Title: Calculate Federal and State Income Taxes in the United States
Description: Calculates federal and state income taxes in the United States. It acts as a wrapper
to the NBER's TAXSIM 35 (<http://taxsim.nber.org/taxsim35/>) tax simulator. TAXSIM 35 conducts
the calculations, while 'usincometaxes' prepares the data for TAXSIM 35, sends the data to
TAXSIM 35's server or communicates with the Web Assembly file, retrieves the data, and places it
into a data frame. All without the user worrying about this process.
Author: Shane Orr [aut, cre, cph],
Thomas Wells [ctb]
Maintainer: Shane Orr <shane.j.orr@gmail.com>
Diff between usincometaxes versions 0.5.4 dated 2022-10-30 and 0.6.0 dated 2023-01-23
usincometaxes-0.5.4/usincometaxes/inst/doc/interface-options.R |only usincometaxes-0.5.4/usincometaxes/inst/doc/interface-options.Rmd |only usincometaxes-0.5.4/usincometaxes/inst/doc/interface-options.html |only usincometaxes-0.5.4/usincometaxes/man/calculate_taxes_http.Rd |only usincometaxes-0.5.4/usincometaxes/man/connect_server_single_ssh.Rd |only usincometaxes-0.5.4/usincometaxes/man/create_ssh_command.Rd |only usincometaxes-0.5.4/usincometaxes/man/import_data_helper.Rd |only usincometaxes-0.5.4/usincometaxes/man/import_data_ssh.Rd |only usincometaxes-0.5.4/usincometaxes/vignettes/interface-options.Rmd |only usincometaxes-0.6.0/usincometaxes/DESCRIPTION | 8 usincometaxes-0.6.0/usincometaxes/MD5 | 59 -- usincometaxes-0.6.0/usincometaxes/NEWS.md | 116 ++-- usincometaxes-0.6.0/usincometaxes/R/calculate_taxes.R | 69 -- usincometaxes-0.6.0/usincometaxes/R/usincometaxes.R | 2 usincometaxes-0.6.0/usincometaxes/R/utils_check_data.R | 13 usincometaxes-0.6.0/usincometaxes/R/utils_connect_server.R | 273 +--------- usincometaxes-0.6.0/usincometaxes/README.md | 48 - usincometaxes-0.6.0/usincometaxes/build/vignette.rds |binary usincometaxes-0.6.0/usincometaxes/inst/doc/send-data-to-taxsim.Rmd | 4 usincometaxes-0.6.0/usincometaxes/inst/doc/send-data-to-taxsim.html | 119 ++-- usincometaxes-0.6.0/usincometaxes/inst/doc/taxsim-input.Rmd | 6 usincometaxes-0.6.0/usincometaxes/inst/doc/taxsim-input.html | 23 usincometaxes-0.6.0/usincometaxes/inst/doc/taxsim-output.html | 14 usincometaxes-0.6.0/usincometaxes/inst/doc/using-usincometaxes.Rmd | 4 usincometaxes-0.6.0/usincometaxes/inst/doc/using-usincometaxes.html | 126 ++-- usincometaxes-0.6.0/usincometaxes/inst/doc/wasm.R |only usincometaxes-0.6.0/usincometaxes/inst/doc/wasm.Rmd |only usincometaxes-0.6.0/usincometaxes/inst/doc/wasm.html |only usincometaxes-0.6.0/usincometaxes/man/check_parameters.Rd | 2 usincometaxes-0.6.0/usincometaxes/man/create_dataset_for_taxsim.Rd | 2 usincometaxes-0.6.0/usincometaxes/man/taxsim_calculate_taxes.Rd | 22 usincometaxes-0.6.0/usincometaxes/man/usincometaxes.Rd | 2 usincometaxes-0.6.0/usincometaxes/tests/testthat/test-calculate_taxes.R | 46 - usincometaxes-0.6.0/usincometaxes/vignettes/send-data-to-taxsim.Rmd | 4 usincometaxes-0.6.0/usincometaxes/vignettes/taxsim-input.Rmd | 6 usincometaxes-0.6.0/usincometaxes/vignettes/using-usincometaxes.Rmd | 4 usincometaxes-0.6.0/usincometaxes/vignettes/wasm.Rmd |only 37 files changed, 319 insertions(+), 653 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and technical writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between inti versions 0.5.8 dated 2022-11-16 and 0.6.0 dated 2023-01-23
inti-0.5.8/inti/R/tarpuy_varlist.R |only inti-0.5.8/inti/man/tarpuy_varlist.Rd |only inti-0.6.0/inti/DESCRIPTION | 10 inti-0.6.0/inti/MD5 | 112 +-- inti-0.6.0/inti/NAMESPACE | 6 inti-0.6.0/inti/NEWS.md | 17 inti-0.6.0/inti/R/design_repblock.R |only inti-0.6.0/inti/R/tarpuy_design.R | 210 +----- inti-0.6.0/inti/R/tarpuy_plex.R | 107 ++- inti-0.6.0/inti/R/tarpuy_plotdesign.R | 119 ++- inti-0.6.0/inti/R/tarpuy_traits.R |only inti-0.6.0/inti/R/yupana_mvr.R | 79 +- inti-0.6.0/inti/build/partial.rdb |binary inti-0.6.0/inti/build/vignette.rds |binary inti-0.6.0/inti/inst/doc/apps.html | 2 inti-0.6.0/inti/inst/doc/rticles.html | 8 inti-0.6.0/inti/inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy.dcf | 6 inti-0.6.0/inti/inst/tarpuy/server.R | 348 +++++++--- inti-0.6.0/inti/inst/tarpuy/ui.R | 154 +++- inti-0.6.0/inti/inst/yupana/rsconnect/shinyapps.io/flavjack/yupana-test.dcf | 6 inti-0.6.0/inti/inst/yupana/rsconnect/shinyapps.io/flavjack/yupana.dcf | 6 inti-0.6.0/inti/inst/yupana/server.R | 2 inti-0.6.0/inti/inst/yupana/ui.R | 18 inti-0.6.0/inti/man/H2cal.Rd | 298 ++++---- inti-0.6.0/inti/man/colortext.Rd | 68 - inti-0.6.0/inti/man/design_repblock.Rd |only inti-0.6.0/inti/man/figure2qmd.Rd | 48 - inti-0.6.0/inti/man/figure2rmd.Rd | 42 - inti-0.6.0/inti/man/footnotes.Rd | 58 - inti-0.6.0/inti/man/gdoc2qmd.Rd | 48 - inti-0.6.0/inti/man/include_figure.Rd | 66 - inti-0.6.0/inti/man/include_table.Rd | 90 +- inti-0.6.0/inti/man/jc_tombola.Rd | 104 +- inti-0.6.0/inti/man/mean_comparison.Rd | 120 +-- inti-0.6.0/inti/man/met.Rd | 68 - inti-0.6.0/inti/man/metamorphosis.Rd | 74 +- inti-0.6.0/inti/man/outliers_remove.Rd | 94 +- inti-0.6.0/inti/man/plot_diag.Rd | 88 +- inti-0.6.0/inti/man/plot_raw.Rd | 202 ++--- inti-0.6.0/inti/man/plot_smr.Rd | 212 +++--- inti-0.6.0/inti/man/potato.Rd | 76 +- inti-0.6.0/inti/man/reexports.Rd | 32 inti-0.6.0/inti/man/split_folder.Rd | 88 +- inti-0.6.0/inti/man/table2qmd.Rd | 34 inti-0.6.0/inti/man/table2rmd.Rd | 38 - inti-0.6.0/inti/man/tarpuy.Rd | 58 - inti-0.6.0/inti/man/tarpuy_design.Rd | 138 ++- inti-0.6.0/inti/man/tarpuy_plex.Rd | 197 ++--- inti-0.6.0/inti/man/tarpuy_plotdesign.Rd | 105 +-- inti-0.6.0/inti/man/tarpuy_traits.Rd |only inti-0.6.0/inti/man/web_table.Rd | 110 +-- inti-0.6.0/inti/man/yupana.Rd | 58 - inti-0.6.0/inti/man/yupana_analysis.Rd | 128 +-- inti-0.6.0/inti/man/yupana_export.Rd | 206 ++--- inti-0.6.0/inti/man/yupana_import.Rd | 70 +- inti-0.6.0/inti/man/yupana_mvr.Rd | 94 +- inti-0.6.0/inti/man/yupana_reshape.Rd | 88 +- inti-0.6.0/inti/vignettes/files/r-cran.svg | 66 - inti-0.6.0/inti/vignettes/files/rstudio.svg | 140 ++-- inti-0.6.0/inti/vignettes/files/zotero.svg | 22 60 files changed, 2491 insertions(+), 2147 deletions(-)
Title: Syntactically Awesome Style Sheets ('Sass')
Description: An 'SCSS' compiler, powered by the 'LibSass' library. With this,
R developers can use variables, inheritance, and functions to generate
dynamic style sheets. The package uses the 'Sass CSS' extension language,
which is stable, powerful, and CSS compatible.
Author: Joe Cheng [aut],
Timothy Mastny [aut],
Richard Iannone [aut] ,
Barret Schloerke [aut] ,
Carson Sievert [aut, cre] ,
Christophe Dervieux [ctb] ,
RStudio [cph, fnd],
Sass Open Source Foundation [ctb, cph] ,
Greter Marcel [ctb, cph] ,
Mifsud Michael [ct [...truncated...]
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between sass versions 0.4.4 dated 2022-11-24 and 0.4.5 dated 2023-01-23
DESCRIPTION | 8 MD5 | 62 +-- NEWS.md | 6 inst/doc/sass.html | 637 ++++++++++++++++++++++++++------ src/libsass/Makefile | 5 src/libsass/Makefile.conf | 87 ++++ src/libsass/Readme.md | 15 src/libsass/docs/build.md | 8 src/libsass/docs/implementations.md | 1 src/libsass/script/ci-build-libsass | 6 src/libsass/script/ci-install-compiler | 10 src/libsass/src/ast.hpp | 6 src/libsass/src/ast_helpers.hpp | 26 + src/libsass/src/ast_sel_unify.cpp | 2 src/libsass/src/ast_selectors.cpp | 33 + src/libsass/src/ast_selectors.hpp | 17 src/libsass/src/ast_values.cpp | 4 src/libsass/src/error_handling.cpp | 6 src/libsass/src/error_handling.hpp | 9 src/libsass/src/extender.cpp | 74 ++- src/libsass/src/fn_numbers.cpp | 23 + src/libsass/src/fn_selectors.cpp | 2 src/libsass/src/inspect.cpp | 11 src/libsass/src/lexer.cpp | 2 src/libsass/src/operators.cpp | 2 src/libsass/src/parser.cpp | 2 src/libsass/src/position.cpp | 16 src/libsass/src/sass_context.cpp | 1 src/libsass/utils |only src/libsass/win/libsass.targets | 126 +++--- src/libsass/win/libsass.vcxproj.filters | 563 +++++++++++++--------------- 31 files changed, 1197 insertions(+), 573 deletions(-)
Title: Create Visuals for Publication
Description: A set of functions to aid in the production of visuals in ggplot2.
Author: Eric Finnesgard [aut, cre]
Maintainer: Eric Finnesgard <efinite@outlook.com>
Diff between utile.visuals versions 0.3.2 dated 2022-11-20 and 0.3.3 dated 2023-01-23
DESCRIPTION | 12 MD5 | 25 +- NAMESPACE | 17 - NEWS.md | 121 ++++++--- R/geoms.R | 145 +++++------ R/themes.R | 589 ++++++++++++++++++++++++------------------------ R/utils.R | 30 +- README.md | 39 +-- man/append_table.Rd | 206 ++++++++-------- man/geom_stepconfint.Rd | 125 +++++----- man/ggrisktable.Rd | 88 +++---- man/panel_border.Rd |only man/theme_basic.Rd | 75 +++--- man/theme_risk.Rd | 71 ++--- 14 files changed, 807 insertions(+), 736 deletions(-)
Title: R Markdown Format for Flexible Dashboards
Description: Format for converting an R Markdown document to a grid oriented
dashboard. The dashboard flexibly adapts the size of it's components to the
containing web page.
Author: Carson Sievert [aut, cre] ,
Richard Iannone [aut] ,
JJ Allaire [aut],
Barbara Borges [aut],
RStudio [cph],
Keen IO [ctb, cph] ,
Abdullah Almsaeed [ctb, cph] ,
Jonas Mosbech [ctb, cph] ,
Noel Bossart [ctb, cph] ,
Lea Verou [ctb, cph] ,
Dmitry Baranovs [...truncated...]
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between flexdashboard versions 0.6.0 dated 2022-08-05 and 0.6.1 dated 2023-01-23
DESCRIPTION | 13 +++++++++---- MD5 | 10 +++++----- NEWS.md | 7 +++++++ inst/www/flex_dashboard/default.html | 2 +- man/flex_dashboard.Rd | 2 +- tests/testthat/test_built_css.R | 1 + 6 files changed, 24 insertions(+), 11 deletions(-)
Title: Power Logit Regression for Modeling Bounded Data
Description: Power logit regression models for bounded
continuous data, in which the density generator may be normal, Student-t,
power exponential, slash, hyperbolic, sinh-normal, or type II logistic.
Diagnostic tools associated with the fitted model, such as the residuals,
local influence measures, leverage measures, and goodness-of-fit statistics,
are implemented. The estimation process follows the maximum likelihood approach
and, currently, the package supports two types of estimators: the usual maximum
likelihood estimator and the penalized maximum likelihood estimator. More details
about power logit regression models are described in
Queiroz and Ferrari (2022) <arXiv:2202.01697>.
Author: Felipe Queiroz [aut, cre],
Silvia Ferrari [aut]
Maintainer: Felipe Queiroz <ffelipeq@outlook.com>
Diff between PLreg versions 0.3.0 dated 2022-12-19 and 0.3.1 dated 2023-01-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 9 ++------- R/PLreg.R | 5 ++--- 4 files changed, 10 insertions(+), 16 deletions(-)
Title: Tensors and Neural Networks with 'GPU' Acceleration
Description: Provides functionality to define and train neural networks similar to
'PyTorch' by Paszke et al (2019) <arXiv:1912.01703> but written entirely in R
using the 'libtorch' library. Also supports low-level tensor operations and
'GPU' acceleration.
Author: Daniel Falbel [aut, cre, cph],
Javier Luraschi [aut],
Dmitriy Selivanov [ctb],
Athos Damiani [ctb],
Christophe Regouby [ctb],
Krzysztof Joachimiak [ctb],
Hamada S. Badr [ctb],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torch versions 0.9.0 dated 2022-10-24 and 0.9.1 dated 2023-01-23
torch-0.9.0/torch/inst/build-version |only torch-0.9.0/torch/man/get_install_libs_url.Rd |only torch-0.9.1/torch/DESCRIPTION | 10 torch-0.9.1/torch/MD5 | 67 - torch-0.9.1/torch/NAMESPACE | 1 torch-0.9.1/torch/NEWS.md | 21 torch-0.9.1/torch/R/gen-namespace-docs.R | 34 torch-0.9.1/torch/R/gen-namespace.R | 8 torch-0.9.1/torch/R/install.R | 72 + torch-0.9.1/torch/R/nn-activation.R | 54 - torch-0.9.1/torch/R/translate.R | 14 torch-0.9.1/torch/R/wrapers.R | 26 torch-0.9.1/torch/build/partial.rdb |binary torch-0.9.1/torch/build/vignette.rds |binary torch-0.9.1/torch/inst/doc/distributions.html | 325 +++++++- torch-0.9.1/torch/inst/doc/extending-autograd.html | 351 +++++++-- torch-0.9.1/torch/inst/doc/indexing.html | 376 ++++++++-- torch-0.9.1/torch/inst/doc/installation.html | 387 ++++++++-- torch-0.9.1/torch/inst/doc/loading-data.html | 435 +++++++++--- torch-0.9.1/torch/inst/doc/python-to-r.html | 319 +++++++- torch-0.9.1/torch/inst/doc/serialization.html | 352 +++++++-- torch-0.9.1/torch/inst/doc/tensor-creation.html | 384 ++++++++-- torch-0.9.1/torch/inst/doc/torchscript.html | 409 +++++++++-- torch-0.9.1/torch/inst/doc/using-autograd.html | 373 ++++++++-- torch-0.9.1/torch/man/install_torch_from_file.Rd | 23 torch-0.9.1/torch/man/torch_fft_fftfreq.Rd |only torch-0.9.1/torch/src/Makevars | 2 torch-0.9.1/torch/src/RcppExports.cpp | 16 torch-0.9.1/torch/src/tensor.cpp | 16 torch-0.9.1/torch/src/xptr.cpp | 6 torch-0.9.1/torch/tests/testthat/test-distribution-normal.R | 11 torch-0.9.1/torch/tests/testthat/test-tensor.R | 1 torch-0.9.1/torch/tests/testthat/test-translate.R | 12 torch-0.9.1/torch/tests/testthat/test-wrapers.R | 15 torch-0.9.1/torch/tests/testthat/tracedmodule.pt |binary torch-0.9.1/torch/tools/torchgen/R/r.R | 3 36 files changed, 3257 insertions(+), 866 deletions(-)
Title: Bayesian Additive Regression Trees with Stan-Sampled Parametric
Extensions
Description: Fits semiparametric linear and multilevel models with non-parametric additive Bayesian additive regression tree (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) components and Stan (Stan Development Team (2021) <https://mc-stan.org/>) sampled parametric ones. Multilevel models can be expressed using 'lme4' syntax (Bates, Maechler, Bolker, and Walker (2015) <doi:10.18637/jss.v067.i01>).
Author: Vincent Dorie [aut, cre] ,
Ben Goodrich [ctb] ,
Jonah Gabry [ctb] ,
Imad Ali [ctb] ,
Sam Brilleman [ctb] ,
Paul-Christian Burkner [ctb] ,
Joshua Pritikin [ctb] ,
Andrew Gelman [ctb] ,
Bob Carpenter [ctb] ,
Matt Hoffman [ctb] ,
Daniel Lee [ctb] ,
Mich [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between stan4bart versions 0.0-3 dated 2022-03-31 and 0.0-5 dated 2023-01-23
stan4bart-0.0-3/stan4bart/src/include/stan/math/prim/fun/F32.hpp |only stan4bart-0.0-3/stan4bart/src/include/stan/math/rev/functor/algebra_solver_newton.hpp |only stan4bart-0.0-3/stan4bart/src/include/stan/math/rev/functor/algebra_solver_powell.hpp |only stan4bart-0.0-3/stan4bart/src/include/stan/math/rev/functor/idas_forward_system.hpp |only stan4bart-0.0-3/stan4bart/src/include/stan/math/rev/functor/idas_system.hpp |only stan4bart-0.0-3/stan4bart/src/include/stan/math/rev/functor/integrate_dae.hpp |only stan4bart-0.0-3/stan4bart/src/include/sundials/sundials/sundials_fconfig.h |only stan4bart-0.0-3/stan4bart/src/include/sundials/sundials/sundials_fconfig.in |only stan4bart-0.0-3/stan4bart/src/include/sundials/sundials/sundials_fnvector.h |only stan4bart-0.0-5/stan4bart/DESCRIPTION | 8 stan4bart-0.0-5/stan4bart/MD5 | 798 +++++----- stan4bart-0.0-5/stan4bart/R/generics.R | 56 stan4bart-0.0-5/stan4bart/R/lme4_functions.R | 5 stan4bart-0.0-5/stan4bart/R/stan4bart.R | 248 ++- stan4bart-0.0-5/stan4bart/R/stan4bart_fit.R | 17 stan4bart-0.0-5/stan4bart/R/test_data.R | 4 stan4bart-0.0-5/stan4bart/configure | 18 stan4bart-0.0-5/stan4bart/configure.ac | 2 stan4bart-0.0-5/stan4bart/inst/NEWS.Rd | 15 stan4bart-0.0-5/stan4bart/man/generics.Rd | 7 stan4bart-0.0-5/stan4bart/man/stan4bart.Rd | 29 stan4bart-0.0-5/stan4bart/src/config.h.win | 4 stan4bart-0.0-5/stan4bart/src/include/misc/adaptiveRadixTree.h | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd.hpp | 1 stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd/core/fvar.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd/fun.hpp | 7 stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd/fun/grad_inc_beta.hpp | 9 stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd/fun/hypergeometric_2F1.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd/fun/hypergeometric_pFq.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd/fun/inv_erfc.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd/fun/inv_inc_beta.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd/fun/lmultiply.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd/fun/norm1.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd/fun/norm2.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd/fun/sum.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd/functor/operands_and_partials.hpp | 60 stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd/prob |only stan4bart-0.0-5/stan4bart/src/include/stan/math/fwd/prob.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/mix.hpp | 10 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/kernel_generator/elt_function_cl.hpp | 3 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/kernel_generator/multi_result_kernel.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/kernel_generator/opencl_code.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/kernel_generator/operation_cl.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/kernels/device_functions/lmultiply.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/matrix_cl.hpp | 19 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/bernoulli_cdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/bernoulli_lccdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/bernoulli_lcdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/bernoulli_logit_glm_lpmf.hpp | 7 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/bernoulli_logit_lpmf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/bernoulli_lpmf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/beta_lpdf.hpp | 10 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/beta_proportion_lpdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/categorical_logit_glm_lpmf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/exp_mod_normal_lpdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/gamma_lpdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/logistic_lpdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/neg_binomial_2_log_glm_lpmf.hpp | 9 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/normal_id_glm_lpdf.hpp | 9 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/num_elements.hpp | 3 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/ordered_logistic_glm_lpmf.hpp | 10 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/ordered_logistic_lpmf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/poisson_log_glm_lpmf.hpp | 7 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/poisson_log_lpmf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/poisson_lpmf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/std_normal_cdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/std_normal_lccdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/std_normal_lcdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/prim/std_normal_lpdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/rev.hpp | 1 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/rev/adjoint_results.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/rev/arena_matrix_cl.hpp | 10 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/rev/lmultiply.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/rev/operands_and_partials.hpp | 3 stan4bart-0.0-5/stan4bart/src/include/stan/math/opencl/zeros_strict_tri.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/core/operator_addition.hpp | 7 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/core/operator_division.hpp | 7 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/core/operator_multiplication.hpp | 10 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/core/operator_subtraction.hpp | 7 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/err/check_flag_sundials.hpp | 403 ++++- stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/err/check_matching_dims.hpp | 1 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/err/hmm_check.hpp | 1 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun.hpp | 16 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/Phi.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/Phi_approx.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/abs.hpp | 34 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/acos.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/acosh.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/arg.hpp | 12 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/asin.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/asinh.hpp | 3 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/atan.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/atan2.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/atanh.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/cbrt.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/ceil.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/complex_schur_decompose.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/conj.hpp | 41 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/constants.hpp | 68 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/cos.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/cosh.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/cumulative_sum.hpp | 11 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/digamma.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/eigenvalues.hpp | 13 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/eigenvectors.hpp | 13 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/erf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/erfc.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/exp.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/exp2.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/expm1.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/fabs.hpp | 6 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/fft.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/floor.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/fmod.hpp | 15 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/get_imag.hpp | 29 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/get_real.hpp | 29 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/gp_matern52_cov.hpp | 1 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/grad_2F1.hpp | 363 +++- stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/grad_inc_beta.hpp | 7 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/grad_pFq.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/grad_reg_lower_inc_gamma.hpp | 7 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/hypergeometric_2F1.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/hypergeometric_2F2.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/hypergeometric_3F2.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/hypergeometric_pFq.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/inv.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/inv_Phi.hpp | 9 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/inv_cloglog.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/inv_erfc.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/inv_inc_beta.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/inv_logit.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/inv_sqrt.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/lambert_w.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/lgamma.hpp | 8 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/lmultiply.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/log.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/log10.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/log1m.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/log1m_exp.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/log1m_inv_logit.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/log1p.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/log1p_exp.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/log2.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/log_inv_logit.hpp | 5 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/log_inv_logit_diff.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/log_mix.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/log_sum_exp_signed.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/logit.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/lub_free.hpp | 18 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/matrix_exp_2x2.hpp | 7 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/max.hpp | 19 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/min.hpp | 15 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/minus.hpp | 16 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/multiply.hpp | 44 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/norm.hpp | 12 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/norm1.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/norm2.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/offset_multiplier_constrain.hpp | 5 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/owens_t.hpp | 5 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/pow.hpp | 39 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/proj.hpp | 13 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/promote_scalar.hpp | 162 -- stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/round.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/scalar_seq_view.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/sin.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/singular_values.hpp | 3 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/sinh.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/size_zero.hpp | 3 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/sqrt.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/square.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/stan_print.hpp | 25 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/step.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/sum.hpp | 13 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/tan.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/tanh.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/tgamma.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/to_complex.hpp | 21 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/to_int.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/to_matrix.hpp | 22 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/trigamma.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/fun/trunc.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/functor/apply_scalar_unary.hpp | 38 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/functor/coupled_ode_system.hpp | 10 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/functor/integrate_1d.hpp | 9 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/functor/ode_ckrk.hpp | 6 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/functor/ode_rk45.hpp | 6 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/functor/operands_and_partials.hpp | 37 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/functor/reduce_sum.hpp | 3 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/meta.hpp | 117 - stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/meta/forward_as.hpp | 16 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/meta/index_apply.hpp | 9 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/meta/is_complex.hpp | 25 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/meta/is_tuple.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/meta/is_var_and_matrix_types.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/meta/possibly_sum.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/meta/promote_scalar_type.hpp | 7 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/meta/require_generics.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob.hpp | 10 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/bernoulli_logit_glm_lpmf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/bernoulli_lpmf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/beta_binomial_cdf.hpp | 6 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/beta_binomial_lccdf.hpp | 6 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/beta_binomial_lcdf.hpp | 6 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/beta_binomial_lpmf.hpp | 1 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/beta_proportion_lpdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/binomial_logit_lpmf.hpp | 5 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/categorical_logit_glm_lpmf.hpp | 6 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/categorical_logit_lpmf.hpp | 11 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/cauchy_lpdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/chi_square_cdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/chi_square_lccdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/chi_square_lcdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/chi_square_lpdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/double_exponential_cdf.hpp | 1 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/double_exponential_lpdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/exp_mod_normal_lpdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/exponential_lccdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/exponential_lpdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/frechet_lpdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/gamma_cdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/gamma_lccdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/gamma_lcdf.hpp | 48 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/gamma_lpdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/gumbel_lpdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/hmm_marginal.hpp | 1 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/inv_chi_square_cdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/inv_chi_square_lccdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/inv_chi_square_lcdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/inv_chi_square_lpdf.hpp | 5 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/inv_gamma_cdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/inv_gamma_lccdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/inv_gamma_lcdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/inv_gamma_lpdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/inv_wishart_cholesky_lpdf.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/inv_wishart_cholesky_rng.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/logistic_lpdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/loglogistic_log.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/lognormal_lpdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/multi_normal_cholesky_lpdf.hpp | 6 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/multi_student_t_cholesky_lpdf.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/multi_student_t_cholesky_rng.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/multi_student_t_lpdf.hpp | 104 - stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/multi_student_t_rng.hpp | 29 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/neg_binomial_2_log_glm_lpmf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/normal_id_glm_lpdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/normal_lpdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/normal_sufficient_lpdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/ordered_logistic_glm_lpmf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/ordered_logistic_lpmf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/ordered_probit_lpmf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/pareto_lpdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/pareto_type_2_lpdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/poisson_log_glm_lpmf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/poisson_log_lpmf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/poisson_lpmf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/rayleigh_lpdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/scaled_inv_chi_square_cdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/scaled_inv_chi_square_lccdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/scaled_inv_chi_square_lcdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/scaled_inv_chi_square_lpdf.hpp | 14 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/skew_double_exponential_cdf.hpp | 1 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/skew_double_exponential_lcdf.hpp | 1 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/skew_double_exponential_lpdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/skew_normal_lpdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/std_normal_log_qf.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/std_normal_rng.hpp | 1 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/student_t_cdf.hpp | 6 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/student_t_lccdf.hpp | 6 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/student_t_lcdf.hpp | 6 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/student_t_lpdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/uniform_lcdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/uniform_lpdf.hpp | 4 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/von_mises_ccdf_log.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/von_mises_cdf.hpp | 1 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/von_mises_cdf_log.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/von_mises_lpdf.hpp | 3 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/weibull_lpdf.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/wishart_cholesky_lpdf.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/prim/prob/wishart_cholesky_rng.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev.hpp | 1 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/core/arena_allocator.hpp | 16 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/core/arena_matrix.hpp | 30 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/core/count_vars.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/core/operator_addition.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/core/operator_divide_equal.hpp | 9 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/core/operator_subtraction.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/core/set_zero_all_adjoints.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/core/var.hpp | 71 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/core/vari.hpp | 61 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun.hpp | 9 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/atan2.hpp | 144 + stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/beta.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/cumulative_sum.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/fft.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/fma.hpp | 6 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/grad_inc_beta.hpp | 10 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/hypergeometric_2F1.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/hypergeometric_pFq.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/inv_erfc.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/inv_inc_beta.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/lmultiply.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/log.hpp | 1 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/log_determinant_spd.hpp | 91 - stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/log_inv_logit.hpp | 21 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/multiply.hpp | 17 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/norm1.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/norm2.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/owens_t.hpp | 112 - stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/pow.hpp | 262 ++- stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/rep_matrix.hpp | 3 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/tan.hpp | 3 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/fun/value_of_rec.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor.hpp | 6 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/algebra_solver_fp.hpp | 44 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/coupled_ode_system.hpp | 9 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/cvodes_integrator.hpp | 90 - stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/cvodes_integrator_adjoint.hpp | 364 ++-- stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/cvodes_utils.hpp | 26 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/dae.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/dae_system.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/gradient.hpp | 69 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/idas_integrator.hpp | 272 --- stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/idas_service.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/integrate_1d.hpp | 11 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/kinsol_data.hpp | 15 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/kinsol_solve.hpp | 56 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/ode_adams.hpp | 3 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/ode_adjoint.hpp | 16 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/ode_bdf.hpp | 3 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/operands_and_partials.hpp | 79 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/reduce_sum.hpp | 8 stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/solve_newton.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/functor/solve_powell.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/prob |only stan4bart-0.0-5/stan4bart/src/include/stan/math/rev/prob.hpp |only stan4bart-0.0-5/stan4bart/src/include/stan/math/version.hpp | 2 stan4bart-0.0-5/stan4bart/src/include/sundials/cvodes/cvodes.h | 49 stan4bart-0.0-5/stan4bart/src/include/sundials/cvodes/cvodes_bandpre.h | 2 stan4bart-0.0-5/stan4bart/src/include/sundials/cvodes/cvodes_bbdpre.h | 2 stan4bart-0.0-5/stan4bart/src/include/sundials/cvodes/cvodes_diag.h | 2 stan4bart-0.0-5/stan4bart/src/include/sundials/cvodes/cvodes_direct.h | 38 stan4bart-0.0-5/stan4bart/src/include/sundials/cvodes/cvodes_ls.h | 11 stan4bart-0.0-5/stan4bart/src/include/sundials/cvodes/cvodes_spils.h | 62 stan4bart-0.0-5/stan4bart/src/include/sundials/idas/idas.h | 8 stan4bart-0.0-5/stan4bart/src/include/sundials/idas/idas_bbdpre.h | 2 stan4bart-0.0-5/stan4bart/src/include/sundials/idas/idas_direct.h | 37 stan4bart-0.0-5/stan4bart/src/include/sundials/idas/idas_ls.h | 2 stan4bart-0.0-5/stan4bart/src/include/sundials/idas/idas_spils.h | 90 - stan4bart-0.0-5/stan4bart/src/include/sundials/kinsol/kinsol.h | 24 stan4bart-0.0-5/stan4bart/src/include/sundials/kinsol/kinsol_bbdpre.h | 2 stan4bart-0.0-5/stan4bart/src/include/sundials/kinsol/kinsol_direct.h | 23 stan4bart-0.0-5/stan4bart/src/include/sundials/kinsol/kinsol_ls.h | 2 stan4bart-0.0-5/stan4bart/src/include/sundials/kinsol/kinsol_spils.h | 40 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_cuda.h | 31 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_hip.h | 54 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_manyvector.h | 14 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_mpimanyvector.h | 20 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_mpiplusx.h | 8 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_openmp.h | 30 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_openmpdev.h | 33 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_parallel.h | 42 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_parhyp.h | 76 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_petsc.h | 36 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_pthreads.h | 76 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_raja.h | 22 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_serial.h | 30 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_sycl.h | 23 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/nvector_trilinos.h | 6 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/trilinos/SundialsTpetraVectorInterface.hpp | 25 stan4bart-0.0-5/stan4bart/src/include/sundials/nvector/trilinos/SundialsTpetraVectorKernels.hpp | 19 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_band.h | 191 +- stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_config.h | 68 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_config.in | 58 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_context.h |only stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_cuda_policies.hpp | 154 + stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_dense.h | 332 ++-- stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_direct.h | 306 ++- stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_futils.h | 2 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_hip_policies.hpp | 160 +- stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_iterative.h | 355 +++- stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_lapack.h | 4 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_linearsolver.h | 20 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_math.h | 38 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_matrix.h | 7 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_memory.h | 39 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_mpi_types.h | 6 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_nonlinearsolver.h | 11 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_nvector.h | 64 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_nvector_senswrapper.h | 4 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_profiler.h |only stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_sycl_policies.hpp | 51 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_types.h | 77 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_version.h | 2 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials/sundials_xbraid.h | 2 stan4bart-0.0-5/stan4bart/src/include/sundials/sundials_debug.h | 21 stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_band.h | 9 stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_cusolversp_batchqr.h | 7 stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_dense.h | 9 stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_klu.h | 13 stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_lapackband.h | 21 stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_lapackdense.h | 21 stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_magmadense.h | 4 stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_onemkldense.h |only stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_pcg.h | 24 stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_spbcgs.h | 25 stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_spfgmr.h | 29 stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_spgmr.h | 28 stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_sptfqmr.h | 25 stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_superludist.h | 7 stan4bart-0.0-5/stan4bart/src/include/sundials/sunlinsol/sunlinsol_superlumt.h | 13 stan4bart-0.0-5/stan4bart/src/include/sundials/sunmatrix/sunmatrix_band.h | 21 stan4bart-0.0-5/stan4bart/src/include/sundials/sunmatrix/sunmatrix_cusparse.h | 11 stan4bart-0.0-5/stan4bart/src/include/sundials/sunmatrix/sunmatrix_dense.h | 14 stan4bart-0.0-5/stan4bart/src/include/sundials/sunmatrix/sunmatrix_magmadense.h | 6 stan4bart-0.0-5/stan4bart/src/include/sundials/sunmatrix/sunmatrix_onemkldense.h |only stan4bart-0.0-5/stan4bart/src/include/sundials/sunmatrix/sunmatrix_slunrloc.h | 4 stan4bart-0.0-5/stan4bart/src/include/sundials/sunmatrix/sunmatrix_sparse.h | 17 stan4bart-0.0-5/stan4bart/src/include/sundials/sunmemory/sunmemory_cuda.h | 33 stan4bart-0.0-5/stan4bart/src/include/sundials/sunmemory/sunmemory_hip.h | 33 stan4bart-0.0-5/stan4bart/src/include/sundials/sunmemory/sunmemory_sycl.h | 37 stan4bart-0.0-5/stan4bart/src/include/sundials/sunmemory/sunmemory_system.h |only stan4bart-0.0-5/stan4bart/src/include/sundials/sunnonlinsol/sunnonlinsol_fixedpoint.h | 20 stan4bart-0.0-5/stan4bart/src/include/sundials/sunnonlinsol/sunnonlinsol_newton.h | 10 stan4bart-0.0-5/stan4bart/src/include/sundials/sunnonlinsol/sunnonlinsol_petscsnes.h | 6 stan4bart-0.0-5/stan4bart/src/init.cpp | 205 ++ stan4bart-0.0-5/stan4bart/src/misc_adaptiveRadixTree.c | 2 stan4bart-0.0-5/stan4bart/src/stan_files/continuous.hpp | 58 stan4bart-0.0-5/stan4bart/src/stan_files/continuous.stan | 10 stan4bart-0.0-5/stan4bart/src/stan_files/continuous_new.hpp |only stan4bart-0.0-5/stan4bart/src/stan_sampler.cpp | 12 stan4bart-0.0-5/stan4bart/src/stan_sampler.hpp | 2 stan4bart-0.0-5/stan4bart/src/stan_sampler_includes.hpp | 5 stan4bart-0.0-5/stan4bart/tests/testthat/test-01-continuous.R | 24 stan4bart-0.0-5/stan4bart/tests/testthat/test-06-no_ranef.R | 2 stan4bart-0.0-5/stan4bart/tests/testthat/test-10-treatment.R |only stan4bart-0.0-5/stan4bart/tests/testthat/test-11-callback.R |only 436 files changed, 6069 insertions(+), 3409 deletions(-)
Title: R Interface to Geochemical Modeling Software
Description: A geochemical modeling program developed by the US Geological
Survey that is designed to perform a wide variety of aqueous geochemical
calculations, including speciation, batch-reaction, one-dimensional
reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton [aut, cre], D.L. Parkhurst [aut], and C.A.J. Appelo [aut], with contributions
from D. Gillespie [ctb] for Chipmunk BASIC and S.D. Cohen [ctb], A.C. Hindmarsh [ctb],
R. Serban [ctb], D. Shumaker [ctb], and A.G. Taylor [ctb] for CVODE/SUN [...truncated...]
Maintainer: S.R. Charlton <charlton@usgs.gov>
Diff between phreeqc versions 3.7.4 dated 2022-03-28 and 3.7.5 dated 2023-01-23
DESCRIPTION | 8 +- MD5 | 50 ++++++------- R/phreeqc.R | 2 build/partial.rdb |binary data/databases.rda |binary data/examples.rda |binary man/phreeqc-package.Rd | 2 src/IPhreeqc.cpp | 10 +- src/IPhreeqc.h | 2 src/R.cpp | 12 +-- src/Version.h | 8 +- src/phreeqcpp/PBasic.cpp | 39 +++++----- src/phreeqcpp/PBasic.h | 1 src/phreeqcpp/PHRQ_io_output.cpp | 4 - src/phreeqcpp/Phreeqc.h | 2 src/phreeqcpp/ReadClass.cpp | 6 - src/phreeqcpp/basicsubs.cpp | 2 src/phreeqcpp/inverse.cpp | 60 ++++++++-------- src/phreeqcpp/kinetics.cpp | 2 src/phreeqcpp/mainsubs.cpp | 22 +++--- src/phreeqcpp/parse.cpp | 4 - src/phreeqcpp/pitzer.cpp | 4 - src/phreeqcpp/print.cpp | 6 - src/phreeqcpp/readtr.cpp | 140 +++++++++++++++++++-------------------- src/phreeqcpp/transport.cpp | 40 +++++------ src/phreeqcpp/utilities.cpp | 22 +++--- 26 files changed, 226 insertions(+), 222 deletions(-)
Title: Functions to Support the ICES Transparent Assessment Framework
Description: Functions to support the ICES Transparent Assessment Framework
<https://taf.ices.dk> to organize data, methods, and results used in ICES
assessments. ICES is an organization facilitating international collaboration
in marine science.
Author: Colin Millar [aut, cre],
Arni Magnusson [aut],
Alexandros Kokkalis [ctb],
Iago Mosqueira [ctb],
Ibrahim Umar [ctb],
Hjalte Parner [ctb]
Maintainer: Colin Millar <colin.millar@ices.dk>
Diff between icesTAF versions 4.0.2 dated 2023-01-11 and 4.1.0 dated 2023-01-23
DESCRIPTION | 12 - MD5 | 21 +-- NAMESPACE | 16 ++ NEWS.md | 12 + R/TAF.R | 311 ++++++++++++++++++++++++++--------------------- R/dir.tree.R |only R/install.deps.R | 5 R/taf.colors.R |only R/taf.skeleton.sa.org.R | 35 +++-- data |only man/dir.tree.Rd |only man/install.deps.Rd | 4 man/taf-reexports.Rd | 316 +++++++++++++++++++++++++----------------------- man/taf.colors.Rd |only 14 files changed, 418 insertions(+), 314 deletions(-)
Title: Gillespie's Stochastic Simulation Algorithm for Impatient People
Description: A fast, scalable, and versatile framework for
simulating large systems with Gillespie's Stochastic Simulation
Algorithm ('SSA'). This package is the spiritual successor to the
'GillespieSSA' package originally written by Mario Pineda-Krch.
Benefits of this package include major speed improvements (>100x),
easier to understand documentation, and many unit tests that try to
ensure the package works as intended. Cannoodt and Saelens et al. (2021)
<doi:10.1038/s41467-021-24152-2>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between GillespieSSA2 versions 0.2.10 dated 2022-09-23 and 0.3.0 dated 2023-01-23
DESCRIPTION | 15 ++-- MD5 | 71 ++++++++++--------- NEWS.md | 7 + R/compile_reactions.R | 20 +++-- README.md | 45 +++++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 12 +-- inst/REFERENCES.bib |only inst/doc/an_introduction.html | 4 - inst/doc/converting_from_GillespieSSA.html | 8 +- inst/doc/decaying_dimer.Rmd | 9 +- inst/doc/decaying_dimer.html | 40 +++++++++-- inst/doc/epi_chain.Rmd | 9 +- inst/doc/epi_chain.html | 38 +++++++++- inst/doc/linear_chain.Rmd | 9 +- inst/doc/linear_chain.html | 38 +++++++++- inst/doc/logistic_growth.Rmd | 43 +++++++----- inst/doc/logistic_growth.html | 103 +++++++++++++++++++---------- inst/doc/lotka_predator_prey.Rmd | 7 + inst/doc/lotka_predator_prey.html | 38 +++++++++- inst/doc/radioactive_decay.Rmd | 9 +- inst/doc/radioactive_decay.html | 38 +++++++++- inst/doc/rm_predator_prey.Rmd | 9 +- inst/doc/rm_predator_prey.html | 42 ++++++++++- inst/doc/sir.Rmd | 8 +- inst/doc/sir.html | 36 +++++++++- man/compile_reactions.Rd | 5 + tests/testthat/test-compile_reactions.R | 30 ++++++-- vignettes/decaying_dimer.Rmd | 9 +- vignettes/epi_chain.Rmd | 9 +- vignettes/linear_chain.Rmd | 9 +- vignettes/logistic_growth.Rmd | 43 +++++++----- vignettes/lotka_predator_prey.Rmd | 7 + vignettes/radioactive_decay.Rmd | 9 +- vignettes/rm_predator_prey.Rmd | 9 +- vignettes/sir.Rmd | 8 +- 37 files changed, 575 insertions(+), 221 deletions(-)
Title: Causal Inference using Bayesian Additive Regression Trees
Description: Contains a variety of methods to generate typical causal inference estimates using Bayesian Additive Regression Trees (BART) as the underlying regression model (Hill (2012) <doi:10.1198/jcgs.2010.08162>).
Author: Vincent Dorie [aut, cre] ,
Jennifer Hill [aut]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between bartCause versions 1.0-4 dated 2020-08-10 and 1.0-6 dated 2023-01-23
DESCRIPTION | 10 MD5 | 50 ++- NAMESPACE | 2 R/argParse.R | 382 ++++++++++++++++++++--------- R/bartc.R | 46 ++- R/bayesOpt.R | 58 ++-- R/generics.R | 117 ++++++--- R/plot.R | 39 +-- R/responseFit.R | 127 +++++++++ R/summary.R | 81 ++++-- R/treatmentFit.R | 100 ++++++- R/utility.R | 47 ++- build |only inst/NEWS.Rd | 30 ++ inst/common/friedmanData.R |only man/bartc.Rd | 389 ++++++++++++++++++------------ man/generics.Rd | 3 man/plot.Rd | 1 tests/testthat/test-01-callConstructors.R | 320 ++++++++++++++++++++---- tests/testthat/test-02-treatmentFit.R | 50 +++ tests/testthat/test-03-responseFit.R | 17 - tests/testthat/test-04-bartc.R | 88 +++--- tests/testthat/test-05-generics.R | 108 +++++++- tests/testthat/test-06-regression.R | 18 - tests/testthat/test-07-commonSupport.R | 13 - tests/testthat/test-09-binary.R | 22 + tests/testthat/test-10-rng.R |only tests/testthat/test-11-stan4bart.R |only 28 files changed, 1534 insertions(+), 584 deletions(-)
Title: Methods to Convert R Data to YAML and Back
Description: Implements the 'libyaml' 'YAML' 1.1 parser and emitter
(<https://pyyaml.org/wiki/LibYAML>) for R.
Author: Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb],
Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb],
Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb],
Michael Quinn [...truncated...]
Maintainer: Shawn Garbett <shawn.garbett@vumc.org>
Diff between yaml versions 2.3.6 dated 2022-10-18 and 2.3.7 dated 2023-01-23
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 8 ++++---- inst/CHANGELOG | 2 ++ src/dumper.c | 2 +- 5 files changed, 12 insertions(+), 10 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement
complex random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
an efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [...truncated...]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.9.1 dated 2022-08-16 and 1.9.2 dated 2023-01-23
DESCRIPTION | 8 MD5 | 42 + NEWS | 16 R/TMB.R | 3 inst/include/TMB.hpp | 4 inst/include/TMBad/TMBad.cpp | 453 +++++++++++++++++--- inst/include/TMBad/TMBad.hpp | 57 ++ inst/include/TMBad/ad_blas.hpp | 103 ++-- inst/include/TMBad/checkpoint.hpp | 71 ++- inst/include/TMBad/config.hpp | 2 inst/include/TMBad/global.hpp | 425 ++++++++++++++---- inst/include/TMBad/vectorize.hpp |only inst/include/checkpoint_macro.hpp | 5 inst/include/dynamic_data.hpp | 2 inst/include/tiny_ad/bessel/bessel.hpp | 1 inst/include/tiny_ad/beta/pbeta.hpp | 1 inst/include/tiny_ad/gamma/gamma.hpp | 1 inst/include/tmb_core.hpp | 24 - inst/include/tmbutils/concat.hpp |only inst/include/tmbutils/sparse_matrix_exponential.hpp |only inst/include/tmbutils/vectorize.hpp |only src/external_metis.c | 3 src/init.c | 2 src/solve_subset.c | 1 24 files changed, 991 insertions(+), 233 deletions(-)
Title: R Interface to 'pytorch''s 'torchaudio'
Description: Provides access to datasets, models and processing
facilities for deep learning in audio.
Author: Sigrid Keydana [aut, cre],
Athos Damiani [aut],
Daniel Falbel [aut]
Maintainer: Sigrid Keydana <sigrid@posit.co>
Diff between torchaudio versions 0.2.1 dated 2023-01-16 and 0.2.2 dated 2023-01-23
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 +++--- R/dataset-utils.R | 6 +++--- man/extract_archive.Rd | 6 +++--- src/AudioFile.h | 1 + 6 files changed, 18 insertions(+), 17 deletions(-)
Title: Data from Access to Information Law
Description: Downloads the public data available from the Brazilian Access to Information Law and and performs a search on information requests and appeals made since 2015.
Author: Igor Laltuf [aut, cre]
Maintainer: Igor Laltuf <igorlaltuf@gmail.com>
Diff between dail versions 1.4.2 dated 2023-01-06 and 1.5 dated 2023-01-23
DESCRIPTION | 9 +++++---- MD5 | 7 +++++-- NAMESPACE | 17 +++++++++-------- R/corporateCardExpenses.R |only man/corporateCardExpenses.Rd |only tests/testthat/test-corporateCardExpenses.R |only 6 files changed, 19 insertions(+), 14 deletions(-)
Title: Two Sample Problem Routines using Permutation
Description: The routine twosample_test() in this package runs the
two sample test using various test statistic. The p values are
found via permutation. The routine twosample_power() allows the
calculation of the power in various cases, and plot_power()
draws the corresponding power graphs.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between R2sample versions 1.0.0 dated 2022-10-26 and 1.1.0 dated 2023-01-23
DESCRIPTION | 6 - MD5 | 74 ++++++++++---------- NEWS.md | 4 + R/RcppExports.R | 25 ++++-- R/plot_power.R | 4 - R/run_shiny.R | 2 R/twosample_power.R | 2 R/twosample_test.R | 2 inst/doc/R2sample.R | 2 inst/doc/R2sample.Rmd | 8 +- inst/doc/R2sample.html | 166 ++++++++++++++++++++++------------------------ man/TS_cont_cpp.Rd | 3 man/TS_disc_cpp.Rd | 3 man/bincounter_cpp.Rd | 1 man/chi_test_cont_cpp.Rd | 1 man/chi_test_disc_cpp.Rd | 3 man/perm_test_cpp.Rd | 3 man/permute_cont_cpp.Rd | 3 man/permute_disc_cpp.Rd | 1 man/plot_power.Rd | 2 man/power_cpp.Rd | 3 man/rep_cpp.Rd | 1 man/run_shiny.Rd | 2 man/twosample_power.Rd | 2 man/twosample_test.Rd | 2 man/weights_cpp.Rd | 3 src/TS_cont_cpp.cpp | 47 +++++-------- src/TS_disc_cpp.cpp | 3 src/bincounter_cpp.cpp | 5 + src/chi_test_cont_cpp.cpp | 8 +- src/chi_test_disc_cpp.cpp | 3 src/perm_test_cpp.cpp | 13 +-- src/permute_cont_cpp.cpp | 3 src/permute_disc_cpp.cpp | 1 src/power_cpp.cpp | 3 src/rep_cpp.cpp | 1 src/weights_cpp.cpp | 3 vignettes/R2sample.Rmd | 8 +- 38 files changed, 226 insertions(+), 200 deletions(-)
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
developed by the research group around Cornelia Dowling through
querying experts.
Author: Cord Hockemeyer [aut, cre],
Wai Wong [aut]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 0.1-4 dated 2022-10-24 and 0.1-5 dated 2023-01-23
Changelog | 10 + DESCRIPTION | 10 - MD5 | 18 +- NAMESPACE | 1 R/kmeqreduction.R |only build/vignette.rds |binary inst/doc/kstMatrix.R | 4 inst/doc/kstMatrix.Rmd | 8 inst/doc/kstMatrix.html | 406 ++++++++++++++++++++++++------------------------ man/kmeqreduction.Rd |only vignettes/kstMatrix.Rmd | 8 11 files changed, 254 insertions(+), 211 deletions(-)
Title: Fast and Easy Eurostat Data Import and Search
Description: Interface to Eurostat’s Bulk Download Facility with fast data.table-based import of
data, labels, and metadata. On top of the core functionality, data search and data
description/comparison functions are also provided.
Use <https://github.com/alekrutkowski/eurodata_codegen> — a point-and-click app for rapid and
easy generation of richly-commented R code — to import a Eurostat dataset or its subset
(based on the eurodata::importData() function).
Author: Aleksander Rutkowski [aut, cre]
Maintainer: Aleksander Rutkowski <alek.rutkowski@gmail.com>
Diff between eurodata versions 1.6.0 dated 2022-12-14 and 1.6.1 dated 2023-01-23
DESCRIPTION | 11 +++-- MD5 | 4 - README.md | 132 ++++++++++++++++++++++++++++++++++++++++-------------------- 3 files changed, 99 insertions(+), 48 deletions(-)
Title: Visual Regression Testing and Graphical Diffing
Description: An extension to the 'testthat' package that makes it easy
to add graphical unit tests. It provides a Shiny application to
manage the test cases.
Author: Lionel Henry [cre, aut],
Thomas Lin Pedersen [aut] ,
RStudio [cph, fnd],
T Jake Luciani [aut] ,
Matthieu Decorde [aut] ,
Vaudor Lise [aut] ,
Tony Plate [ctb] ,
David Gohel [ctb] ,
Yixuan Qiu [ctb] ,
Hakon Malmedal [ctb]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between vdiffr versions 1.0.4 dated 2022-03-15 and 1.0.5 dated 2023-01-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ src/devSVG.cpp | 1 + 4 files changed, 12 insertions(+), 6 deletions(-)
Title: Neural Networks using the Stuttgart Neural Network Simulator
(SNNS)
Description: The Stuttgart Neural Network Simulator (SNNS) is a library
containing many standard implementations of neural networks. This
package wraps the SNNS functionality to make it available from
within R. Using the 'RSNNS' low-level interface, all of the
algorithmic functionality and flexibility of SNNS can be accessed.
Furthermore, the package contains a convenient high-level
interface, so that the most common neural network topologies and
learning algorithms integrate seamlessly into R.
Author: Christoph Bergmeir [aut, cre, cph],
Jose M. Benitez [ths],
Andreas Zell [ctb] ,
Niels Mache [ctb] ,
Guenter Mamier [ctb] ,
Michael Vogt [ctb] ,
Sven Doering [ctb] ,
Ralf Huebner [ctb] ,
Kai-Uwe Herrmann [ctb] ,
Tobias Soyez [ctb] ,
Michael Schmalzl [ctb [...truncated...]
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>
Diff between RSNNS versions 0.4-14 dated 2021-08-13 and 0.4-15 dated 2023-01-23
ChangeLog | 12 DESCRIPTION | 10 MD5 | 116 ++-- R/util.R | 2 demo/mlp_plot_with_my_predict.R | 2 src/SnnsCLib.cpp | 46 - src/SnnsCLib.h | 8 src/SnnsCLibWrapper.cpp | 126 ++--- src/arttr_f.cpp | 54 +- src/arttr_f.h | 6 src/bn_JordElm.cpp | 18 src/bn_art1.cpp | 64 +- src/bn_art2.cpp | 32 - src/bn_artmap.cpp | 166 +++---- src/bn_assoz.cpp | 4 src/bn_kohonen.cpp | 2 src/cc_glob.cpp | 66 +- src/cc_learn.cpp | 48 +- src/cc_mac.h | 40 - src/cc_modify.cpp | 14 src/cc_prune.cpp | 14 src/dlvq_learn.cpp | 40 - src/func_mac.h | 6 src/glob_typ.h | 2 src/init_f.cpp | 368 +++++++-------- src/kernel.cpp | 202 ++++---- src/kernel.h | 2 src/kr_JordElm.cpp | 2 src/kr_amap.cpp | 160 +++--- src/kr_art.cpp | 12 src/kr_art1.cpp | 72 +-- src/kr_art2.cpp | 106 ++-- src/kr_funcs.cpp | 6 src/kr_inversion.cpp | 26 - src/kr_io.cpp | 280 +++++------ src/kr_mem.cpp | 18 src/kr_newpattern.cpp | 48 +- src/kr_pat_parse.cpp | 23 src/kr_pat_scan.cpp | 220 ++++----- src/kr_td.cpp | 90 +-- src/kr_typ.h | 7 src/kr_ui.cpp | 76 +-- src/krart_df.h | 12 src/learn_f.cpp | 936 ++++++++++++++++++++-------------------- src/matrix.cpp | 58 +- src/prun_f.cpp | 104 ++-- src/prun_f.h | 8 src/remap_f.cpp | 34 - src/scaled_conj_grad.cpp | 28 - src/scaled_conj_grad.h | 6 src/sigmoid_tbl.h | 408 ++++++++--------- src/stochastic_learn_f.cpp | 62 +- src/tacoma_learn.cpp | 120 ++--- src/tacoma_learn.h | 4 src/tbl_func.cpp | 6 src/trans_f.cpp | 408 ++++++++--------- src/trans_f.h | 12 src/update_f.cpp | 158 +++--- tests/testAllDemos.R | 2 59 files changed, 2496 insertions(+), 2486 deletions(-)
Title: Read and Write ODS Files
Description: Read ODS (OpenDocument Spreadsheet) into R as data frame. Also support writing data frame into ODS file.
Author: Gerrit-Jan Schutten [aut],
Chung-hong Chan [aut, cre] ,
Thomas J. Leeper [aut] ,
John Foster [ctb],
Sergio Oller [ctb],
Jim Hester [ctb] ,
Stephen Watts [ctb],
Arthur Katossky [ctb],
Stas Malavin [ctb],
Duncan Garmonsway [ctb],
Mehrad Mahmoudian [ctb [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between readODS versions 1.7.0 dated 2020-07-10 and 1.8.0 dated 2023-01-23
DESCRIPTION | 37 ++ MD5 | 53 ++-- NAMESPACE | 1 R/readODS-package.R |only R/readODS.R | 213 ++++++++++------ R/sysdata.rda |only R/writeODS.R | 231 ++++++++++------- README.md | 91 ++++-- build/vignette.rds |binary inst/doc/overview.R | 3 inst/doc/overview.Rmd | 14 - inst/doc/overview.html | 344 +++++++++++++------------- man/get_num_sheets_in_ods.Rd | 4 man/list_ods_sheets.Rd | 2 man/readODS-package.Rd |only man/read_ods.Rd | 34 +- man/write_ods.Rd | 26 + tests/testdata/eating_spaces.ods |only tests/testdata/excel_repeat.ods |only tests/testdata/fuzz.txt |only tests/testdata/issue81.ods |only tests/testdata/na_test2.ods |only tests/testdata/na_test3.ods |only tests/testdata/perform.ods |only tests/testdata/rep_check.ods |only tests/testdata/repeat_rows.ods |only tests/testdata/reprow.ods |only tests/testdata/starwars.ods |only tests/testdata/test_naming.ods |only tests/testthat/test_issue81.R |only tests/testthat/test_legacy.R | 54 ++-- tests/testthat/test_na.R | 36 ++ tests/testthat/test_read_ods.R | 30 ++ tests/testthat/test_write_ods_append_update.R | 12 tests/testthat/test_xml_fuzz.R |only vignettes/overview.Rmd | 14 - 36 files changed, 747 insertions(+), 452 deletions(-)
Title: Visualizations for 'mlr3'
Description: Visualization package of the 'mlr3' ecosystem. It features plots
for mlr3 objects such as tasks, learners, predictions, benchmark results,
tuning instances and filters via the 'autoplot()' generic of 'ggplot2'.
The package draws plots with the 'viridis' color palette and applies the
minimal theme. Visualizations include barplots, boxplots, histograms, ROC
curves, and Precision-Recall curves.
Author: Michel Lang [cre, aut] ,
Patrick Schratz [aut] ,
Raphael Sonabend [aut] ,
Marc Becker [aut] ,
Jakob Richter [aut] ,
Damir Pulatov [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3viz versions 0.6.0 dated 2023-01-12 and 0.6.1 dated 2023-01-23
DESCRIPTION | 8 ++-- MD5 | 20 +++++----- NEWS.md | 6 +++ R/OptimInstanceSingleCrit.R | 4 +- R/PredictionRegr.R | 7 ++- R/ResampleResult.R | 7 ++- README.md | 9 +++- man/autoplot.PredictionRegr.Rd | 5 ++ man/autoplot.ResampleResult.Rd | 4 ++ man/mlr3viz-package.Rd | 2 - tests/testthat/_snaps/TuningInstanceSingleCrit/tisc-performance.svg | 2 - 11 files changed, 49 insertions(+), 25 deletions(-)
Title: Lightweight Utilities for 'DIZ' R Package Development
Description: Lightweight utility functions used for the R package
development infrastructure inside the data integration centers ('DIZ')
to standardize and facilitate repetitive tasks such as setting up a
database connection or issuing notification messages and to avoid
redundancy.
Author: Jonathan M. Mang [aut, cre] ,
Lorenz A. Kapsner [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between DIZtools versions 0.0.6 dated 2022-11-21 and 0.0.7 dated 2023-01-23
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/feedback.R | 7 +++++-- README.md | 4 ++-- man/check_if_unique_rows.Rd | 2 +- man/feedback.Rd | 2 +- man/feedback_get_formatted_string.Rd | 2 +- man/feedback_to_console.Rd | 2 +- man/feedback_to_logfile.Rd | 2 +- man/log_set_defaults.Rd | 2 +- 10 files changed, 27 insertions(+), 24 deletions(-)
Title: Bayesian Inference for Directed Acyclic Graphs
Description: Implementation of a collection of MCMC methods for Bayesian structure learning
of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient
inference on larger DAGs, the space of DAGs is pruned according to the data. To filter
the search space, the algorithm employs a hybrid approach, combining constraint-based
learning with search and score. A reduced search space is initially defined on the basis
of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with
search and score. Search and score is then performed following two approaches:
Order MCMC, or Partition MCMC.
The BGe score is implemented for continuous data and the BDe score is implemented
for binary data or categorical data. The algorithms may provide the maximum a posteriori
(MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data.
All algorithms are also applicable for structure learning and sampling for dynamic Bayesian networks.
Refe [...truncated...]
Author: Polina Suter [aut, cre], Jack Kuipers [aut]
Maintainer: Polina Suter <polina.suter@gmail.com>
Diff between BiDAG versions 2.1.2 dated 2022-12-21 and 2.1.3 dated 2023-01-23
DESCRIPTION | 9 +++++---- MD5 | 3 ++- inst |only 3 files changed, 7 insertions(+), 5 deletions(-)
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 11. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood est [...truncated...]
Author: Anthony Hammond
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 0.2.5 dated 2023-01-22 and 0.2.6 dated 2023-01-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/All.R | 25 +++++++++++++++++-------- man/BivarSim.Rd | 7 +++++-- man/POTextract.Rd | 10 ++++++---- 5 files changed, 35 insertions(+), 21 deletions(-)
Title: Functions to Support the ICES Transparent Assessment Framework
Description: Functions to support the ICES Transparent Assessment Framework
<https://taf.ices.dk> to organize data, methods, and results used in ICES
assessments. ICES is an organization facilitating international collaboration
in marine science.
Author: Arni Magnusson [aut, cre],
Colin Millar [aut],
Alexandros Kokkalis [ctb],
Iago Mosqueira [ctb],
Ibrahim Umar [ctb],
Hjalte Parner [ctb]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Diff between TAF versions 4.0.0 dated 2021-04-07 and 4.1.0 dated 2023-01-23
TAF-4.0.0/TAF/R/makeAll.R |only TAF-4.0.0/TAF/R/makeTAF.R |only TAF-4.0.0/TAF/R/sourceAll.R |only TAF-4.0.0/TAF/R/sourceDir.R |only TAF-4.0.0/TAF/R/sourceTAF.R |only TAF-4.0.0/TAF/R/taf.bootstrap.R |only TAF-4.0.0/TAF/man/makeAll.Rd |only TAF-4.0.0/TAF/man/makeTAF.Rd |only TAF-4.0.0/TAF/man/sourceAll.Rd |only TAF-4.0.0/TAF/man/sourceDir.Rd |only TAF-4.0.0/TAF/man/sourceTAF.Rd |only TAF-4.0.0/TAF/man/taf.bootstrap.Rd |only TAF-4.1.0/TAF/DESCRIPTION | 10 - TAF-4.1.0/TAF/MD5 | 156 +++++++++--------- TAF-4.1.0/TAF/NAMESPACE | 7 TAF-4.1.0/TAF/NEWS.md | 26 +++ TAF-4.1.0/TAF/R/TAF-package.R | 31 ++- TAF-4.1.0/TAF/R/access.vocab.R | 3 TAF-4.1.0/TAF/R/clean.data.R | 6 TAF-4.1.0/TAF/R/clean.library.R | 17 +- TAF-4.1.0/TAF/R/clean.software.R | 10 - TAF-4.1.0/TAF/R/deps.R | 10 - TAF-4.1.0/TAF/R/download.R | 4 TAF-4.1.0/TAF/R/download.github.R | 10 - TAF-4.1.0/TAF/R/draft.data.R | 7 TAF-4.1.0/TAF/R/draft.software.R | 2 TAF-4.1.0/TAF/R/file.encoding.R | 13 - TAF-4.1.0/TAF/R/get.remote.sha.R | 4 TAF-4.1.0/TAF/R/lim.R | 7 TAF-4.1.0/TAF/R/make.R | 8 TAF-4.1.0/TAF/R/make.all.R |only TAF-4.1.0/TAF/R/make.taf.R |only TAF-4.1.0/TAF/R/msg.R | 2 TAF-4.1.0/TAF/R/process.bibfile.R | 13 - TAF-4.1.0/TAF/R/process.entry.R | 34 ++-- TAF-4.1.0/TAF/R/read.bib.R | 37 ++-- TAF-4.1.0/TAF/R/read.taf.R | 24 ++ TAF-4.1.0/TAF/R/rnd.R | 4 TAF-4.1.0/TAF/R/source.all.R |only TAF-4.1.0/TAF/R/source.dir.R |only TAF-4.1.0/TAF/R/source.taf.R |only TAF-4.1.0/TAF/R/taf.boot.R |only TAF-4.1.0/TAF/R/taf.boot.path.R | 38 ++-- TAF-4.1.0/TAF/R/taf.data.path.R | 44 +++-- TAF-4.1.0/TAF/R/taf.install.R | 10 - TAF-4.1.0/TAF/R/taf.libPaths.R | 2 TAF-4.1.0/TAF/R/taf.library.R | 18 +- TAF-4.1.0/TAF/R/taf.skeleton.R | 12 + TAF-4.1.0/TAF/R/taf.sources.R | 40 +++- TAF-4.1.0/TAF/R/taf2html.R |only TAF-4.1.0/TAF/R/taf2long.R | 6 TAF-4.1.0/TAF/R/write.taf.R | 24 +- TAF-4.1.0/TAF/build/partial.rdb |binary TAF-4.1.0/TAF/data/catage.long.rda |binary TAF-4.1.0/TAF/data/catage.taf.rda |binary TAF-4.1.0/TAF/data/catage.xtab.rda |binary TAF-4.1.0/TAF/data/summary.taf.rda |binary TAF-4.1.0/TAF/data/taf.colors.rda |binary TAF-4.1.0/TAF/man/TAF-package.Rd | 31 ++- TAF-4.1.0/TAF/man/clean.data.Rd | 6 TAF-4.1.0/TAF/man/clean.library.Rd | 8 TAF-4.1.0/TAF/man/clean.software.Rd | 9 - TAF-4.1.0/TAF/man/cp.Rd | 3 TAF-4.1.0/TAF/man/deps.Rd | 4 TAF-4.1.0/TAF/man/download.Rd | 4 TAF-4.1.0/TAF/man/download.github.Rd | 8 TAF-4.1.0/TAF/man/draft.data.Rd | 7 TAF-4.1.0/TAF/man/draft.software.Rd | 2 TAF-4.1.0/TAF/man/file.encoding.Rd | 6 TAF-4.1.0/TAF/man/get.remote.sha.Rd | 4 TAF-4.1.0/TAF/man/lim.Rd | 7 TAF-4.1.0/TAF/man/make.Rd | 8 TAF-4.1.0/TAF/man/make.all.Rd |only TAF-4.1.0/TAF/man/make.taf.Rd |only TAF-4.1.0/TAF/man/msg.Rd | 2 TAF-4.1.0/TAF/man/read.bib.Rd | 38 ++-- TAF-4.1.0/TAF/man/read.taf.Rd | 4 TAF-4.1.0/TAF/man/rnd.Rd | 4 TAF-4.1.0/TAF/man/source.all.Rd |only TAF-4.1.0/TAF/man/source.dir.Rd |only TAF-4.1.0/TAF/man/source.taf.Rd |only TAF-4.1.0/TAF/man/taf.boot.Rd |only TAF-4.1.0/TAF/man/taf.boot.path.Rd | 34 ++-- TAF-4.1.0/TAF/man/taf.data.path.Rd | 38 ++-- TAF-4.1.0/TAF/man/taf.install.Rd | 8 TAF-4.1.0/TAF/man/taf.libPaths.Rd | 2 TAF-4.1.0/TAF/man/taf.library.Rd | 9 - TAF-4.1.0/TAF/man/taf.skeleton.Rd | 5 TAF-4.1.0/TAF/man/taf.sources.Rd | 33 +++ TAF-4.1.0/TAF/man/taf2html.Rd |only TAF-4.1.0/TAF/man/write.taf.Rd | 14 - TAF-4.1.0/TAF/tests/Examples/TAF-Ex.Rout.save | 215 ++++++++++++++++++++++---- 92 files changed, 749 insertions(+), 403 deletions(-)
Title: Rendering Font into 'data.frame'
Description: Extract glyph information from font data, and translate the
outline curves to flattened paths or tessellated polygons. The converted
data is returned as a 'data.frame' in easy-to-plot format.
Author: Hiroaki Yutani [aut, cre] ,
The authors of the dependency Rust crates [ctb]
Maintainer: Hiroaki Yutani <yutani.ini@gmail.com>
Diff between string2path versions 0.1.2 dated 2022-12-17 and 0.1.3 dated 2023-01-23
DESCRIPTION | 6 +- MD5 | 18 +++---- NEWS.md | 5 ++ src/cargo_vendor_config.toml | 12 ++--- src/rust/Cargo.lock | 98 ++++++++++++++++++++++++++++--------------- src/rust/Cargo.toml | 11 +++- src/rust/src/font.rs | 2 src/rust/src/lib.rs | 14 ++++-- src/rust/vendor.tar.xz |binary tools/configure.R | 7 +++ 10 files changed, 113 insertions(+), 60 deletions(-)
Title: Extract Statistics from Articles and Recompute P-Values
Description: A "spellchecker" for statistics. It checks whether your p-values match their accompanying test statistic and
degrees of freedom. statcheck searches for null-hypothesis significance test
(NHST) in APA style (e.g., t(28) = 2.2, p < .05). It recalculates the p-value
using the reported test statistic and degrees of freedom. If the reported and
computed p-values don't match, statcheck will flag the result as an error. If
the reported p-value is statistically significant and the recomputed one is not,
or vice versa, the result will be flagged as a decision error.
You can use statcheck directly on a string of text, but you can also scan a PDF
or HTML file, or even a folder of PDF and/or HTML files.
Statcheck needs an external program to convert PDF to text: Xpdf. Instructions
on where and how to download this program, how to install statcheck, and more
details on what statcheck can and cannot do can be found in the online manual:
<https://rpubs.com/michelenuijten/statcheckmanual>.
Yo [...truncated...]
Author: Michele B. Nuijten [aut, cre] ,
Sacha Epskamp [aut] ,
Willem Sleegers [ctb] ,
Sean Rife [ctb] ,
John Sakaluk [ctb] ,
Paul van der Laken [ctb] ,
Chris Hartgerink [ctb] ,
Steve Haroz [ctb]
Maintainer: Michele B. Nuijten <m.b.nuijten@uvt.nl>
Diff between statcheck versions 1.3.0 dated 2018-05-06 and 1.4.0 dated 2023-01-23
statcheck-1.3.0/statcheck/COPYING |only statcheck-1.3.0/statcheck/R/PDFimport.R |only statcheck-1.3.0/statcheck/R/htmlImport.R |only statcheck-1.3.0/statcheck/man/checkHTML.Rd |only statcheck-1.3.0/statcheck/man/checkHTMLdir.Rd |only statcheck-1.3.0/statcheck/man/checkPDF.Rd |only statcheck-1.3.0/statcheck/man/checkPDFdir.Rd |only statcheck-1.3.0/statcheck/man/checkdir.Rd |only statcheck-1.4.0/statcheck/DESCRIPTION | 64 statcheck-1.4.0/statcheck/MD5 | 77 statcheck-1.4.0/statcheck/NAMESPACE | 45 statcheck-1.4.0/statcheck/NEWS.md |only statcheck-1.4.0/statcheck/R/calc_APA_factor.R |only statcheck-1.4.0/statcheck/R/checkHTML.R |only statcheck-1.4.0/statcheck/R/checkHTMLdir.R |only statcheck-1.4.0/statcheck/R/checkPDF.R |only statcheck-1.4.0/statcheck/R/checkPDFdir.R |only statcheck-1.4.0/statcheck/R/checkdir.R | 9 statcheck-1.4.0/statcheck/R/compute_p.R |only statcheck-1.4.0/statcheck/R/constants.R |only statcheck-1.4.0/statcheck/R/decision_error_test.R |only statcheck-1.4.0/statcheck/R/doc-checkdirs.R |only statcheck-1.4.0/statcheck/R/doc-checkfiles.R |only statcheck-1.4.0/statcheck/R/error_test.R |only statcheck-1.4.0/statcheck/R/extract_1tail.R |only statcheck-1.4.0/statcheck/R/extract_stats.R |only statcheck-1.4.0/statcheck/R/file-to-txt.R |only statcheck-1.4.0/statcheck/R/helpers-parse-stats.R |only statcheck-1.4.0/statcheck/R/identify.statcheck.R | 43 statcheck-1.4.0/statcheck/R/plot.statcheck.R | 103 - statcheck-1.4.0/statcheck/R/process_stats.R |only statcheck-1.4.0/statcheck/R/regex.R |only statcheck-1.4.0/statcheck/R/statcheck-package.R |only statcheck-1.4.0/statcheck/R/statcheck.R | 1713 +++----------------- statcheck-1.4.0/statcheck/R/statcheckReport.R | 54 statcheck-1.4.0/statcheck/R/summary.statcheck.R | 45 statcheck-1.4.0/statcheck/README.md |only statcheck-1.4.0/statcheck/inst/COPYRIGHT.txt |only statcheck-1.4.0/statcheck/inst/GPL3.txt |only statcheck-1.4.0/statcheck/man/checkdirs.Rd |only statcheck-1.4.0/statcheck/man/checkfiles.Rd |only statcheck-1.4.0/statcheck/man/figures |only statcheck-1.4.0/statcheck/man/identify.statcheck.Rd | 76 statcheck-1.4.0/statcheck/man/plot.statcheck.Rd | 79 statcheck-1.4.0/statcheck/man/statcheck-package.Rd | 136 + statcheck-1.4.0/statcheck/man/statcheck.Rd | 203 +- statcheck-1.4.0/statcheck/man/statcheckReport.Rd | 84 statcheck-1.4.0/statcheck/man/summary.statcheck.Rd | 60 statcheck-1.4.0/statcheck/tests |only 49 files changed, 1041 insertions(+), 1750 deletions(-)
Title: Stochastic Island Biogeography Theory Made Easy
Description: Develops stochastic models based on the Theory of Island
Biogeography (TIB) of MacArthur and Wilson (1967) <doi:10.1023/A:1016393430551>
and extensions. It implements methods to estimate colonization and
extinction rates (including environmental variables) given presence-absence
data, simulates community assembly, and performs model selection.
Author: Vicente Jimenez [aut, cre],
David Alonso [aut]
Maintainer: Vicente Jimenez <vicente.jimenez.ontiveros@gmail.com>
Diff between island versions 0.2.8 dated 2022-10-05 and 0.2.9 dated 2023-01-23
island-0.2.8/island/tests/testthat/Best_Model_Colonization_Extinction_Results.tex |only island-0.2.8/island/tests/testthat/Model_Selection_Results.tex |only island-0.2.9/island/DESCRIPTION | 8 island-0.2.9/island/MD5 | 30 island-0.2.9/island/NEWS.md | 5 island-0.2.9/island/R/da_upgma_AIC_cedp.R | 2 island-0.2.9/island/R/idaho.R | 2 island-0.2.9/island/build/partial.rdb |binary island-0.2.9/island/configure | 1847 +++++----- island-0.2.9/island/configure.ac | 4 island-0.2.9/island/inst/doc/IBDmodels.html | 4 island-0.2.9/island/inst/doc/detectability.html | 36 island-0.2.9/island/inst/doc/island.html | 4 island-0.2.9/island/man/idaho.Rd | 2 island-0.2.9/island/man/upgma_model_selection.Rd | 2 island-0.2.9/island/src/IO_AKAIKE_Model_Selection.c | 47 island-0.2.9/island/src/config.h | 8 17 files changed, 1142 insertions(+), 859 deletions(-)
More information about fwildclusterboot at CRAN
Permanent link
Title: Core Functions for Data Quality Assessment
Description: Perform data quality assessment ('DQA') of electronic health
records ('EHR'). Publication: Kapsner et al. (2021)
<doi:10.1055/s-0041-1733847>.
Author: Lorenz A. Kapsner [cre, aut] ,
Jonathan M. Mang [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen [cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@uk-erlangen.de>
Diff between DQAstats versions 0.3.1 dated 2022-06-27 and 0.3.2 dated 2023-01-23
DQAstats-0.3.1/DQAstats/man/export_affected_ids.Rd |only DQAstats-0.3.2/DQAstats/DESCRIPTION | 10 DQAstats-0.3.2/DQAstats/MD5 | 64 DQAstats-0.3.2/DQAstats/NAMESPACE | 1 DQAstats-0.3.2/DQAstats/R/DQA.R | 1048 ++++------ DQAstats-0.3.2/DQAstats/R/categorical_analysis.R | 104 DQAstats-0.3.2/DQAstats/R/completeness.R | 354 +-- DQAstats-0.3.2/DQAstats/R/conformance.R | 216 -- DQAstats-0.3.2/DQAstats/R/create_markdown.R | 438 ++-- DQAstats-0.3.2/DQAstats/R/dataloading.R | 190 + DQAstats-0.3.2/DQAstats/R/datetime_restrictions.R | 8 DQAstats-0.3.2/DQAstats/R/descriptive_results.R | 576 ++--- DQAstats-0.3.2/DQAstats/R/export_results.R | 727 ++---- DQAstats-0.3.2/DQAstats/R/format_value_conformance_results.R | 476 ++-- DQAstats-0.3.2/DQAstats/R/mdr.R | 782 +++---- DQAstats-0.3.2/DQAstats/R/plausibilities.R | 792 +++---- DQAstats-0.3.2/DQAstats/R/plausibility_results.R | 4 DQAstats-0.3.2/DQAstats/R/report.R | 574 ++--- DQAstats-0.3.2/DQAstats/R/test_csv.R | 280 +- DQAstats-0.3.2/DQAstats/R/utils.R | 434 ++-- DQAstats-0.3.2/DQAstats/R/zzz.R |only DQAstats-0.3.2/DQAstats/build/vignette.rds |binary DQAstats-0.3.2/DQAstats/inst/demo_data/utilities/RMD/DQA_report.Rmd | 416 +-- DQAstats-0.3.2/DQAstats/inst/doc/DQAstats2SHIPdataset.Rmd | 996 ++++----- DQAstats-0.3.2/DQAstats/inst/doc/DQAstats2SHIPdataset.html | 554 ++--- DQAstats-0.3.2/DQAstats/tests/testthat/_snaps/datetime_restrictions.md | 6 DQAstats-0.3.2/DQAstats/tests/testthat/test-MDR.R | 190 - DQAstats-0.3.2/DQAstats/tests/testthat/test-datetime_restrictions.R | 224 +- DQAstats-0.3.2/DQAstats/tests/testthat/test-export.R | 427 +--- DQAstats-0.3.2/DQAstats/tests/testthat/test-helper_vars.R | 292 +- DQAstats-0.3.2/DQAstats/tests/testthat/test-import.R | 210 +- DQAstats-0.3.2/DQAstats/tests/testthat/test-lints.R | 64 DQAstats-0.3.2/DQAstats/tests/testthat/test-stats.R | 108 - DQAstats-0.3.2/DQAstats/vignettes/DQAstats2SHIPdataset.Rmd | 996 ++++----- 34 files changed, 5546 insertions(+), 6015 deletions(-)
Title: Graphical User Interface for Data Quality Assessment
Description: A graphical user interface (GUI) to the functions implemented in the R package 'DQAstats'. . Publication: Mang et al. (2021)
<doi:10.1186/s12911-022-01961-z>.
Author: Lorenz A. Kapsner [cre, aut] ,
Jonathan M. Mang [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen [cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@uk-erlangen.de>
Diff between DQAgui versions 0.2.1 dated 2022-07-04 and 0.2.2 dated 2023-01-23
DESCRIPTION | 13 MD5 | 30 R/app_utils.R | 1642 +++++++++++++++++++------------------- R/custom_buttons.R | 234 ++--- R/launch_app.R | 4 R/moduleAtempPlausibility.R | 876 ++++++++++---------- R/moduleConfig.R | 4 R/moduleDashboard.R | 1352 +++++++++++++++---------------- R/moduleLog.R | 480 +++++------ R/moduleReport.R | 462 ++++------ R/zzz.R |only inst/CITATION |only inst/application/global.R | 134 +-- inst/application/server.R | 756 ++++++++--------- inst/application/ui.R | 334 +++---- tests/testthat/_snaps/shinyapp.md | 36 tests/testthat/test-shinyapp.R | 230 ++--- 17 files changed, 3247 insertions(+), 3340 deletions(-)
Title: Tools for Reading, Writing, Viewing and Manipulating CIFTI Files
Description: CIFTI files contain brain imaging data in "grayordinates," which
represent the gray matter as cortical surface vertices (left and right) and
subcortical voxels (cerebellum, basal ganglia, and other deep gray matter).
'ciftiTools' provides a unified environment for reading, writing,
visualizing and manipulating CIFTI-format data. It supports the "dscalar,"
"dlabel," and "dtseries" intents. Grayordinate data is read in as a "xifti"
object, which is structured for convenient access to the data and metadata,
and includes support for surface geometry files to enable
spatially-dependent functionality such as static or interactive
visualizations and smoothing.
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] ,
John Muschelli [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between ciftiTools versions 0.10.2 dated 2022-07-01 and 0.11.0 dated 2023-01-23
DESCRIPTION | 8 MD5 | 119 ++++---- NAMESPACE | 8 NEWS.md | 46 ++- R/add_surf.R | 44 +-- R/convert_xifti.R | 137 +++++----- R/edit_mask.R | 24 + R/is.xifti.R | 12 R/load_surf.R | 7 R/make_xifti.R | 126 ++++----- R/make_xifti_components.R | 2 R/read_cifti.R | 37 ++ R/read_cifti_separate.R | 27 - R/resample_cifti.R | 48 ++- R/resample_cifti_components.R | 72 +++-- R/resample_gifti.R | 67 ++++ R/resample_surf.R | 9 R/rox_args_docs.R | 245 +++++++++++------- R/smooth_cifti.R | 10 R/transform_xifti.R | 18 + R/utils.R | 4 R/utils_surf.R | 421 ++++++++++++++++++++++++++++++- R/utils_xifti.R | 11 R/view_xifti.R | 4 R/view_xifti_surface.R | 35 +- R/view_xifti_volume.R | 83 ++++-- R/write_cifti_from_separate.R | 16 - R/write_gifti.R | 72 ++--- R/write_xifti2.R | 47 +-- README.md | 47 ++- inst/CITATION | 9 man/add_surf.Rd | 4 man/boundary_mask_surf.Rd |only man/ciftiTools_msg.Rd | 2 man/ciftiTools_warn.Rd | 2 man/convert_xifti.Rd | 15 - man/dist_from_mask_surf.Rd |only man/edit_mask_surf.Rd | 19 + man/faces_Param.Rd |only man/load_surf.Rd | 7 man/mask_Param_vertices.Rd |only man/mask_surf.Rd |only man/mask_with_boundary_surf.Rd |only man/radial_order_surf.Rd |only man/read_cifti.Rd | 34 ++ man/read_cifti_separate.Rd | 25 + man/resamp_area_Param.Rd |only man/resamp_method_Param.Rd |only man/resample_cifti.Rd | 34 ++ man/resample_cifti_components.Rd | 29 ++ man/resample_cifti_wrapper.Rd | 3 man/resample_gifti.Rd | 18 + man/resample_surf.Rd | 4 man/rgl_interactive_plots_Description.Rd | 4 man/surface_plot_Params.Rd | 2 man/unmask_cortex.Rd | 1 man/vert_adjacency.Rd |only man/vertices_Param.Rd |only man/view_surf.Rd | 6 man/view_xifti.cbar.Rd | 2 man/view_xifti_surface.Rd | 13 man/view_xifti_volume.Rd | 25 + tests/testthat/test-misc.R | 64 +++- tests/testthat/test-plotting_sub.R | 6 tests/testthat/test-plotting_surf.R | 4 tests/testthat/test-resampling.R | 17 + 66 files changed, 1604 insertions(+), 551 deletions(-)
Title: Vector Helpers
Description: Defines new notions of prototype and size that are
used to provide tools for consistent and well-founded type-coercion
and size-recycling, and are in turn connected to ideas of type- and
size-stability useful for analysing function interfaces.
Author: Hadley Wickham [aut],
Lionel Henry [aut, cre],
Davis Vaughan [aut],
data.table team [cph] and
their contribution to R's order),
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between vctrs versions 0.5.1 dated 2022-11-16 and 0.5.2 dated 2023-01-23
DESCRIPTION | 8 MD5 | 75 +- NAMESPACE | 5 NEWS.md | 19 R/expand.R |only R/runs.R | 10 R/set.R |only build/vignette.rds |binary inst/doc/pillar.html | 426 ++++++++++++--- inst/doc/s3-vector.html | 1074 +++++++++++++++++++++++++++++++--------- inst/doc/stability.html | 551 ++++++++++++++++---- inst/doc/type-size.html | 521 +++++++++++++++---- man/vec-set.Rd |only man/vec_expand_grid.Rd |only src/bind.c | 1 src/decl/expand-decl.h |only src/decl/runs-decl.h | 86 --- src/decl/set-decl.h |only src/decl/size-decl.h | 3 src/dictionary.c | 18 src/expand.c |only src/expand.h |only src/hash.c | 16 src/init.c | 22 src/order.c | 4 src/rep.c | 2 src/rep.h |only src/rlang/dyn-array.c | 14 src/rlang/dyn-array.h | 77 +- src/rlang/stack.c | 13 src/runs.c | 517 +++++++------------ src/set.c |only src/set.h |only src/size.c | 1 src/size.h | 2 src/vctrs.h | 3 src/version.c | 2 tests/testthat/_snaps/expand.md |only tests/testthat/_snaps/hash.md | 64 +- tests/testthat/_snaps/order.md | 16 tests/testthat/_snaps/runs.md | 28 - tests/testthat/_snaps/set.md |only tests/testthat/test-expand.R |only tests/testthat/test-order.R | 54 ++ tests/testthat/test-runs.R | 40 - tests/testthat/test-set.R |only 46 files changed, 2569 insertions(+), 1103 deletions(-)
Title: Functions for the Courses Multivariate Analysis and Computer
Intensive Methods
Description: Provides utility functions for multivariate analysis (factor analysis, discriminant analysis, and others). The package is primary written for the course Multivariate analysis and for the course Computer intensive methods at the masters program of Applied Statistics at University of Ljubljana.
Author: Ziberna Ales [aut],
Cugmas Marjan [cre, aut],
Torgo Luis [cph],
Ki-Yeol Kim [cph],
Gwan-Su Yi [cph],
Liaw Andy [cph],
Leisch Friedrich [cph]
Maintainer: Cugmas Marjan <marjan.cugmas@fdv.uni-lj.si>
Diff between multiUS versions 1.1.0 dated 2022-02-16 and 1.2.3 dated 2023-01-23
multiUS-1.1.0/multiUS/man/printCorTestDf.Rd |only multiUS-1.2.3/multiUS/DESCRIPTION | 10 ++-- multiUS-1.2.3/multiUS/MD5 | 53 +++++++++++++++----------- multiUS-1.2.3/multiUS/NAMESPACE | 7 +++ multiUS-1.2.3/multiUS/R/Omega.R |only multiUS-1.2.3/multiUS/R/Theta.R |only multiUS-1.2.3/multiUS/R/breakString.R |only multiUS-1.2.3/multiUS/R/cancorPlus.R | 8 +-- multiUS-1.2.3/multiUS/R/compLoad.R | 2 multiUS-1.2.3/multiUS/R/corTestDf.R | 18 +++----- multiUS-1.2.3/multiUS/R/freqTab.R | 2 multiUS-1.2.3/multiUS/R/ldaPlus.R | 21 ++++------ multiUS-1.2.3/multiUS/R/makeFactorLabels.R | 2 multiUS-1.2.3/multiUS/R/plotCCA.R |only multiUS-1.2.3/multiUS/R/plotMeans.R | 4 - multiUS-1.2.3/multiUS/R/printCorTestDf.R | 45 +++++++++++----------- multiUS-1.2.3/multiUS/R/small2other.R |only multiUS-1.2.3/multiUS/R/toLik.R | 6 +- multiUS-1.2.3/multiUS/R/wardKF.R | 9 ++-- multiUS-1.2.3/multiUS/man/Omega.Rd |only multiUS-1.2.3/multiUS/man/Theta.Rd |only multiUS-1.2.3/multiUS/man/breakString.Rd |only multiUS-1.2.3/multiUS/man/cancorPlus.Rd | 8 +-- multiUS-1.2.3/multiUS/man/compLoad.Rd | 2 multiUS-1.2.3/multiUS/man/corTestDf.Rd | 32 +++++++++------ multiUS-1.2.3/multiUS/man/discretize.Rd | 6 +- multiUS-1.2.3/multiUS/man/freqTab.Rd | 2 multiUS-1.2.3/multiUS/man/ldaPlus.Rd | 18 ++++---- multiUS-1.2.3/multiUS/man/makeFactorLabels.Rd | 2 multiUS-1.2.3/multiUS/man/plotCCA.Rd |only multiUS-1.2.3/multiUS/man/plotMeans.Rd | 4 - multiUS-1.2.3/multiUS/man/small2other.Rd |only multiUS-1.2.3/multiUS/man/wardKF.Rd | 7 ++- 33 files changed, 146 insertions(+), 122 deletions(-)
Title: A Toolbox for Manipulating and Assessing Colors and Palettes
Description: Carries out mapping between assorted color spaces including RGB, HSV, HLS,
CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB.
Qualitative, sequential, and diverging color palettes based on HCL colors
are provided along with corresponding ggplot2 color scales.
Color palette choice is aided by an interactive app (with either a Tcl/Tk
or a shiny graphical user interface) and shiny apps with an HCL color picker and a
color vision deficiency emulator. Plotting functions for displaying
and assessing palettes include color swatches, visualizations of the
HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation
functions include: desaturation, lightening/darkening, mixing, and
simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly).
Details can be found on the project web page at <https://colorspace.R-Forge.R-project.org/>
and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical
Software, <doi:10.18637/ [...truncated...]
Author: Ross Ihaka [aut],
Paul Murrell [aut] ,
Kurt Hornik [aut] ,
Jason C. Fisher [aut] ,
Reto Stauffer [aut] ,
Claus O. Wilke [aut] ,
Claire D. McWhite [aut] ,
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between colorspace versions 2.0-3 dated 2022-02-21 and 2.1-0 dated 2023-01-23
DESCRIPTION | 11 MD5 | 34 +- NEWS.md | 41 +++ R/desaturate.R | 5 R/scale_diverging.R | 1 R/scale_divergingx.R | 1 R/scale_qualitative.R | 1 R/scale_sequential.R | 1 R/simulate_cvd.R | 167 ++++++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/colorspace.html | 378 ++++++++++++++++++++------------- inst/doc/hcl-colors.pdf |binary man/desaturate.Rd | 5 man/simulate_cvd.Rd | 60 +++-- tests/Examples/colorspace-Ex.Rout.save | 32 +- tests/cvd.R | 32 ++ tests/cvd.Rout.save | 50 +++- 18 files changed, 564 insertions(+), 255 deletions(-)
Title: Alternating Optimization
Description: Alternating optimization of (high-dimensional) functions is an
iterative procedure for optimizing jointly over all parameters by
alternately optimizing parameter subsets.
For a reference on the method, see Bezdek and Hathaway (2002)
"Some Notes on Alternating Optimization"
<doi:10.1007/3-540-45631-7_39>.
Author: Lennart Oelschlaeger [aut, cre]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between ao versions 0.2.4 dated 2022-12-04 and 0.2.5 dated 2023-01-23
DESCRIPTION | 10 +- MD5 | 32 +++--- NEWS.md | 8 + R/ao.R | 34 ++++--- R/package.R | 68 +++++++------- R/utils.R | 48 ++++----- README.md | 166 +++++++++++++++++----------------- inst/doc/ao.R | 2 inst/doc/ao.Rmd | 164 +++++++++++++++++----------------- inst/doc/ao.html | 37 +++---- man/ao.Rd | 202 +++++++++++++++++++++--------------------- man/is_number.Rd | 52 +++++----- tests/testthat.R | 8 - tests/testthat/test-ao.R | 28 ++++- tests/testthat/test-package.R | 8 - tests/testthat/test-utils.R | 12 +- vignettes/ao.Rmd | 164 +++++++++++++++++----------------- 17 files changed, 535 insertions(+), 508 deletions(-)
Title: Phylogenetic Reconstruction and Analysis
Description: Allows for estimation of phylogenetic trees and networks
using Maximum Likelihood, Maximum Parsimony, distance methods and
Hadamard conjugation (Schliep 2011). Offers methods for tree comparison,
model selection and visualization of phylogenetic networks as described in
Schliep et al. (2017).
Author: Klaus Schliep [aut, cre] ,
Emmanuel Paradis [aut] ,
Leonardo de Oliveira Martins [aut]
,
Alastair Potts [aut],
Iris Bardel-Kahr [aut] ,
Tim W. White [ctb],
Cyrill Stachniss [ctb],
Michelle Kendall [ctb],
Keren Halabi [ctb],
Richel Bilderbeek [ctb],
K [...truncated...]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between phangorn versions 2.10.0 dated 2022-09-18 and 2.11.1 dated 2023-01-23
phangorn-2.10.0/phangorn/inst/phangorn_sticker.png |only phangorn-2.10.0/phangorn/vignettes/exdna.txt |only phangorn-2.10.0/phangorn/vignettes/primates.dna |only phangorn-2.11.1/phangorn/DESCRIPTION | 36 phangorn-2.11.1/phangorn/MD5 | 156 - phangorn-2.11.1/phangorn/NAMESPACE | 7 phangorn-2.11.1/phangorn/NEWS | 25 phangorn-2.11.1/phangorn/R/Densi.R | 9 phangorn-2.11.1/phangorn/R/F3X4.R | 4 phangorn-2.11.1/phangorn/R/addConfidences.R |only phangorn-2.11.1/phangorn/R/ancestral_pml.R | 7 phangorn-2.11.1/phangorn/R/bab.R | 3 phangorn-2.11.1/phangorn/R/baseFreq.R | 2 phangorn-2.11.1/phangorn/R/bootstrap.R | 164 - phangorn-2.11.1/phangorn/R/candidate_tree.R | 4 phangorn-2.11.1/phangorn/R/codonTest.R | 15 phangorn-2.11.1/phangorn/R/draw_CI.R |only phangorn-2.11.1/phangorn/R/maxCladeCred.R |only phangorn-2.11.1/phangorn/R/modelTest.R | 133 - phangorn-2.11.1/phangorn/R/networx.R | 226 -- phangorn-2.11.1/phangorn/R/phangorn-package.R | 28 phangorn-2.11.1/phangorn/R/phyDat.R | 26 phangorn-2.11.1/phangorn/R/phylo.R | 202 + phangorn-2.11.1/phangorn/R/pmlMix.R | 60 phangorn-2.11.1/phangorn/R/pml_bb.R | 44 phangorn-2.11.1/phangorn/R/pml_control.R | 4 phangorn-2.11.1/phangorn/R/read.nexus.splits.R | 12 phangorn-2.11.1/phangorn/R/read.phyDat.R | 24 phangorn-2.11.1/phangorn/R/splits.R | 12 phangorn-2.11.1/phangorn/R/transferBootstrap.R | 2 phangorn-2.11.1/phangorn/README.md | 1 phangorn-2.11.1/phangorn/TODO | 52 phangorn-2.11.1/phangorn/build/vignette.rds |binary phangorn-2.11.1/phangorn/data/chloroplast.RData |binary phangorn-2.11.1/phangorn/data/mites.RData |only phangorn-2.11.1/phangorn/inst/doc/AdvancedFeatures.R | 29 phangorn-2.11.1/phangorn/inst/doc/AdvancedFeatures.Rmd | 101 phangorn-2.11.1/phangorn/inst/doc/AdvancedFeatures.html | 435 ++-- phangorn-2.11.1/phangorn/inst/doc/Ancestral.Rmd | 7 phangorn-2.11.1/phangorn/inst/doc/Ancestral.html | 299 ++ phangorn-2.11.1/phangorn/inst/doc/IntertwiningTreesAndNetworks.Rmd | 5 phangorn-2.11.1/phangorn/inst/doc/IntertwiningTreesAndNetworks.html | 267 ++ phangorn-2.11.1/phangorn/inst/doc/MLbyHand.R |only phangorn-2.11.1/phangorn/inst/doc/MLbyHand.Rmd |only phangorn-2.11.1/phangorn/inst/doc/MLbyHand.html |only phangorn-2.11.1/phangorn/inst/doc/Morphological.R |only phangorn-2.11.1/phangorn/inst/doc/Morphological.Rmd |only phangorn-2.11.1/phangorn/inst/doc/Morphological.html |only phangorn-2.11.1/phangorn/inst/doc/Networx.Rmd | 10 phangorn-2.11.1/phangorn/inst/doc/Networx.html | 319 ++- phangorn-2.11.1/phangorn/inst/doc/Trees.R | 158 - phangorn-2.11.1/phangorn/inst/doc/Trees.Rmd | 284 -- phangorn-2.11.1/phangorn/inst/doc/Trees.html | 1022 ++++------ phangorn-2.11.1/phangorn/inst/extdata/mites.csv |only phangorn-2.11.1/phangorn/inst/extdata/mites.nex |only phangorn-2.11.1/phangorn/inst/tinytest/test_ancestral.R | 24 phangorn-2.11.1/phangorn/inst/tinytest/test_phyDat.R | 10 phangorn-2.11.1/phangorn/inst/tinytest/test_pml.R | 14 phangorn-2.11.1/phangorn/inst/tinytest/test_pmlMix.R | 74 phangorn-2.11.1/phangorn/inst/tinytest/test_pml_generics.R |only phangorn-2.11.1/phangorn/man/addConfidences.Rd | 18 phangorn-2.11.1/phangorn/man/add_ci.Rd |only phangorn-2.11.1/phangorn/man/add_edge_length.Rd |only phangorn-2.11.1/phangorn/man/bab.Rd | 3 phangorn-2.11.1/phangorn/man/bootstrap.pml.Rd | 5 phangorn-2.11.1/phangorn/man/maxCladeCred.Rd | 7 phangorn-2.11.1/phangorn/man/mites.Rd |only phangorn-2.11.1/phangorn/man/phangorn-package.Rd | 5 phangorn-2.11.1/phangorn/man/phyDat.Rd | 13 phangorn-2.11.1/phangorn/man/plot.networx.Rd | 5 phangorn-2.11.1/phangorn/man/plotBS.Rd | 2 phangorn-2.11.1/phangorn/man/pml.Rd | 6 phangorn-2.11.1/phangorn/man/pml.control.Rd | 4 phangorn-2.11.1/phangorn/man/pml.fit.Rd | 4 phangorn-2.11.1/phangorn/man/pml_bb.Rd | 5 phangorn-2.11.1/phangorn/man/transferBootstrap.Rd | 2 phangorn-2.11.1/phangorn/src/RcppExports.cpp | 28 phangorn-2.11.1/phangorn/src/fitch64.cpp | 42 phangorn-2.11.1/phangorn/src/ml.c | 2 phangorn-2.11.1/phangorn/src/sprdist.c | 124 - phangorn-2.11.1/phangorn/vignettes/AF.RData |only phangorn-2.11.1/phangorn/vignettes/AdvancedFeatures.Rmd | 101 phangorn-2.11.1/phangorn/vignettes/Ancestral.Rmd | 7 phangorn-2.11.1/phangorn/vignettes/IntertwiningTreesAndNetworks.Rmd | 5 phangorn-2.11.1/phangorn/vignettes/MLbyHand.Rmd |only phangorn-2.11.1/phangorn/vignettes/Morphological.Rmd |only phangorn-2.11.1/phangorn/vignettes/Networx.Rmd | 10 phangorn-2.11.1/phangorn/vignettes/Trees.RData |binary phangorn-2.11.1/phangorn/vignettes/Trees.Rmd | 284 -- phangorn-2.11.1/phangorn/vignettes/phangorn.bib | 152 + 90 files changed, 2950 insertions(+), 2200 deletions(-)
Title: Cross-Platform File System Operations Based on 'libuv'
Description: A cross-platform interface to file system operations, built
on top of the 'libuv' C library.
Author: Jim Hester [aut],
Hadley Wickham [aut],
Gabor Csardi [aut, cre],
libuv project contributors [cph] ,
Joyent, Inc. and other Node contributors [cph] ,
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between fs versions 1.5.2 dated 2021-12-08 and 1.6.0 dated 2023-01-23
fs-1.5.2/fs/src/libuv-1.38.1 |only fs-1.5.2/fs/tests/testthat/ref-tree-1 |only fs-1.5.2/fs/tests/testthat/ref-tree-2 |only fs-1.5.2/fs/tests/testthat/ref-tree-3 |only fs-1.6.0/fs/DESCRIPTION | 43 + fs-1.6.0/fs/MD5 | 544 ++++++++++++++++--------- fs-1.6.0/fs/NEWS.md | 6 fs-1.6.0/fs/R/fs-package.R | 14 fs-1.6.0/fs/R/path.R | 6 fs-1.6.0/fs/R/utils.R | 9 fs-1.6.0/fs/README.md | 148 +++--- fs-1.6.0/fs/build/vignette.rds |binary fs-1.6.0/fs/cleanup |only fs-1.6.0/fs/inst/WORDLIST | 27 - fs-1.6.0/fs/inst/doc/function-comparisons.html | 95 ++-- fs-1.6.0/fs/man/fs-package.Rd | 10 fs-1.6.0/fs/src/Makevars | 2 fs-1.6.0/fs/src/Makevars.win | 2 fs-1.6.0/fs/src/file.cc | 12 fs-1.6.0/fs/src/init.cc | 2 fs-1.6.0/fs/src/libuv-1.44.2 |only fs-1.6.0/fs/tests/testthat/_snaps |only fs-1.6.0/fs/tests/testthat/helper.R | 4 fs-1.6.0/fs/tests/testthat/test-access.R | 1 fs-1.6.0/fs/tests/testthat/test-copy.R | 28 - fs-1.6.0/fs/tests/testthat/test-create.R | 11 fs-1.6.0/fs/tests/testthat/test-delete.R | 17 fs-1.6.0/fs/tests/testthat/test-file.R | 98 ++-- fs-1.6.0/fs/tests/testthat/test-file_exists.R | 1 fs-1.6.0/fs/tests/testthat/test-fs_bytes.R | 1 fs-1.6.0/fs/tests/testthat/test-fs_path.R | 15 fs-1.6.0/fs/tests/testthat/test-fs_perms.R | 5 fs-1.6.0/fs/tests/testthat/test-id.R | 9 fs-1.6.0/fs/tests/testthat/test-is.R | 1 fs-1.6.0/fs/tests/testthat/test-link.R | 1 fs-1.6.0/fs/tests/testthat/test-list.R | 82 ++- fs-1.6.0/fs/tests/testthat/test-path.R | 543 ++++++++++++++++-------- fs-1.6.0/fs/tests/testthat/test-path_package.R | 11 fs-1.6.0/fs/tests/testthat/test-sanitize.R | 1 fs-1.6.0/fs/tests/testthat/test-temp.R | 7 fs-1.6.0/fs/tests/testthat/test-tree.R | 10 fs-1.6.0/fs/tests/testthat/test-utils.R | 1 42 files changed, 1105 insertions(+), 662 deletions(-)
Title: Utilities for 'DIZ' R Package Development
Description: Utility functions used for the R package development
infrastructure inside the data integration centers ('DIZ') to
standardize and facilitate repetitive tasks such as setting up a
database connection or issuing notification messages and to avoid
redundancy.
Author: Jonathan M. Mang [aut, cre] ,
Lorenz A. Kapsner [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between DIZutils versions 0.1.1 dated 2022-06-27 and 0.1.2 dated 2023-01-23
DESCRIPTION | 10 - MD5 | 12 +- R/db_connection.R | 14 ++ R/get_config_env.R | 187 ++++++++++++++++++++--------------- README.md | 4 man/get_config_env.Rd | 4 man/get_default_config_elements.Rd |only tests/testthat/test-get_config_env.R |only 8 files changed, 139 insertions(+), 92 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-08 2.9.1
2022-09-14 2.8.0
2022-05-10 2.7.3
2021-12-16 2.3.7
2021-06-18 2.2.3
2021-06-11 2.2.1
2020-11-05 1.1.0
2020-05-17 1.0.0
2020-03-22 0.9.0
2019-05-29 0.8.2
2019-03-22 0.7.4
2019-03-19 0.7.3
2016-11-10 0.2.2
2016-11-09 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-25 0.1-2
2020-11-18 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-08 0.3.9
Title: A Framework for Data-Driven Stochastic Disease Spread
Simulations
Description: Provides an efficient and very flexible framework to
conduct data-driven epidemiological modeling in realistic large
scale disease spread simulations. The framework integrates
infection dynamics in subpopulations as continuous-time Markov
chains using the Gillespie stochastic simulation algorithm and
incorporates available data such as births, deaths and movements
as scheduled events at predefined time-points. Using C code for
the numerical solvers and 'OpenMP' (if available) to divide work
over multiple processors ensures high performance when simulating
a sample outcome. One of our design goals was to make the package
extendable and enable usage of the numerical solvers from other R
extension packages in order to facilitate complex epidemiological
research. The package contains template models and can be extended
with user-defined models. For more details see the paper by
Widgren, Bauer, Eriksson and Engblom (2019)
<doi:10.18637/jss.v091.i12>. The package also provides
function [...truncated...]
Author: Stefan Widgren [aut, cre] ,
Robin Eriksson [aut] ,
Stefan Engblom [aut] ,
Pavol Bauer [aut] ,
Thomas Rosendal [ctb] ,
Ivana Rodriguez Ewerloef [ctb] ,
Attractive Chaos [cph]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between SimInf versions 9.4.0 dated 2023-01-06 and 9.5.0 dated 2023-01-23
DESCRIPTION | 6 - MD5 | 52 ++++++------ NEWS.md | 6 + build/partial.rdb |binary build/vignette.rds |binary configure | 32 +++---- configure.ac | 9 -- inst/doc/SimInf.pdf |binary src/SimInf.c | 9 +- src/init.c | 3 src/misc/SimInf_abc.c | 10 +- src/misc/SimInf_arg.c | 28 +++++- src/misc/SimInf_distance_matrix.c | 3 src/misc/SimInf_forward_euler_linear_decay.c | 18 +++- src/misc/SimInf_ldata.c | 8 + src/misc/SimInf_local_spread.c | 5 - src/misc/SimInf_particle_filter.c | 11 +- src/models/SEIR.c | 19 +++- src/models/SIR.c | 16 ++- src/models/SIS.c | 14 ++- src/models/SISe.c | 16 ++- src/models/SISe3.c | 28 ++++-- src/models/SISe3_sp.c | 28 ++++-- src/models/SISe_sp.c | 16 ++- src/solvers/SimInf_solver.c | 112 ++++++++++++++++++--------- src/solvers/aem/SimInf_solver_aem.c | 31 +++++-- src/solvers/ssm/SimInf_solver_ssm.c | 7 + 27 files changed, 316 insertions(+), 171 deletions(-)
Title: Implementation of the 'PROCESS' Macro
Description: Perform moderation, mediation, moderated mediation and moderated moderation.
Inspired from famous 'PROCESS' macro for 'SPSS' and 'SAS' created by Andrew Hayes.
Author: Keon-Woong Moon [aut, cre],
Sokyoung Hong [ctb]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>
Diff between processR versions 0.2.6 dated 2021-01-07 and 0.2.7 dated 2023-01-23
DESCRIPTION | 10 - MD5 | 98 +++++++------- NEWS.md | 11 + R/catMediation.R | 2 R/conceptDiagram.R | 2 R/condPlot.R | 4 R/condPlot2.R | 4 R/condPlotCat2.R | 4 R/conditionalEffectPlot.R | 2 R/densityPlot.R | 2 R/drawCatModel.R | 6 R/drawConcept.R | 2 R/drawModel.R | 10 - R/meanSummary.R | 14 +- R/modSummary.R | 2 R/modSummary2.R | 2 R/modmedSummary.R | 4 R/r2diff.R | 2 R/statisticalDiagram.R | 42 +++--- R/teachers.R | 2 R/tripleInteraction.R | 2 build/vignette.rds |binary inst/doc/processR.html | 290 +++++++++++++++++++------------------------ man/adjustypos.Rd | 2 man/condPlot.Rd | 2 man/condPlot2.Rd | 2 man/condPlotCat2.Rd | 2 man/conditionalEffectPlot.Rd | 2 man/deleteSingleNumber.Rd | 4 man/drawCatModel.Rd | 6 man/drawConcept.Rd | 2 man/drawModel.Rd | 4 man/eq2df.Rd | 2 man/fit2table.Rd | 4 man/getMeanSd.Rd | 4 man/getYhat1.Rd | 2 man/jnPlot.Rd | 2 man/makeLabel.Rd | 2 man/meanSummary.Rd | 4 man/meanSummaryTable.Rd | 2 man/modSummary.Rd | 2 man/modSummary2.Rd | 2 man/modmedSummary.Rd | 2 man/modmedSummary2Table.Rd | 2 man/myarrow.Rd | 2 man/print.meanSummary.Rd | 2 man/productEq.Rd | 2 man/r2diff.Rd | 2 man/statisticalDiagram.Rd | 6 man/teachers.Rd | 2 50 files changed, 283 insertions(+), 306 deletions(-)
Title: Metabolomics Data Analysis Functions
Description: A collection of functions for processing and analyzing metabolite data.
The namesake function mrbin() converts 1D
or 2D Nuclear Magnetic Resonance data into a matrix of values suitable for further data analysis and
performs basic processing steps in a reproducible way. Negative values, a
common issue in such data, can be replaced by positive values (<doi:10.1021/acs.jproteome.0c00684>). All used
parameters are stored in a readable text file and can be restored from that
file to enable exact reproduction of the data at a later time. The function fia() ranks features according
to their impact on classifier models, especially artificial neural network models.
Author: Matthias Klein [aut, cre]
Maintainer: Matthias Klein <matthias.s.klein@gmx.net>
Diff between mrbin versions 1.7.1 dated 2022-11-07 and 1.7.2 dated 2023-01-23
DESCRIPTION | 6 MD5 | 18 +- NEWS.md | 9 + R/mrbin.R | 437 +++++++++++++++++++++++++++++++++++++--------------- inst/doc/mrbin.R | 4 inst/doc/mrbin.Rnw | 6 inst/doc/mrbin.pdf |binary man/contPlus.Rd | 2 man/plotNMR.Rd | 5 vignettes/mrbin.Rnw | 6 10 files changed, 352 insertions(+), 141 deletions(-)
Title: Lookup for IP Address Information
Description: Enables the user to find the country, region, city, coordinates, zip code, time zone, ISP, domain name, connection type, area code, weather station code, weather station name, mobile, usage type, address type and IAB category that any IP address or hostname originates from. Supported IPv4 and IPv6.
Please visit <https://www.ip2location.com> to learn more. You may also want to visit <https://lite.ip2location.com> for free database download.
This package requires 'IP2Location Python' module. At the terminal, please run 'pip install IP2Location' to install the module.
Author: IP2Location
Maintainer: IP2Location <support@ip2location.com>
Diff between ip2location versions 8.0.1 dated 2021-06-03 and 8.1.1 dated 2023-01-23
DESCRIPTION | 11 ++++++----- MD5 | 15 +++++++++------ NAMESPACE | 5 +++++ R/IP2Location.R | 6 +++--- R/IP2Location_plotmap.R |only README.md | 9 ++++++++- inst |only man/get_all.Rd | 2 +- man/open.Rd | 4 ++-- man/plot_map.Rd |only 10 files changed, 34 insertions(+), 18 deletions(-)
Title: Adaptive Multivariate Integration over Hypercubes
Description: R wrappers around the cubature C library of Steven
G. Johnson for adaptive multivariate integration over hypercubes
and the Cuba C library of Thomas Hahn for deterministic and
Monte Carlo integration. Scalar and vector interfaces for
cubature and Cuba routines are provided; the vector interfaces
are highly recommended as demonstrated in the package
vignette.
Author: Balasubramanian Narasimhan [aut, cre],
Manuel Koller [ctb],
Steven G. Johnson [aut],
Thomas Hahn [aut],
Annie Bouvier [aut],
Kien Kieu [aut],
Simen Gaure [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.stanford.edu>
Diff between cubature versions 2.0.4.5 dated 2022-08-16 and 2.0.4.6 dated 2023-01-23
DESCRIPTION | 10 MD5 | 42 - NEWS.md | 9 R/cuhre.R | 2 README.md | 5 build/vignette.rds |binary inst/doc/cubature.html | 1066 +++++++++++++++---------------- inst/doc/version2.html | 144 +--- inst/include/cuba.h | 4 man/cuhre.Rd | 2 src/Cuba-4.2-nonwin/cuba.h | 4 src/Cuba-4.2-nonwin/src/common/Fork.c | 23 src/Cuba-4.2-nonwin/src/common/stddecl.h | 8 src/Cuba-4.2-win/cuba.h | 4 src/Cuba-4.2-win/src/common/Fork.c | 17 src/Cuba-4.2/config.log | 228 +++--- src/Cuba-4.2/config.status | 22 src/Cuba-4.2/cuba.h | 4 src/Cuba-4.2/makefile | 4 src/Makevars | 14 src/Makevars.win | 7 src/Rcpp-cubature.cpp | 2 22 files changed, 794 insertions(+), 827 deletions(-)
Title: Access, Retrieve, and Work with Canadian Census Data and
Geography
Description: Integrated, convenient, and uniform access to Canadian
Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready
tidy data frames and spatial data in multiple formats, as well as convenience functions
for working with Census variables, variable hierarchies, and region selection. API
keys are freely available with free registration at <https://censusmapper.ca/api>.
Census data and boundary geometries are reproduced and distributed on an "as
is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006;
2011; 2016; 2021).
Author: Jens von Bergmann [aut] ,
Dmitry Shkolnik [aut, cre] ,
Aaron Jacobs [aut]
Maintainer: Dmitry Shkolnik <shkolnikd@gmail.com>
Diff between cancensus versions 0.5.4 dated 2022-11-07 and 0.5.5 dated 2023-01-23
DESCRIPTION | 8 MD5 | 61 NAMESPACE | 6 NEWS.md | 20 R/geo_suite.R |only R/geographies.R |only R/helpers.R | 6 R/local_server_setup.R |only R/sysdata.rda |only R/wds.R |only README.md | 10 build/vignette.rds |binary inst/doc/Dwellings_by_document_type_cross_tabulation.R | 86 inst/doc/Dwellings_by_document_type_cross_tabulation.html | 133 inst/doc/Making_maps_with_cancensus.R | 68 inst/doc/Making_maps_with_cancensus.html | 5024 +++++++++++++- inst/doc/Taxfiler_Data.R | 100 inst/doc/Taxfiler_Data.html | 155 inst/doc/cancensus.R | 76 inst/doc/cancensus.html | 229 inst/doc/data_discovery.R | 2 inst/doc/data_discovery.Rmd | 12 inst/doc/data_discovery.html | 1445 +++- inst/doc/intersecting_geometries.R | 130 inst/doc/intersecting_geometries.html | 114 inst/doc/statcan_attribute_files.R |only inst/doc/statcan_attribute_files.Rmd |only inst/doc/statcan_attribute_files.html |only inst/doc/statcan_wds.R |only inst/doc/statcan_wds.Rmd |only inst/doc/statcan_wds.html |only man/CODES_TABLE.Rd | 2 man/get_statcan_geo_suite.Rd |only man/get_statcan_geographic_attributes.Rd |only man/get_statcan_geographies.Rd |only man/get_statcan_geography_relationships.Rd |only man/get_statcan_wds_data.Rd |only man/get_statcan_wds_metadata.Rd |only vignettes/data_discovery.Rmd | 12 vignettes/statcan_attribute_files.Rmd |only vignettes/statcan_wds.Rmd |only 41 files changed, 7032 insertions(+), 667 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-16 1.1.0
2019-01-09 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-28 2.0.0
2018-06-15 1.4.2
2018-06-05 1.4.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-18 1.6.0
2022-03-08 1.4.0
2021-03-16 1.2.0
2020-09-28 1.0.1
2020-07-22 1.0.0
2020-05-04 0.5.0
2020-03-19 0.3.0
2019-12-12 0.2.0
2019-07-23 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-31 1.5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-04 1.9.90
2015-11-22 1.9.89
2014-12-22 1.9.73
2014-04-29 1.9.5
2014-01-22 1.7.6
2013-12-04 1.6.1
2013-10-01 1.5.5
2013-09-11 1.5.3
2013-05-22 1.5.0
2013-04-01 1.4.6
2013-03-05 1.4.4
2013-01-26 1.4.2
2013-01-04 1.3.6
2012-11-08 1.3.2
2012-10-05 1.2.3
2012-09-12 1.2.2
2012-08-14 1.0
Title: Functions for Kriging and Point Pattern Analysis
Description: Functions for kriging and point pattern analysis.
Author: Brian Ripley [aut, cre, cph],
Roger Bivand [ctb],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between spatial versions 7.3-15.1 dated 2022-05-30 and 7.3-16 dated 2023-01-23
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: World Map Data from Natural Earth
Description: Facilitates mapping by making natural earth map data from <https://www.naturalearthdata.com/> more easily available to R users.
Author: Philippe Massicotte [aut, cre]
,
Andy South [aut],
Koen Hufkens [ctb]
Maintainer: Philippe Massicotte <pmassicotte@hotmail.com>
Diff between rnaturalearth versions 0.1.0 dated 2017-03-21 and 0.3.2 dated 2023-01-23
rnaturalearth-0.1.0/rnaturalearth/R/check_data_exist.r |only rnaturalearth-0.1.0/rnaturalearth/R/check_scale.r |only rnaturalearth-0.1.0/rnaturalearth/R/datasets.r |only rnaturalearth-0.1.0/rnaturalearth/R/get_data.r |only rnaturalearth-0.1.0/rnaturalearth/R/install-rnaturalearthdata.r |only rnaturalearth-0.1.0/rnaturalearth/R/install-rnaturalearthhires.r |only rnaturalearth-0.1.0/rnaturalearth/R/ne_as_sf.r |only rnaturalearth-0.1.0/rnaturalearth/R/ne_coastline.r |only rnaturalearth-0.1.0/rnaturalearth/R/ne_countries.r |only rnaturalearth-0.1.0/rnaturalearth/R/ne_download.r |only rnaturalearth-0.1.0/rnaturalearth/R/ne_file_name.r |only rnaturalearth-0.1.0/rnaturalearth/R/ne_load.r |only rnaturalearth-0.1.0/rnaturalearth/R/ne_states.r |only rnaturalearth-0.1.0/rnaturalearth/R/rnaturalearth-package.r |only rnaturalearth-0.1.0/rnaturalearth/man/ne_as_sf.Rd |only rnaturalearth-0.3.2/rnaturalearth/DESCRIPTION | 55 rnaturalearth-0.3.2/rnaturalearth/LICENSE | 2 rnaturalearth-0.3.2/rnaturalearth/MD5 | 123 - rnaturalearth-0.3.2/rnaturalearth/NAMESPACE | 3 rnaturalearth-0.3.2/rnaturalearth/NEWS.md | 29 rnaturalearth-0.3.2/rnaturalearth/R/check_data_exist.R |only rnaturalearth-0.3.2/rnaturalearth/R/check_scale.R |only rnaturalearth-0.3.2/rnaturalearth/R/datasets.R |only rnaturalearth-0.3.2/rnaturalearth/R/find_data.R |only rnaturalearth-0.3.2/rnaturalearth/R/get_data.R |only rnaturalearth-0.3.2/rnaturalearth/R/install-rnaturalearthdata.R |only rnaturalearth-0.3.2/rnaturalearth/R/install-rnaturalearthhires.R |only rnaturalearth-0.3.2/rnaturalearth/R/ne_as_sp.R |only rnaturalearth-0.3.2/rnaturalearth/R/ne_coastline.R |only rnaturalearth-0.3.2/rnaturalearth/R/ne_countries.R |only rnaturalearth-0.3.2/rnaturalearth/R/ne_download.R |only rnaturalearth-0.3.2/rnaturalearth/R/ne_file_name.R |only rnaturalearth-0.3.2/rnaturalearth/R/ne_load.R |only rnaturalearth-0.3.2/rnaturalearth/R/ne_states.R |only rnaturalearth-0.3.2/rnaturalearth/R/rnaturalearth-package.R |only rnaturalearth-0.3.2/rnaturalearth/README.md | 364 +-- rnaturalearth-0.3.2/rnaturalearth/build/vignette.rds |binary rnaturalearth-0.3.2/rnaturalearth/data/countries110.rda |binary rnaturalearth-0.3.2/rnaturalearth/data/df_layers_cultural.rda |only rnaturalearth-0.3.2/rnaturalearth/data/df_layers_physical.rda |only rnaturalearth-0.3.2/rnaturalearth/inst/doc/language-support.R |only rnaturalearth-0.3.2/rnaturalearth/inst/doc/language-support.Rmd |only rnaturalearth-0.3.2/rnaturalearth/inst/doc/language-support.html |only rnaturalearth-0.3.2/rnaturalearth/inst/doc/rnaturalearth.R | 119 - rnaturalearth-0.3.2/rnaturalearth/inst/doc/rnaturalearth.Rmd | 226 +- rnaturalearth-0.3.2/rnaturalearth/inst/doc/rnaturalearth.html | 1088 ++++++++-- rnaturalearth-0.3.2/rnaturalearth/inst/doc/what-is-a-country.R | 110 - rnaturalearth-0.3.2/rnaturalearth/inst/doc/what-is-a-country.Rmd | 200 - rnaturalearth-0.3.2/rnaturalearth/inst/doc/what-is-a-country.html | 620 ++++- rnaturalearth-0.3.2/rnaturalearth/inst/extdata/data_list_cultural.csv | 36 rnaturalearth-0.3.2/rnaturalearth/inst/extdata/data_list_physical.csv | 3 rnaturalearth-0.3.2/rnaturalearth/man/check_data_exist.Rd | 77 rnaturalearth-0.3.2/rnaturalearth/man/check_rnaturalearthdata.Rd | 24 rnaturalearth-0.3.2/rnaturalearth/man/check_rnaturalearthhires.Rd | 24 rnaturalearth-0.3.2/rnaturalearth/man/check_scale.Rd | 41 rnaturalearth-0.3.2/rnaturalearth/man/countries.Rd | 14 rnaturalearth-0.3.2/rnaturalearth/man/df_layers_cultural.Rd |only rnaturalearth-0.3.2/rnaturalearth/man/df_layers_physical.Rd |only rnaturalearth-0.3.2/rnaturalearth/man/get_data.Rd | 44 rnaturalearth-0.3.2/rnaturalearth/man/install_rnaturalearthdata.Rd | 22 rnaturalearth-0.3.2/rnaturalearth/man/install_rnaturalearthhires.Rd | 22 rnaturalearth-0.3.2/rnaturalearth/man/ne_as_sp.Rd |only rnaturalearth-0.3.2/rnaturalearth/man/ne_coastline.Rd | 59 rnaturalearth-0.3.2/rnaturalearth/man/ne_countries.Rd | 121 - rnaturalearth-0.3.2/rnaturalearth/man/ne_download.Rd | 204 - rnaturalearth-0.3.2/rnaturalearth/man/ne_file_name.Rd | 32 rnaturalearth-0.3.2/rnaturalearth/man/ne_find_vector_data.Rd |only rnaturalearth-0.3.2/rnaturalearth/man/ne_git_contents.Rd |only rnaturalearth-0.3.2/rnaturalearth/man/ne_git_layer_names.Rd |only rnaturalearth-0.3.2/rnaturalearth/man/ne_load.Rd | 127 - rnaturalearth-0.3.2/rnaturalearth/man/ne_states.Rd | 27 rnaturalearth-0.3.2/rnaturalearth/man/rnaturalearth.Rd | 28 rnaturalearth-0.3.2/rnaturalearth/tests/testthat.R | 8 rnaturalearth-0.3.2/rnaturalearth/tests/testthat/test-ne_countries.r | 107 rnaturalearth-0.3.2/rnaturalearth/tests/testthat/test-ne_file_name.r | 89 rnaturalearth-0.3.2/rnaturalearth/tests/testthat/test-ne_states.r | 121 - rnaturalearth-0.3.2/rnaturalearth/tools/README-unnamed-chunk-2-1.png |binary rnaturalearth-0.3.2/rnaturalearth/tools/README-unnamed-chunk-2-1.svg |only rnaturalearth-0.3.2/rnaturalearth/tools/README-unnamed-chunk-2-2.png |binary rnaturalearth-0.3.2/rnaturalearth/tools/README-unnamed-chunk-2-2.svg |only rnaturalearth-0.3.2/rnaturalearth/tools/README-unnamed-chunk-2-3.png |binary rnaturalearth-0.3.2/rnaturalearth/tools/README-unnamed-chunk-2-3.svg |only rnaturalearth-0.3.2/rnaturalearth/vignettes/language-support.Rmd |only rnaturalearth-0.3.2/rnaturalearth/vignettes/rnaturalearth.Rmd | 226 +- rnaturalearth-0.3.2/rnaturalearth/vignettes/what-is-a-country.Rmd | 200 - 85 files changed, 2909 insertions(+), 1686 deletions(-)
Title: Discrete Bayesian Additive Regression Trees Sampler
Description: Fits Bayesian additive regression trees (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/Metropolis-Hastings sampler. Also serves as a drop-in replacement for package 'BayesTree'.
Author: Vincent Dorie [aut, cre] ,
Hugh Chipman [aut],
Robert McCulloch [aut],
Armon Dadgar [ctb] ,
R Core Team [ctb] ,
Guido U Draheim [ctb] ,
Maarten Bosmans [ctb] ,
Christophe Tournayre [ctb] ,
Michael Petch [ctb] ,
Rafael de Lucena Valle [ctb] ,
Steven G [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between dbarts versions 0.9-22 dated 2022-03-29 and 0.9-23 dated 2023-01-23
dbarts-0.9-22/dbarts/src/external/linearAlgebra.c |only dbarts-0.9-22/dbarts/src/include/external/linearAlgebra.h |only dbarts-0.9-23/dbarts/DESCRIPTION | 8 dbarts-0.9-23/dbarts/MD5 | 156 +- dbarts-0.9-23/dbarts/R/A_class.R | 46 dbarts-0.9-23/dbarts/R/bart.R | 23 dbarts-0.9-23/dbarts/R/data.R | 23 dbarts-0.9-23/dbarts/R/dbarts.R | 4 dbarts-0.9-23/dbarts/R/generics.R | 60 dbarts-0.9-23/dbarts/R/partialDependence.R | 12 dbarts-0.9-23/dbarts/R/rbart.R | 295 ++-- dbarts-0.9-23/dbarts/R/xbart.R | 8 dbarts-0.9-23/dbarts/build/vignette.rds |binary dbarts-0.9-23/dbarts/configure | 161 +- dbarts-0.9-23/dbarts/configure.ac | 3 dbarts-0.9-23/dbarts/inst/NEWS.Rd | 30 dbarts-0.9-23/dbarts/inst/doc/gibbs_sampler_mixture_model.pdf |binary dbarts-0.9-23/dbarts/inst/doc/working_with_saved_trees.pdf |binary dbarts-0.9-23/dbarts/inst/include/dbarts/scratch.hpp | 7 dbarts-0.9-23/dbarts/inst/include/dbarts/state.hpp | 8 dbarts-0.9-23/dbarts/man/bart.Rd | 15 dbarts-0.9-23/dbarts/man/dbarts.Rd | 2 dbarts-0.9-23/dbarts/man/dbartsControl.Rd | 2 dbarts-0.9-23/dbarts/man/pdbart.Rd | 2 dbarts-0.9-23/dbarts/man/rbart.Rd | 17 dbarts-0.9-23/dbarts/man/xbart.Rd | 10 dbarts-0.9-23/dbarts/src/Makevars.in | 12 dbarts-0.9-23/dbarts/src/Makevars.win | 2 dbarts-0.9-23/dbarts/src/R_interface.cpp | 2 dbarts-0.9-23/dbarts/src/R_interface_common.cpp | 15 dbarts-0.9-23/dbarts/src/R_interface_crossvalidate.cpp | 141 +- dbarts-0.9-23/dbarts/src/R_interface_sampler.cpp | 14 dbarts-0.9-23/dbarts/src/config.hpp.in | 19 dbarts-0.9-23/dbarts/src/config.hpp.win | 4 dbarts-0.9-23/dbarts/src/crossvalidate.cpp | 134 +- dbarts-0.9-23/dbarts/src/crossvalidate.hpp | 4 dbarts-0.9-23/dbarts/src/dbarts/bartFit.cpp | 300 +++- dbarts-0.9-23/dbarts/src/dbarts/binaryIO.cpp | 8 dbarts-0.9-23/dbarts/src/dbarts/binaryIO.hpp | 4 dbarts-0.9-23/dbarts/src/dbarts/birthDeathRule.cpp | 31 dbarts-0.9-23/dbarts/src/dbarts/changeRule.cpp | 6 dbarts-0.9-23/dbarts/src/dbarts/config.hpp.in | 2 dbarts-0.9-23/dbarts/src/dbarts/node.cpp | 29 dbarts-0.9-23/dbarts/src/dbarts/node.hpp | 4 dbarts-0.9-23/dbarts/src/dbarts/parameterPrior.cpp | 3 dbarts-0.9-23/dbarts/src/dbarts/state.cpp | 52 dbarts-0.9-23/dbarts/src/dbarts/swapRule.cpp | 4 dbarts-0.9-23/dbarts/src/dbarts/tree.hpp | 6 dbarts-0.9-23/dbarts/src/external/Makefile | 8 dbarts-0.9-23/dbarts/src/external/config.h.in | 6 dbarts-0.9-23/dbarts/src/external/config.h.win | 4 dbarts-0.9-23/dbarts/src/external/random.c | 21 dbarts-0.9-23/dbarts/src/external/randomBase.c | 37 dbarts-0.9-23/dbarts/src/include/external/random.h | 7 dbarts-0.9-23/dbarts/src/include/misc/adaptiveRadixTree.h | 2 dbarts-0.9-23/dbarts/src/include/misc/intrinsic.h | 37 dbarts-0.9-23/dbarts/src/include/misc/linearAlgebra.h | 24 dbarts-0.9-23/dbarts/src/include/misc/memalign.h | 8 dbarts-0.9-23/dbarts/src/include/misc/simd.h | 18 dbarts-0.9-23/dbarts/src/misc/Makefile | 26 dbarts-0.9-23/dbarts/src/misc/adaptiveRadixTree.c | 10 dbarts-0.9-23/dbarts/src/misc/config.h.in | 11 dbarts-0.9-23/dbarts/src/misc/config.h.win | 12 dbarts-0.9-23/dbarts/src/misc/linearAlgebra.c | 266 ++-- dbarts-0.9-23/dbarts/src/misc/linearAlgebra_avx.c | 636 +++++++++- dbarts-0.9-23/dbarts/src/misc/linearAlgebra_neon.c |only dbarts-0.9-23/dbarts/src/misc/linearAlgebra_sse2.c | 562 ++++++++ dbarts-0.9-23/dbarts/src/misc/moments.c | 4 dbarts-0.9-23/dbarts/src/misc/partition.c | 4 dbarts-0.9-23/dbarts/src/misc/partition_avx2.c | 4 dbarts-0.9-23/dbarts/src/misc/partition_body.c | 72 + dbarts-0.9-23/dbarts/src/misc/partition_neon.c |only dbarts-0.9-23/dbarts/src/misc/partition_sse2.c | 4 dbarts-0.9-23/dbarts/src/misc/partition_sse4_1.c | 4 dbarts-0.9-23/dbarts/src/misc/simd.c | 170 ++ dbarts-0.9-23/dbarts/tests/testthat/test-01-dbartsDataArgs.R | 32 dbarts-0.9-23/dbarts/tests/testthat/test-08-xbart.R | 19 dbarts-0.9-23/dbarts/tests/testthat/test-14-rbart.R | 75 - dbarts-0.9-23/dbarts/tests/testthat/test-15-simd.R | 130 +- dbarts-0.9-23/dbarts/tests/testthat/test-18-extractedTrees.R | 2 dbarts-0.9-23/dbarts/tools/m4/ax_compiler_ext.m4 | 147 +- 81 files changed, 3077 insertions(+), 973 deletions(-)
Title: Functions for Classification
Description: Various functions for classification, including k-nearest
neighbour, Learning Vector Quantization and Self-Organizing Maps.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between class versions 7.3-20.1 dated 2022-05-30 and 7.3-21 dated 2023-01-23
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] ,
Albrecht Gebhardt [trl] ,
David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between MASS versions 7.3-58.1 dated 2022-07-27 and 7.3-58.2 dated 2023-01-23
ChangeLog | 5 +++++ DESCRIPTION | 8 +++++--- MD5 |only NAMESPACE | 2 +- build/partial.rdb |binary man/bacteria.Rd | 2 +- man/fractions.Rd | 9 ++++++++- man/gamma.shape.glm.Rd | 4 +++- man/lm.ridge.Rd | 9 +++++++-- man/stdres.Rd | 3 +-- 10 files changed, 31 insertions(+), 11 deletions(-)