurfer' completely in R, where you pass R objects of class 'nifti',
implemented by package 'oro.nifti', and the function executes an 'Freesurfer'
command and returns an R object of class 'nifti' or necessary output.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between freesurfer versions 1.6.1 dated 2017-10-10 and 1.6.5 dated 2019-07-18
DESCRIPTION | 10 MD5 | 36 +- NAMESPACE | 1 NEWS.md | 9 R/fs_setup.R | 18 - R/mnc2nii.R | 8 R/mri_deface.R |only R/read_label.R | 3 R/recon.R | 2 build/vignette.rds |binary inst/doc/exploring_included_data.html | 537 ++++++++++++++++++++++++---------- man/asegstats2table.Rd | 4 man/construct_subj_dir.Rd | 5 man/mri_deface.Rd |only man/mri_surf2surf.Rd | 8 man/read_fs_label.Rd | 3 man/read_fs_table.Rd | 4 man/recon.Rd | 14 man/recon_all.Rd | 4 man/reconner.Rd | 4 20 files changed, 471 insertions(+), 199 deletions(-)
Title: Fingertips Data for Public Health
Description: Fingertips (<http://fingertips.phe.org.uk/>) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API.
Author: Sebastian Fox [aut, cre],
Julian Flowers [aut, ctb],
Simon Thelwall [ctb] (<https://orcid.org/0000-0002-0434-2724>),
Duncan Gormansway [ctb],
Carl Ganz [ctb],
David Whiting [ctb],
Crown Copyright 2018 [cph]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>
Diff between fingertipsR versions 0.2.6 dated 2019-06-07 and 0.2.7 dated 2019-07-18
DESCRIPTION | 6 MD5 | 32 ++--- NAMESPACE | 1 NEWS.md | 10 + R/area_types.R | 18 ++ R/fingertipsR.R | 3 R/fingertips_data.R | 215 ++++++++++++++++++++++++++++------- R/retrieve_data.R | 51 +++++++- R/utils.R | 2 README.md | 6 inst/doc/lifeExpectancy.html | 28 ++-- inst/doc/selectIndicatorsRedRed.html | 2 man/area_types.Rd | 5 man/fingertips_data.Rd | 9 + man/indicator_order.Rd | 4 tests/testthat/test-area_types.R | 2 tests/testthat/test-extract.R | 13 +- 17 files changed, 316 insertions(+), 91 deletions(-)
Title: Efficient Effect Size Computation
Description: A collection of functions to compute the standardized
effect sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha-Delaney A).
The computation algorithms have been optimized to allow efficient computation even
with very large data sets.
Author: Marco Torchiano [aut, cre]
Maintainer: Marco Torchiano <marco.torchiano@polito.it>
Diff between effsize versions 0.7.4 dated 2018-12-21 and 0.7.6 dated 2019-07-18
DESCRIPTION | 8 ++-- MD5 | 14 +++---- NAMESPACE | 2 - R/CohenD.R | 73 +++++++++++++++++++++++++++----------- man/cohen.d.Rd | 2 - man/effsize-package.Rd | 2 + tests/testthat/testCliff.R | 14 +++++-- tests/testthat/testCohenD.R | 84 ++++++++++++++++++++++++++++++++++---------- 8 files changed, 142 insertions(+), 57 deletions(-)
Title: Create Interactive Graphs with 'Echarts JavaScript' Version 4
Description: Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes
34 chart types, themes, 'Shiny' proxies and animations.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between echarts4r versions 0.2.2 dated 2019-04-09 and 0.2.3 dated 2019-07-18
echarts4r-0.2.2/echarts4r/R/add__.R |only echarts4r-0.2.3/echarts4r/DESCRIPTION | 14 - echarts4r-0.2.3/echarts4r/MD5 | 165 +++++++++---------- echarts4r-0.2.3/echarts4r/NAMESPACE | 1 echarts4r-0.2.3/echarts4r/NEWS.md | 13 + echarts4r-0.2.3/echarts4r/R/actions.R | 12 - echarts4r-0.2.3/echarts4r/R/add.R | 46 ++--- echarts4r-0.2.3/echarts4r/R/add_.R | 6 echarts4r-0.2.3/echarts4r/R/calendar.R | 2 echarts4r-0.2.3/echarts4r/R/callbacks.R | 2 echarts4r-0.2.3/echarts4r/R/color.R | 4 echarts4r-0.2.3/echarts4r/R/geo.R | 2 echarts4r-0.2.3/echarts4r/R/graphic.R | 28 +-- echarts4r-0.2.3/echarts4r/R/grid.R | 10 - echarts4r-0.2.3/echarts4r/R/helpers.R | 8 echarts4r-0.2.3/echarts4r/R/map.R | 8 echarts4r-0.2.3/echarts4r/R/mark.R | 6 echarts4r-0.2.3/echarts4r/R/nesting.R | 6 echarts4r-0.2.3/echarts4r/R/opts.R | 57 ++++-- echarts4r-0.2.3/echarts4r/R/plugins.R | 4 echarts4r-0.2.3/echarts4r/R/proxies.R | 8 echarts4r-0.2.3/echarts4r/R/timeline.R | 2 echarts4r-0.2.3/echarts4r/R/utils.R | 9 - echarts4r-0.2.3/echarts4r/README.md | 2 echarts4r-0.2.3/echarts4r/man/angle_axis.Rd | 2 echarts4r-0.2.3/echarts4r/man/axis.Rd | 4 echarts4r-0.2.3/echarts4r/man/callbacks.Rd | 2 echarts4r-0.2.3/echarts4r/man/e-tooltip.Rd | 10 - echarts4r-0.2.3/echarts4r/man/e_add.Rd | 6 echarts4r-0.2.3/echarts4r/man/e_animation.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_area.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_aria.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_axis_pointer.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_bar.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_boxplot.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_brush.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_calendar.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_candle.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_capture.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_cloud.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_color.Rd | 4 echarts4r-0.2.3/echarts4r/man/e_datazoom.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_dispatch_action_p.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_funnel.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_gauge.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_geo.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_grid.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_heatmap.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_labels.Rd | 4 echarts4r-0.2.3/echarts4r/man/e_legend.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_line.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_lines.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_liquid.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_map_register.Rd | 4 echarts4r-0.2.3/echarts4r/man/e_parallel.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_pictorial.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_pie.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_polar.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_river.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_sankey.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_step.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_sunburst.Rd | 4 echarts4r-0.2.3/echarts4r/man/e_text_style.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_title.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_tree.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_treemap.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_visual_map.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_visual_map_range.Rd | 2 echarts4r-0.2.3/echarts4r/man/e_zoom.Rd | 2 echarts4r-0.2.3/echarts4r/man/graph.Rd | 2 echarts4r-0.2.3/echarts4r/man/graph_action.Rd | 2 echarts4r-0.2.3/echarts4r/man/graphic.Rd | 28 +-- echarts4r-0.2.3/echarts4r/man/line3D.Rd | 2 echarts4r-0.2.3/echarts4r/man/map.Rd | 4 echarts4r-0.2.3/echarts4r/man/map_actions.Rd | 2 echarts4r-0.2.3/echarts4r/man/mark.Rd | 6 echarts4r-0.2.3/echarts4r/man/node_adjacency.Rd | 2 echarts4r-0.2.3/echarts4r/man/pie_action.Rd | 2 echarts4r-0.2.3/echarts4r/man/radius_axis.Rd | 2 echarts4r-0.2.3/echarts4r/man/scatter.Rd | 4 echarts4r-0.2.3/echarts4r/man/timeline-opts.Rd | 2 echarts4r-0.2.3/echarts4r/man/toolbox.Rd | 2 echarts4r-0.2.3/echarts4r/man/tooltip_action.Rd | 2 echarts4r-0.2.3/echarts4r/man/tooltip_proxy.Rd | 2 84 files changed, 314 insertions(+), 277 deletions(-)
Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Baltagi (2011) <doi:10.1007/978-3-642-20059-5> for more information.
Author: Haydar Demirhan [aut, cre, cph] (<https://orcid.org/0000-0002-8565-4710>)
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>
Diff between dLagM versions 1.0.12 dated 2019-05-02 and 1.0.15 dated 2019-07-18
DESCRIPTION | 8 ++++---- MD5 | 15 +++++++++------ NEWS.md | 4 ++++ R/ardlDlmForecast.main.R | 12 ++++++++++-- R/dlmForecast.main.R | 24 ++++++++++++++++++++---- build |only data/wheat.RData |only man/dLagM-package.Rd | 15 +++++++++++---- man/forecast.Rd | 2 +- man/wheat.Rd |only 10 files changed, 59 insertions(+), 21 deletions(-)
Title: Package Directives and Collaboration Networks in CRAN
Description: Core visualizations and summaries for the CRAN package database. The package provides comprehensive methods for cleaning up and organizing the information in the CRAN package database, for building package directives networks (depends, imports, suggests, enhances, linking to) and collaboration networks, producing package dependence trees, and for computing useful summaries and producing interactive visualizations from the resulting networks and summaries. The resulting networks can be coerced to 'igraph' <https://CRAN.R-project.org/package=igraph> objects for further analyses and modelling.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>)
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between cranly versions 0.3 dated 2019-02-14 and 0.5.2 dated 2019-07-18
cranly-0.3/cranly/man/build_network.Rd |only cranly-0.3/cranly/man/package_by.Rd |only cranly-0.5.2/cranly/DESCRIPTION | 10 cranly-0.5.2/cranly/MD5 | 90 cranly-0.5.2/cranly/NAMESPACE | 61 cranly-0.5.2/cranly/NEWS.md | 31 cranly-0.5.2/cranly/R/build_network.R | 66 cranly-0.5.2/cranly/R/clean_CRAN_db.R | 85 cranly-0.5.2/cranly/R/coerce.R | 39 cranly-0.5.2/cranly/R/cranly-package.R | 185 + cranly-0.5.2/cranly/R/dependence_tree.R | 65 cranly-0.5.2/cranly/R/extractors.R | 1020 ++++++++-- cranly-0.5.2/cranly/R/plot_network.R | 32 cranly-0.5.2/cranly/R/plot_summary.R | 12 cranly-0.5.2/cranly/R/plot_tree.R | 12 cranly-0.5.2/cranly/R/subset.R | 48 cranly-0.5.2/cranly/R/summary.R | 44 cranly-0.5.2/cranly/R/utilities.R | 2 cranly-0.5.2/cranly/R/wordcloud.R |only cranly-0.5.2/cranly/R/zzz_aliases.R |only cranly-0.5.2/cranly/build/vignette.rds |binary cranly-0.5.2/cranly/inst/art |only cranly-0.5.2/cranly/inst/doc/cranly.Rmd | 12 cranly-0.5.2/cranly/inst/doc/cranly.html | 171 - cranly-0.5.2/cranly/inst/doc/dependence_trees.Rmd | 6 cranly-0.5.2/cranly/inst/doc/dependence_trees.html | 151 - cranly-0.5.2/cranly/inst/doc/extractors.R |only cranly-0.5.2/cranly/inst/doc/extractors.Rmd |only cranly-0.5.2/cranly/inst/doc/extractors.html |only cranly-0.5.2/cranly/inst/doc/glms.Rmd | 6 cranly-0.5.2/cranly/inst/doc/glms.html | 184 + cranly-0.5.2/cranly/man/as.igraph.cranly_network.Rd | 36 cranly-0.5.2/cranly/man/build_dependence_tree.cranly_network.Rd | 16 cranly-0.5.2/cranly/man/build_network.cranly_db.Rd | 23 cranly-0.5.2/cranly/man/clean_CRAN_db.Rd | 49 cranly-0.5.2/cranly/man/clean_up_author.Rd | 4 cranly-0.5.2/cranly/man/clean_up_directives.Rd | 4 cranly-0.5.2/cranly/man/compute_dependence_tree.Rd | 6 cranly-0.5.2/cranly/man/compute_term_frequency.Rd |only cranly-0.5.2/cranly/man/cranly.Rd | 8 cranly-0.5.2/cranly/man/extractor-functions.Rd |only cranly-0.5.2/cranly/man/plot.cranly_dependence_tree.Rd | 20 cranly-0.5.2/cranly/man/plot.cranly_network.Rd | 40 cranly-0.5.2/cranly/man/plot.summary_cranly_network.Rd | 10 cranly-0.5.2/cranly/man/subset.cranly_network.Rd | 29 cranly-0.5.2/cranly/man/summary.cranly_dependence_tree.Rd | 29 cranly-0.5.2/cranly/man/summary.cranly_network.Rd | 26 cranly-0.5.2/cranly/man/word_cloud.cranly_network.Rd |only cranly-0.5.2/cranly/vignettes/cranly.Rmd | 12 cranly-0.5.2/cranly/vignettes/dependence_trees.Rmd | 6 cranly-0.5.2/cranly/vignettes/extractors.Rmd |only cranly-0.5.2/cranly/vignettes/glms.Rmd | 6 52 files changed, 1780 insertions(+), 876 deletions(-)
Title: Check for Namespace Collisions with Other Packages and Functions
on CRAN
Description: Check for namespace collisions between a string input (your function or package name) and a quarter of a million packages and functions on CRAN.
Author: Steve Condylios [aut, cre] (<https://orcid.org/0000-0003-0599-844X>)
Maintainer: Steve Condylios <steve.condylios@gmail.com>
Diff between collidr versions 0.1.0 dated 2019-05-04 and 0.1.1 dated 2019-07-18
collidr-0.1.0/collidr/R/packages_and_functions_dataframe-data.R |only collidr-0.1.0/collidr/data/packages_and_functions_dataframe.RData |only collidr-0.1.0/collidr/man/packages_and_functions_dataframe.Rd |only collidr-0.1.1/collidr/DESCRIPTION | 10 collidr-0.1.1/collidr/MD5 | 27 - collidr-0.1.1/collidr/NAMESPACE | 2 collidr-0.1.1/collidr/R/CRANdf-data.R |only collidr-0.1.1/collidr/R/collisions.R | 167 ++++++---- collidr-0.1.1/collidr/data/CRANdf.RData |only collidr-0.1.1/collidr/data/datalist | 2 collidr-0.1.1/collidr/man/CRAN_collisions.Rd | 4 collidr-0.1.1/collidr/man/CRAN_function_collisions.Rd | 4 collidr-0.1.1/collidr/man/CRAN_functions.Rd | 12 collidr-0.1.1/collidr/man/CRAN_package_collisions.Rd | 4 collidr-0.1.1/collidr/man/CRAN_packages.Rd | 12 collidr-0.1.1/collidr/man/CRAN_packages_and_functions.Rd | 12 collidr-0.1.1/collidr/man/CRANdf.Rd |only collidr-0.1.1/collidr/man/getCRAN.Rd |only 18 files changed, 166 insertions(+), 90 deletions(-)
Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids
and Affinity Propagation Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>; (iv) "Clustering by Passing Messages Between Data Points" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, <doi:10.1126/science.1136800>.
Author: Lampros Mouselimis [aut, cre],
Conrad Sanderson [cph] (Author of the C++ Armadillo library),
Ryan Curtin [cph] (Author of the C++ Armadillo library),
Siddharth Agrawal [cph] (Author of the C code of the Mini-Batch-Kmeans
algorithm
(https://github.com/siddharth-agrawal/Mini-Batch-K-Means)),
Brendan Frey [cph] (Author of the matlab code of the Affinity
propagation algorithm (for commercial use please contact the author
of the matlab code)),
Delbert Dueck [cph] (Author of the matlab code of the Affinity
propagation algorithm)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between ClusterR versions 1.1.9 dated 2019-04-14 and 1.2.0 dated 2019-07-18
DESCRIPTION | 8 MD5 | 34 NEWS.md | 7 R/clustering_functions.R | 1250 +++++++++++++-------------- inst/doc/the_clusterR_package.html | 35 inst/include/ClusterRHeader.h | 39 man/AP_affinity_propagation.Rd | 18 man/AP_preferenceRange.Rd | 6 man/Clara_Medoids.Rd | 2 man/Cluster_Medoids.Rd | 2 man/GMM.Rd | 2 man/KMeans_arma.Rd | 2 man/Optimal_Clusters_GMM.Rd | 4 man/Optimal_Clusters_KMeans.Rd | 12 man/Optimal_Clusters_Medoids.Rd | 4 man/distance_matrix.Rd | 2 man/predict_Medoids.Rd | 2 tests/testthat/test-dissimilarity_matrices.R | 526 +++++------ 18 files changed, 1011 insertions(+), 944 deletions(-)
Title: Google's Compact Language Detector 3
Description: Google's Compact Language Detector 3 is a neural network model for language
identification and the successor of 'cld2' (available from CRAN). The algorithm is still
experimental and takes a novel approach to language detection with different properties
and outcomes. It can be useful to combine this with the Bayesian classifier results
from 'cld2'. See <https://github.com/google/cld3#readme> for more information.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Google Inc [cph] (CLD3 C++ library)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between cld3 versions 1.1 dated 2018-06-28 and 1.2 dated 2019-07-18
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 4 ++++ configure | 5 +++++ src/Makevars.win | 25 ++++++++++++------------- 5 files changed, 28 insertions(+), 20 deletions(-)
Title: Accessing Statistics Canada Data Table and Vectors
Description: Searches for, accesses, and retrieves new-format and old-format Statistics Canada data
tables, as well as individual vectors, as tidy data frames. This package deals with encoding issues, allows for
bilingual English or French language data retrieval, and bundles convenience functions
to make it easier to work with retrieved table data. Optional caching features are provided.
Author: Jens von Bergmann [cre],
Dmitry Shkolnik [aut]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between cansim versions 0.2.3 dated 2019-01-07 and 0.3.0 dated 2019-07-18
DESCRIPTION | 6 - MD5 | 45 ++++++----- NAMESPACE | 1 NEWS.md | 11 ++ R/cansim.R | 100 +++++++++++++++++++------- R/cansim_helpers.R | 57 +++++++++++++- R/cansim_tables_list.R | 2 R/sysdata.rda |binary README.md | 11 +- build/vignette.rds |binary inst/Statistics_Canada_Open_Licence_Agreement |only inst/doc/cansim.Rmd | 2 inst/doc/cansim.html | 87 +++++++++++++++------- man/add_provincial_abbreviations.Rd |only man/figures |only man/get_cansim.Rd | 5 + man/get_cansim_column_categories.Rd | 4 - man/get_cansim_column_list.Rd | 4 - man/get_cansim_ndm.Rd | 4 - man/get_cansim_table_info.Rd | 4 - man/get_cansim_table_notes.Rd | 4 - man/get_cansim_table_subject.Rd | 4 - man/get_cansim_table_survey.Rd | 4 - man/normalize_cansim_values.Rd | 7 + vignettes/cansim.Rmd | 2 25 files changed, 267 insertions(+), 97 deletions(-)
Title: Call R from R
Description: It is sometimes useful to perform a computation in a
separate R process, without affecting the current R process at all.
This packages does exactly that.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>),
Winston Chang [aut],
RStudio [cph, fnd],
Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between callr versions 3.3.0 dated 2019-07-04 and 3.3.1 dated 2019-07-18
DESCRIPTION | 6 - MD5 | 23 ++-- NEWS.md | 10 +- R/hook.R | 2 R/r-session.R | 163 +++++++++++++++++++++++++++++++-- R/script.R | 8 + R/utils.R | 8 + inst/WORDLIST | 2 inst/doc/Task-queue-with-callr.html | 92 +++++++++--------- man/r_session.Rd | 8 + man/r_session_debug.Rd |only tests/testthat/test-clean-subprocess.R | 22 ++++ tests/testthat/test-r-session.R | 3 13 files changed, 279 insertions(+), 68 deletions(-)
Title: Stepwise Selection for Large Data Sets
Description: Selecting linear and generalized linear models for large data sets
using modified stepwise procedure and modern selection criteria (like
modifications of Bayesian Information Criterion). Selection can be
performed on data which exceed RAM capacity.
Author: Piotr Szulc [aut, cre]
Maintainer: Piotr Szulc <piotr.michal.szulc@gmail.com>
Diff between bigstep versions 1.0.1 dated 2019-03-21 and 1.0.2 dated 2019-07-18
DESCRIPTION | 10 MD5 | 16 - R/criteria.R | 32 +- build/vignette.rds |binary inst/doc/bigstep.html | 484 +++++++++++++++++++++++++++++------------ man/maic.Rd | 2 man/maic2.Rd | 5 tests/testthat/test_all.R | 22 - tests/testthat/test_criteria.R | 14 - 9 files changed, 404 insertions(+), 181 deletions(-)
Title: Themes for Base Graphics Plots
Description: Functions to create and select graphical themes for the base plotting system. Contains: 1) several custom pre-made themes 2) mechanism for creating new themes by making persistent changes to the graphical parameters of base plots.
Author: Karolis Koncevičius [aut, cre]
Maintainer: Karolis Koncevičius <karolis.koncevicius@gmail.com>
Diff between basetheme versions 0.1.0 dated 2019-06-14 and 0.1.1 dated 2019-07-18
DESCRIPTION | 6 +- MD5 | 7 +-- NEWS |only R/themes.R | 136 +++++++++++++++++++++++++++++++++++++++++++++++++++--------- README.md | 63 +++++++++++++++++++++++---- 5 files changed, 178 insertions(+), 34 deletions(-)
Title: Interface to 'Azure Resource Manager'
Description: A lightweight but powerful R interface to the 'Azure Resource Manager' REST API. The package exposes classes and methods for 'OAuth' authentication and working with subscriptions and resource groups. It also provides functionality for creating and deleting 'Azure' resources and deploying templates. While 'AzureRMR' can be used to manage any 'Azure' service, it can also be extended by other packages to provide extra functionality for specific services. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureRMR versions 2.1.2 dated 2019-06-04 and 2.1.3 dated 2019-07-18
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- NEWS.md | 6 ++++++ R/az_login.R | 14 +++++++------- R/az_resgroup.R | 2 +- R/az_resource.R | 12 +++++++----- R/az_rm.R | 2 +- R/az_template.R | 2 +- R/build_tpl_json.R | 2 +- R/call_azure_rm.R | 33 +++++++++++++++++++++------------ R/format.R | 6 +++--- R/locks.R | 4 ++-- R/rbac.R | 6 +++--- R/utils.R | 4 ++-- man/azure_login.Rd | 2 +- man/call_azure.Rd | 11 ++++++++--- man/lock.Rd | 2 +- man/rbac.Rd | 2 +- 18 files changed, 87 insertions(+), 65 deletions(-)
Title: An R Package for Smith's Mean Measure of Divergence (MMD)
Description: Offers a graphical user interface for the calculation of the mean measure of divergence, with facilities for trait selection and graphical representations <doi:10.1002/ajpa.23336>.
Author: Frédéric Santos [aut, cre] (<https://orcid.org/0000-0003-1445-3871>)
Maintainer: Frédéric Santos <frederic.santos@u-bordeaux.fr>
Diff between AnthropMMD versions 3.0.0 dated 2019-07-05 and 3.0.1 dated 2019-07-18
DESCRIPTION | 6 MD5 | 22 +-- NEWS.md | 6 R/mmd.R | 8 - R/select_traits.R | 2 build/vignette.rds |binary inst/doc/intro_AnthropMMD.R | 2 inst/doc/intro_AnthropMMD.Rmd | 10 - inst/doc/intro_AnthropMMD.html | 248 ++++++++++++++++++++--------------------- man/AnthropMMD-package.Rd | 4 man/plot_mmd.Rd | 4 vignettes/intro_AnthropMMD.Rmd | 10 - 12 files changed, 167 insertions(+), 155 deletions(-)
Title: Test ANOVA Replications by Means of the Prior Predictive p-Value
Description: Allows for the computation of a prior predictive p-value to test replication of relevant features of original ANOVA studies. Relevant features are captured in informative hypotheses. The package also allows for the computation of sample sizes for new studies, post-hoc power calculations, and comes with a Shiny application in which all calculations can be conducted as well. The statistical underpinnings are described in Zondervan-Zwijnenburg (2019) <doi:10.31234/osf.io/6myqh>.
Author: M.A.J. Zondervan-Zwijnenburg [aut, cre],
Herbert Hoijtink [ths],
Caspar J van Lissa [ctb],
Consortium Individual Development [fnd] (NWO grant number 024.001.003)
Maintainer: M.A.J. Zondervan-Zwijnenburg <m.a.j.zwijnenburg@uu.nl>
Diff between ANOVAreplication versions 1.1.3 dated 2018-01-27 and 1.1.4 dated 2019-07-18
DESCRIPTION | 24 + MD5 | 45 +- NAMESPACE | 14 R/Gibbs.ANOVA.R | 6 R/create_matrices.R |only R/generate.data.R |only R/internal_functions.R |only R/pooled.sd.R | 1 R/power.calc.R | 4 R/prior.predictive.check.R | 6 R/sample.size.calc.R | 18 - build |only inst/doc |only inst/shiny-examples/myapp/helpers.R | 566 +++++++++++++++++++++++++++++++----- inst/shiny-examples/myapp/server.R | 201 ++++++++---- inst/shiny-examples/myapp/ui.R | 116 +++++-- man/Fbar.dif.Rd | 15 man/Fbar.ineq.Rd | 8 man/Gibbs.ANOVA.Rd | 2 man/create_matrices.Rd |only man/generate.data.Rd |only man/pooled.sd.Rd | 2 man/power.calc.Rd | 40 +- man/prior.predictive.check.Rd | 38 ++ man/sample.size.calc.Rd | 39 ++ vignettes |only 26 files changed, 913 insertions(+), 232 deletions(-)
More information about ANOVAreplication at CRAN
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