Title: Unified and Automatic 'Theming' of 'ggplot2', 'lattice', and
'base' R Graphics
Description: Theme 'ggplot2', 'lattice', and 'base' graphics based on a few choices, including foreground color, background color, accent color,
and font family. Fonts that aren't available on the system, but are available via download on 'Google Fonts',
can be automatically downloaded, cached, and registered for use with the 'showtext' and 'ragg' packages.
Author: Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>),
Barret Schloerke [aut] (<https://orcid.org/0000-0001-9986-114X>),
Joe Cheng [aut],
RStudio [cph]
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between thematic versions 0.1.2 dated 2021-03-29 and 0.1.2.1 dated 2021-06-09
DESCRIPTION | 10 +- MD5 | 38 +++++----- NEWS.md | 4 + tests/testthat/CairoPNG_rmd/tests/shinytest/mytest-expected-linux/001.png |binary tests/testthat/CairoPNG_rmd/tests/shinytest/mytest-expected-mac/001.png |binary tests/testthat/CairoPNG_rmd/tests/shinytest/mytest-expected-win/001.png |binary tests/testthat/auto_theme_rmd/darkly_rmd/tests/shinytest/mytest-expected-mac/001.png |binary tests/testthat/auto_theme_shiny/lattice/tests/shinytest/mytest-expected-mac/001.png |binary tests/testthat/auto_theme_shiny/local_theme/tests/shinytest/mytest-expected-mac/001.json | 2 tests/testthat/auto_theme_shiny/local_theme/tests/shinytest/mytest-expected-mac/001.png |binary tests/testthat/auto_theme_shiny/with_theme/tests/shinytest/mytest-expected-mac/001.json | 2 tests/testthat/auto_theme_shiny/with_theme/tests/shinytest/mytest-expected-mac/001.png |binary tests/testthat/cairo_svg/tests/shinytest/mytest-current |only tests/testthat/helper-vdiffr.R | 5 + tests/testthat/quartz_png_rmd/tests/shinytest/mytest-expected-mac/001.png |binary tests/testthat/shiny_runtime/tests/shinytest/mytest-expected-win/001.json | 2 tests/testthat/test-ggthemes.R | 1 tests/testthat/test-lattice.R | 2 tests/testthat/test-sequential-gradient.R | 4 - tests/testthat/test-state.R | 4 - 20 files changed, 42 insertions(+), 32 deletions(-)
Title: Fast Gaussian Process Computation Using Vecchia's Approximation
Description: Functions for fitting and doing predictions with
Gaussian process models using Vecchia's (1988) approximation.
Package also includes functions for reordering input locations,
finding ordered nearest neighbors (with help from 'FNN' package),
grouping operations, and conditional simulations.
Covariance functions for spatial and spatial-temporal data
on Euclidean domains and spheres are provided. The original
approximation is due to Vecchia (1988)
<http://www.jstor.org/stable/2345768>, and the reordering and
grouping methods are from Guinness (2018)
<doi:10.1080/00401706.2018.1437476>.
Model fitting employs a Fisher scoring algorithm described
in Guinness (2019) <arXiv:1905.08374>.
Author: Joseph Guinness [aut, cre],
Matthias Katzfuss [aut],
Youssef Fahmy [aut]
Maintainer: Joseph Guinness <joeguinness@gmail.com>
Diff between GpGp versions 0.3.2 dated 2021-01-27 and 0.4.0 dated 2021-06-09
DESCRIPTION | 8 - MD5 | 35 +++-- NEWS.md | 5 R/GpGp.R | 18 ++ R/RcppExports.R | 135 ++++++++++++++++++++ R/fisher_scoring.R | 32 ++++ R/fit_model.R | 98 +++++++++++++- R/predictions.R | 21 ++- man/GpGp.Rd | 18 ++ man/exponential_anisotropic3D_alt.Rd |only man/matern_anisotropic3D_alt.Rd | 4 man/matern_categorical.Rd |only man/matern_spacetime_categorical.Rd |only man/matern_spacetime_categorical_local.Rd |only src/RcppExports.cpp | 104 +++++++++++++++ src/covmatrix_funs.h | 21 +++ src/covmatrix_funs_01.h | 24 ++- src/covmatrix_funs_02.h | 200 ++++++++++++++++++++++++++++-- src/covmatrix_funs_13.h |only src/onepass.h | 191 ++++++++++++++++++++++++++-- tests/testthat/test_covfuns.R | 14 +- 21 files changed, 851 insertions(+), 77 deletions(-)
Title: An API Wrapper for 'Cryptowatch'
Description: An API wrapper for 'Cryptowatch' to get prices and other information (e.g., volume, trades, order books, bid and ask prices, live quotes, and more) about cryptocurrencies and crypto exchanges. See <https://docs.cryptowat.ch/rest-api> for a detailed documentation.
Author: Lorenz Brachtendorf [aut, cre]
(<https://orcid.org/0000-0001-7066-0838>)
Maintainer: Lorenz Brachtendorf <lorenz.brachtendorf@gmx.de>
Diff between cryptowatchR versions 0.1.0 dated 2021-05-25 and 0.2.0 dated 2021-06-09
DESCRIPTION | 8 ++--- MD5 | 42 ++++++++++++++++++++--------- NAMESPACE | 7 ++++ NEWS.md |only R/get_assets.R | 18 +++++++----- R/get_current_price.R |only R/get_exchanges.R | 16 +++++++---- R/get_markets.R | 57 ++++++++++++++++++++++++++++------------ R/get_ohlc.R |only R/get_orderbook.R |only R/get_orderbook_calculator.R |only R/get_orderbook_liquidity.R |only R/get_pairs.R | 16 +++++++---- R/get_summary.R |only R/get_trades.R |only R/markets.R | 29 +++++++++++++------- R/utils-get_data.R | 15 +++++++--- README.md |only man/get_assets.Rd | 16 +++++++---- man/get_current_price.Rd |only man/get_exchanges.Rd | 14 +++++++-- man/get_markets.Rd | 29 ++++++++++++-------- man/get_ohlc.Rd |only man/get_orderbook.Rd |only man/get_orderbook_calculator.Rd |only man/get_orderbook_liquidity.Rd |only man/get_pairs.Rd | 14 +++++++-- man/get_summary.Rd |only man/get_trades.Rd |only man/markets.Rd | 16 +++++------ 30 files changed, 199 insertions(+), 98 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here this package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of the package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
it gives users more convenience and freedom to design figures for
better understanding complex patterns behind multiple dimensional data.
The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.4.12 dated 2021-01-08 and 0.4.13 dated 2021-06-09
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 5 +++++ R/genomic.R | 2 +- R/link.R | 6 ++++-- R/low_level.R | 23 +++++++++++++++++------ R/random_color.R | 19 ++++++++++++++----- build/vignette.rds |binary 8 files changed, 52 insertions(+), 25 deletions(-)
Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between parallelly versions 1.25.0 dated 2021-04-30 and 1.26.0 dated 2021-06-09
parallelly-1.25.0/parallelly/man/getOptionOrEnvVar.Rd |only parallelly-1.26.0/parallelly/DESCRIPTION | 6 parallelly-1.26.0/parallelly/MD5 | 47 - parallelly-1.26.0/parallelly/NAMESPACE | 1 parallelly-1.26.0/parallelly/NEWS | 33 parallelly-1.26.0/parallelly/R/availableConnections.R | 4 parallelly-1.26.0/parallelly/R/availableCores.R | 9 parallelly-1.26.0/parallelly/R/availableWorkers.R | 15 parallelly-1.26.0/parallelly/R/getOptionOrEnvVar.R | 19 parallelly-1.26.0/parallelly/R/makeClusterMPI.R | 2 parallelly-1.26.0/parallelly/R/makeClusterPSOCK.R | 506 +++++++++----- parallelly-1.26.0/parallelly/R/options.R | 192 ++++- parallelly-1.26.0/parallelly/R/ports.R |only parallelly-1.26.0/parallelly/R/stealth_sample.R |only parallelly-1.26.0/parallelly/R/supportsMulticore.R | 4 parallelly-1.26.0/parallelly/R/utils.R | 43 - parallelly-1.26.0/parallelly/README.md | 16 parallelly-1.26.0/parallelly/man/availableWorkers.Rd | 2 parallelly-1.26.0/parallelly/man/canPortBeUsed.Rd |only parallelly-1.26.0/parallelly/man/freePort.Rd |only parallelly-1.26.0/parallelly/man/getOption2.Rd |only parallelly-1.26.0/parallelly/man/makeClusterMPI.Rd | 2 parallelly-1.26.0/parallelly/man/makeClusterPSOCK.Rd | 39 - parallelly-1.26.0/parallelly/man/parallelly.options.Rd | 121 ++- parallelly-1.26.0/parallelly/tests/freePort.R |only parallelly-1.26.0/parallelly/tests/incl/start,load-only.R | 2 parallelly-1.26.0/parallelly/tests/makeClusterPSOCK.R | 12 parallelly-1.26.0/parallelly/tests/options-and-envvars.R | 14 28 files changed, 760 insertions(+), 329 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to
encode spatial vector data. Binds to 'GDAL' for reading and writing
data, to 'GEOS' for geometrical operations, and to 'PROJ' for
projection conversions and datum transformations. Optionally uses the 's2'
package for spherical geometry operations on geographic coordinates.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>),
Etienne Racine [ctb],
Michael Sumner [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Kirill Müller [ctb],
Thomas Lin Pedersen [ctb],
Dan Baston [ctb],
Dewey Dunnington [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 0.9-8 dated 2021-03-17 and 1.0-0 dated 2021-06-09
sf-0.9-8/sf/man/st_interpolate_aw.Rd |only sf-1.0-0/sf/DESCRIPTION | 28 - sf-1.0-0/sf/MD5 | 144 +++---- sf-1.0-0/sf/NAMESPACE | 2 sf-1.0-0/sf/NEWS.md | 195 +++++----- sf-1.0-0/sf/R/RcppExports.R | 20 - sf-1.0-0/sf/R/aggregate.R | 12 sf-1.0-0/sf/R/crs.R | 17 sf-1.0-0/sf/R/geom-measures.R | 16 sf-1.0-0/sf/R/geom-predicates.R | 6 sf-1.0-0/sf/R/geom-transformers.R | 49 +- sf-1.0-0/sf/R/grid.R | 19 + sf-1.0-0/sf/R/init.R | 11 sf-1.0-0/sf/R/nearest.R | 43 +- sf-1.0-0/sf/R/plot.R | 10 sf-1.0-0/sf/R/read.R | 15 sf-1.0-0/sf/R/s2.R | 31 - sf-1.0-0/sf/R/sfc.R | 2 sf-1.0-0/sf/R/sgbp.R | 5 sf-1.0-0/sf/R/sp.R | 16 sf-1.0-0/sf/R/stars.R | 21 + sf-1.0-0/sf/R/tidyverse.R | 10 sf-1.0-0/sf/R/valid.R | 62 ++- sf-1.0-0/sf/build/vignette.rds |binary sf-1.0-0/sf/inst/doc/sf1.R | 21 - sf-1.0-0/sf/inst/doc/sf1.Rmd | 53 -- sf-1.0-0/sf/inst/doc/sf1.html | 375 +++++++++----------- sf-1.0-0/sf/inst/doc/sf2.html | 60 +-- sf-1.0-0/sf/inst/doc/sf3.html | 19 - sf-1.0-0/sf/inst/doc/sf4.html | 35 - sf-1.0-0/sf/inst/doc/sf5.R | 13 sf-1.0-0/sf/inst/doc/sf5.Rmd | 13 sf-1.0-0/sf/inst/doc/sf5.html | 150 +++----- sf-1.0-0/sf/inst/doc/sf6.R | 3 sf-1.0-0/sf/inst/doc/sf6.Rmd | 16 sf-1.0-0/sf/inst/doc/sf6.html | 106 ++--- sf-1.0-0/sf/inst/doc/sf7.html | 71 ++- sf-1.0-0/sf/inst/docker/geos/Dockerfile | 32 - sf-1.0-0/sf/man/gdal.Rd | 16 sf-1.0-0/sf/man/geos_binary_ops.Rd | 2 sf-1.0-0/sf/man/geos_binary_pred.Rd | 2 sf-1.0-0/sf/man/interpolate_aw.Rd |only sf-1.0-0/sf/man/plot.Rd | 2 sf-1.0-0/sf/man/s2.Rd | 4 sf-1.0-0/sf/man/st_nearest_feature.Rd | 21 - sf-1.0-0/sf/man/st_write.Rd | 7 sf-1.0-0/sf/man/valid.Rd | 24 + sf-1.0-0/sf/src/RcppExports.cpp | 58 ++- sf-1.0-0/sf/src/gdal.cpp | 4 sf-1.0-0/sf/src/gdal.h | 1 sf-1.0-0/sf/src/gdal_read.cpp | 15 sf-1.0-0/sf/src/gdal_utils.cpp | 19 + sf-1.0-0/sf/src/gdal_write.cpp | 25 + sf-1.0-0/sf/src/geos.cpp | 2 sf-1.0-0/sf/src/mdim.cpp |only sf-1.0-0/sf/src/polygonize.cpp | 10 sf-1.0-0/sf/src/proj.cpp | 8 sf-1.0-0/sf/src/stars.cpp | 3 sf-1.0-0/sf/tests/crs.Rout.save | 6 sf-1.0-0/sf/tests/dist.Rout.save | 30 - sf-1.0-0/sf/tests/dplyr.Rout.save | 8 sf-1.0-0/sf/tests/gdal_geom.Rout.save | 68 +-- sf-1.0-0/sf/tests/geos.Rout.save | 41 +- sf-1.0-0/sf/tests/plot.Rout.save | 10 sf-1.0-0/sf/tests/read.Rout.save | 7 sf-1.0-0/sf/tests/roundtrip.Rout.save | 7 sf-1.0-0/sf/tests/s2.Rout.save |only sf-1.0-0/sf/tests/sfc.Rout.save | 6 sf-1.0-0/sf/tests/spatstat.Rout.save | 7 sf-1.0-0/sf/tests/stars.Rout.save | 135 ++++--- sf-1.0-0/sf/tests/testthat/test_geos.R | 10 sf-1.0-0/sf/tests/testthat/test_postgis_RPostgres.R | 26 - sf-1.0-0/sf/vignettes/sf1.Rmd | 53 -- sf-1.0-0/sf/vignettes/sf5.Rmd | 13 sf-1.0-0/sf/vignettes/sf6.Rmd | 16 75 files changed, 1232 insertions(+), 1135 deletions(-)
Title: Stochastic Blockmodels
Description: A collection of tools and functions to adjust a variety of stochastic blockmodels (SBM).
Supports at the moment Simple, Bipartite, 'Multipartite' and Multiplex SBM (undirected or directed with Bernoulli,
Poisson or Gaussian emission laws on the edges, and possibly covariate for Simple and Bipartite SBM).
See Léger (2016) <arxiv:1602.07587>, 'Barbillon et al.' (2020) <doi:10.1111/rssa.12193> and
'Bar-Hen et al.' (2020) <arxiv:1807.10138>.
Author: Julien Chiquet [aut, cre] (<https://orcid.org/0000-0002-3629-3429>),
Sophie Donnet [aut] (<https://orcid.org/0000-0003-4370-7316>),
großBM team [ctb],
Pierre Barbillon [aut] (<https://orcid.org/0000-0002-7766-7693>)
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between sbm versions 0.4.2 dated 2021-05-31 and 0.4.3 dated 2021-06-09
sbm-0.4.2/sbm/tests/testthat/Rplots.pdf |only sbm-0.4.3/sbm/DESCRIPTION | 8 sbm-0.4.3/sbm/MD5 | 40 sbm-0.4.3/sbm/NAMESPACE | 1 sbm-0.4.3/sbm/NEWS.md | 7 sbm-0.4.3/sbm/R/plotMyMatrix.R | 2 sbm-0.4.3/sbm/R/utils_plot.R | 23 sbm-0.4.3/sbm/inst/doc/Multipartite_EcologicalNetwork.R | 2 sbm-0.4.3/sbm/inst/doc/Multipartite_EcologicalNetwork.Rmd | 2 sbm-0.4.3/sbm/inst/doc/Multipartite_EcologicalNetwork.html | 26 sbm-0.4.3/sbm/inst/doc/MultiplexNetwork_principle.html | 58 sbm-0.4.3/sbm/inst/doc/Multiplex_allianceNwar_case_study.R | 7 sbm-0.4.3/sbm/inst/doc/Multiplex_allianceNwar_case_study.Rmd | 10 sbm-0.4.3/sbm/inst/doc/Multiplex_allianceNwar_case_study.html | 63 sbm-0.4.3/sbm/inst/doc/SBM_fungus_tree_network.html | 73 sbm-0.4.3/sbm/tests/testthat/test-BipartiteSBM_fit_covariates.R | 474 ++-- sbm-0.4.3/sbm/tests/testthat/test-MultipartiteSBM.R | 153 - sbm-0.4.3/sbm/tests/testthat/test-MultiplexSBM_fit.R | 163 - sbm-0.4.3/sbm/tests/testthat/test-SimpleSBM_fit_covariates.R | 989 +++++----- sbm-0.4.3/sbm/vignettes/Multipartite_EcologicalNetwork.Rmd | 2 sbm-0.4.3/sbm/vignettes/Multiplex_allianceNwar_case_study.Rmd | 10 sbm-0.4.3/sbm/vignettes/Multiplex_allianceNwar_case_study.rds |only 22 files changed, 1011 insertions(+), 1102 deletions(-)
Title: List Comprehension for R
Description: Syntactic shortcuts for creating synthetic lists, vectors,
data frames, and matrices using list comprehension.
Author: Patrick Roocks <mail@p-roocks.de>
Maintainer: Patrick Roocks <mail@p-roocks.de>
Diff between listcompr versions 0.2.0 dated 2021-04-02 and 0.3.0 dated 2021-06-09
listcompr-0.2.0/listcompr/man/gen.list.char.Rd |only listcompr-0.3.0/listcompr/DESCRIPTION | 14 listcompr-0.3.0/listcompr/MD5 | 36 listcompr-0.3.0/listcompr/NAMESPACE | 4 listcompr-0.3.0/listcompr/NEWS.md | 16 listcompr-0.3.0/listcompr/R/eval.r |only listcompr-0.3.0/listcompr/R/expand.r |only listcompr-0.3.0/listcompr/R/gen-list.r | 866 ++----------------- listcompr-0.3.0/listcompr/R/listcompr.r | 7 listcompr-0.3.0/listcompr/README.md | 6 listcompr-0.3.0/listcompr/build/vignette.rds |binary listcompr-0.3.0/listcompr/inst/doc/introduction.R | 37 listcompr-0.3.0/listcompr/inst/doc/introduction.Rmd | 50 - listcompr-0.3.0/listcompr/inst/doc/introduction.html | 496 +++++----- listcompr-0.3.0/listcompr/man/gen.list.Rd | 74 + listcompr-0.3.0/listcompr/man/gen.list.expr.Rd | 5 listcompr-0.3.0/listcompr/man/gen.logical.and.Rd | 11 listcompr-0.3.0/listcompr/man/gen.named.list.Rd |only listcompr-0.3.0/listcompr/man/listcompr.Rd | 7 listcompr-0.3.0/listcompr/tests/testthat/testbase.r | 106 ++ listcompr-0.3.0/listcompr/vignettes/introduction.Rmd | 50 - 21 files changed, 688 insertions(+), 1097 deletions(-)
Title: Simple Fisheries Stock Assessment Methods
Description: A variety of simple fish stock assessment methods.
Detailed vignettes are available on the fishR website <http://derekogle.com/fishR/>.
Author: Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>),
Jason Doll [aut],
Powell Wheeler [aut],
Alexis Dinno [aut] (Provided base functionality of dunnTest())
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSA versions 0.8.32 dated 2021-01-15 and 0.9.0 dated 2021-06-09
FSA-0.8.32/FSA/R/comparisonsDVR.R |only FSA-0.8.32/FSA/R/fitPlot.R |only FSA-0.8.32/FSA/R/mapvalues.R |only FSA-0.8.32/FSA/R/plotBinResp.R |only FSA-0.8.32/FSA/R/residPlot.R |only FSA-0.8.32/FSA/man/FSAUtils.Rd |only FSA-0.8.32/FSA/man/Subset.Rd |only FSA-0.8.32/FSA/man/bootCase.Rd |only FSA-0.8.32/FSA/man/chooseColors.Rd |only FSA-0.8.32/FSA/man/compIntercepts.Rd |only FSA-0.8.32/FSA/man/compSlopes.Rd |only FSA-0.8.32/FSA/man/diags.Rd |only FSA-0.8.32/FSA/man/hoCoef.Rd |only FSA-0.8.32/FSA/man/mapvalues.Rd |only FSA-0.8.32/FSA/man/oddeven.Rd |only FSA-0.8.32/FSA/man/plotBinResp.Rd |only FSA-0.8.32/FSA/man/stockRecruitment.Rd |only FSA-0.8.32/FSA/tests/testthat/testthat_comparisonsDVR.R |only FSA-0.8.32/FSA/tests/testthat/testthat_fitResidPlots.R |only FSA-0.9.0/FSA/DESCRIPTION | 14 FSA-0.9.0/FSA/MD5 | 164 - FSA-0.9.0/FSA/NAMESPACE | 15 FSA-0.9.0/FSA/NEWS.md | 2492 ++++++---------- FSA-0.9.0/FSA/R/CIDists.R | 13 FSA-0.9.0/FSA/R/Ecoli.R | 2 FSA-0.9.0/FSA/R/FSA-defunct.R |only FSA-0.9.0/FSA/R/FSA-internals.R | 130 FSA-0.9.0/FSA/R/FSAUtils.R | 295 - FSA-0.9.0/FSA/R/Mirex.R | 2 FSA-0.9.0/FSA/R/PSDlit.R | 1 FSA-0.9.0/FSA/R/addZeroCatch.R | 2 FSA-0.9.0/FSA/R/ageComparisons.R | 3 FSA-0.9.0/FSA/R/alkPlot.R | 113 FSA-0.9.0/FSA/R/bootstrap.R | 155 FSA-0.9.0/FSA/R/catchCurve.R | 71 FSA-0.9.0/FSA/R/chapmanRobson.R | 64 FSA-0.9.0/FSA/R/depletion.R | 5 FSA-0.9.0/FSA/R/deprecated-residPlot.R |only FSA-0.9.0/FSA/R/deprecated_fitPlot.R |only FSA-0.9.0/FSA/R/mrClosed.R | 11 FSA-0.9.0/FSA/R/mrOpen.R | 27 FSA-0.9.0/FSA/R/nlsTracePlot.R | 14 FSA-0.9.0/FSA/R/psdAdd.R | 17 FSA-0.9.0/FSA/R/psdCI.R | 4 FSA-0.9.0/FSA/R/psdCalc.R | 6 FSA-0.9.0/FSA/R/psdPlot.R | 2 FSA-0.9.0/FSA/R/psdVal.R | 70 FSA-0.9.0/FSA/R/removal.R | 25 FSA-0.9.0/FSA/R/stockRecruitment.R | 8 FSA-0.9.0/FSA/R/wrAdd.R | 24 FSA-0.9.0/FSA/R/wsVal.R | 10 FSA-0.9.0/FSA/data/PSDlit.rdata |binary FSA-0.9.0/FSA/data/WSlit.rdata |binary FSA-0.9.0/FSA/inst/extdata/bootCase1.RData |binary FSA-0.9.0/FSA/inst/helpers/installTester.R | 14 FSA-0.9.0/FSA/man/Ecoli.Rd | 63 FSA-0.9.0/FSA/man/FSA-defunct.Rd |only FSA-0.9.0/FSA/man/FSA-internals.Rd | 60 FSA-0.9.0/FSA/man/Mirex.Rd | 85 FSA-0.9.0/FSA/man/PSDlit.Rd | 1 FSA-0.9.0/FSA/man/addZeroCatch.Rd | 270 - FSA-0.9.0/FSA/man/alkAgeDist.Rd | 150 FSA-0.9.0/FSA/man/alkIndivAge.Rd | 252 - FSA-0.9.0/FSA/man/alkMeanVar.Rd | 172 - FSA-0.9.0/FSA/man/alkPlot.Rd | 214 - FSA-0.9.0/FSA/man/boot.Rd |only FSA-0.9.0/FSA/man/capFirst.Rd |only FSA-0.9.0/FSA/man/catchCurve.Rd | 388 +- FSA-0.9.0/FSA/man/chapmanRobson.Rd | 340 +- FSA-0.9.0/FSA/man/filterD.Rd |only FSA-0.9.0/FSA/man/fitPlot.Rd | 572 +-- FSA-0.9.0/FSA/man/is.odd.Rd |only FSA-0.9.0/FSA/man/nlsBoot.Rd | 226 - FSA-0.9.0/FSA/man/nlsTracePlot.Rd | 202 - FSA-0.9.0/FSA/man/psdAdd.Rd | 257 - FSA-0.9.0/FSA/man/psdVal.Rd | 6 FSA-0.9.0/FSA/man/repeatedRows2Keep.Rd | 92 FSA-0.9.0/FSA/man/residPlot.Rd | 526 +-- FSA-0.9.0/FSA/man/srFuns.Rd |only FSA-0.9.0/FSA/man/wrAdd.Rd | 161 - FSA-0.9.0/FSA/tests/testthat/Rplots.pdf |binary FSA-0.9.0/FSA/tests/testthat/testthat_AgeLengthKey.R | 8 FSA-0.9.0/FSA/tests/testthat/testthat_FSAUtils.R | 273 - FSA-0.9.0/FSA/tests/testthat/testthat_Internals.R | 22 FSA-0.9.0/FSA/tests/testthat/testthat_PSD.R | 55 FSA-0.9.0/FSA/tests/testthat/testthat_VonBertalanffy.R | 4 FSA-0.9.0/FSA/tests/testthat/testthat_WSWR.R | 1 FSA-0.9.0/FSA/tests/testthat/testthat_bootstrap.R | 18 FSA-0.9.0/FSA/tests/testthat/testthat_capHist.R | 4 FSA-0.9.0/FSA/tests/testthat/testthat_catchCurve.R | 13 FSA-0.9.0/FSA/tests/testthat/testthat_ciDists.R | 3 FSA-0.9.0/FSA/tests/testthat/testthat_depletion.R | 2 FSA-0.9.0/FSA/tests/testthat/testthat_expandCounts.R | 6 FSA-0.9.0/FSA/tests/testthat/testthat_mrClosed.R | 4 FSA-0.9.0/FSA/tests/testthat/testthat_mrOpen.R | 42 FSA-0.9.0/FSA/tests/testthat/testthat_nlsTracePlot.R | 4 FSA-0.9.0/FSA/tests/testthat/testthat_removal.R | 12 97 files changed, 3828 insertions(+), 4453 deletions(-)
Title: Calculation of Slope-Dependant Accumulated Cost Surface,
Least-Cost Paths, and Least-Cost Corridors Related to Human
Movement Across the Landscape
Description: Provides the facility to calculate non-isotropic accumulated cost surface, least-cost paths, and least-cost corridors using a number of human-movement-related cost functions that can be selected by the user. It just requires a Digital Terrain Model, a start location and (optionally) destination locations. See Alberti (2019) <doi:10.1016/j.softx.2019.100331>.
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Diff between movecost versions 0.9 dated 2021-05-31 and 1.0 dated 2021-06-09
DESCRIPTION | 6 - MD5 | 14 +-- NEWS.md | 52 +------------- R/movecorr.R | 57 +++++++++++---- R/movecost.R | 206 ++++++++++++++++++++++++++++++++++++++++++++++---------- README.md | 12 ++- man/movecorr.Rd | 16 ++-- man/movecost.Rd | 81 +++++++++++++++++++--- 8 files changed, 319 insertions(+), 125 deletions(-)
Title: Ecological Inference by Linear Programming under Homogeneity
Description: Provides a bunch of algorithms based on linear programming for estimating RxC ecological contingency tables (vote transitions matrices) using exclusively aggregate results from voting units under the homogeneity hypothesis. References: Romero, Pavia, Martin and Romero (2020) <doi:10.1080/02664763.2020.1804842>. Pavia and Romero (2021) Improving estimates accuracy of voter transitions. Two new algorithms for ecological inference based on linear programming.
Author: Jose M. Pavía [aut, cre] (<https://orcid.org/0000-0002-0129-726X>),
Rafael Romero [aut]
Maintainer: Jose M. Pavía <jose.m.pavia@uv.es>
Diff between lphom versions 0.1.3 dated 2021-06-02 and 0.1.4 dated 2021-06-09
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- R/auxiliar.R | 5 ++++- R/confidence_intervals_pjk.R | 9 ++++----- R/error_lphom.R | 5 ++--- R/lphom.R | 3 ++- R/nslphom.R | 4 ++-- R/tslphom.R | 4 ++-- build/partial.rdb |binary data/France2017P.rda |binary man/confidence_intervals_pjk.Rd | 5 ++--- man/error_lphom.Rd | 5 ++--- man/lphom.Rd | 3 ++- man/nslphom.Rd | 4 ++-- man/tslphom.Rd | 4 ++-- 15 files changed, 43 insertions(+), 42 deletions(-)
Title: Analyse Biological Invasion Costs with the 'InvaCost' Database
Description: Provides an up-to-date version of the 'InvaCost' database
(<doi:10.6084/m9.figshare.12668570>) in R, and
several functions to analyse the costs of invasive alien species.
Author: Boris Leroy [cre, aut], Andrew Kramer [aut], Anne-Charlotte Vaissière [ctb], Christophe Diagne [ctb]
Maintainer: Boris Leroy <leroy.boris@gmail.com>
Diff between invacost versions 1.0 dated 2020-12-18 and 1.1 dated 2021-06-09
DESCRIPTION | 8 MD5 | 39 ++-- NEWS | 5 R/expandYearlyCosts.R | 2 R/genericfunctions.R | 4 R/getInvaCostVersion.R | 10 - R/invacost.R | 349 +++++++-------------------------------- R/modelcosts.R | 2 R/prettySummary.R | 2 R/summarizeCosts.R | 4 build |only data/invacost.rda |binary man/computeAvgTotCost.Rd | 2 man/expandYearlyCosts.Rd | 2 man/getInvaCostVersion.Rd | 4 man/invacost.Rd | 347 +++++++------------------------------- man/modelCosts.Rd | 2 man/plot.invacost.costmodel.Rd | 2 man/plot.invacost.costsummary.Rd | 2 man/prettySummary.Rd | 2 man/summarizeCosts.Rd | 2 21 files changed, 188 insertions(+), 602 deletions(-)
Title: Graphic Devices Based on AGG
Description: Anti-Grain Geometry (AGG) is a high-quality and high-performance
2D drawing library. The 'ragg' package provides a set of graphic devices
based on AGG to use as alternative to the raster devices provided through
the 'grDevices' package.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
Maxim Shemanarev [aut, cph] (Author of AGG),
Tony Juricic [ctb, cph] (Contributor to AGG),
Milan Marusinec [ctb, cph] (Contributor to AGG),
Spencer Garrett [ctb] (Contributor to AGG),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between ragg versions 1.1.2 dated 2021-03-17 and 1.1.3 dated 2021-06-09
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS.md | 7 +++++++ R/aaa.R | 9 +++++++++ src/AggDevice.h | 10 ++++++---- src/AggDeviceTiff.h | 4 ++-- src/Makevars.ucrt |only src/Makevars.win | 2 +- src/ragg.h | 3 +++ 9 files changed, 39 insertions(+), 17 deletions(-)
Title: Meta-Analysis Package for R
Description: A comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat, bubble, and GOSH plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted. An introduction to the package can be found in Viechtbauer (2010) <doi:10.18637/jss.v036.i03>.
Author: Wolfgang Viechtbauer [aut, cre]
(<https://orcid.org/0000-0003-3463-4063>)
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>
Diff between metafor versions 3.0-1 dated 2021-06-03 and 3.0-2 dated 2021-06-09
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 2 +- NEWS.md | 2 +- R/tes.default.r | 6 +++++- R/zzz.r | 2 +- README.md | 2 +- build/metafor.pdf |binary tests/testthat/test_misc_reporter.r | 2 ++ 9 files changed, 23 insertions(+), 17 deletions(-)
Title: Tools for Matrix Algebra, Optimization and Inference
Description: Matrix is an universal and sometimes primary object/unit in applied mathematics and statistics. We provide a number of algorithms for selected problems in optimization and statistical inference. For general exposition to the topic with focus on statistical context, see the book by Banerjee and Roy (2014, ISBN:9781420095388).
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kisungyou@outlook.com>
Diff between maotai versions 0.1.9 dated 2021-04-24 and 0.2.0 dated 2021-06-09
DESCRIPTION | 14 +++++------ MD5 | 18 +++++++------- NAMESPACE | 1 NEWS.md | 6 +++- R/aux_hiddenDAS.R | 67 +++++++++++++++++++++++++++++++++++++++++++++++++++++ R/aux_hiddenR.R | 54 +++++++++++++++++++++++++++++++++++++----- R/package-maotai.R | 2 - R/zzz.R | 4 +-- README.md | 25 +++++++++++++------ build/partial.rdb |binary 10 files changed, 156 insertions(+), 35 deletions(-)
Title: Interface to 'Interpretable AI' Modules
Description: An interface to the algorithms of 'Interpretable AI'
<https://www.interpretable.ai> from the R programming language.
'Interpretable AI' provides various modules, including 'Optimal Trees' for
classification, regression, prescription and survival analysis, 'Optimal
Imputation' for missing data imputation and outlier detection, and 'Optimal
Feature Selection' for exact sparse regression. The 'iai' package is an
open-source project. The 'Interpretable AI' software modules are proprietary
products, but free academic and evaluation licenses are available.
Author: Jack Dunn [aut, cre],
Ying Zhuo [aut],
Interpretable AI LLC [cph]
Maintainer: Jack Dunn <jack@interpretable.ai>
Diff between iai versions 1.5.0 dated 2021-02-03 and 1.6.0 dated 2021-06-09
DESCRIPTION | 11 MD5 | 317 ++++++++------ NAMESPACE | 34 + NEWS.md | 11 R/heuristics.R | 78 +++ R/iaibase.R | 162 +++++-- R/iaitrees.R | 453 ++++++++++++++++++--- R/install.R | 73 ++- R/interface.R | 62 ++ R/optimalfeatureselection.R | 83 +++ R/optimaltrees.R | 14 R/optimpute.R | 18 R/rewardestimation.R | 237 ++++++++++ R/utils.R | 28 + man/add_julia_processes.Rd |only man/all_treatment_combinations.Rd | 2 man/apply.Rd | 2 man/apply_nodes.Rd | 2 man/as.mixeddata.Rd | 2 man/autoplot.grid_search.Rd |only man/autoplot.roc_curve.Rd |only man/autoplot.similarity_comparison.Rd |only man/autoplot.stability_analysis.Rd |only man/categorical_classification_reward_estimator.Rd |only man/categorical_regression_reward_estimator.Rd |only man/categorical_reward_estimator.Rd | 5 man/categorical_survival_reward_estimator.Rd |only man/clone.Rd | 2 man/convert_treatments_to_numeric.Rd | 2 man/decision_path.Rd | 2 man/delete_rich_output_param.Rd | 2 man/equal_propensity_estimator.Rd | 2 man/fit.Rd | 2 man/fit_cv.Rd | 2 man/fit_predict.Rd | 11 man/fit_transform.Rd | 6 man/fit_transform_cv.Rd | 2 man/get_best_params.Rd | 2 man/get_classification_label.Rd | 2 man/get_classification_proba.Rd | 2 man/get_cluster_assignments.Rd |only man/get_cluster_details.Rd |only man/get_cluster_distances.Rd |only man/get_depth.Rd | 2 man/get_estimation_densities.Rd |only man/get_features_used.Rd |only man/get_grid_result_details.Rd | 2 man/get_grid_result_summary.Rd | 2 man/get_learner.Rd | 2 man/get_lower_child.Rd | 2 man/get_num_fits.Rd | 2 man/get_num_nodes.Rd | 2 man/get_num_samples.Rd | 2 man/get_params.Rd | 2 man/get_parent.Rd | 2 man/get_policy_treatment_outcome.Rd | 2 man/get_policy_treatment_rank.Rd | 2 man/get_prediction_constant.Rd | 2 man/get_prediction_weights.Rd | 2 man/get_prescription_treatment_rank.Rd | 2 man/get_regression_constant.Rd | 2 man/get_regression_weights.Rd | 2 man/get_rich_output_params.Rd | 2 man/get_roc_curve_data.Rd | 4 man/get_split_categories.Rd | 2 man/get_split_feature.Rd | 2 man/get_split_threshold.Rd | 2 man/get_split_weights.Rd | 2 man/get_stability_results.Rd |only man/get_survival_curve.Rd | 2 man/get_survival_curve_data.Rd | 6 man/get_survival_expected_time.Rd | 2 man/get_survival_hazard.Rd | 2 man/get_train_errors.Rd |only man/get_tree.Rd |only man/get_upper_child.Rd | 2 man/glmnetcv_regressor.Rd | 2 man/grid_search.Rd | 2 man/iai_setup.Rd | 2 man/imputation_learner.Rd | 2 man/impute.Rd | 2 man/impute_cv.Rd | 2 man/install_julia.Rd | 2 man/install_system_image.Rd | 2 man/is_categoric_split.Rd | 2 man/is_hyperplane_split.Rd | 2 man/is_leaf.Rd | 2 man/is_mixed_ordinal_split.Rd | 2 man/is_mixed_parallel_split.Rd | 2 man/is_ordinal_split.Rd | 2 man/is_parallel_split.Rd | 2 man/mean_imputation_learner.Rd | 2 man/missing_goes_lower.Rd | 2 man/multi_questionnaire.Rd | 2 man/multi_questionnaire.default.Rd | 9 man/multi_questionnaire.grid_search.Rd | 2 man/multi_tree_plot.Rd | 2 man/multi_tree_plot.default.Rd | 9 man/multi_tree_plot.grid_search.Rd | 2 man/numeric_classification_reward_estimator.Rd |only man/numeric_regression_reward_estimator.Rd |only man/numeric_reward_estimator.Rd | 5 man/numeric_survival_reward_estimator.Rd |only man/opt_knn_imputation_learner.Rd | 2 man/opt_svm_imputation_learner.Rd | 2 man/opt_tree_imputation_learner.Rd | 2 man/optimal_feature_selection_classifier.Rd | 2 man/optimal_feature_selection_regressor.Rd | 2 man/optimal_tree_classifier.Rd | 2 man/optimal_tree_policy_maximizer.Rd | 2 man/optimal_tree_policy_minimizer.Rd | 2 man/optimal_tree_prescription_maximizer.Rd | 2 man/optimal_tree_prescription_minimizer.Rd | 2 man/optimal_tree_regressor.Rd | 2 man/optimal_tree_survival_learner.Rd | 2 man/plot.grid_search.Rd |only man/plot.roc_curve.Rd |only man/plot.similarity_comparison.Rd |only man/plot.stability_analysis.Rd |only man/predict.Rd | 2 man/predict_expected_survival_time.Rd | 2 man/predict_hazard.Rd | 2 man/predict_outcomes.Rd | 2 man/predict_proba.Rd | 2 man/predict_shap.Rd |only man/predict_treatment_outcome.Rd | 2 man/predict_treatment_rank.Rd | 2 man/print_path.Rd | 2 man/questionnaire.Rd | 4 man/rand_imputation_learner.Rd | 2 man/random_forest_classifier.Rd | 2 man/random_forest_regressor.Rd | 2 man/random_forest_survival_learner.Rd |only man/read_json.Rd | 2 man/reset_display_label.Rd | 2 man/reward_estimator.Rd | 2 man/roc_curve.Rd | 2 man/roc_curve.default.Rd | 2 man/roc_curve.learner.Rd | 2 man/score.Rd | 2 man/set_display_label.Rd | 2 man/set_params.Rd | 2 man/set_reward_kernel_bandwidth.Rd |only man/set_rich_output_param.Rd | 2 man/set_threshold.Rd | 2 man/show_in_browser.Rd | 2 man/show_questionnaire.Rd | 2 man/similarity_comparison.Rd |only man/single_knn_imputation_learner.Rd | 2 man/split_data.Rd | 2 man/stability_analysis.Rd |only man/transform.Rd | 2 man/tree_plot.Rd | 4 man/tune_reward_kernel_bandwidth.Rd |only man/variable_importance.Rd | 2 man/variable_importance_similarity.Rd |only man/write_booster.Rd | 2 man/write_dot.Rd | 2 man/write_html.Rd | 2 man/write_json.Rd | 2 man/write_pdf.Rd | 2 man/write_png.Rd | 2 man/write_questionnaire.Rd | 2 man/write_svg.Rd | 2 man/xgboost_classifier.Rd | 2 man/xgboost_regressor.Rd | 2 man/xgboost_survival_learner.Rd |only tests/testthat.R | 6 tests/testthat/helper.R | 4 tests/testthat/test_heuristics.R | 28 + tests/testthat/test_iaibase.R | 41 + tests/testthat/test_iaitrees.R | 53 +- tests/testthat/test_optimalfeatureselection.R | 12 tests/testthat/test_optimaltrees.R | 4 tests/testthat/test_rewardestimation.R | 126 +++++ 175 files changed, 1631 insertions(+), 511 deletions(-)
Title: Permutations Tests and Performance Indicator for Zero-Inflated
Proportions Response
Description: Permutations tests to identify factor correlated to zero-inflated proportions response. Provide a performance indicator based on Spearman correlation to quantify the part of correlation explained by the selected set of factors. See details for the method at the following preprint e.g.: <https://hal.archives-ouvertes.fr/hal-02936779v3>.
Author: Melina Ribaud
Maintainer: Melina Ribaud <melina.ribaud@gmail.com>
Diff between ZIprop versions 0.1.0 dated 2021-04-08 and 0.1.1 dated 2021-06-09
DESCRIPTION | 11 +++++++---- MD5 | 15 ++++++++++++++- NEWS.md |only R/diffFactors.R |only R/equineDiffFactors.R |only build |only data/diffFactors.rda |only data/equineDiffFactors.rda |only inst |only man/diffFactors.Rd |only man/equineDiffFactors.Rd |only vignettes |only 12 files changed, 21 insertions(+), 5 deletions(-)
Title: Vault Client for Secrets and Sensitive Data
Description: Provides an interface to a 'HashiCorp' vault server over
its http API (typically these are self-hosted; see
<https://www.vaultproject.io>). This allows for secure storage and
retrieval of secrets over a network, such as tokens, passwords and
certificates. Authentication with vault is supported through
several backends including user name/password and authentication via
'GitHub'.
Author: Rich FitzJohn [aut, cre],
Robert Ashton [aut],
Wes Hinsley [aut],
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between vaultr versions 1.0.2 dated 2019-05-16 and 1.1.0 dated 2021-06-09
vaultr-1.0.2/vaultr/tests/testthat/helper-travis.R |only vaultr-1.1.0/vaultr/DESCRIPTION | 11 vaultr-1.1.0/vaultr/MD5 | 123 - vaultr-1.1.0/vaultr/NEWS.md | 8 vaultr-1.1.0/vaultr/R/aaa.R | 23 vaultr-1.1.0/vaultr/R/server_manager.R | 97 vaultr-1.1.0/vaultr/R/util.R | 15 vaultr-1.1.0/vaultr/R/vault_api_client.R | 100 vaultr-1.1.0/vaultr/R/vault_client.R | 170 + vaultr-1.1.0/vaultr/R/vault_client_audit.R | 35 vaultr-1.1.0/vaultr/R/vault_client_auth.R | 57 vaultr-1.1.0/vaultr/R/vault_client_auth_approle.R | 144 + vaultr-1.1.0/vaultr/R/vault_client_auth_github.R | 63 vaultr-1.1.0/vaultr/R/vault_client_auth_userpass.R | 66 vaultr-1.1.0/vaultr/R/vault_client_cubbyhole.R | 49 vaultr-1.1.0/vaultr/R/vault_client_kv1.R | 79 vaultr-1.1.0/vaultr/R/vault_client_kv2.R | 169 + vaultr-1.1.0/vaultr/R/vault_client_operator.R | 75 vaultr-1.1.0/vaultr/R/vault_client_policy.R | 30 vaultr-1.1.0/vaultr/R/vault_client_secrets.R | 45 vaultr-1.1.0/vaultr/R/vault_client_token.R | 266 ++ vaultr-1.1.0/vaultr/R/vault_client_tools.R | 36 vaultr-1.1.0/vaultr/R/vault_client_transit.R | 433 +++- vaultr-1.1.0/vaultr/R/vault_resolve_secrets.R | 44 vaultr-1.1.0/vaultr/R/vault_server_instance.R | 55 vaultr-1.1.0/vaultr/R/vaultr.R | 26 vaultr-1.1.0/vaultr/README.md | 4 vaultr-1.1.0/vaultr/build/vignette.rds |binary vaultr-1.1.0/vaultr/inst/WORDLIST | 8 vaultr-1.1.0/vaultr/inst/doc/packages.html | 36 vaultr-1.1.0/vaultr/inst/doc/vaultr.html | 36 vaultr-1.1.0/vaultr/man/vault_api_client.Rd | 396 ++- vaultr-1.1.0/vaultr/man/vault_client.Rd | 445 ++-- vaultr-1.1.0/vaultr/man/vault_client_audit.Rd | 178 + vaultr-1.1.0/vaultr/man/vault_client_auth.Rd | 203 + vaultr-1.1.0/vaultr/man/vault_client_auth_approle.Rd | 552 +++-- vaultr-1.1.0/vaultr/man/vault_client_auth_github.Rd | 263 +- vaultr-1.1.0/vaultr/man/vault_client_auth_userpass.Rd | 326 ++- vaultr-1.1.0/vaultr/man/vault_client_cubbyhole.Rd | 204 + vaultr-1.1.0/vaultr/man/vault_client_kv1.Rd | 254 +- vaultr-1.1.0/vaultr/man/vault_client_kv2.Rd | 547 +++-- vaultr-1.1.0/vaultr/man/vault_client_object.Rd |only vaultr-1.1.0/vaultr/man/vault_client_operator.Rd | 336 ++- vaultr-1.1.0/vaultr/man/vault_client_policy.Rd | 161 + vaultr-1.1.0/vaultr/man/vault_client_secrets.Rd | 205 + vaultr-1.1.0/vaultr/man/vault_client_token.Rd | 858 +++++--- vaultr-1.1.0/vaultr/man/vault_client_tools.Rd | 133 - vaultr-1.1.0/vaultr/man/vault_client_transit.Rd | 1045 ++++++---- vaultr-1.1.0/vaultr/man/vault_resolve_secrets.Rd | 32 vaultr-1.1.0/vaultr/man/vault_test_server.Rd | 272 +- vaultr-1.1.0/vaultr/man/vaultr.Rd | 26 vaultr-1.1.0/vaultr/tests/testthat/helper-ci.R |only vaultr-1.1.0/vaultr/tests/testthat/helper-vault.R | 27 vaultr-1.1.0/vaultr/tests/testthat/test-server-manager.R | 12 vaultr-1.1.0/vaultr/tests/testthat/test-util.R | 1 vaultr-1.1.0/vaultr/tests/testthat/test-vault-api.R | 1 vaultr-1.1.0/vaultr/tests/testthat/test-vault-auth-approle.R | 3 vaultr-1.1.0/vaultr/tests/testthat/test-vault-kv1.R | 22 vaultr-1.1.0/vaultr/tests/testthat/test-vault-kv2.R | 25 vaultr-1.1.0/vaultr/tests/testthat/test-vault-operator.R | 1 vaultr-1.1.0/vaultr/tests/testthat/test-vault-policy.R | 2 vaultr-1.1.0/vaultr/tests/testthat/test-vault-resolve-secrets.R | 43 vaultr-1.1.0/vaultr/tests/testthat/test-vault-transit.R | 14 vaultr-1.1.0/vaultr/tests/testthat/test-vaultr-tools.R | 8 64 files changed, 6470 insertions(+), 2428 deletions(-)
Title: Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text
Shaping
Description: Provides access to the text shaping functionality in the 'HarfBuzz'
library and the bidirectional algorithm in the 'Fribidi' library.
'textshaping' is a low-level utility package mainly for graphic devices that
expands upon the font tool-set provided by the 'systemfonts' package.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between textshaping versions 0.3.4 dated 2021-05-11 and 0.3.5 dated 2021-06-09
DESCRIPTION | 6 - MD5 | 14 +- NEWS.md | 5 inst/doc/c_interface.html | 253 ++++----------------------------------------- inst/include/textshaping.h | 5 src/face_feature.cpp | 4 src/string_metrics.cpp | 10 - src/string_metrics.h | 7 - 8 files changed, 49 insertions(+), 255 deletions(-)
Title: Download and Display Map Tiles
Description: To create maps from tiles, 'maptiles' downloads, composes and
displays tiles from a large number of providers (e.g. 'OpenStreetMap',
'Stamen', 'Esri', 'CARTO', or 'Thunderforest').
Author: Timothée Giraud [cre, aut] (<https://orcid.org/0000-0002-1932-3323>),
Diego Hernangómez [ctb] (<https://orcid.org/0000-0001-8457-4658>),
Robert J. Hijmans [ctb] (<https://orcid.org/0000-0001-5872-2872>),
Hugh A. Graham [ctb]
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between maptiles versions 0.1.3 dated 2021-04-28 and 0.2.0 dated 2021-06-09
DESCRIPTION | 20 +++++++++++--------- MD5 | 8 ++++---- NAMESPACE | 1 + NEWS.md | 8 ++++++++ R/get_tiles.R | 44 +++++++++++++++++++++++++++++++++++++++++--- 5 files changed, 65 insertions(+), 16 deletions(-)
Title: Estimations using Conley Standard Errors
Description: Merges and extends multiple packages and other published scripts calculating Conley (1999) <doi:10.1016/S0304-4076(98)00084-0> standard errors. Details are
available in the function documentation and in the vignette.
Author: Christian Düben [aut, cre],
Richard Bluhm [cph],
Luis Calderon [cph],
Darin Christensen [cph],
Timothy Conley [cph],
Thiemo Fetzer [cph],
Leander Heldring [cph]
Maintainer: Christian Düben <christian.dueben@uni-hamburg.de>
Diff between conleyreg versions 0.1.1 dated 2021-05-27 and 0.1.2 dated 2021-06-09
DESCRIPTION | 11 +++++------ MD5 | 9 +++++---- NEWS.md |only R/conleyreg.R | 4 ++-- build/partial.rdb |binary inst/doc/conleyreg_introduction.html | 1 + 6 files changed, 13 insertions(+), 12 deletions(-)
Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrGraph versions 1.2.3 dated 2021-04-11 and 1.2.4 dated 2021-06-09
DESCRIPTION | 6 MD5 | 36 +- NAMESPACE | 1 R/MAplotW.R | 4 R/VolcanoPlotW.R | 62 ++- R/addBagPlot.R | 30 - R/foldChangeArrow.R |only R/imageW.R | 18 - R/legendHist.R | 1 R/plotPCAw.R | 101 ++++-- R/vioplotW.R | 16 build/vignette.rds |binary inst/doc/wrGraphVignette1.Rmd | 2 inst/doc/wrGraphVignette1.html | 689 +++++++++++++---------------------------- man/VolcanoPlotW.Rd | 4 man/addBagPlot.Rd | 3 man/foldChangeArrow.Rd |only man/imageW.Rd | 8 man/plotPCAw.Rd | 30 + vignettes/wrGraphVignette1.Rmd | 2 20 files changed, 440 insertions(+), 573 deletions(-)
Title: Inferring Developmental Chronologies from Single-Cell RNA
Sequencing Data
Description: An accurate and easy tool for performing linear trajectory inference on
single cells using single-cell RNA sequencing data. In addition, SCORPIUS
provides functions for discovering the most important genes with respect to
the reconstructed trajectory, as well as nice visualisation tools.
Cannoodt et al. (2016) <doi:10.1101/079509>.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Wouter Saelens [ctb] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between SCORPIUS versions 1.0.7 dated 2020-05-11 and 1.0.8 dated 2021-06-09
SCORPIUS-1.0.7/SCORPIUS/data/datalist |only SCORPIUS-1.0.8/SCORPIUS/DESCRIPTION | 14 SCORPIUS-1.0.8/SCORPIUS/MD5 | 38 - SCORPIUS-1.0.8/SCORPIUS/NEWS.md | 4 SCORPIUS-1.0.8/SCORPIUS/R/data.R | 2 SCORPIUS-1.0.8/SCORPIUS/R/dynwrap_integration.R | 16 SCORPIUS-1.0.8/SCORPIUS/R/package.R | 7 SCORPIUS-1.0.8/SCORPIUS/R/plotting.R | 43 + SCORPIUS-1.0.8/SCORPIUS/README.md | 75 +- SCORPIUS-1.0.8/SCORPIUS/build/partial.rdb |only SCORPIUS-1.0.8/SCORPIUS/build/vignette.rds |binary SCORPIUS-1.0.8/SCORPIUS/inst/CITATION | 4 SCORPIUS-1.0.8/SCORPIUS/inst/doc/ginhoux.html | 275 ++-------- SCORPIUS-1.0.8/SCORPIUS/inst/doc/simulated-data.html | 275 ++-------- SCORPIUS-1.0.8/SCORPIUS/inst/dynwrap/definition.yml | 3 SCORPIUS-1.0.8/SCORPIUS/inst/dynwrap/run.R | 2 SCORPIUS-1.0.8/SCORPIUS/man/SCORPIUS-package.Rd | 7 SCORPIUS-1.0.8/SCORPIUS/man/figures/README_infer_trajectory-1.png |binary SCORPIUS-1.0.8/SCORPIUS/man/figures/README_reduce_dimensionality-1.png |binary SCORPIUS-1.0.8/SCORPIUS/man/ginhoux.Rd | 2 SCORPIUS-1.0.8/SCORPIUS/man/ti_scorpius.Rd | 2 21 files changed, 222 insertions(+), 547 deletions(-)
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with
details from statistical tests included in the plots themselves. It
provides an easier syntax to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports the most common types of
statistical approaches and tests: parametric, nonparametric, robust,
and Bayesian versions of t-test/ANOVA, correlation analyses,
contingency table analysis, meta-analysis, and regression analyses.
Author: Indrajeet Patil [cre, aut, cph]
(<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 0.7.2 dated 2021-04-12 and 0.8.0 dated 2021-06-09
ggstatsplot-0.7.2/ggstatsplot/R/helpers_messages.R |only ggstatsplot-0.7.2/ggstatsplot/R/helpers_theme_ggstatsplot.R |only ggstatsplot-0.7.2/ggstatsplot/man/aesthetic_addon.Rd |only ggstatsplot-0.7.2/ggstatsplot/man/centrality_ggrepel.Rd |only ggstatsplot-0.7.2/ggstatsplot/man/ggsignif_adder.Rd |only ggstatsplot-0.7.2/ggstatsplot/man/histo_labeller.Rd |only ggstatsplot-0.7.2/ggstatsplot/tests/figs |only ggstatsplot-0.7.2/ggstatsplot/tests/testthat/_snaps/ggcoefstats_dataframes.md |only ggstatsplot-0.7.2/ggstatsplot/tests/testthat/test-ggcoefstats_dataframes.R |only ggstatsplot-0.7.2/ggstatsplot/vignettes/web_only/theme_ggstatsplot.Rmd |only ggstatsplot-0.8.0/ggstatsplot/DESCRIPTION | 21 ggstatsplot-0.8.0/ggstatsplot/LICENSE | 1348 - ggstatsplot-0.8.0/ggstatsplot/MD5 | 360 ggstatsplot-0.8.0/ggstatsplot/NAMESPACE | 226 ggstatsplot-0.8.0/ggstatsplot/NEWS.md | 2791 +- ggstatsplot-0.8.0/ggstatsplot/R/attach.R | 14 ggstatsplot-0.8.0/ggstatsplot/R/combine_plots.R | 142 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ggstatsplot-0.8.0/ggstatsplot/tests/testthat/test-grouped_ggdotplotstats.R | 177 ggstatsplot-0.8.0/ggstatsplot/tests/testthat/test-grouped_gghistostats.R | 152 ggstatsplot-0.8.0/ggstatsplot/tests/testthat/test-grouped_ggpiestats.R | 229 ggstatsplot-0.8.0/ggstatsplot/tests/testthat/test-grouped_ggscatterstats.R | 388 ggstatsplot-0.8.0/ggstatsplot/tests/testthat/test-grouped_ggwithinstats.R | 228 ggstatsplot-0.8.0/ggstatsplot/tests/testthat/test-helpers.R | 82 ggstatsplot-0.8.0/ggstatsplot/tests/testthat/test-pairwise_ggsignif.R | 481 ggstatsplot-0.8.0/ggstatsplot/tests/testthat/test-vdiffr_figs.R | 329 ggstatsplot-0.8.0/ggstatsplot/tests/testthat/test-z_ggcoefstats_dataframes.R |only ggstatsplot-0.8.0/ggstatsplot/vignettes/additional.Rmd | 250 ggstatsplot-0.8.0/ggstatsplot/vignettes/web_only/apa.csl | 886 ggstatsplot-0.8.0/ggstatsplot/vignettes/web_only/benchmarking.Rmd | 440 ggstatsplot-0.8.0/ggstatsplot/vignettes/web_only/combine_plots.Rmd | 538 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More information about contTimeCausal at CRAN
Permanent link
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018)
<DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] (<https://orcid.org/0000-0002-2089-3956>),
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 1.12.0 dated 2021-05-05 and 1.13.0 dated 2021-06-09
DESCRIPTION | 8 MD5 | 662 +-- NAMESPACE | 564 +- NEWS.md | 552 +- R/abfit.R | 2707 ++++++------ R/amp_scaling.R | 516 +- R/basis_set.R | 610 +- R/benchmark.R | 84 R/data.R | 4 R/dicom_reader.R | 300 - R/fit_display.R | 902 ++-- R/fitting.R | 1626 +++---- R/gsl_functions.R | 454 +- R/image_reg.R | 988 ++-- R/interactive_plotting.R | 988 ++-- R/mol_parameters.R | 2502 +++++------ R/mrs_data_display.R | 1464 +++--- R/mrs_data_io.R | 708 +-- R/mrs_data_proc.R | 6486 +++++++++++++++--------------- R/mrs_read_dicom.R | 470 +- R/mrs_read_ima.R | 140 R/mrs_read_lcm_raw.R | 58 R/mrs_read_list_data.R | 197 R/mrs_read_nifti.R | 182 R/mrs_read_paravis.R | 136 R/mrs_read_pfile.R | 382 - R/mrs_read_rda.R | 192 R/mrs_read_spar_sdat.R | 362 - R/mrs_read_twix.R | 1001 ++-- R/mrs_read_varian.R | 146 R/mrs_write_nifti.R | 122 R/pnnls.R | 134 R/precomp.R | 152 R/pulse_sequences.R | 1070 ++-- R/pulse_shapes.R | 24 R/qm_simulation.R | 998 ++-- R/rats.R | 330 - R/spant.R | 386 - R/svs_batch_fit.R | 462 +- R/tdsr.R | 144 R/utils.R | 946 ++-- R/varpro.R | 502 +- R/varpro_3_para.R | 460 +- build/vignette.rds |binary inst/WORDLIST | 380 - inst/doc/abfit-baseline-opts.R | 106 inst/doc/abfit-baseline-opts.Rmd | 184 inst/doc/abfit-baseline-opts.html | 427 - inst/doc/spant-basis-simulation.R | 84 inst/doc/spant-basis-simulation.Rmd | 146 inst/doc/spant-basis-simulation.html | 389 - inst/doc/spant-intro.R | 99 inst/doc/spant-intro.Rmd | 170 inst/doc/spant-intro.html | 569 +- inst/doc/spant-metabolite-simulation.R | 150 inst/doc/spant-metabolite-simulation.Rmd | 248 - inst/doc/spant-metabolite-simulation.html | 597 +- inst/doc/spant-preprocessing.R | 92 inst/doc/spant-preprocessing.Rmd | 152 inst/doc/spant-preprocessing.html | 395 - inst/reports/mpress_gaba.Rmd | 86 man/Arg.mrs_data.Rd | 34 man/Conj.mrs_data.Rd | 34 man/Im.mrs_data.Rd | 34 man/Mod.mrs_data.Rd | 34 man/Ncoils.Rd | 28 man/Ndyns.Rd | 28 man/Npts.Rd | 34 man/Nspec.Rd | 28 man/Nx.Rd | 28 man/Ny.Rd | 28 man/Nz.Rd | 28 man/Re.mrs_data.Rd | 34 man/abfit_opts.Rd | 328 - man/abfit_opts_v1_9_0.Rd | 38 man/acquire.Rd | 46 man/add_noise.Rd |only man/align.Rd | 70 man/apodise_xy.Rd | 42 man/append_basis.Rd | 38 man/append_coils.Rd | 38 man/append_dyns.Rd | 38 man/apply_axes.Rd | 60 man/apply_mrs.Rd | 44 man/apply_pvc.Rd | 52 man/array2mrs_data.Rd | 72 man/auto_phase.Rd | 50 man/back_extrap_ar.Rd | 74 man/basis2mrs_data.Rd | 54 man/bbase.Rd | 46 man/bc_als.Rd | 42 man/bc_constant.Rd | 40 man/beta2lw.Rd | 38 man/calc_coil_noise_cor.Rd | 34 man/calc_coil_noise_sd.Rd | 34 man/calc_ed_from_lambda.Rd | 42 man/calc_peak_info_vec.Rd | 40 man/calc_sd_poly.Rd | 42 man/calc_spec_diff.Rd | 42 man/calc_spec_snr.Rd | 88 man/check_lcm.Rd | 22 man/check_tqn.Rd | 22 man/circ_mask.Rd | 42 man/collapse_to_dyns.Rd | 52 man/comb_coils.Rd | 88 man/comb_csv_results.Rd | 42 man/comb_fit_list_fit_tables.Rd | 76 man/comb_fit_list_result_tables.Rd | 48 man/comb_fit_tables.Rd | 46 man/comb_metab_ref.Rd | 38 man/conv_mrs.Rd | 38 man/crop_spec.Rd | 46 man/crop_td_pts.Rd | 42 man/crop_xy.Rd | 42 man/crossprod_3d.Rd | 42 man/decimate_mrs_fd.Rd | 38 man/decimate_mrs_td.Rd | 46 man/def_N.Rd | 28 man/def_acq_paras.Rd | 80 man/def_fs.Rd | 28 man/def_ft.Rd | 28 man/def_nuc.Rd | 28 man/def_ref.Rd | 28 man/dicom_reader.Rd | 64 man/diff_mrs.Rd | 38 man/downsample_mrs_fd.Rd | 34 man/downsample_mrs_td.Rd | 42 man/ecc.Rd | 52 man/est_noise_sd.Rd | 46 man/fd2td.Rd | 34 man/fd_conv_filt.Rd | 36 man/fit_amps.Rd | 58 man/fit_diags.Rd | 38 man/fit_mrs.Rd | 160 man/fit_res2csv.Rd | 36 man/fp_phase.Rd | 34 man/fp_phase_correct.Rd | 44 man/fp_scale.Rd | 38 man/fs.Rd | 34 man/ft_shift.Rd | 34 man/ft_shift_mat.Rd | 38 man/gen_F.Rd | 42 man/gen_F_xy.Rd | 42 man/get_1h_brain_basis_paras.Rd | 48 man/get_1h_brain_basis_paras_v1.Rd | 48 man/get_1h_brain_basis_paras_v2.Rd | 48 man/get_1h_brain_basis_paras_v3.Rd | 48 man/get_2d_psf.Rd | 46 man/get_acq_paras.Rd | 34 man/get_dyns.Rd | 40 man/get_even_dyns.Rd | 34 man/get_fh_dyns.Rd | 34 man/get_fit_map.Rd | 32 man/get_fp.Rd | 34 man/get_guassian_pulse.Rd | 36 man/get_lcm_cmd.Rd | 22 man/get_metab.Rd | 34 man/get_mol_names.Rd | 32 man/get_mol_paras.Rd | 32 man/get_mrs_affine.Rd | 46 man/get_mrsi2d_seg.Rd | 48 man/get_mrsi_voi.Rd | 46 man/get_mrsi_voxel.Rd | 50 man/get_mrsi_voxel_xy_psf.Rd | 50 man/get_odd_dyns.Rd | 34 man/get_ref.Rd | 34 man/get_seg_ind.Rd | 42 man/get_sh_dyns.Rd | 34 man/get_slice.Rd | 38 man/get_subset.Rd | 82 man/get_svs_voi.Rd | 38 man/get_td_amp.Rd | 50 man/get_tqn_cmd.Rd | 22 man/get_uncoupled_mol.Rd | 74 man/get_voi_cog.Rd | 34 man/get_voi_seg.Rd | 38 man/get_voi_seg_psf.Rd | 38 man/get_voxel.Rd | 54 man/grid_shift_xy.Rd | 42 man/gridplot.Rd | 32 man/gridplot.mrs_data.Rd | 76 man/hsvd.Rd | 52 man/hsvd_filt.Rd | 70 man/hsvd_vec.Rd | 58 man/hz.Rd | 42 man/ift_shift.Rd | 34 man/ift_shift_mat.Rd | 38 man/image.mrs_data.Rd | 124 man/img2kspace_xy.Rd | 34 man/int_spec.Rd | 50 man/interleave_dyns.Rd | 34 man/inv_even_dyns.Rd | 34 man/inv_odd_dyns.Rd | 34 man/is.def.Rd | 34 man/is_fd.Rd | 38 man/kspace2img_xy.Rd | 34 man/l2_reg.Rd | 58 man/lb.Rd | 54 man/lw2alpha.Rd | 38 man/lw2beta.Rd | 38 man/mask_dyns.Rd | 40 man/mask_xy.Rd | 42 man/mask_xy_mat.Rd | 44 man/mat2mrs_data.Rd | 72 man/max_mrs.Rd | 34 man/max_mrs_interp.Rd | 38 man/mean.mrs_data.Rd | 38 man/mean_dyn_blocks.Rd | 38 man/mean_dyn_pairs.Rd | 34 man/mean_dyns.Rd | 34 man/median_dyns.Rd | 34 man/mrs_data2basis.Rd | 42 man/mrs_data2mat.Rd | 44 man/mrs_data2vec.Rd | 54 man/mvfftshift.Rd | 38 man/mvifftshift.Rd | 38 man/n2coord.Rd | 32 man/nifti_flip_lr.Rd | 42 man/norm_mrs.Rd | 50 man/ortho3.Rd | 116 man/ortho3_inter.Rd | 68 man/peak_info.Rd | 72 man/pg_extrap_xy.Rd | 80 man/phase.Rd | 42 man/plot.fit_result.Rd | 154 man/plot.mrs_data.Rd | 210 man/plot_bc.Rd | 36 man/plot_slice_fit.Rd | 66 man/plot_slice_fit_inter.Rd | 72 man/plot_slice_map.Rd | 94 man/plot_slice_map_inter.Rd | 122 man/plot_voi_overlay.Rd | 44 man/plot_voi_overlay_seg.Rd | 40 man/ppm.Rd | 70 man/precomp.Rd | 40 man/print.fit_result.Rd | 32 man/print.mrs_data.Rd | 36 man/qn_states.Rd | 34 man/rats.Rd | 96 man/re_weighting.Rd | 42 man/read_basis.Rd | 38 man/read_ima_coil_dir.Rd | 48 man/read_ima_dyn_dir.Rd | 48 man/read_lcm_coord.Rd | 36 man/read_mrs.Rd | 112 man/read_mrs_tqn.Rd | 64 man/read_siemens_txt_hdr.Rd | 38 man/read_tqn_fit.Rd | 44 man/read_tqn_result.Rd | 48 man/reexports.Rd | 42 man/rep_array_dim.Rd | 42 man/rep_dyn.Rd | 38 man/rep_mrs.Rd | 54 man/resample_img.Rd | 42 man/resample_voi.Rd | 42 man/reslice_to_mrs.Rd | 38 man/reson_table2mrs_data.Rd | 52 man/rm_dyns.Rd | 40 man/scale_amp_molal_pvc.Rd | 54 man/scale_amp_molar.Rd | 56 man/scale_amp_ratio.Rd | 40 man/scale_amp_water_ratio.Rd | 42 man/scale_mrs.Rd |only man/sd.Rd | 38 man/sd.mrs_data.Rd | 38 man/seconds.Rd | 34 man/seq_cpmg_ideal.Rd | 50 man/seq_mega_press_ideal.Rd | 84 man/seq_press_ideal.Rd | 50 man/seq_pulse_acquire.Rd | 42 man/seq_pulse_acquire_31p.Rd | 42 man/seq_slaser_ideal.Rd | 54 man/seq_spin_echo_ideal.Rd | 46 man/seq_spin_echo_ideal_31p.Rd | 46 man/seq_steam_ideal.Rd | 50 man/set_def_acq_paras.Rd | 56 man/set_lcm_cmd.Rd | 28 man/set_lw.Rd | 42 man/set_precomp_mode.Rd | 28 man/set_precomp_verbose.Rd | 28 man/set_ref.Rd | 32 man/set_td_pts.Rd | 42 man/set_tqn_cmd.Rd | 28 man/shift.Rd | 42 man/shift_basis.Rd |only man/sim_basis.Rd | 64 man/sim_basis_1h_brain.Rd | 70 man/sim_basis_1h_brain_press.Rd | 70 man/sim_basis_tqn.Rd | 66 man/sim_brain_1h.Rd | 82 man/sim_mol.Rd | 80 man/sim_noise.Rd | 74 man/sim_resonances.Rd | 96 man/spant-package.Rd | 94 man/spant_abfit_benchmark.Rd | 40 man/spant_mpress_drift.Rd | 32 man/spin_sys.Rd | 42 man/spm_pve2categorical.Rd | 38 man/ssp.Rd | 48 man/stackplot.Rd | 32 man/stackplot.fit_result.Rd | 178 man/stackplot.mrs_data.Rd | 206 man/sum_coils.Rd | 34 man/sum_dyns.Rd | 34 man/sum_mrs.Rd |only man/svs_1h_brain_analysis.Rd | 152 man/svs_1h_brain_batch_analysis.Rd | 86 man/td2fd.Rd | 34 man/td_conv_filt.Rd | 42 man/tdsr.Rd | 52 man/varpro_3_para_opts.Rd | 100 man/varpro_opts.Rd | 96 man/vec2mrs_data.Rd | 74 man/write_basis.Rd | 36 man/write_basis_tqn.Rd | 46 man/write_mrs.Rd | 40 man/write_mrs_nifti.Rd | 32 man/zero_nzoc.Rd | 38 man/zf.Rd | 52 man/zf_xy.Rd | 44 tests/testthat.R | 8 tests/testthat/abfit_res_coarse.rds |binary tests/testthat/abfit_res_default.rds |binary tests/testthat/abfit_res_fine.rds |binary tests/testthat/abfit_res_no_optim.rds |binary tests/testthat/test_fitting.R | 147 tests/testthat/test_nifti.R | 72 tests/testthat/test_preproc.R | 8 tests/testthat/test_qm_sim.R | 10 vignettes/abfit-baseline-opts.Rmd | 184 vignettes/spant-basis-simulation.Rmd | 146 vignettes/spant-intro.Rmd | 170 vignettes/spant-metabolite-simulation.Rmd | 248 - vignettes/spant-preprocessing.Rmd | 152 334 files changed, 24916 insertions(+), 24580 deletions(-)
Title: Calculate Predicted Means for Linear Models
Description: Providing functions to diagnose
and make inferences from various linear models, such as those obtained from 'aov',
'lm', 'glm', 'gls', 'lme', and 'lmer'. Inferences include predicted
means and standard errors, contrasts, multiple comparisons, permutation tests and graphs.
Author: Dongwen Luo, Siva Ganesh and John Koolaard
Maintainer: Dongwen Luo <dongwen.luo@agresearch.co.nz>
Diff between predictmeans versions 1.0.4 dated 2020-04-15 and 1.0.6 dated 2021-06-09
predictmeans-1.0.4/predictmeans/R/varcomp.lmer.R |only predictmeans-1.0.4/predictmeans/man/varcomp.lmer.Rd |only predictmeans-1.0.6/predictmeans/DESCRIPTION | 14 predictmeans-1.0.6/predictmeans/MD5 | 30 - predictmeans-1.0.6/predictmeans/NAMESPACE | 41 +- predictmeans-1.0.6/predictmeans/R/Kmatrix.R | 48 +- predictmeans-1.0.6/predictmeans/R/anovalmer.R | 3 predictmeans-1.0.6/predictmeans/R/covariatemeans.R | 25 + predictmeans-1.0.6/predictmeans/R/misc.R | 295 +++++++++++++++--- predictmeans-1.0.6/predictmeans/R/mymodelparm.R | 2 predictmeans-1.0.6/predictmeans/R/permlmer.R | 24 - predictmeans-1.0.6/predictmeans/R/predictmeans.R | 69 ++-- predictmeans-1.0.6/predictmeans/R/rsplot.gls.R | 10 predictmeans-1.0.6/predictmeans/R/varcomp.R |only predictmeans-1.0.6/predictmeans/man/Kmatrix.Rd | 8 predictmeans-1.0.6/predictmeans/man/anovalmer.Rd | 2 predictmeans-1.0.6/predictmeans/man/covariatemeans.Rd | 3 predictmeans-1.0.6/predictmeans/man/varcomp.Rd |only 18 files changed, 417 insertions(+), 157 deletions(-)
Title: An Interface to Specify Causal Graphs and Compute Bounds on
Causal Effects
Description: When causal quantities are not identifiable from the observed data, it still may be possible
to bound these quantities using the observed data. We outline a class of problems for which the
derivation of tight bounds is always a linear programming problem and can therefore, at least
theoretically, be solved using a symbolic linear optimizer. We extend and generalize the
approach of Balke and Pearl (1994) <doi:10.1016/B978-1-55860-332-5.50011-0> and we provide
a user friendly graphical interface for setting up such problems via directed acyclic
graphs (DAG), which only allow for problems within this class to be depicted. The user can
then define linear constraints to further refine their assumptions to meet their specific
problem, and then specify a causal query using a text interface. The program converts this
user defined DAG, query, and constraints, and returns tight bounds. The bounds can be
converted to R functions to evaluate them for specific datasets, and to latex code for
publication. The methods and proofs of tightness and validity of the bounds are described in
a preprint by Sachs, Gabriel, and Sjölander (2020)
<https://sachsmc.github.io/causaloptim/articles/CausalBoundsMethods.pdf>.
Author: Michael C Sachs [aut, cre],
Erin E Gabriel [aut],
Arvid Sjölander [aut],
Gustav Jonzon [ctb] ((improved vertex enumeration)),
Alexander A Balke [ctb] ((C++ code)),
Colorado Reed [ctb] ((graph-creator.js))
Maintainer: Michael C Sachs <sachsmc@gmail.com>
Diff between causaloptim versions 0.7.1 dated 2020-05-07 and 0.8.2 dated 2021-06-09
DESCRIPTION | 16 MD5 | 90 ++- NAMESPACE | 8 NEWS.md | 16 R/process-optimizer.R | 127 +++++ R/response-functional.R | 431 ++----------------- R/text-parsing.R | 13 R/translation-modules.R |only R/update-effect.R |only R/utils.R | 60 ++ README.md | 4 build/vignette.rds |binary inst/doc/CausalBoundsMethods.pdf |binary inst/doc/example-code.R | 10 inst/doc/example-code.Rmd | 10 inst/doc/example-code.html | 608 +++++++++------------------ inst/doc/shinyapp.Rmd | 2 inst/doc/shinyapp.html | 315 +++---------- inst/doc/vertexenum-speed.R |only inst/doc/vertexenum-speed.Rmd |only inst/doc/vertexenum-speed.html |only inst/shiny/interface/server.R | 2 man/analyze_graph.Rd | 101 ++-- man/btm_var.Rd | 38 - man/causaloptim-package.Rd | 46 +- man/constant_term.Rd |only man/create_R_matrix.Rd |only man/create_effect_vector.Rd |only man/create_q_matrix.Rd |only man/create_response_function.Rd |only man/evaluate_objective.Rd |only man/interpret_bounds.Rd | 62 +- man/latex_bounds.Rd | 64 +- man/linear_expression.Rd |only man/linear_term.Rd |only man/list_to_path.Rd | 38 - man/opt_effect.Rd |only man/optimize_effect.Rd | 56 +- man/optimize_effect_2.Rd |only man/parse_constraints.Rd | 38 - man/parse_effect.Rd | 52 +- man/plot.linearcausalproblem.Rd | 38 - man/print.linearcausalproblem.Rd | 38 - man/simulate_bounds.Rd | 64 +- man/update_effect.Rd |only src/EquationSet.cpp | 2 tests/test-graphs-for-known-bounds.R | 160 ++++++- tests/test-graphs/MIV-bounds-result.RData |only tests/test-graphs/multi-instrument-graph.rds |only vignettes/Canonical_Partitions.png |only vignettes/Causal_Graph.png |only vignettes/MIV-bounds-result.RData |only vignettes/TwoIVs.png |only vignettes/User_Input_DAG.png |only vignettes/example-code.Rmd | 10 vignettes/example.RData |binary vignettes/shinyapp.Rmd | 2 vignettes/vertexenum-speed.Rmd |only 58 files changed, 1124 insertions(+), 1397 deletions(-)
Title: Weighting and Weighted Statistics
Description: Provides a variety of functions for producing simple weighted statistics, such as weighted Pearson's correlations, partial correlations, Chi-Squared statistics, histograms, and t-tests. Also now includes some software for quickly recoding survey data and plotting estimates from interaction terms in regressions (and multiply imputed regressions) both with and without weights. NOTE: Weighted partial correlation calculations pulled to address a bug.
Author: Josh Pasek [aut, cre], with some assistance from Alex Tahk and some code modified from R-core; Additional contributions by Gene Culter and Marcus Schwemmle.
Maintainer: Josh Pasek <josh@joshpasek.com>
Diff between weights versions 1.0.2 dated 2021-05-27 and 1.0.3 dated 2021-06-09
DESCRIPTION | 8 ++-- MD5 | 8 ++-- R/findwtdinteraction.default.R | 4 +- R/plotinteractpreds.interactpreds.R | 69 ++++++++++++++++++------------------ R/plotwtdinteraction.R | 2 - 5 files changed, 46 insertions(+), 45 deletions(-)
Title: Data Structures for Single Cell Data
Description: Defines S4 classes for single-cell genomic data and associated
information, such as dimensionality reduction embeddings, nearest-neighbor
graphs, and spatially-resolved coordinates. Provides data access methods and
R-native hooks to ensure the Seurat object is familiar to other R users. See
Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>,
Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>,
and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for
more details.
Author: Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>),
Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>),
Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>),
Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>),
Jeff Farrell [ctb],
Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>),
Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>),
Patrick Roelli [ctb],
Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)
Maintainer: Paul Hoffman <seurat@nygenome.org>
Diff between SeuratObject versions 4.0.1 dated 2021-05-08 and 4.0.2 dated 2021-06-09
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 5 +++++ R/utils.R | 2 +- 4 files changed, 13 insertions(+), 8 deletions(-)
Title: P-Model
Description: Implements the P-model
(Stocker et al., 2020 <doi:10.5194/gmd-13-1545-2020>),
predicting acclimated parameters of the enzyme kinetics of C3 photosynthesis,
assimilation, and dark respiration rates as a function of the environment
(temperature, CO2, vapour pressure deficit, light, atmospheric pressure).
Author: Benjamin Stocker [aut, cre] (<https://orcid.org/0000-0002-5070-8109>),
Koen Hufkens [ctb] (<https://orcid.org/0000-0002-5070-8109>)
Maintainer: Benjamin Stocker <benjamin.stocker@gmail.com>
Diff between rpmodel versions 1.0.4 dated 2019-12-04 and 1.2.0 dated 2021-06-09
rpmodel-1.0.4/rpmodel/NEWS.md |only rpmodel-1.0.4/rpmodel/R/calc_ftemp_arrh.R |only rpmodel-1.0.4/rpmodel/R/calc_ftemp_inst_rd.R |only rpmodel-1.0.4/rpmodel/R/calc_ftemp_inst_vcmax.R |only rpmodel-1.0.4/rpmodel/R/calc_ftemp_kphio.R |only rpmodel-1.0.4/rpmodel/R/calc_gammastar.R |only rpmodel-1.0.4/rpmodel/R/calc_kmm.R |only rpmodel-1.0.4/rpmodel/R/calc_patm.R |only rpmodel-1.0.4/rpmodel/R/calc_soilmstress.R |only rpmodel-1.0.4/rpmodel/README.md |only rpmodel-1.0.4/rpmodel/man/calc_ftemp_arrh.Rd |only rpmodel-1.0.4/rpmodel/man/calc_ftemp_inst_rd.Rd |only rpmodel-1.0.4/rpmodel/man/calc_ftemp_inst_vcmax.Rd |only rpmodel-1.0.4/rpmodel/man/calc_ftemp_kphio.Rd |only rpmodel-1.0.4/rpmodel/man/calc_gammastar.Rd |only rpmodel-1.0.4/rpmodel/man/calc_kmm.Rd |only rpmodel-1.0.4/rpmodel/man/calc_patm.Rd |only rpmodel-1.0.4/rpmodel/man/calc_soilmstress.Rd |only rpmodel-1.2.0/rpmodel/DESCRIPTION | 39 rpmodel-1.2.0/rpmodel/MD5 | 56 - rpmodel-1.2.0/rpmodel/NAMESPACE | 21 rpmodel-1.2.0/rpmodel/R/rpmodel.R | 849 +++++++-------------- rpmodel-1.2.0/rpmodel/R/subroutines.R |only rpmodel-1.2.0/rpmodel/build/vignette.rds |binary rpmodel-1.2.0/rpmodel/inst/CITATION | 20 rpmodel-1.2.0/rpmodel/inst/doc/usage.R | 132 +-- rpmodel-1.2.0/rpmodel/inst/doc/usage.Rmd | 165 ++-- rpmodel-1.2.0/rpmodel/inst/doc/usage.html | 206 ++--- rpmodel-1.2.0/rpmodel/man/co2_to_ca.Rd |only rpmodel-1.2.0/rpmodel/man/dampen_vec.Rd |only rpmodel-1.2.0/rpmodel/man/density_h2o.Rd |only rpmodel-1.2.0/rpmodel/man/ftemp_arrh.Rd |only rpmodel-1.2.0/rpmodel/man/ftemp_inst_jmax.Rd |only rpmodel-1.2.0/rpmodel/man/ftemp_inst_rd.Rd |only rpmodel-1.2.0/rpmodel/man/ftemp_inst_vcmax.Rd |only rpmodel-1.2.0/rpmodel/man/ftemp_kphio.Rd |only rpmodel-1.2.0/rpmodel/man/gammastar.Rd |only rpmodel-1.2.0/rpmodel/man/kmm.Rd |only rpmodel-1.2.0/rpmodel/man/patm.Rd |only rpmodel-1.2.0/rpmodel/man/rpmodel.Rd | 303 ++++--- rpmodel-1.2.0/rpmodel/man/soilmstress.Rd |only rpmodel-1.2.0/rpmodel/man/viscosity_h2o.Rd |only rpmodel-1.2.0/rpmodel/tests |only rpmodel-1.2.0/rpmodel/vignettes/fig |only rpmodel-1.2.0/rpmodel/vignettes/usage.Rmd | 165 ++-- 45 files changed, 956 insertions(+), 1000 deletions(-)
Title: Computation and Plots of Influence Functions for Risk and
Performance Measures
Description: Computes the influence functions time series of the returns for the risk and
performance measures as mentioned in Chen and Martin (2018)
<https://www.ssrn.com/abstract=3085672>, as well as in Zhang et al. (2019)
<https://www.ssrn.com/abstract=3415903>. Also evaluates estimators influence
functions at a set of parameter values and plots them to display the shapes of
the influence functions.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Shengyu Zhang <syzhang@uw.edu>,
Douglas Martin <doug@amath.washington.edu>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RPEIF versions 1.2.2 dated 2021-05-13 and 1.2.3 dated 2021-06-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 3 +++ README.md | 6 +++--- inst/doc/RPEIFVignette.pdf |binary 5 files changed, 14 insertions(+), 11 deletions(-)
Title: Set of Tools to Data Analysis using Generalized Linear Models
Description: Set of tools to the statistical analysis of data using: (1) normal linear models; (2) generalized linear models; (3) negative binomial regression models as alternative to the Poisson regression models under the presence of overdispersion; (4) beta-binomial regression models as alternative to the binomial regression models under the presence of overdispersion; (5) generalized estimating equations for cluster correlated data.
Author: Luis Hernando Vanegas [aut, cre],
Luz Marina Rondón [aut],
Gilberto A. Paula [aut]
Maintainer: Luis Hernando Vanegas <lhvanegasp@unal.edu.co>
Diff between glmtoolbox versions 0.1.0 dated 2021-04-13 and 0.1.1 dated 2021-06-09
glmtoolbox-0.1.0/glmtoolbox/man/DEW.Rd |only glmtoolbox-0.1.1/glmtoolbox/DESCRIPTION | 8 glmtoolbox-0.1.1/glmtoolbox/MD5 | 68 - glmtoolbox-0.1.1/glmtoolbox/NAMESPACE | 8 glmtoolbox-0.1.1/glmtoolbox/R/data.R | 44 - glmtoolbox-0.1.1/glmtoolbox/R/geeglm.R | 548 +++++++++++---- glmtoolbox-0.1.1/glmtoolbox/R/glms.R | 138 +++ glmtoolbox-0.1.1/glmtoolbox/R/overglm.R | 36 glmtoolbox-0.1.1/glmtoolbox/man/AGPC.Rd |only glmtoolbox-0.1.1/glmtoolbox/man/CIC.Rd | 20 glmtoolbox-0.1.1/glmtoolbox/man/GHYC.Rd |only glmtoolbox-0.1.1/glmtoolbox/man/QIC.Rd | 16 glmtoolbox-0.1.1/glmtoolbox/man/RJC.Rd | 16 glmtoolbox-0.1.1/glmtoolbox/man/SGPC.Rd |only glmtoolbox-0.1.1/glmtoolbox/man/anova.glmgee.Rd | 2 glmtoolbox-0.1.1/glmtoolbox/man/cellular.Rd | 4 glmtoolbox-0.1.1/glmtoolbox/man/confint2.Rd |only glmtoolbox-0.1.1/glmtoolbox/man/depression.Rd | 6 glmtoolbox-0.1.1/glmtoolbox/man/dfbeta.glmgee.Rd | 7 glmtoolbox-0.1.1/glmtoolbox/man/envelope.glm.Rd | 2 glmtoolbox-0.1.1/glmtoolbox/man/envelope.lm.Rd | 2 glmtoolbox-0.1.1/glmtoolbox/man/envelope.overglm.Rd | 8 glmtoolbox-0.1.1/glmtoolbox/man/estequa.glm.Rd | 1 glmtoolbox-0.1.1/glmtoolbox/man/estequa.overglm.Rd | 1 glmtoolbox-0.1.1/glmtoolbox/man/glmgee.Rd | 8 glmtoolbox-0.1.1/glmtoolbox/man/ossification.Rd | 4 glmtoolbox-0.1.1/glmtoolbox/man/races.Rd | 5 glmtoolbox-0.1.1/glmtoolbox/man/residuals.glmgee.Rd | 8 glmtoolbox-0.1.1/glmtoolbox/man/residuals.overglm.Rd | 8 glmtoolbox-0.1.1/glmtoolbox/man/richness.Rd | 5 glmtoolbox-0.1.1/glmtoolbox/man/skincancer.Rd | 3 glmtoolbox-0.1.1/glmtoolbox/man/spruce.Rd | 12 glmtoolbox-0.1.1/glmtoolbox/man/stepCriterion.glm.Rd | 2 glmtoolbox-0.1.1/glmtoolbox/man/stepCriterion.glmgee.Rd | 6 glmtoolbox-0.1.1/glmtoolbox/man/stepCriterion.lm.Rd | 4 glmtoolbox-0.1.1/glmtoolbox/man/stepCriterion.overglm.Rd | 2 glmtoolbox-0.1.1/glmtoolbox/man/swimmers.Rd | 5 glmtoolbox-0.1.1/glmtoolbox/man/vcov.glmgee.Rd |only 38 files changed, 700 insertions(+), 307 deletions(-)
Title: VITA, IG and PLSIM Simulation for Given Covariance and Marginals
Description: User specifies population covariance matrix. Marginal information may be fully
specified, for which the package implements the VITA (VIne-To-Anything) algorithm.
Groenneberg and Foldnes (2017) <doi:10.1007/s11336-017-9569-6>.
Alternatively, marginal skewness and kurtosis may be specified, for which the package
implements the IG (independent generator) and PLSIM (piecewise linear) algorithms. Foldnes and Olsson (2016) <doi:10.1080/00273171.2015.1133274>.
Foldnes and Groenneberg (2021).
Author: Njaal Foldnes [aut, cre],
Steffen Groenneberg [aut]
Maintainer: Njaal Foldnes <njal.foldnes@gmail.com>
Diff between covsim versions 0.1.0 dated 2020-05-12 and 0.2.0 dated 2021-06-09
DESCRIPTION | 27 ++++++----- MD5 | 20 ++++---- NAMESPACE | 1 NEWS.md | 6 +- R/IG.R | 3 - R/PLSIM.R |only R/auxiliary.R | 134 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ R/vita.R | 13 +++-- README.md | 10 +++- inst/CITATION | 19 -------- man/rIG.Rd | 9 +++ man/rPLSIM.Rd |only 12 files changed, 192 insertions(+), 50 deletions(-)
Title: Automatic Structural Time Series Models
Description: Automatic model selection for structural time series decomposition into trend, cycle, and seasonal components using the Kalman filter.
Koopman, Siem Jan and Marius Ooms (2012) "Forecasting Economic Time Series Using Unobserved Components Time Series Models" <doi:10.1093/oxfordhb/9780195398649.013.0006>.
Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Diff between autostsm versions 1.3 dated 2021-05-04 and 1.4 dated 2021-06-09
DESCRIPTION | 19 +++++------ MD5 | 41 ++++++++++++----------- R/RcppExports.R | 4 +- R/stsm_data_checks.R | 1 R/stsm_detect_anomalies.R | 3 - R/stsm_detect_breaks.R | 3 - R/stsm_detect_cycle.R | 27 ++++++++++++--- R/stsm_detect_multiplicative.R | 4 +- R/stsm_detect_seasonality.R | 28 ++++++++++++---- R/stsm_detect_trend.R | 32 ++++-------------- R/stsm_estimate.R | 44 +++++++++++++++---------- R/stsm_forecast.R | 5 +- R/stsm_init_vals.R | 10 ++--- R/stsm_prior.R | 14 ++++---- R/stsm_ssm.R | 69 +++++++++++++++++++++------------------- inst/doc/autostsm_vignette.R | 1 inst/doc/autostsm_vignette.Rmd | 7 +--- inst/doc/autostsm_vignette.html | 37 ++++++++++----------- man/stsm_bdiag.Rd |only src/RcppExports.cpp | 26 +++++---------- src/kalmanfilter.cpp | 26 +++++++++------ vignettes/autostsm_vignette.Rmd | 7 +--- 22 files changed, 214 insertions(+), 194 deletions(-)
Title: Estimates of Standard Errors for Risk and Performance Measures
Description: Estimates of standard errors of popular risk and performance
measures for asset or portfolio returns using methods as described in
Chen and Martin (2018) <https://www.ssrn.com/abstract=3085672>.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Xin Chen <chenx26@uw.edu>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RPESE versions 1.2.2 dated 2021-05-13 and 1.2.3 dated 2021-06-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 3 +++ README.md | 9 ++++----- inst/doc/RPESEVignette.pdf |binary 5 files changed, 15 insertions(+), 13 deletions(-)
Title: Geographic Profiling Methods for Serial Crime Analysis
Description: An implementation of functions for the analysis of serial crime
incidents. The package implements algorithms for the geographical profiling
of serial incidents in attempt to prioritize the area in which the anchor
point or home base of the perpetrator is located. The geographic profiling
methods in the package are implemented based upon the 'Dragnet' software
by Canter, Coffey, Huntley, and Missen (2000) <doi:10.1023/A:1007551316253>,
the 'CrimeStat' software by Levine (2013)
<https://nij.ojp.gov/topics/articles/crimestat-spatial-statistics-program-analysis-crime-incident-locations>,
and the criminal geographic targeting model outlined in Rossmo (2000, ISBN:978-0849381294)
and Rossmo (1995) <http://summit.sfu.ca/item/6820>.
Author: Jamie Spaulding and Keith Morris
Maintainer: Jamie Spaulding <jspaulding02@hamline.edu>
Diff between rgeoprofile versions 0.2.1 dated 2021-03-28 and 0.2.2 dated 2021-06-09
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 1 - NEWS.md | 14 +++++++++----- R/cmd_pred.R | 18 ++++++++++++++++-- 5 files changed, 34 insertions(+), 17 deletions(-)
Title: Ratio Benchmarking for Multivariate Small Area Estimation
Description: Implements multivariate ratio benchmarking small area estimation. This package provides ratio benchmarking estimation for univariate and multivariate small area estimation and its MSE. In fact, MSE estimators for ratio benchmark are not readily available, so resampling method that called parametric bootstrap is applied. The ratio benchmark model and parametric bootstrap in this package are based on the model proposed in small area estimation. J.N.K Rao and Isabel Molina (2015, ISBN: 978-1-118-73578-7).
Author: Zenda Oka Briantiko [aut, cre],
Azka Ubaidillah [aut]
Maintainer: Zenda Oka Briantiko <221710087@stis.ac.id>
Diff between msaeRB versions 0.1.5 dated 2021-05-03 and 0.2.0 dated 2021-06-09
DESCRIPTION | 6 +++--- MD5 | 19 +++++++++++++++---- NAMESPACE | 6 ++++++ R/datamsaeRBns.R |only R/est_msaeRBns.R |only R/est_saeRBns.R |only R/mse_msaeRB.R | 6 +++--- R/mse_msaeRBns.R |only R/mse_saeRBns.R |only data/datamsaeRBns.rda |only man/datamsaeRBns.Rd |only man/est_msaeRBns.Rd |only man/est_saeRBns.Rd |only man/mse_msaeRB.Rd | 2 +- man/mse_msaeRBns.Rd |only man/mse_saeRBns.Rd |only 16 files changed, 28 insertions(+), 11 deletions(-)
Title: Electronic Health Record (EHR) Data Processing and Analysis Tool
Description: Process and analyze electronic health record (EHR) data. The 'EHR'
package provides modules to perform diverse medication-related studies using
data from EHR databases. Especially, the package includes modules to perform
pharmacokinetic/pharmacodynamic (PK/PD) analyses using EHRs, as outlined in
Choi, Beck, McNeer, Weeks, Williams, James, Niu, Abou-Khalil, Birdwell, Roden,
Stein, Bejan, Denny, and Van Driest (2020) <doi:10.1002/cpt.1787>. Additional
modules will be added in future. In addition, this package provides various
functions useful to perform Phenome Wide Association Study (PheWAS) to explore
associations between drug exposure and phenotypes obtained from EHR data, as
outlined in Choi, Carroll, Beck, Mosley, Roden, Denny, and Van Driest (2018)
<doi:10.1093/bioinformatics/bty306>.
Author: Leena Choi [aut, cre] (<https://orcid.org/0000-0002-2544-7090>),
Cole Beck [aut] (<https://orcid.org/0000-0002-6849-6255>),
Hannah Weeks [aut] (<https://orcid.org/0000-0002-0262-6790>),
Elizabeth McNeer [aut],
Nathan James [aut] (<https://orcid.org/0000-0001-7079-9151>),
Michael Williams [aut]
Maintainer: Leena Choi <naturechoi@gmail.com>
Diff between EHR versions 0.4-0 dated 2021-06-05 and 0.4-1 dated 2021-06-09
EHR-0.4-0/EHR/inst/doc/DoseBuilding_vignette.R |only EHR-0.4-0/EHR/inst/doc/DoseBuilding_vignette.Rmd |only EHR-0.4-0/EHR/inst/doc/DoseBuilding_vignette.pdf |only EHR-0.4-0/EHR/inst/doc/ehr_vignette_Build_PK_Oral.R |only EHR-0.4-0/EHR/inst/doc/ehr_vignette_Build_PK_Oral.Rmd |only EHR-0.4-0/EHR/inst/doc/ehr_vignette_Build_PK_Oral.pdf |only EHR-0.4-0/EHR/inst/doc/ehr_vignette_mxr.R |only EHR-0.4-0/EHR/inst/doc/ehr_vignette_mxr.Rmd |only EHR-0.4-0/EHR/inst/doc/ehr_vignette_mxr.pdf |only EHR-0.4-0/EHR/inst/doc/ehr_vignette_str.R |only EHR-0.4-0/EHR/inst/doc/ehr_vignette_str.Rmd |only EHR-0.4-0/EHR/inst/doc/ehr_vignette_str.pdf |only EHR-0.4-0/EHR/inst/examples/str_ex1/checks |only EHR-0.4-0/EHR/inst/examples/str_ex2/Fentanyl_alb_mod_id.rds |only EHR-0.4-0/EHR/inst/examples/str_ex2/Fentanyl_conc_mod_id.rds |only EHR-0.4-0/EHR/inst/examples/str_ex2/Fentanyl_creat_mod_id.rds |only EHR-0.4-0/EHR/inst/examples/str_ex2/Fentanyl_demo_mod_id.rds |only EHR-0.4-0/EHR/inst/examples/str_ex2/Fentanyl_flow_mod_id.rds |only EHR-0.4-0/EHR/inst/examples/str_ex2/Fentanyl_mar_mod_id.rds |only EHR-0.4-0/EHR/inst/examples/str_ex2/Fentanyl_module_id.rds |only EHR-0.4-0/EHR/inst/examples/str_ex2/Fentanyl_samp_mod_id.rds |only EHR-0.4-0/EHR/inst/examples/str_ex2/checks |only EHR-0.4-0/EHR/vignettes/DoseBuilding_vignette.Rmd |only EHR-0.4-0/EHR/vignettes/ehr_vignette_Build_PK_Oral.Rmd |only EHR-0.4-0/EHR/vignettes/ehr_vignette_mxr.Rmd |only EHR-0.4-0/EHR/vignettes/ehr_vignette_str.Rmd |only EHR-0.4-1/EHR/DESCRIPTION | 8 - EHR-0.4-1/EHR/MD5 | 51 +++------- EHR-0.4-1/EHR/R/extractMed.R | 6 - EHR-0.4-1/EHR/build/vignette.rds |binary EHR-0.4-1/EHR/inst/doc/ehr_vignette_01_mxr.R |only EHR-0.4-1/EHR/inst/doc/ehr_vignette_01_mxr.Rmd |only EHR-0.4-1/EHR/inst/doc/ehr_vignette_01_mxr.html |only EHR-0.4-1/EHR/inst/doc/ehr_vignette_02_str.R |only EHR-0.4-1/EHR/inst/doc/ehr_vignette_02_str.Rmd |only EHR-0.4-1/EHR/inst/doc/ehr_vignette_02_str.html |only EHR-0.4-1/EHR/inst/doc/ehr_vignette_03_DoseBuilding.R |only EHR-0.4-1/EHR/inst/doc/ehr_vignette_03_DoseBuilding.Rmd |only EHR-0.4-1/EHR/inst/doc/ehr_vignette_03_DoseBuilding.html |only EHR-0.4-1/EHR/inst/doc/ehr_vignette_04_Build_PK_Oral.R |only EHR-0.4-1/EHR/inst/doc/ehr_vignette_04_Build_PK_Oral.Rmd |only EHR-0.4-1/EHR/inst/doc/ehr_vignette_04_Build_PK_Oral.html |only EHR-0.4-1/EHR/vignettes/ehr_vignette_01_mxr.Rmd |only EHR-0.4-1/EHR/vignettes/ehr_vignette_02_str.Rmd |only EHR-0.4-1/EHR/vignettes/ehr_vignette_03_DoseBuilding.Rmd |only EHR-0.4-1/EHR/vignettes/ehr_vignette_04_Build_PK_Oral.Rmd |only 46 files changed, 26 insertions(+), 39 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-08 1.0.2
2019-03-06 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-13 1.0-7
2017-07-28 1.0-6
2014-02-02 1.0-5
2011-03-31 1.0-4
2011-03-17 1.0-3
2010-05-12 1.0-2
2010-05-05 1.0
2010-05-05 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-03 1.0.6
2020-01-20 1.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-02 1.0-9
2014-02-02 1.0-8
2011-03-31 1.0-7
2011-03-17 1.0-6
2011-01-16 1.0-5
2010-09-16 1.0-4
2010-05-26 1.0-3
2010-05-12 1.0-2
2010-05-05 1.0
2010-05-05 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-13 1.0-11
2015-01-11 1.0-10
2014-03-02 1.0-9
2014-02-04 1.0-8
2012-01-04 1.0-7
2011-03-31 1.0-6
2011-01-16 1.0-5
2010-09-17 1.0-4
2010-05-26 1.0-3
2010-05-12 1.0-2
2010-05-05 1.0
2010-05-05 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-21 1.1
2016-04-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-17 1.0.9
2020-01-09 1.0.7
2019-12-04 1.0.6
2019-06-14 1.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-01 1.0.4
2020-11-11 1.0.3
2019-10-31 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-13 1.0.2
2016-08-16 1.0.1
2016-06-13 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-11 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-19 1.0.1
2012-03-28 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-04 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-11 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-01-16 1.4.3
2015-09-09 1.3.1
2015-08-28 1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-08-13 0.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-21 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2006-05-24 0.1
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization
for biological sequence (DNA and protein) data. Seqinr includes
utilities for sequence data management under the ACNUC system
described in Gouy, M. et al. (1984) Nucleic Acids Res.
12:121-127 <doi:10.1093/nar/12.1Part1.121>.
Author: Delphine Charif [aut],
Olivier Clerc [ctb],
Carolin Frank [ctb],
Jean R. Lobry [aut, cph],
Anamaria Necşulea [ctb],
Leonor Palmeira [ctb],
Simon Penel [cre],
Guy Perrière [ctb]
Maintainer: Simon Penel <simon.penel@univ-lyon1.fr>
Diff between seqinr versions 4.2-5 dated 2020-12-17 and 4.2-8 dated 2021-06-09
seqinr-4.2-5/seqinr/R/get.ncbi.R |only seqinr-4.2-5/seqinr/man/get.ncbi.Rd |only seqinr-4.2-8/seqinr/DESCRIPTION | 12 +-- seqinr-4.2-8/seqinr/MD5 | 95 +++++++++++++-------------- seqinr-4.2-8/seqinr/R/ClassSeq.R | 26 +++++-- seqinr-4.2-8/seqinr/R/comp.R | 21 ++--- seqinr-4.2-8/seqinr/R/dia.bactgensize.R | 77 ++++++++------------- seqinr-4.2-8/seqinr/R/dist.alignment.R | 12 +-- seqinr-4.2-8/seqinr/R/gbk2g2.R | 27 +++---- seqinr-4.2-8/seqinr/R/s2n.R | 6 + seqinr-4.2-8/seqinr/build |only seqinr-4.2-8/seqinr/data/AnoukResult.RData |binary seqinr-4.2-8/seqinr/data/ECH.RData |binary seqinr-4.2-8/seqinr/data/EXP.RData |binary seqinr-4.2-8/seqinr/data/JLO.RData |binary seqinr-4.2-8/seqinr/data/SEQINR.UTIL.RData |binary seqinr-4.2-8/seqinr/data/aacost.RData |binary seqinr-4.2-8/seqinr/data/aaindex.RData |binary seqinr-4.2-8/seqinr/data/caitab.RData |binary seqinr-4.2-8/seqinr/data/chargaff.RData |binary seqinr-4.2-8/seqinr/data/clustal.RData |binary seqinr-4.2-8/seqinr/data/dinucl.RData |binary seqinr-4.2-8/seqinr/data/ec999.RData |binary seqinr-4.2-8/seqinr/data/fasta.RData |binary seqinr-4.2-8/seqinr/data/gcO2.rda |binary seqinr-4.2-8/seqinr/data/gcT.rda |binary seqinr-4.2-8/seqinr/data/gs500liz.RData |binary seqinr-4.2-8/seqinr/data/identifiler.RData |binary seqinr-4.2-8/seqinr/data/kaksTorture.RData |binary seqinr-4.2-8/seqinr/data/m16j.RData |binary seqinr-4.2-8/seqinr/data/mase.RData |binary seqinr-4.2-8/seqinr/data/msf.RData |binary seqinr-4.2-8/seqinr/data/pK.RData |binary seqinr-4.2-8/seqinr/data/phylip.RData |binary seqinr-4.2-8/seqinr/data/prochlo.RData |binary seqinr-4.2-8/seqinr/data/revaligntest.RData |binary seqinr-4.2-8/seqinr/data/sysdata.rda |binary seqinr-4.2-8/seqinr/data/toyaa.RData |binary seqinr-4.2-8/seqinr/data/toycodon.RData |binary seqinr-4.2-8/seqinr/data/waterabs.RData |binary seqinr-4.2-8/seqinr/man/AAstat.Rd | 7 + seqinr-4.2-8/seqinr/man/SEQINR.UTIL.Rd | 14 +-- seqinr-4.2-8/seqinr/man/dia.bactgensize.Rd | 11 +-- seqinr-4.2-8/seqinr/man/dist.alignment.Rd | 20 +++-- seqinr-4.2-8/seqinr/man/gbk2g2.Rd | 4 - seqinr-4.2-8/seqinr/man/getTrans.Rd | 24 +++++- seqinr-4.2-8/seqinr/man/oriloc.Rd | 50 +++++++------- seqinr-4.2-8/seqinr/man/print.SeqAcnucWeb.Rd | 12 +-- seqinr-4.2-8/seqinr/man/translate.Rd | 54 +++++++++++---- seqinr-4.2-8/seqinr/man/uco.Rd | 39 ++++++----- 50 files changed, 277 insertions(+), 234 deletions(-)
Title: Analytics, Data Mining & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine learning
tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Exploratory, and Scrapper, it helps the analyst or data scientist to get quick and robust
results, without the need of repetitive coding or extensive programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.0.0 dated 2021-06-03 and 5.0.1 dated 2021-06-09
lares-5.0.0/lares/man/file_type.Rd |only lares-5.0.1/lares/DESCRIPTION | 17 +++++++++-------- lares-5.0.1/lares/MD5 | 33 ++++++++++++++++----------------- lares-5.0.1/lares/NAMESPACE | 2 +- lares-5.0.1/lares/R/apis.R | 2 +- lares-5.0.1/lares/R/clusters.R | 11 +++++------ lares-5.0.1/lares/R/correlations.R | 28 +++++++++++++--------------- lares-5.0.1/lares/R/forecasting.R | 2 +- lares-5.0.1/lares/R/lares.R | 26 ++++++++++++-------------- lares-5.0.1/lares/R/onehotencoding.R | 27 ++++++++++++++------------- lares-5.0.1/lares/R/other_functions.R | 10 +++++----- lares-5.0.1/lares/R/shapley.R | 4 +--- lares-5.0.1/lares/README.md | 8 ++++---- lares-5.0.1/lares/man/corr.Rd | 18 ++++++++++-------- lares-5.0.1/lares/man/file_name.Rd | 16 ++++++++++++---- lares-5.0.1/lares/man/h2o_shap.Rd | 4 +--- lares-5.0.1/lares/man/ohse.Rd | 7 ++++--- lares-5.0.1/lares/man/shap_var.Rd | 4 +--- 18 files changed, 110 insertions(+), 109 deletions(-)
Title: Clean and Analyze Continuous Glucose Monitor Data
Description: This code provides several different functions for cleaning and analyzing continuous glucose monitor data. Currently it works with 'Dexcom', 'iPro 2', 'Diasend', 'Libre', or 'Carelink' data. The cleandata() function takes a directory of CGM data files and prepares them for analysis. cgmvariables() iterates through a directory of cleaned CGM data files and produces a single spreadsheet with data for each file in either rows or columns. The column format of this spreadsheet is compatible with REDCap data upload. cgmreport() also iterates through a directory of cleaned data, and produces PDFs of individual and aggregate AGP plots. Please visit <https://github.com/childhealthbiostatscore/R-Packages/> to download the new-user guide.
Author: Tim Vigers [aut, cre]
Maintainer: Tim Vigers <timvigers@mailbox.org>
Diff between cgmanalysis versions 2.7.1 dated 2021-02-15 and 2.7.2 dated 2021-06-09
DESCRIPTION | 11 +++++------ MD5 | 4 ++-- R/cgmvariables.R | 11 ++++++++--- 3 files changed, 15 insertions(+), 11 deletions(-)