Title: A GUI for Planar Location Problems
Description: A GUI for the orloca package is provided as a Rcmdr plug-in. The package deals with continuos planar location problems.
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between RcmdrPlugin.orloca versions 4.7 dated 2018-11-05 and 4.8.2 dated 2021-05-12
RcmdrPlugin.orloca-4.7/RcmdrPlugin.orloca/inst/po |only RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/ChangeLog | 7 RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/DESCRIPTION | 19 RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/MD5 | 31 RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/build/vignette.rds |binary RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/inst/doc/localizacionplanaRcmdr.R | 22 RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/inst/doc/localizacionplanaRcmdr.Rmd | 9 RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/inst/doc/localizacionplanaRcmdr.html | 454 ++++++++-- RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/inst/doc/planarlocationRcmdr.R | 22 RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/inst/doc/planarlocationRcmdr.Rmd | 7 RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/inst/doc/planarlocationRcmdr.html | 446 ++++++++- RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/man/RcmdrPlugin.orloca-package.Rd | 12 RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/man/RcmdrPlugin.orloca.es-package.Rd | 14 RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/po/R-RcmdrPlugin.orloca-es.mo |binary RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/po/R-RcmdrPlugin.orloca-es.po | 24 RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/vignettes/localizacionplanaRcmdr.Rmd | 9 RcmdrPlugin.orloca-4.8.2/RcmdrPlugin.orloca/vignettes/planarlocationRcmdr.Rmd | 7 17 files changed, 826 insertions(+), 257 deletions(-)
More information about RcmdrPlugin.orloca at CRAN
Permanent link
Title: Enhancements for 'broom' and 'easystats' Package Families
Description: Provides helper functions that assist in data
analysis workflows involving regression analyses. The goal is to
combine the functionality offered by different set of packages
('broom', 'broom.mixed', 'parameters', and 'performance') through a
common syntax to return tidy dataframes containing model parameters
and performance measure summaries. The 'grouped_' variants of the
generics provides a convenient way to execute functions across a
combination of grouping variable(s) in a dataframe.
Author: Indrajeet Patil [aut, cre, cph]
(<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between broomExtra versions 4.2.1 dated 2021-02-21 and 4.2.3 dated 2021-05-12
broomExtra-4.2.1/broomExtra/build |only broomExtra-4.2.1/broomExtra/man/figures/lifecycle-archived.svg |only broomExtra-4.2.1/broomExtra/man/figures/lifecycle-defunct.svg |only broomExtra-4.2.1/broomExtra/man/figures/lifecycle-deprecated.svg |only broomExtra-4.2.1/broomExtra/man/figures/lifecycle-experimental.svg |only broomExtra-4.2.1/broomExtra/man/figures/lifecycle-maturing.svg |only broomExtra-4.2.1/broomExtra/man/figures/lifecycle-questioning.svg |only broomExtra-4.2.1/broomExtra/man/figures/lifecycle-stable.svg |only broomExtra-4.2.1/broomExtra/man/figures/lifecycle-superseded.svg |only broomExtra-4.2.3/broomExtra/DESCRIPTION | 11 broomExtra-4.2.3/broomExtra/LICENSE | 1348 ++++---- broomExtra-4.2.3/broomExtra/MD5 | 61 broomExtra-4.2.3/broomExtra/NAMESPACE | 88 broomExtra-4.2.3/broomExtra/NEWS.md | 239 - broomExtra-4.2.3/broomExtra/R/generics.R | 224 - broomExtra-4.2.3/broomExtra/R/global_vars.R | 14 broomExtra-4.2.3/broomExtra/R/grouped_generics.R | 307 - broomExtra-4.2.3/broomExtra/R/hybrid_easystats.R | 255 - broomExtra-4.2.3/broomExtra/R/reexports.R | 59 broomExtra-4.2.3/broomExtra/README.md | 1662 ++++------ broomExtra-4.2.3/broomExtra/inst/WORDLIST | 61 broomExtra-4.2.3/broomExtra/man/augment.Rd | 9 broomExtra-4.2.3/broomExtra/man/glance.Rd | 9 broomExtra-4.2.3/broomExtra/man/glance_performance.Rd | 64 broomExtra-4.2.3/broomExtra/man/grouped_augment.Rd | 7 broomExtra-4.2.3/broomExtra/man/grouped_glance.Rd | 7 broomExtra-4.2.3/broomExtra/man/grouped_tidy.Rd | 7 broomExtra-4.2.3/broomExtra/man/reexports.Rd | 52 broomExtra-4.2.3/broomExtra/man/tidy.Rd | 9 broomExtra-4.2.3/broomExtra/man/tidy_parameters.Rd | 76 broomExtra-4.2.3/broomExtra/tests/spelling.R | 12 broomExtra-4.2.3/broomExtra/tests/testthat.R | 8 broomExtra-4.2.3/broomExtra/tests/testthat/_snaps |only broomExtra-4.2.3/broomExtra/tests/testthat/test-generics.R | 140 broomExtra-4.2.3/broomExtra/tests/testthat/test-grouped_generics.R | 204 - broomExtra-4.2.3/broomExtra/tests/testthat/test-hybrid_generics.R | 164 36 files changed, 2513 insertions(+), 2584 deletions(-)
Title: Multivariate Generalized Kernel Smoothing and Related
Statistical Methods
Description: Probability mass functions (PMFs), probability density functions (PDFs), cumulative distribution functions (CDFs) and quantile functions, mainly via (optionally bounded/truncated) kernel smoothing. In the continuous case, there's support for univariate, multivariate and conditional distributions, including distributions that are both multivariate and conditional. Refer to the book "Kernel Smoothing" by Wand and Jones (1995), whose methods are generalized by the methods here. Also, supports categorical distributions, mixed conditional distributions (with mixed input types) and smooth empirical-like distributions, some of which, can be used for statistical classification. There are extensions for computing distance matrices (between distributions), multivariate probabilities, multivariate random numbers, moment-based statistics and mode estimates.
Author: Abby Spurdle
Maintainer: Abby Spurdle <spurdle.a@gmail.com>
Diff between probhat versions 0.4.0 dated 2021-04-02 and 0.4.1 dated 2021-05-12
probhat-0.4.0/probhat/man/80_mockup_function_objects.Rd |only probhat-0.4.1/probhat/DESCRIPTION | 10 probhat-0.4.1/probhat/MD5 | 86 +-- probhat-0.4.1/probhat/NAMESPACE | 3 probhat-0.4.1/probhat/R/init.r | 2 probhat-0.4.1/probhat/R/intd.r | 2 probhat-0.4.1/probhat/R/kernel.r | 4 probhat-0.4.1/probhat/R/ph.r | 31 - probhat-0.4.1/probhat/R/ph2.r | 2 probhat-0.4.1/probhat/R/ph_categorical.r | 2 probhat-0.4.1/probhat/R/ph_cks_constructors.r | 36 - probhat-0.4.1/probhat/R/ph_cks_eval1.r | 111 +--- probhat-0.4.1/probhat/R/ph_cks_eval2.r | 56 +- probhat-0.4.1/probhat/R/ph_cks_init.r | 255 +++++------ probhat-0.4.1/probhat/R/ph_dks_eval.r | 2 probhat-0.4.1/probhat/R/ph_dks_init.r | 2 probhat-0.4.1/probhat/R/ph_empirical.r | 2 probhat-0.4.1/probhat/R/ph_mix.r | 14 probhat-0.4.1/probhat/R/pk_distribution_set.r | 28 - probhat-0.4.1/probhat/R/plots_cpd.r | 9 probhat-0.4.1/probhat/R/plots_dpd.r | 2 probhat-0.4.1/probhat/R/plots_mv.r | 2 probhat-0.4.1/probhat/R/plots_other.r | 31 - probhat-0.4.1/probhat/R/x_kubik_ext.r | 4 probhat-0.4.1/probhat/R/x_math1.r | 2 probhat-0.4.1/probhat/R/x_math2.r | 2 probhat-0.4.1/probhat/R/x_probmv.r | 68 ++ probhat-0.4.1/probhat/R/x_stats.r | 4 probhat-0.4.1/probhat/R/y_dataprep.r | 4 probhat-0.4.1/probhat/inst/doc/probhat.R | 216 +++++---- probhat-0.4.1/probhat/inst/doc/probhat.Rnw | 134 ++++- probhat-0.4.1/probhat/inst/doc/probhat.pdf |binary probhat-0.4.1/probhat/inst/doc/probhatx_kernels.pdf |binary probhat-0.4.1/probhat/man/11_names_methods.Rd | 4 probhat-0.4.1/probhat/man/20_discrete_kernel_smoothing.Rd | 4 probhat-0.4.1/probhat/man/21_continuous_kernel_smoothing.Rd | 32 - probhat-0.4.1/probhat/man/22_categorical_distributions.Rd | 2 probhat-0.4.1/probhat/man/23_mixed_conditional.Rd | 30 - probhat-0.4.1/probhat/man/24_empirical-like_distributions.Rd | 2 probhat-0.4.1/probhat/man/31_distribution_sets.Rd | 54 +- probhat-0.4.1/probhat/man/44_other_plot_methods.Rd | 4 probhat-0.4.1/probhat/man/60_distance_matrices.Rd | 47 +- probhat-0.4.1/probhat/man/80_runtime_function_objects.Rd |only probhat-0.4.1/probhat/man/91_other_functions.Rd | 10 probhat-0.4.1/probhat/vignettes/probhat.Rnw | 134 ++++- 45 files changed, 848 insertions(+), 601 deletions(-)
Title: Multi-Trait Dissimilarity with more Uniform Contributions
Description: R function gawdis() produces multi-trait dissimilarity with more uniform contributions of different traits. de Bello et al. (2021) <doi:10.1111/2041-210X.13537> presented the approach based on minimizing the differences in the correlation between the dissimilarity of each trait, or groups of traits, and the multi-trait dissimilarity. This is done using either an analytic or a numerical solution, both available in the function.
Author: Francesco de Bello [aut],
Zoltan Botta-Dukat [aut],
Jan Leps [aut],
Pavel Fibich [aut, cre]
Maintainer: Pavel Fibich <pavel.fibich@prf.jcu.cz>
Diff between gawdis versions 0.1.2 dated 2020-12-17 and 0.1.3 dated 2021-05-12
DESCRIPTION | 6 MD5 | 12 - R/gawdis.R | 4 README.md | 2 build/vignette.rds |binary inst/CITATION | 2 inst/doc/gawdis.html | 565 ++++++++++++++++----------------------------------- 7 files changed, 199 insertions(+), 392 deletions(-)
Title: Running Commands Remotely on 'Gridengine' Clusters
Description: Run lapply() calls in parallel by submitting them to
'gridengine' clusters using the 'qsub' command.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between qsub versions 1.1.1 dated 2021-01-29 and 1.1.2 dated 2021-05-12
DESCRIPTION | 7 +++---- MD5 | 10 +++++----- NAMESPACE | 1 - NEWS.md | 8 ++++++++ R/qsub_config.R | 19 +++++++++++++++++-- tests/testthat/test-config_file_location.R | 7 ++++++- 6 files changed, 39 insertions(+), 13 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] (<https://orcid.org/0000-0003-3925-190X>),
Barret Schloerke [aut] (<https://orcid.org/0000-0001-9986-114X>),
Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>),
Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>),
RStudio [cph, fnd],
Sass Open Source Foundation [ctb, cph] (LibSass library),
Greter Marcel [ctb, cph] (LibSass library),
Mifsud Michael [ctb, cph] (LibSass library),
Hampton Catlin [ctb, cph] (LibSass library),
Natalie Weizenbaum [ctb, cph] (LibSass library),
Chris Eppstein [ctb, cph] (LibSass library),
Adams Joseph [ctb, cph] (json.cpp),
Trifunovic Nemanja [ctb, cph] (utf8.h)
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between sass versions 0.3.1 dated 2021-01-24 and 0.4.0 dated 2021-05-12
DESCRIPTION | 15 MD5 | 88 +- NAMESPACE | 14 NEWS.md | 22 R/as_sass.R | 87 +- R/fonts.R |only R/format.R | 13 R/layers.R | 116 ++- R/options.R | 128 ++- R/sass.R | 46 - R/sass_cache.R | 74 - R/utils.R | 20 inst/doc/sass.R | 49 - inst/doc/sass.Rmd | 133 ++- inst/doc/sass.html | 915 ++++++++++-------------- man/as_sass.Rd | 24 man/font_face.Rd |only man/output_template.Rd | 13 man/sass.Rd | 17 man/sass_cache_context_dir.Rd | 17 man/sass_cache_get.Rd | 46 - man/sass_import.Rd | 5 man/sass_layer.Rd | 56 - man/sass_options.Rd | 46 - man/sass_partial.Rd | 5 tests/testthat/_snaps |only tests/testthat/test-assets/test-layer-file.scss |only tests/testthat/test-cache.R | 30 tests/testthat/test-compile.R | 2 tests/testthat/test-extend.R | 2 tests/testthat/test-font-objects.R |only tests/testthat/test-html-dependencies.R | 20 tests/testthat/test-import.R | 2 tests/testthat/test-include-paths.R | 2 tests/testthat/test-layers-list.R | 9 tests/testthat/test-layers.R | 47 - tests/testthat/test-mixins.R | 2 tests/testthat/test-nesting.R | 2 tests/testthat/test-option-errors.R | 47 + tests/testthat/test-options.R | 2 tests/testthat/test-output.R | 2 tests/testthat/test-unicode.R | 2 tests/testthat/test-utils.R | 33 tests/testthat/test-variables.R | 2 vignettes/hello-pacifico.png |only vignettes/sass.Rmd | 133 ++- 46 files changed, 1326 insertions(+), 962 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from 'RevMan 5';
- prediction interval, Hartung-Knapp method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression;
- generalised linear mixed models;
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.18-0 dated 2021-03-05 and 4.18-1 dated 2021-05-12
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 34 ++++++++++++++++++++++++++++++++++ R/calcH.R | 4 ++-- R/forest.R | 20 ++++++++++++++++---- R/linregcore.R | 28 +++++++++++++++++++--------- R/metabias.R | 18 ++++++++++-------- R/metabind.R | 3 ++- R/metagen.R | 2 +- man/forest.meta.Rd | 8 ++++++++ man/metabias.Rd | 3 ++- 11 files changed, 108 insertions(+), 40 deletions(-)
Title: Easily Create Presentation-Ready Display Tables
Description: Build display tables from tabular data with an easy-to-use set of
functions. With its progressive approach, we can construct display tables
with a cohesive set of table parts. Table values can be formatted using any
of the included formatting functions. Footnotes and cell styles can be
precisely added through a location targeting system. The way in which 'gt'
handles things for you means that you don't often have to worry about the
fine details.
Author: Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>),
Joe Cheng [aut],
Barret Schloerke [aut] (<https://orcid.org/0000-0001-9986-114X>),
RStudio [cph, fnd]
Maintainer: Richard Iannone <rich@rstudio.com>
Diff between gt versions 0.2.2 dated 2020-08-05 and 0.3.0 dated 2021-05-12
gt-0.2.2/gt/R/dt_stub_others.R |only gt-0.2.2/gt/README.md |only gt-0.2.2/gt/man/cells_data.Rd |only gt-0.2.2/gt/man/figures/rstudio-cloud-example.png |only gt-0.2.2/gt/tests/testthat/test-resolver_core.R |only gt-0.3.0/gt/DESCRIPTION | 26 gt-0.3.0/gt/LICENSE | 2 gt-0.3.0/gt/MD5 | 520 +-- gt-0.3.0/gt/NAMESPACE | 12 gt-0.3.0/gt/NEWS.md | 69 gt-0.3.0/gt/R/build_data.R | 51 gt-0.3.0/gt/R/data_color.R | 12 gt-0.3.0/gt/R/datasets.R | 9 gt-0.3.0/gt/R/dt_body.R | 2 gt-0.3.0/gt/R/dt_boxhead.R | 55 gt-0.3.0/gt/R/dt_cols_merge.R | 2 gt-0.3.0/gt/R/dt_groups_rows.R | 49 gt-0.3.0/gt/R/dt_heading.R | 5 gt-0.3.0/gt/R/dt_options.R | 6 gt-0.3.0/gt/R/dt_row_groups.R | 4 gt-0.3.0/gt/R/dt_spanners.R | 41 gt-0.3.0/gt/R/dt_stub_df.R | 56 gt-0.3.0/gt/R/dt_stubhead.R | 2 gt-0.3.0/gt/R/dt_summary.R | 77 gt-0.3.0/gt/R/dt_transforms.R | 13 gt-0.3.0/gt/R/export.R | 114 gt-0.3.0/gt/R/format_data.R | 654 ++-- gt-0.3.0/gt/R/gt-package.R | 1 gt-0.3.0/gt/R/gt.R | 68 gt-0.3.0/gt/R/gt_preview.R | 11 gt-0.3.0/gt/R/helpers.R | 1258 ++++++--- gt-0.3.0/gt/R/image.R | 6 gt-0.3.0/gt/R/info_tables.R | 142 - gt-0.3.0/gt/R/knitr-utils.R |only gt-0.3.0/gt/R/location_methods.R | 98 gt-0.3.0/gt/R/modify_columns.R | 574 +++- gt-0.3.0/gt/R/modify_rows.R | 73 gt-0.3.0/gt/R/opts.R | 46 gt-0.3.0/gt/R/print.R | 33 gt-0.3.0/gt/R/reexports.R | 4 gt-0.3.0/gt/R/render_as_html.R | 29 gt-0.3.0/gt/R/resolver.R | 396 +- gt-0.3.0/gt/R/summary_rows.R | 31 gt-0.3.0/gt/R/sysdata.rda |binary gt-0.3.0/gt/R/tab_create_modify.R | 529 ++- gt-0.3.0/gt/R/text_transform.R | 38 gt-0.3.0/gt/R/utils.R | 326 ++ gt-0.3.0/gt/R/utils_formatters.R | 134 gt-0.3.0/gt/R/utils_render_common.R | 228 + gt-0.3.0/gt/R/utils_render_footnotes.R | 229 - gt-0.3.0/gt/R/utils_render_html.R | 489 ++- gt-0.3.0/gt/R/utils_render_latex.R | 89 gt-0.3.0/gt/R/utils_render_rtf.R | 1789 ++++++++++--- gt-0.3.0/gt/R/zzz.R | 11 gt-0.3.0/gt/inst/css/gt_styles_default.scss | 1 gt-0.3.0/gt/man/adjust_luminance.Rd | 12 gt-0.3.0/gt/man/as_rtf.Rd | 8 gt-0.3.0/gt/man/cell_borders.Rd | 10 gt-0.3.0/gt/man/cell_fill.Rd | 12 gt-0.3.0/gt/man/cell_text.Rd | 12 gt-0.3.0/gt/man/cells_body.Rd | 63 gt-0.3.0/gt/man/cells_column_labels.Rd | 65 gt-0.3.0/gt/man/cells_column_spanners.Rd | 67 gt-0.3.0/gt/man/cells_footnotes.Rd |only gt-0.3.0/gt/man/cells_grand_summary.Rd | 67 gt-0.3.0/gt/man/cells_group.Rd | 1 gt-0.3.0/gt/man/cells_row_groups.Rd | 65 gt-0.3.0/gt/man/cells_source_notes.Rd |only gt-0.3.0/gt/man/cells_stub.Rd | 71 gt-0.3.0/gt/man/cells_stub_grand_summary.Rd |only gt-0.3.0/gt/man/cells_stub_summary.Rd |only gt-0.3.0/gt/man/cells_stubhead.Rd | 59 gt-0.3.0/gt/man/cells_summary.Rd | 79 gt-0.3.0/gt/man/cells_title.Rd | 62 gt-0.3.0/gt/man/cols_align.Rd | 12 gt-0.3.0/gt/man/cols_hide.Rd | 25 gt-0.3.0/gt/man/cols_label.Rd | 2 gt-0.3.0/gt/man/cols_merge.Rd | 23 gt-0.3.0/gt/man/cols_merge_n_pct.Rd |only gt-0.3.0/gt/man/cols_merge_range.Rd | 17 gt-0.3.0/gt/man/cols_merge_uncert.Rd | 18 gt-0.3.0/gt/man/cols_move.Rd | 6 gt-0.3.0/gt/man/cols_move_to_end.Rd | 6 gt-0.3.0/gt/man/cols_move_to_start.Rd | 6 gt-0.3.0/gt/man/cols_unhide.Rd |only gt-0.3.0/gt/man/cols_width.Rd | 8 gt-0.3.0/gt/man/currency.Rd | 8 gt-0.3.0/gt/man/data_color.Rd | 5 gt-0.3.0/gt/man/default_fonts.Rd | 8 gt-0.3.0/gt/man/escape_latex.Rd | 6 gt-0.3.0/gt/man/extract_summary.Rd | 8 gt-0.3.0/gt/man/figures/man_adjust_luminance_1.png |binary gt-0.3.0/gt/man/figures/man_cell_borders_1.png |binary gt-0.3.0/gt/man/figures/man_cell_text_1.png |binary gt-0.3.0/gt/man/figures/man_cells_body_1.png |binary gt-0.3.0/gt/man/figures/man_cells_column_spanners_1.png |binary gt-0.3.0/gt/man/figures/man_cells_footnotes_1.png |only gt-0.3.0/gt/man/figures/man_cells_grand_summary_1.png |binary gt-0.3.0/gt/man/figures/man_cells_row_groups_1.png |binary gt-0.3.0/gt/man/figures/man_cells_source_notes_1.png |only gt-0.3.0/gt/man/figures/man_cells_stub_grand_summary_1.png |only gt-0.3.0/gt/man/figures/man_cells_stub_summary_1.png |only gt-0.3.0/gt/man/figures/man_cells_stubhead_1.png |binary gt-0.3.0/gt/man/figures/man_cells_summary_1.png |binary gt-0.3.0/gt/man/figures/man_cells_title_1.png |binary gt-0.3.0/gt/man/figures/man_cols_align_1.png |binary gt-0.3.0/gt/man/figures/man_cols_hide_1.png |binary gt-0.3.0/gt/man/figures/man_cols_hide_2.png |binary gt-0.3.0/gt/man/figures/man_cols_label_1.png |binary gt-0.3.0/gt/man/figures/man_cols_label_2.png |binary gt-0.3.0/gt/man/figures/man_cols_merge_1.png |binary gt-0.3.0/gt/man/figures/man_cols_merge_n_pct_1.png |only gt-0.3.0/gt/man/figures/man_cols_merge_range_1.png |binary gt-0.3.0/gt/man/figures/man_cols_merge_uncert_1.png |binary gt-0.3.0/gt/man/figures/man_cols_move_1.png |binary gt-0.3.0/gt/man/figures/man_cols_move_to_end_1.png |binary gt-0.3.0/gt/man/figures/man_cols_move_to_end_2.png |binary gt-0.3.0/gt/man/figures/man_cols_move_to_start_1.png |binary gt-0.3.0/gt/man/figures/man_cols_move_to_start_2.png |binary gt-0.3.0/gt/man/figures/man_cols_unhide_1.png 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gt-0.3.0/gt/man/grand_summary_rows.Rd | 4 gt-0.3.0/gt/man/gt-options.Rd | 1 gt-0.3.0/gt/man/gt-package.Rd | 2 gt-0.3.0/gt/man/gt.Rd | 6 gt-0.3.0/gt/man/gt_latex_dependencies.Rd | 6 gt-0.3.0/gt/man/gtsave.Rd | 5 gt-0.3.0/gt/man/html.Rd | 4 gt-0.3.0/gt/man/local_image.Rd | 2 gt-0.3.0/gt/man/md.Rd | 4 gt-0.3.0/gt/man/opt_align_table_header.Rd | 4 gt-0.3.0/gt/man/opt_all_caps.Rd | 7 gt-0.3.0/gt/man/opt_css.Rd | 4 gt-0.3.0/gt/man/opt_footnote_marks.Rd | 1 gt-0.3.0/gt/man/opt_row_striping.Rd | 4 gt-0.3.0/gt/man/opt_table_font.Rd | 3 gt-0.3.0/gt/man/opt_table_lines.Rd | 4 gt-0.3.0/gt/man/opt_table_outline.Rd | 4 gt-0.3.0/gt/man/pct.Rd | 6 gt-0.3.0/gt/man/print.rtf_text.Rd |only gt-0.3.0/gt/man/px.Rd | 6 gt-0.3.0/gt/man/random_id.Rd | 6 gt-0.3.0/gt/man/reexports.Rd | 3 gt-0.3.0/gt/man/row_group_order.Rd | 24 gt-0.3.0/gt/man/summary_rows.Rd | 4 gt-0.3.0/gt/man/tab_footnote.Rd | 35 gt-0.3.0/gt/man/tab_options.Rd | 27 gt-0.3.0/gt/man/tab_row_group.Rd | 43 gt-0.3.0/gt/man/tab_spanner.Rd | 17 gt-0.3.0/gt/man/tab_spanner_delim.Rd | 20 gt-0.3.0/gt/man/tab_style.Rd | 24 gt-0.3.0/gt/man/text_transform.Rd | 8 gt-0.3.0/gt/man/web_image.Rd | 2 gt-0.3.0/gt/tests/testthat/_snaps |only gt-0.3.0/gt/tests/testthat/helper-gt_attr_expectations.R | 13 gt-0.3.0/gt/tests/testthat/test-cols_align.R | 10 gt-0.3.0/gt/tests/testthat/test-cols_merge.R | 140 - gt-0.3.0/gt/tests/testthat/test-cols_move.R | 18 gt-0.3.0/gt/tests/testthat/test-cols_width.R | 604 +++- gt-0.3.0/gt/tests/testthat/test-cols_width_rtf.R |only gt-0.3.0/gt/tests/testthat/test-conditional_fmt.R | 37 gt-0.3.0/gt/tests/testthat/test-data_color.R | 66 gt-0.3.0/gt/tests/testthat/test-fmt_bytes.R |only gt-0.3.0/gt/tests/testthat/test-fmt_markdown.R | 2 gt-0.3.0/gt/tests/testthat/test-fmt_missing.R | 8 gt-0.3.0/gt/tests/testthat/test-fmt_number.R | 442 +-- gt-0.3.0/gt/tests/testthat/test-fmt_percent.R | 224 + gt-0.3.0/gt/tests/testthat/test-gt_object.R | 179 + gt-0.3.0/gt/tests/testthat/test-gtsave.R | 334 ++ gt-0.3.0/gt/tests/testthat/test-h_md_html.R | 12 gt-0.3.0/gt/tests/testthat/test-image.R | 2 gt-0.3.0/gt/tests/testthat/test-info_tables.R | 2 gt-0.3.0/gt/tests/testthat/test-input_data_validation.R | 58 gt-0.3.0/gt/tests/testthat/test-l_cols_align.R | 6 gt-0.3.0/gt/tests/testthat/test-l_cols_merge.R | 48 gt-0.3.0/gt/tests/testthat/test-l_cols_move.R | 8 gt-0.3.0/gt/tests/testthat/test-l_conditional_fmt.R | 36 gt-0.3.0/gt/tests/testthat/test-l_fmt_markdown.R | 2 gt-0.3.0/gt/tests/testthat/test-l_fmt_missing.R | 8 gt-0.3.0/gt/tests/testthat/test-l_fmt_number.R | 206 - gt-0.3.0/gt/tests/testthat/test-l_fmt_percent.R | 166 - gt-0.3.0/gt/tests/testthat/test-l_row_group_order.R | 16 gt-0.3.0/gt/tests/testthat/test-l_tab_spanner_delim.R | 31 gt-0.3.0/gt/tests/testthat/test-l_table_parts.R | 180 + gt-0.3.0/gt/tests/testthat/test-location_cells.R | 275 + gt-0.3.0/gt/tests/testthat/test-r_table_parts.R |only gt-0.3.0/gt/tests/testthat/test-resolver.R |only gt-0.3.0/gt/tests/testthat/test-row_group_order.R | 23 gt-0.3.0/gt/tests/testthat/test-rtf_column_widths.R |only gt-0.3.0/gt/tests/testthat/test-rtf_page_numbering.R |only gt-0.3.0/gt/tests/testthat/test-summary_rows.R | 187 + gt-0.3.0/gt/tests/testthat/test-summary_rows_rtf.R |only gt-0.3.0/gt/tests/testthat/test-tab_footnote.R | 67 gt-0.3.0/gt/tests/testthat/test-tab_options.R | 4 gt-0.3.0/gt/tests/testthat/test-tab_spanner_delim.R | 377 ++ gt-0.3.0/gt/tests/testthat/test-tab_style.R | 64 gt-0.3.0/gt/tests/testthat/test-table_parts.R | 502 +++ gt-0.3.0/gt/tests/testthat/test-text_transform.R | 162 + gt-0.3.0/gt/tests/testthat/test-util_functions.R | 32 gt-0.3.0/gt/tests/testthat/test-utils.R |only gt-0.3.0/gt/tests/testthat/test-utils_render_html.R |only 277 files changed, 10370 insertions(+), 4164 deletions(-)
Title: Make 'ggplot2' Graphics Interactive
Description: Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Author: David Gohel [aut, cre],
Panagiotis Skintzos [aut],
Mike Bostock [cph] (d3.js),
Speros Kokenes [cph] (d3-lasso),
Eric Shull [cph] (saveSvgAsPng js library),
Eric Book [ctb] (hline and vline geoms)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between ggiraph versions 0.7.8 dated 2020-07-01 and 0.7.9 dated 2021-05-12
ggiraph-0.7.8/ggiraph/inst/htmlwidgets/lib/d3-5.7.0 |only ggiraph-0.7.8/ggiraph/inst/htmlwidgets/lib/d3-lasso-0.0.5/lasso.js |only ggiraph-0.7.8/ggiraph/inst/htmlwidgets/lib/ggiraphjs-0.3.0 |only ggiraph-0.7.9/ggiraph/DESCRIPTION | 47 +- ggiraph-0.7.9/ggiraph/MD5 | 97 ++-- ggiraph-0.7.9/ggiraph/NAMESPACE | 16 ggiraph-0.7.9/ggiraph/NEWS | 23 + ggiraph-0.7.9/ggiraph/R/dsvg.R | 36 + ggiraph-0.7.9/ggiraph/R/element_interactive.R | 19 ggiraph-0.7.9/ggiraph/R/fonts.R | 84 +++ ggiraph-0.7.9/ggiraph/R/geom_dotplot_interactive.R |only ggiraph-0.7.9/ggiraph/R/geom_label_interactive.R | 3 ggiraph-0.7.9/ggiraph/R/girafe.R | 2 ggiraph-0.7.9/ggiraph/R/girafe_options.R | 45 + ggiraph-0.7.9/ggiraph/R/interactive_circle_grob.R |only ggiraph-0.7.9/ggiraph/R/interactive_rect_grob.R | 7 ggiraph-0.7.9/ggiraph/R/interactive_roundrect_grob.R | 5 ggiraph-0.7.9/ggiraph/R/ipar.R | 23 - ggiraph-0.7.9/ggiraph/R/labeller_interactive.R |only ggiraph-0.7.9/ggiraph/R/svg.R | 2 ggiraph-0.7.9/ggiraph/R/utils.R | 25 - ggiraph-0.7.9/ggiraph/README.md | 55 +- ggiraph-0.7.9/ggiraph/build/vignette.rds |binary ggiraph-0.7.9/ggiraph/cleanup |only ggiraph-0.7.9/ggiraph/configure |only ggiraph-0.7.9/ggiraph/configure.win |only ggiraph-0.7.9/ggiraph/inst/doc/overview.Rmd | 4 ggiraph-0.7.9/ggiraph/inst/doc/overview.html | 227 ---------- ggiraph-0.7.9/ggiraph/inst/examples/rmd/xaringan |only ggiraph-0.7.9/ggiraph/inst/examples/shiny/maps/server.R | 2 ggiraph-0.7.9/ggiraph/inst/htmlwidgets/girafe.js | 113 ---- ggiraph-0.7.9/ggiraph/inst/htmlwidgets/girafe.yaml | 19 ggiraph-0.7.9/ggiraph/inst/htmlwidgets/lib/d3-bundle-5.16.0 |only ggiraph-0.7.9/ggiraph/inst/htmlwidgets/lib/ggiraphjs-0.4.1 |only ggiraph-0.7.9/ggiraph/inst/htmlwidgets/lib/save-svg-as-png-1.4.17 |only ggiraph-0.7.9/ggiraph/man/dsvg.Rd | 26 - ggiraph-0.7.9/ggiraph/man/font_family_exists.Rd |only ggiraph-0.7.9/ggiraph/man/geom_dotplot_interactive.Rd |only ggiraph-0.7.9/ggiraph/man/ggiraph-ggproto.Rd | 20 ggiraph-0.7.9/ggiraph/man/girafe.Rd | 2 ggiraph-0.7.9/ggiraph/man/id_label.Rd |only ggiraph-0.7.9/ggiraph/man/interactive_circle_grob.Rd |only ggiraph-0.7.9/ggiraph/man/ipar.Rd | 20 ggiraph-0.7.9/ggiraph/man/label_interactive.Rd | 22 ggiraph-0.7.9/ggiraph/man/labeller_interactive.Rd |only ggiraph-0.7.9/ggiraph/man/match_family.Rd |only ggiraph-0.7.9/ggiraph/man/opts_hover.Rd | 8 ggiraph-0.7.9/ggiraph/man/opts_selection.Rd | 8 ggiraph-0.7.9/ggiraph/man/opts_sizing.Rd | 4 ggiraph-0.7.9/ggiraph/man/opts_tooltip.Rd | 15 ggiraph-0.7.9/ggiraph/man/validated_fonts.Rd |only ggiraph-0.7.9/ggiraph/src/Makevars.in |only ggiraph-0.7.9/ggiraph/src/Makevars.win |only ggiraph-0.7.9/ggiraph/src/dsvg.cpp | 79 +-- ggiraph-0.7.9/ggiraph/src/fonts.cpp | 56 -- ggiraph-0.7.9/ggiraph/src/fonts.h | 9 ggiraph-0.7.9/ggiraph/src/raster.cpp |only ggiraph-0.7.9/ggiraph/src/raster.h |only ggiraph-0.7.9/ggiraph/tests/testthat/test-svg-text.R | 3 ggiraph-0.7.9/ggiraph/tools |only ggiraph-0.7.9/ggiraph/vignettes/overview.Rmd | 4 61 files changed, 549 insertions(+), 581 deletions(-)
Title: Run 'roxygen2' on (Chunks of) Single Code Files
Description: Have you ever been tempted to create 'roxygen2'-style documentation
comments for one of your functions that was not part of one of your
packages (yet)?
This is exactly what this package is about: running 'roxygen2' on
(chunks of) a single code file.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between document versions 3.3.1 dated 2021-03-31 and 3.3.2 dated 2021-05-12
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 ++++- build/vignette.rds |binary inst/files/minimal.html | 10 ++++++---- inst/runit_tests/expected_files.r | 3 ++- tests/testthat/test_basic.R | 15 +++++++++------ 7 files changed, 30 insertions(+), 21 deletions(-)
Title: Dive Analysis and Calibration
Description: Utilities to represent, visualize, filter, analyse, and summarize
time-depth recorder (TDR) data. Miscellaneous functions for
handling location data are also provided.
Author: Sebastian P. Luque <spluque@gmail.com>
Maintainer: Sebastian P. Luque <spluque@gmail.com>
Diff between diveMove versions 1.5.4 dated 2021-04-20 and 1.6.0 dated 2021-05-12
diveMove-1.5.4/diveMove/man/bout-methods.Rd |only diveMove-1.5.4/diveMove/man/bout-misc.Rd |only diveMove-1.5.4/diveMove/man/bouts2MLE.Rd |only diveMove-1.5.4/diveMove/man/bouts2NLS.Rd |only diveMove-1.5.4/diveMove/man/bouts3NLS.Rd |only diveMove-1.5.4/diveMove/man/extractDive-methods.Rd |only diveMove-1.5.4/diveMove/man/plotDiveModel-methods.Rd |only diveMove-1.5.4/diveMove/man/plotTDR-methods.Rd |only diveMove-1.5.4/diveMove/man/plotZOC-methods.Rd |only diveMove-1.5.4/diveMove/man/readTDR.Rd |only diveMove-1.5.4/diveMove/man/runquantile-internal.Rd |only diveMove-1.5.4/diveMove/man/timeBudget-methods.Rd |only diveMove-1.6.0/diveMove/DESCRIPTION | 17 diveMove-1.6.0/diveMove/MD5 | 104 + diveMove-1.6.0/diveMove/NAMESPACE | 41 diveMove-1.6.0/diveMove/NEWS | 13 diveMove-1.6.0/diveMove/R/AllClass.R | 211 +++ diveMove-1.6.0/diveMove/R/AllGenerics.R | 45 diveMove-1.6.0/diveMove/R/AllMethod.R | 1063 ++++++++++++++++++- diveMove-1.6.0/diveMove/R/austFilter.R | 194 ++- diveMove-1.6.0/diveMove/R/bouts.R | 701 +----------- diveMove-1.6.0/diveMove/R/bouts_helpers.R |only diveMove-1.6.0/diveMove/R/calibrate.R | 409 ++++++- diveMove-1.6.0/diveMove/R/detDive.R | 48 diveMove-1.6.0/diveMove/R/detPhase.R | 61 - diveMove-1.6.0/diveMove/R/distSpeed.R | 50 diveMove-1.6.0/diveMove/R/diveMove-defunct.R |only diveMove-1.6.0/diveMove/R/diveMove-deprecated.R |only diveMove-1.6.0/diveMove/R/diveStats.R | 114 +- diveMove-1.6.0/diveMove/R/oneDiveStats.R | 4 diveMove-1.6.0/diveMove/R/readLocs.R | 64 - diveMove-1.6.0/diveMove/R/readTDR.R | 1 diveMove-1.6.0/diveMove/R/runquantile.R | 182 +++ diveMove-1.6.0/diveMove/R/stampDive.R | 7 diveMove-1.6.0/diveMove/build/vignette.rds |binary diveMove-1.6.0/diveMove/inst/doc/diveMove.html | 4 diveMove-1.6.0/diveMove/man/Bouts-class.Rd |only diveMove-1.6.0/diveMove/man/TDR-class.Rd | 112 -- diveMove-1.6.0/diveMove/man/TDRcalibrate-class.Rd | 197 +-- diveMove-1.6.0/diveMove/man/austFilter.Rd | 234 ++-- diveMove-1.6.0/diveMove/man/boutfreqs.Rd |only diveMove-1.6.0/diveMove/man/boutinit.Rd |only diveMove-1.6.0/diveMove/man/bouts-internal.Rd |only diveMove-1.6.0/diveMove/man/boutsBEC.Rd |only diveMove-1.6.0/diveMove/man/boutsCDF.Rd |only diveMove-1.6.0/diveMove/man/boutsMLEll.Rd |only diveMove-1.6.0/diveMove/man/boutsNLSll.Rd |only diveMove-1.6.0/diveMove/man/calibrateDepth.Rd | 597 +++++----- diveMove-1.6.0/diveMove/man/calibrateSpeed.Rd | 124 +- diveMove-1.6.0/diveMove/man/createTDR.Rd |only diveMove-1.6.0/diveMove/man/detDive-internal.Rd | 73 - diveMove-1.6.0/diveMove/man/detPhase-internal.Rd | 100 - diveMove-1.6.0/diveMove/man/distSpeed.Rd | 70 - diveMove-1.6.0/diveMove/man/diveModel-class.Rd | 130 -- diveMove-1.6.0/diveMove/man/diveMove-defunct.Rd |only diveMove-1.6.0/diveMove/man/diveMove-deprecated.Rd |only diveMove-1.6.0/diveMove/man/diveMove-package.Rd | 12 diveMove-1.6.0/diveMove/man/diveStats.Rd | 190 +-- diveMove-1.6.0/diveMove/man/dot-runquantile.Rd |only diveMove-1.6.0/diveMove/man/extractDive.Rd |only diveMove-1.6.0/diveMove/man/fitMLEbouts.Rd |only diveMove-1.6.0/diveMove/man/fitNLSbouts.Rd |only diveMove-1.6.0/diveMove/man/labelBouts.Rd |only diveMove-1.6.0/diveMove/man/plotBouts.Rd |only diveMove-1.6.0/diveMove/man/plotBoutsCDF.Rd |only diveMove-1.6.0/diveMove/man/plotDiveModel.Rd |only diveMove-1.6.0/diveMove/man/plotTDR.Rd |only diveMove-1.6.0/diveMove/man/plotZOC.Rd |only diveMove-1.6.0/diveMove/man/readLocs.Rd | 123 +- diveMove-1.6.0/diveMove/man/rmixexp.Rd |only diveMove-1.6.0/diveMove/man/rqPlot.Rd | 103 - diveMove-1.6.0/diveMove/man/timeBudget.Rd |only 72 files changed, 3411 insertions(+), 1987 deletions(-)
Title: An R Port of the 'ImageJ' Plugin 'Auto Threshold'
Description: Algorithms for automatically finding appropriate
thresholds for numerical data, with special functions for thresholding
images. Provides the 'ImageJ' 'Auto Threshold' plugin functionality to
R users. See <https://imagej.net/Auto_Threshold> and Landini et al.
(2017) <DOI:10.1111/jmi.12474>.
Author: Rory Nolan [aut, cre, trl] (<https://orcid.org/0000-0002-5239-4043>),
Luis Alvarez [ctb] (<https://orcid.org/0000-0003-1316-1906>),
Sergi Padilla-Parra [ctb, ths]
(<https://orcid.org/0000-0002-8010-9481>),
Gabriel Landini [ctb, cph] (<https://orcid.org/0000-0002-9689-0989>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between autothresholdr versions 1.3.10 dated 2021-04-19 and 1.3.11 dated 2021-05-12
autothresholdr-1.3.10/autothresholdr/man/arr_mask.Rd |only autothresholdr-1.3.11/autothresholdr/DESCRIPTION | 6 - autothresholdr-1.3.11/autothresholdr/MD5 | 27 ++--- autothresholdr-1.3.11/autothresholdr/NAMESPACE | 2 autothresholdr-1.3.11/autothresholdr/NEWS.md | 6 + autothresholdr-1.3.11/autothresholdr/R/class_constructors.R | 24 +++- autothresholdr-1.3.11/autothresholdr/R/thresh.R | 21 +--- autothresholdr-1.3.11/autothresholdr/R/utils.R | 10 - autothresholdr-1.3.11/autothresholdr/inst/doc/finding-thresholds.html | 52 +++++----- autothresholdr-1.3.11/autothresholdr/inst/doc/thresholding-image-stacks.html | 4 autothresholdr-1.3.11/autothresholdr/inst/doc/thresholding-images.html | 10 - autothresholdr-1.3.11/autothresholdr/man/auto_thresh.Rd | 2 autothresholdr-1.3.11/autothresholdr/man/masked_arr.Rd |only autothresholdr-1.3.11/autothresholdr/tests/testthat/test-class-constructors.R |only autothresholdr-1.3.11/autothresholdr/tests/testthat/test_thresh.R | 8 - autothresholdr-1.3.11/autothresholdr/tests/testthat/test_utils.R | 7 + 16 files changed, 99 insertions(+), 80 deletions(-)
More information about autothresholdr at CRAN
Permanent link
Title: Mass Spectrometry Metabolomics Feature Clustering and
Interpretation
Description: A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. This method is compatible with gas and liquid chromatography coupled mass spectrometry, including indiscriminant tandem mass spectrometry <DOI: 10.1021/ac501530d> data.
Author: Corey D. Broeckling, Fayyaz Afsar, Steffan Neumann, Asa Ben-Hur, Jessica Prenni.
Maintainer: "Broeckling,Corey" <Corey.Broeckling@ColoState.EDU>
Diff between RAMClustR versions 1.2.0 dated 2021-04-22 and 1.2.1 dated 2021-05-12
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/annotation.summary.R | 32 +++++++++++++++++++++++++++++++- R/rc.calibrate.ri.R | 8 ++++---- R/rc.cmpd.get.pubchem.R | 43 ++++++++++++++++++++++++++++++++++--------- inst/doc/RAMClustR.html | 4 ++-- man/rc.cmpd.get.pubchem.Rd | 2 +- 8 files changed, 86 insertions(+), 28 deletions(-)
Title: Fitting Finite Mixture of Scale Mixture of Skew-Normal
Distributions
Description: Functions to fit finite mixture of scale mixture of skew-normal (FM-SMSN) distributions, details in Prates, Lachos and Cabral (2013) <doi: 10.18637/jss.v054.i12>, Cabral, Lachos and Prates (2012) <doi:10.1016/j.csda.2011.06.026> and Basso, Lachos, Cabral and Ghosh (2010) <doi:10.1016/j.csda.2009.09.031>.
Author: Marcos Prates [aut, cre, trl],
Victor Lachos [aut],
Celso Cabral [aut]
Maintainer: Marcos Prates <marcosop@est.ufmg.br>
Diff between mixsmsn versions 1.1-8 dated 2020-10-08 and 1.1-9 dated 2021-05-12
ChangeLog | 4 +++ DESCRIPTION | 8 +++--- MD5 | 6 ++-- R/mixsmsn.R | 73 +++++++++++++++++++++++++++++++++++++++++------------------- 4 files changed, 61 insertions(+), 30 deletions(-)
Title: Regression-Based Causal Mediation Analysis with an Interaction
Term
Description: 'R' implementation of the regression-based causal mediation analysis with a treatment-mediator interaction term, as originally implemented in the 'SAS' macro by Valeri and VanderWeele (2013) <doi:10.1037/a0031034> and Valeri and VanderWeele (2015) <doi:10.1097/EDE.0000000000000253>. Linear and logistic models are supported for the mediator model. Linear, logistic, loglinear, Poisson, negative binomial, Cox, and accelerated failure time (exponential and Weibull) models are supported for the outcome model.
Author: Kazuki Yoshida [cre, aut] (<https://orcid.org/0000-0002-2030-3549>),
Yi Li [ctb, aut] (<https://orcid.org/0000-0002-9359-210X>),
Maya Mathur [ctb] (<https://orcid.org/0000-0001-6698-2607>)
Maintainer: Kazuki Yoshida <kazukiyoshida@mail.harvard.edu>
Diff between regmedint versions 0.2.0 dated 2020-11-16 and 0.2.1 dated 2021-05-12
DESCRIPTION | 10 - MD5 | 38 ++--- NEWS.md | 5 build/vignette.rds |binary inst/doc/vig_01_introduction.R | 2 inst/doc/vig_01_introduction.Rmd | 2 inst/doc/vig_01_introduction.html | 250 +--------------------------------- inst/doc/vig_02_formulas.R | 2 inst/doc/vig_02_formulas.Rmd | 2 inst/doc/vig_02_formulas.html | 266 +++--------------------------------- inst/doc/vig_03_bootstrap.R | 2 inst/doc/vig_03_bootstrap.Rmd | 2 inst/doc/vig_03_bootstrap.html | 250 +--------------------------------- inst/doc/vig_04_mi.R | 2 inst/doc/vig_04_mi.Rmd | 2 inst/doc/vig_04_mi.html | 274 +++----------------------------------- vignettes/vig_01_introduction.Rmd | 2 vignettes/vig_02_formulas.Rmd | 2 vignettes/vig_03_bootstrap.Rmd | 2 vignettes/vig_04_mi.Rmd | 2 20 files changed, 117 insertions(+), 1000 deletions(-)
Title: Data Science for Psychologists
Description: All datasets and functions required for the examples and exercises of the book "Data Science for Psychologists" (by Hansjoerg Neth, Konstanz University, 2021), available at <https://bookdown.org/hneth/ds4psy/>. The book and course introduce principles and methods of data science to students of psychology and other biological or social sciences. The 'ds4psy' package primarily provides datasets, but also functions for data generation and manipulation (e.g., of text and time data) and graphics that are used in the book and its exercises. All functions included in 'ds4psy' are designed to be explicit and instructive, rather than efficient or elegant.
Author: Hansjoerg Neth [aut, cre] (<https://orcid.org/0000-0001-5427-3141>)
Maintainer: Hansjoerg Neth <h.neth@uni.kn>
Diff between ds4psy versions 0.6.0 dated 2021-04-08 and 0.7.0 dated 2021-05-12
ds4psy-0.6.0/ds4psy/man/is_vector.Rd |only ds4psy-0.7.0/ds4psy/DESCRIPTION | 10 ds4psy-0.7.0/ds4psy/MD5 | 99 ds4psy-0.7.0/ds4psy/NAMESPACE | 8 ds4psy-0.7.0/ds4psy/NEWS.md | 78 ds4psy-0.7.0/ds4psy/R/color_fun.R | 4 ds4psy-0.7.0/ds4psy/R/data.R | 2 ds4psy-0.7.0/ds4psy/R/data_fun.R | 34 ds4psy-0.7.0/ds4psy/R/plot_fun.R | 899 +++++++- ds4psy-0.7.0/ds4psy/R/text_fun.R | 2824 +++++++++++++++++++++------ ds4psy-0.7.0/ds4psy/R/theme_fun.R | 44 ds4psy-0.7.0/ds4psy/R/time_fun.R | 34 ds4psy-0.7.0/ds4psy/R/util_fun.R | 99 ds4psy-0.7.0/ds4psy/README.md | 10 ds4psy-0.7.0/ds4psy/build/partial.rdb |binary ds4psy-0.7.0/ds4psy/data/Trumpisms.rda |binary ds4psy-0.7.0/ds4psy/inst/CITATION | 4 ds4psy-0.7.0/ds4psy/inst/WORDLIST | 85 ds4psy-0.7.0/ds4psy/inst/doc/ds4psy.R | 2 ds4psy-0.7.0/ds4psy/inst/doc/ds4psy.Rmd | 6 ds4psy-0.7.0/ds4psy/inst/doc/ds4psy.html | 8 ds4psy-0.7.0/ds4psy/man/Umlaut.Rd | 5 ds4psy-0.7.0/ds4psy/man/capitalize.Rd | 5 ds4psy-0.7.0/ds4psy/man/caseflip.Rd | 5 ds4psy-0.7.0/ds4psy/man/cclass.Rd | 11 ds4psy-0.7.0/ds4psy/man/count_chars.Rd | 27 ds4psy-0.7.0/ds4psy/man/count_chars_words.Rd |only ds4psy-0.7.0/ds4psy/man/count_words.Rd | 21 ds4psy-0.7.0/ds4psy/man/is_equal.Rd | 2 ds4psy-0.7.0/ds4psy/man/is_vect.Rd |only ds4psy-0.7.0/ds4psy/man/is_wholenumber.Rd | 2 ds4psy-0.7.0/ds4psy/man/l33t_rul35.Rd | 5 ds4psy-0.7.0/ds4psy/man/map_text_chars.Rd |only ds4psy-0.7.0/ds4psy/man/map_text_coord.Rd |only ds4psy-0.7.0/ds4psy/man/map_text_regex.Rd |only ds4psy-0.7.0/ds4psy/man/metachar.Rd | 11 ds4psy-0.7.0/ds4psy/man/num_as_char.Rd | 2 ds4psy-0.7.0/ds4psy/man/num_as_ordinal.Rd | 2 ds4psy-0.7.0/ds4psy/man/num_equal.Rd | 2 ds4psy-0.7.0/ds4psy/man/plot_charmap.Rd |only ds4psy-0.7.0/ds4psy/man/plot_chars.Rd |only ds4psy-0.7.0/ds4psy/man/plot_fn.Rd | 2 ds4psy-0.7.0/ds4psy/man/plot_fun.Rd | 2 ds4psy-0.7.0/ds4psy/man/plot_n.Rd | 2 ds4psy-0.7.0/ds4psy/man/plot_text.Rd | 97 ds4psy-0.7.0/ds4psy/man/plot_tiles.Rd | 2 ds4psy-0.7.0/ds4psy/man/read_ascii.Rd | 42 ds4psy-0.7.0/ds4psy/man/text_to_chars.Rd |only ds4psy-0.7.0/ds4psy/man/text_to_sentences.Rd | 50 ds4psy-0.7.0/ds4psy/man/text_to_words.Rd | 17 ds4psy-0.7.0/ds4psy/man/theme_clean.Rd | 2 ds4psy-0.7.0/ds4psy/man/theme_ds4psy.Rd | 2 ds4psy-0.7.0/ds4psy/man/theme_empty.Rd | 16 ds4psy-0.7.0/ds4psy/man/transl33t.Rd | 5 ds4psy-0.7.0/ds4psy/vignettes/ds4psy.Rmd | 6 55 files changed, 3585 insertions(+), 1010 deletions(-)
Title: Derivatives of the Diffusion Density and Cumulative Distribution
Function
Description: Calculates the partial derivative of the first-passage time diffusion probability density function (PDF) and cumulative distribution function (CDF)
with respect to the first-passage time t (only for PDF), the upper barrier a, the drift rate v, the relative starting point w, the non-decision time t0,
the inter-trial variability of the drift rate sv, the inter-trial variability of the rel. starting point sw, and the inter-trial variability of the
non-decision time st0. In addition the PDF and CDF themselves are also provided. Most calculations are done on the logarithmic scale to make it more stable.
Since the PDF, CDF, and their derivatives are represented as infinite series, we give the user the option to control the approximation errors with the argument
'precision'. For the numerical integration we used the C library cubature by Johnson, S. G. (2005-2013) <https://github.com/stevengj/cubature>. Numerical integration is
required whenever sv, sw, and/or st0 is not zero. Note that numerical integration reduces speed of the computation and the precision cannot be guaranteed
anymore. Therefore, whenever numerical integration is used an estimate of the approximation error is provided in the output list.
Author: Raphael Hartmann [aut, cre],
Karl C. Klauer [cph, aut, ctb, ths],
Steven G. Johnson [ctb],
Jean M. Linhart [ctb],
Brian Gough [ctb],
Gerard Jungman [ctb],
Rudolf Schuerer [ctb],
Przemyslaw Sliwa [ctb],
Jason H. Stover [ctb]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between WienR versions 0.1-9 dated 2021-05-07 and 0.2-0 dated 2021-05-11
DESCRIPTION | 17 + MD5 | 106 +++++------ R/WienerDens.R | 51 ++--- R/WienerDist.R | 45 ++--- R/daWienerDens.R | 47 ++--- R/daWienerDist.R | 49 ++--- R/dst0WienerDens.R | 7 R/dst0WienerDist.R | 7 R/dsvWienerDens.R | 7 R/dsvWienerDist.R | 7 R/dswWienerDens.R | 7 R/dswWienerDist.R | 7 R/dt0WienerDens.R | 9 - R/dt0WienerDist.R | 57 +++--- R/dtWienerDens.R | 49 ++--- R/dvWienerDens.R | 49 ++--- R/dvWienerDist.R | 49 ++--- R/dwWienerDens.R | 9 - R/dwWienerDist.R | 49 ++--- R/dxWienerDens.R | 9 - R/dxWienerDist.R | 9 - man/WienerCDF.Rd | 5 man/WienerPDF.Rd | 3 man/daWienerCDF.Rd | 5 man/daWienerPDF.Rd | 5 man/dst0WienerCDF.Rd | 5 man/dst0WienerPDF.Rd | 5 man/dsvWienerCDF.Rd | 5 man/dsvWienerPDF.Rd | 5 man/dswWienerCDF.Rd | 5 man/dswWienerPDF.Rd | 5 man/dt0WienerCDF.Rd | 5 man/dt0WienerPDF.Rd | 5 man/dtWienerPDF.Rd | 5 man/dvWienerCDF.Rd | 5 man/dvWienerPDF.Rd | 5 man/dwWienerCDF.Rd | 5 man/dwWienerPDF.Rd | 5 man/gradWienerCDF.Rd | 5 man/gradWienerPDF.Rd | 5 src/R_wrapper.cpp | 356 ++++++++++++++++++++++++++++++++++++++-- src/WienR_init.c | 4 src/adaptive_rejection_samp.cpp | 2 src/adaptive_rejection_samp.h | 1 src/cdf_fncs.cpp | 8 src/derivs.cpp | 121 +++++++------ src/derivs.h | 8 src/fncs_seven.cpp | 6 src/fncs_seven.h | 4 src/hcubature.c | 14 - src/rwiener.cpp | 48 +++-- src/rwiener.h | 2 src/tools.cpp | 1 src/tools.h | 19 +- 54 files changed, 877 insertions(+), 456 deletions(-)
Title: Nonparametric Estimation of the Trend and Its Derivatives in TS
Description: The nonparametric trend and its derivatives in equidistant time
series (TS) with short-memory stationary errors can be estimated. The
estimation is conducted via local polynomial regression using an
automatically selected bandwidth obtained by a built-in iterative plug-in
algorithm or a bandwidth fixed by the user. A Nadaraya-Watson kernel
smoother is also built-in as a comparison. With version 1.1.0, a linearity
test for the trend function, forecasting methods and backtesting
approaches are implemented as well.
The smoothing methods of the package are described in Feng, Y., Gries, T.,
and Fritz, M. (2020) <doi:10.1080/10485252.2020.1759598>.
Author: Yuanhua Feng [aut] (Paderborn University, Germany),
Sebastian Letmathe [aut] (Paderborn University, Germany),
Dominik Schulz [aut, cre] (Paderborn University, Germany),
Thomas Gries [ctb] (Paderborn University, Germany),
Marlon Fritz [ctb] (Paderborn University, Germany)
Maintainer: Dominik Schulz <schulzd@mail.uni-paderborn.de>
Diff between smoots versions 1.0.1 dated 2019-12-02 and 1.1.0 dated 2021-05-11
DESCRIPTION | 31 - MD5 | 104 +++-- NAMESPACE | 19 NEWS.md | 26 + R/RcppExports.R |only R/Welcome.R | 10 R/algorithms.R | 2 R/bootCast.R |only R/cf0.LW.est.R | 71 --- R/col.alpha.R |only R/color.name.R |only R/confBounds.R |only R/critMatrix.R |only R/dsmooth.R | 290 +++++++++------ R/fitted.R |only R/gdpUS.R | 2 R/gsmooth.R | 251 +++++++------ R/knsmooth.R | 97 +++-- R/maInfty.R |only R/modelCast.R |only R/msmooth.R | 418 +++++++++++++-------- R/msmoothCalc.R |only R/normCast.R |only R/optOrd.R |only R/plot.smoots.R | 277 ++++++++++---- R/print.smoots.R | 105 ++++- R/rescale.R |only R/residuals.R |only R/rollCast.R |only R/smoots.R | 132 +++++- R/sysdata.rda |binary R/tempNH.R | 4 R/trendCast.R |only R/tsmooth.R | 652 ++++++++++++++------------------- R/tsmoothCalc.R |only README.md | 188 ++++++--- man/bootCast.Rd |only man/confBounds.Rd |only man/critMatrix.Rd |only man/dax.Rd | 64 +-- man/dsmooth.Rd | 425 ++++++++++++---------- man/figures/README-confbounds-1.pdf |only man/figures/README-confbounds-1.png |only man/figures/README-fcast-1.pdf |only man/figures/README-fcast-1.png |only man/figures/README-plot1-1.pdf |only man/figures/README-plot1-1.png |binary man/figures/README-plot1-2.pdf |only man/figures/README-plot1-2.png |binary man/fitted.smoots.Rd |only man/gdpUS.Rd | 56 +- man/gsmooth.Rd | 343 +++++++++-------- man/knsmooth.Rd | 222 +++++------ man/modelCast.Rd |only man/msmooth.Rd | 650 +++++++++++++++++---------------- man/normCast.Rd |only man/optOrd.Rd |only man/plot.smoots.Rd | 76 +-- man/print.smoots.Rd | 54 +- man/rescale.Rd |only man/residuals.smoots.Rd |only man/rollCast.Rd |only man/smoots.Rd | 228 +++++++---- man/tempNH.Rd | 56 +- man/trendCast.Rd |only man/tsmooth.Rd | 695 +++++++++++++++++++----------------- man/vix.Rd | 64 +-- src |only 68 files changed, 3162 insertions(+), 2450 deletions(-)
Title: Optimal Project Prioritization
Description: A decision support tool for prioritizing conservation projects.
Prioritizations can be developed by maximizing expected feature richness,
expected phylogenetic diversity, the number of features that meet
persistence targets, or identifying a set of projects that meet persistence
targets for minimal cost. Constraints (e.g. lock in specific actions) and
feature weights can also be specified to further customize prioritizations.
After defining a project prioritization problem, solutions can be obtained
using exact algorithms, heuristic algorithms, or random processes. In
particular, it is recommended to install the 'Gurobi' optimizer (available
from <https://www.gurobi.com>) because it can identify optimal solutions
very quickly. Finally, methods are provided for comparing different
prioritizations and evaluating their benefits. For more information, see
Hanson et al. (2019) <doi:10.1111/2041-210X.13264>.
Author: Jeffrey O Hanson [aut, cre] (<https://orcid.org/0000-0002-4716-6134>),
Richard Schuster [aut] (<https://orcid.org/0000-0003-3191-7869>),
Matthew Strimas-Mackey [aut] (<https://orcid.org/0000-0001-8929-7776>),
Joseph R Bennett [aut] (<https://orcid.org/0000-0002-3901-9513>)
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between oppr versions 1.0.2 dated 2020-05-20 and 1.0.3 dated 2021-05-11
DESCRIPTION | 18 MD5 | 324 ++--- NEWS.md | 48 R/ArrayParameter-proto.R | 56 R/Collection-proto.R | 46 R/Constraint-proto.R | 8 R/Decision-proto.R | 8 R/Id.R | 6 R/MiscParameter-proto.R | 34 R/Objective-proto.R | 6 R/OptimizationProblem-methods.R | 58 R/OptimizationProblem-proto.R | 94 - R/Parameter-proto.R | 36 R/Parameters-proto.R | 48 R/ProjectModifier-proto.R | 90 - R/ProjectProblem-proto.R | 210 +-- R/ScalarParameter-proto.R | 46 R/Solver-proto.R | 28 R/Target-proto.R | 6 R/Weight-proto.R | 6 R/action_names.R | 4 R/add_absolute_targets.R | 26 R/add_binary_decisions.R | 12 R/add_default_solver.R | 24 R/add_feature_weights.R | 20 R/add_gurobi_solver.R | 100 - R/add_heuristic_solver.R | 35 R/add_locked_in_constraints.R | 32 R/add_locked_out_constraints.R | 6 R/add_lpsolveapi_solver.R | 28 R/add_lpsymphony_solver.R | 31 R/add_manual_locked_constraints.R | 20 R/add_manual_targets.R | 38 R/add_max_phylo_div_objective.R | 40 R/add_max_richness_objective.R | 26 R/add_max_targets_met_objective.R | 45 R/add_min_set_objective.R | 24 R/add_random_solver.R | 10 R/add_relative_targets.R | 9 R/add_rsymphony_solver.R | 33 R/branch_matrix.R | 10 R/compile.R | 10 R/constraints.R | 16 R/data.R | 116 - R/decisions.R | 10 R/feature_names.R | 4 R/internal.R | 57 R/magrittr-operators.R | 8 R/misc.R | 2 R/new_optimization_problem.R | 6 R/number_of_actions.R | 6 R/number_of_features.R | 6 R/number_of_projects.R | 6 R/objectives.R | 54 R/package.R | 38 R/parameters.R | 84 - R/plot.R | 26 R/plot_feature_persistence.R | 10 R/plot_phylo_persistence.R | 28 R/pproto.R | 12 R/predefined_optimization_problem.R | 46 R/print.R | 2 R/problem.R | 88 - R/project_cost_effectiveness.R | 22 R/project_names.R | 4 R/rake_phylogeny.R | 10 R/replacement_costs.R | 40 R/show.R | 2 R/simulate_ppp_data.R | 120 - R/simulate_ptm_data.R | 157 +- R/solution_statistics.R | 30 R/solve.R | 44 R/solvers.R | 42 R/star_phylogeny.R | 8 R/targets.R | 24 R/tbl_df.R | 12 R/waiver.R | 8 R/weights.R | 12 R/zzz.R | 1 README.md | 161 ++ build/vignette.rds |binary inst/doc/oppr.Rmd | 18 inst/doc/oppr.html | 1668 ++++++++++++++------------- man/ArrayParameter-class.Rd | 24 man/Collection-class.Rd | 20 man/Constraint-class.Rd | 6 man/Decision-class.Rd | 6 man/MiscParameter-class.Rd | 16 man/Objective-class.Rd | 4 man/OptimizationProblem-class.Rd | 12 man/OptimizationProblem-methods.Rd | 32 man/Parameter-class.Rd | 12 man/Parameters-class.Rd | 18 man/ProjectModifier-class.Rd | 46 man/ProjectProblem-class.Rd | 118 - man/ScalarParameter-class.Rd | 20 man/Solver-class.Rd | 14 man/Target-class.Rd | 6 man/Weight-class.Rd | 6 man/action_names.Rd | 2 man/add_absolute_targets.Rd | 56 man/add_binary_decisions.Rd | 20 man/add_default_solver.Rd | 24 man/add_feature_weights.Rd | 64 - man/add_gurobi_solver.Rd | 73 - man/add_heuristic_solver.Rd | 197 +-- man/add_locked_in_constraints.Rd | 50 man/add_locked_out_constraints.Rd | 6 man/add_lpsolveapi_solver.Rd | 45 man/add_lsymphony_solver.Rd | 51 man/add_manual_locked_constraints.Rd | 30 man/add_manual_targets.Rd | 72 - man/add_max_phylo_div_objective.Rd | 206 +-- man/add_max_richness_objective.Rd | 118 - man/add_max_targets_met_objective.Rd | 167 +- man/add_min_set_objective.Rd | 138 +- man/add_random_solver.Rd | 58 man/add_relative_targets.Rd | 59 man/add_rsymphony_solver.Rd | 45 man/array_parameters.Rd | 20 man/as.list.Rd | 4 man/branch_matrix.Rd | 8 man/compile.Rd | 12 man/constraints.Rd | 24 man/decisions.Rd | 18 man/feature_names.Rd | 2 man/figures/README-readme-plot-1.png |binary man/matrix_parameters.Rd | 2 man/misc_parameter.Rd | 2 man/new_id.Rd | 4 man/new_optimization_problem.Rd | 6 man/number_of_actions.Rd | 4 man/number_of_features.Rd | 4 man/number_of_projects.Rd | 4 man/objectives.Rd | 66 - man/oppr.Rd | 50 man/parameters.Rd | 6 man/pipe.Rd | 4 man/plot.ProjectProblem.Rd | 48 man/plot_feature_persistence.Rd | 34 man/plot_phylo_persistence.Rd | 48 man/print.Rd | 2 man/problem.Rd | 100 - man/project_cost_effectiveness.Rd | 54 man/project_names.Rd | 2 man/replacement_costs.Rd | 80 - man/scalar_parameters.Rd | 22 man/show.Rd | 2 man/sim_data.Rd | 135 -- man/simulate_ppp_data.Rd | 206 +-- man/simulate_ptm_data.Rd | 209 +-- man/solution_statistics.Rd | 40 man/solve.Rd | 90 - man/solvers.Rd | 114 - man/targets.Rd | 46 man/tee.Rd | 4 man/tibble-methods.Rd | 18 man/weights.Rd | 16 tests/testthat/helper_functions.R | 6 tests/testthat/test_decisions.R | 2 tests/testthat/test_plot.R | 1 tests/testthat/test_plot_phylo_persistence.R | 4 vignettes/oppr.Rmd | 18 163 files changed, 4112 insertions(+), 4037 deletions(-)
Title: Multivariate Kernel Density Estimation with Vine Copulas
Description: Implements the vine copula based kernel density estimator of
Nagler and Czado (2016) <doi:10.1016/j.jmva.2016.07.003>. The estimator does
not suffer from the curse of dimensionality and is therefore well suited for
high-dimensional applications.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between kdevine versions 0.4.2 dated 2018-12-17 and 0.4.3 dated 2021-05-11
DESCRIPTION | 10 +- MD5 | 12 +-- NEWS.md | 10 ++ R/kdevine-package.R | 2 R/kdevinecop.R | 1 R/structure_select2.R | 1 README.md | 168 ++++++++++++++++++++++++++++++-------------------- 7 files changed, 122 insertions(+), 82 deletions(-)
Title: Analytical Tool for Aquatic Respirometry
Description: Calculates metabolic rate of fish and other aquatic organisms measured using
an intermittent-flow respirometry approach. The tool is used to run a set of graphical
QC tests of raw respirometry data, correct it for background respiration and chamber
effect, filter and extract target values of absolute and mass-specific metabolic rate.
Experimental design should include background respiration tests and measuring of one
or more metabolic rate traits. The R package is ideally integrated with the pump
controller 'PumpResp' and the DO meter 'SensResp' (open-source hardware by FishResp).
Raw respirometry data can be also imported from 'AquaResp' (free software), 'AutoResp'
('LoligoSystems'), 'OxyView' ('PreSens'), 'Pyro Oxygen Logger' ('PyroScience') and
'Q-box Aqua' ('QubitSystems'). More information about the R package 'FishResp'is
available in the publication by Morozov et al. (2019) <doi:10.1093/conphys/coz003>.
Author: Sergey Morozov [aut, cre],
Scott McCairns [aut, ths],
Juha Merila [ths],
Federico Calboli [ctb],
Jenni Prokkola [dtc],
Stephen White [dtc],
Daniel Montgomery [dtc],
Laura Almodovar-Acevedo [dtc],
Niclas Kolm [dtc],
Alexander Kotrschal [dtc],
Erik Gill [dtc]
Maintainer: Sergey Morozov <sergey.morozov@helsinki.fi>
Diff between FishResp versions 1.0.3 dated 2019-03-07 and 1.1.0 dated 2021-05-11
DESCRIPTION | 37 +++++++++++++--------- MD5 | 71 ++++++++++++++++++++++++-------------------- NAMESPACE | 3 + NEWS.md |only R/FishResp.R | 2 - R/QC.activity.R | 1 R/QC.slope.R | 6 +-- R/convert.rMR.R | 3 + R/convert.respirometry.R | 3 + R/export.MR.R | 2 + R/extract.slope.R | 6 +-- R/prepare.data.R |only R/presens.aquaresp.R | 17 ++++++++-- R/pyroscience.aquaresp.R | 16 ++++++--- R/pyroscience.pumpresp.R |only README.md |only inst/extdata/amphipod |only inst/extdata/salmon |only man/AMR.Rd | 6 ++- man/AMR.clean.Rd | 6 ++- man/AMR.raw.Rd | 6 ++- man/AMR.slope.Rd | 6 ++- man/FishResp.Rd | 3 - man/QC.slope.Rd | 2 - man/SMR.Rd | 6 ++- man/SMR.clean.Rd | 6 ++- man/SMR.raw.Rd | 6 ++- man/SMR.slope.Rd | 6 ++- man/convert.rMR.Rd | 3 + man/convert.respirometry.Rd | 3 + man/export.MR.Rd | 2 + man/extract.slope.Rd | 2 - man/info.Rd | 6 ++- man/post.Rd | 6 ++- man/pre.Rd | 6 ++- man/prepare.data.Rd |only man/presens.aquaresp.Rd | 7 ++-- man/pyroscience.aquaresp.Rd | 10 +++--- man/pyroscience.pumpresp.Rd |only man/results.Rd | 6 ++- 40 files changed, 168 insertions(+), 103 deletions(-)
Title: Estimation Methods for Markets in Equilibrium and Disequilibrium
Description: Provides estimation methods for markets in equilibrium and
disequilibrium. Supports the estimation of an equilibrium and
four disequilibrium models with both correlated and independent shocks.
Also provides post-estimation analysis tools, such as aggregation,
marginal effect, and shortage calculations. The estimation methods are
based on full information maximum likelihood techniques given in
Maddala and Nelson (1974) <doi:10.2307/1914215>. They are implemented
using the analytic derivative expressions calculated in
Karapanagiotis (2020) <doi:10.2139/ssrn.3525622>. Standard
errors can be estimated by adjusting for heteroscedasticity or clustering.
The equilibrium estimation constitutes a case of a system of linear,
simultaneous equations. Instead, the disequilibrium models replace the
market-clearing condition with a non-linear,
short-side rule and allow for different specifications of price dynamics.
Author: Pantelis Karapanagiotis [aut, cre]
(<https://orcid.org/0000-0001-9871-1908>)
Maintainer: Pantelis Karapanagiotis <pikappa.devel@gmail.com>
Diff between diseq versions 0.2.1 dated 2021-04-14 and 0.3.1 dated 2021-05-11
diseq-0.2.1/diseq/man/aggregate_demand.Rd |only diseq-0.2.1/diseq/man/aggregate_supply.Rd |only diseq-0.2.1/diseq/man/demand_descriptives.Rd |only diseq-0.2.1/diseq/man/demanded_quantities.Rd |only diseq-0.2.1/diseq/man/diseq_basic-class.Rd |only diseq-0.2.1/diseq/man/diseq_deterministic_adjustment-class.Rd |only diseq-0.2.1/diseq/man/diseq_directional-class.Rd |only diseq-0.2.1/diseq/man/diseq_stochastic_adjustment-class.Rd |only diseq-0.2.1/diseq/man/disequilibrium_model-class.Rd |only diseq-0.2.1/diseq/man/equation_base-class.Rd |only diseq-0.2.1/diseq/man/equation_basic-class.Rd |only diseq-0.2.1/diseq/man/equation_deterministic_adjustment-class.Rd |only diseq-0.2.1/diseq/man/equation_directional-class.Rd |only diseq-0.2.1/diseq/man/equation_stochastic_adjustment-class.Rd |only diseq-0.2.1/diseq/man/equilibrium_model-class.Rd |only diseq-0.2.1/diseq/man/has_shortage.Rd |only diseq-0.2.1/diseq/man/marginal_effect_at_mean.Rd |only diseq-0.2.1/diseq/man/market_model-class.Rd |only diseq-0.2.1/diseq/man/mean_marginal_effect.Rd |only diseq-0.2.1/diseq/man/model_description.Rd |only diseq-0.2.1/diseq/man/normalized_shortages.Rd |only diseq-0.2.1/diseq/man/prefixed_const_variable.Rd |only diseq-0.2.1/diseq/man/prefixed_control_variables.Rd |only diseq-0.2.1/diseq/man/prefixed_independent_variables.Rd |only diseq-0.2.1/diseq/man/prefixed_price_variable.Rd |only diseq-0.2.1/diseq/man/prefixed_variance_variable.Rd |only diseq-0.2.1/diseq/man/relative_shortages.Rd |only diseq-0.2.1/diseq/man/shortage_probabilities.Rd |only diseq-0.2.1/diseq/man/simulate_model_data.Rd |only diseq-0.2.1/diseq/man/supplied_quantities.Rd |only diseq-0.2.1/diseq/man/supply_descriptives.Rd |only diseq-0.3.1/diseq/DESCRIPTION | 8 diseq-0.3.1/diseq/MD5 | 166 - diseq-0.3.1/diseq/NAMESPACE | 21 diseq-0.3.1/diseq/NEWS.md | 37 diseq-0.3.1/diseq/R/data.R | 88 diseq-0.3.1/diseq/R/diseq.R | 75 diseq-0.3.1/diseq/R/diseq_basic.R | 41 diseq-0.3.1/diseq/R/diseq_deterministic_adjustment.R | 57 diseq-0.3.1/diseq/R/diseq_directional.R | 63 diseq-0.3.1/diseq/R/diseq_stochastic_adjustment.R | 64 diseq-0.3.1/diseq/R/disequilibrium_model.R | 427 +--- diseq-0.3.1/diseq/R/equation_base.R | 202 +- diseq-0.3.1/diseq/R/equation_basic.R | 16 diseq-0.3.1/diseq/R/equation_deterministic_adjustment.R | 14 diseq-0.3.1/diseq/R/equation_directional.R | 5 diseq-0.3.1/diseq/R/equation_stochastic_adjustment.R | 6 diseq-0.3.1/diseq/R/equilibrium_model.R | 77 diseq-0.3.1/diseq/R/hessian_basic.R | 3 diseq-0.3.1/diseq/R/hessian_directional.R | 1 diseq-0.3.1/diseq/R/likelihood_deterministic_adjustment.R | 4 diseq-0.3.1/diseq/R/likelihood_stochastic_adjustment.R | 15 diseq-0.3.1/diseq/R/market_model.R | 649 +++--- diseq-0.3.1/diseq/R/model_simulation.R | 487 ++--- diseq-0.3.1/diseq/R/system_base.R | 64 diseq-0.3.1/diseq/R/system_basic.R | 18 diseq-0.3.1/diseq/R/system_deterministic_adjustment.R | 18 diseq-0.3.1/diseq/R/system_directional.R | 2 diseq-0.3.1/diseq/R/system_equilibrium.R | 12 diseq-0.3.1/diseq/R/system_stochastic_adjustment.R | 67 diseq-0.3.1/diseq/README.md | 39 diseq-0.3.1/diseq/build/partial.rdb |binary diseq-0.3.1/diseq/build/vignette.rds |binary diseq-0.3.1/diseq/configure | 32 diseq-0.3.1/diseq/configure.ac | 2 diseq-0.3.1/diseq/inst/doc/basic_usage.R | 42 diseq-0.3.1/diseq/inst/doc/basic_usage.Rmd | 44 diseq-0.3.1/diseq/inst/doc/basic_usage.html | 944 +++++----- diseq-0.3.1/diseq/inst/doc/diseq.pdf |only diseq-0.3.1/diseq/inst/doc/market_clearing_assessment.R | 2 diseq-0.3.1/diseq/inst/doc/market_clearing_assessment.Rmd | 2 diseq-0.3.1/diseq/inst/doc/market_clearing_assessment.html | 760 ++++---- diseq-0.3.1/diseq/inst/doc/package.Rmd |only diseq-0.3.1/diseq/inst/doc/package.html |only diseq-0.3.1/diseq/man/diseq.Rd | 74 diseq-0.3.1/diseq/man/equation_classes.Rd |only diseq-0.3.1/diseq/man/estimate.Rd | 66 diseq-0.3.1/diseq/man/figures/implementation.png |only diseq-0.3.1/diseq/man/gradient.Rd |only diseq-0.3.1/diseq/man/hessian.Rd |only diseq-0.3.1/diseq/man/houses.Rd | 69 diseq-0.3.1/diseq/man/initialize_market_model.Rd | 169 + diseq-0.3.1/diseq/man/marginal_effects.Rd |only diseq-0.3.1/diseq/man/market_aggregation.Rd |only diseq-0.3.1/diseq/man/market_descriptives.Rd |only diseq-0.3.1/diseq/man/market_models.Rd |only diseq-0.3.1/diseq/man/market_quantities.Rd |only diseq-0.3.1/diseq/man/market_simulation.Rd |only diseq-0.3.1/diseq/man/maximize_log_likelihood.Rd | 36 diseq-0.3.1/diseq/man/minus_log_likelihood.Rd | 4 diseq-0.3.1/diseq/man/model_name.Rd |only diseq-0.3.1/diseq/man/number_of_observations.Rd | 6 diseq-0.3.1/diseq/man/plot.Rd | 25 diseq-0.3.1/diseq/man/scores.Rd | 27 diseq-0.3.1/diseq/man/shortage_analysis.Rd |only diseq-0.3.1/diseq/man/show.Rd | 34 diseq-0.3.1/diseq/man/summary.Rd | 29 diseq-0.3.1/diseq/man/system_classes.Rd |only diseq-0.3.1/diseq/man/variable_names.Rd |only diseq-0.3.1/diseq/tests/testthat/helper-common.R | 33 diseq-0.3.1/diseq/tests/testthat/test-basic.R | 16 diseq-0.3.1/diseq/tests/testthat/test-deterministic_adjustment.R | 18 diseq-0.3.1/diseq/tests/testthat/test-directional.R | 20 diseq-0.3.1/diseq/tests/testthat/test-equilibrium.R | 14 diseq-0.3.1/diseq/tests/testthat/test-stochastic_adjustment.R | 20 diseq-0.3.1/diseq/vignettes/.install_extras |only diseq-0.3.1/diseq/vignettes/basic_usage.Rmd | 44 diseq-0.3.1/diseq/vignettes/diseq.pdf |only diseq-0.3.1/diseq/vignettes/market_clearing_assessment.Rmd | 2 diseq-0.3.1/diseq/vignettes/package.Rmd |only 110 files changed, 2946 insertions(+), 2334 deletions(-)
Title: Bootstrap cis-QTL Method that Corrects for the Winner's Curse
Description: Identifies genome-related molecular traits with significant
evidence of genetic regulation and performs a bootstrap procedure to
correct estimated effect sizes for over-estimation present in cis-QTL
mapping studies (The "Winner's Curse"), described in Huang QQ *et al.*
2018 <doi: 10.1093/nar/gky780>.
Author: Qin Qin Huang [aut],
Scott Ritchie [aut, cre]
Maintainer: Scott Ritchie <sritchie73@gmail.com>
Diff between BootstrapQTL versions 1.0.2 dated 2018-09-21 and 1.0.5 dated 2021-05-11
DESCRIPTION | 9 ++---- MD5 | 8 ++--- R/BootstrapQTL.R | 75 ++++++++++++++++++++++++++------------------------ R/utils.R | 12 +------- tests/testthat/test.R | 35 ++++++++++++++++++----- 5 files changed, 77 insertions(+), 62 deletions(-)
Title: Bayesian Aggregate Treatment Effects
Description: Running and comparing meta-analyses of data with hierarchical
Bayesian models in Stan, including convenience functions for formatting
data, plotting and pooling measures specific to meta-analysis. This implements many models
from Meager (2019) <doi:10.1257/app.20170299>.
Author: Witold Wiecek [cre, aut],
Rachael Meager [aut],
Brice Green [ctb] (predict(), loo_compare, many visuals),
Trustees of Columbia University [cph] (tools/make_cc.R)
Maintainer: Witold Wiecek <witold.wiecek@gmail.com>
Diff between baggr versions 0.4.0 dated 2020-02-28 and 0.6.4 dated 2021-05-11
baggr-0.4.0/baggr/R/baggr_code.R |only baggr-0.4.0/baggr/inst/include/meta_header.hpp |only baggr-0.4.0/baggr/man/print.plot_list.Rd |only baggr-0.4.0/baggr/man/show_model.Rd |only baggr-0.4.0/baggr/src/init.cpp |only baggr-0.4.0/baggr/src/stan_files |only baggr-0.4.0/baggr/tools |only baggr-0.6.4/baggr/DESCRIPTION | 25 baggr-0.6.4/baggr/MD5 | 217 +++-- baggr-0.6.4/baggr/NAMESPACE | 7 baggr-0.6.4/baggr/NEWS.md | 78 ++ baggr-0.6.4/baggr/R/auto_prior.R | 296 ++++--- baggr-0.6.4/baggr/R/baggr-package.R | 7 baggr-0.6.4/baggr/R/baggr.R | 169 +++- baggr-0.6.4/baggr/R/baggr_compare.R | 357 +++++---- baggr-0.6.4/baggr/R/baggr_plot.R | 21 baggr-0.6.4/baggr/R/binary_to_individual.R |only baggr-0.6.4/baggr/R/check_cols.R | 6 baggr-0.6.4/baggr/R/convert_inputs.R | 179 ++-- baggr-0.6.4/baggr/R/fixed_effects.R | 3 baggr-0.6.4/baggr/R/forest_plot.R | 4 baggr-0.6.4/baggr/R/group_effects.R | 79 +- baggr-0.6.4/baggr/R/labbe.R |only baggr-0.6.4/baggr/R/loocv.R | 48 - baggr-0.6.4/baggr/R/microcredit.R | 24 baggr-0.6.4/baggr/R/names.R | 26 baggr-0.6.4/baggr/R/plot_quantiles.R |only baggr-0.6.4/baggr/R/pooling_metrics.R | 113 +-- baggr-0.6.4/baggr/R/predict.R | 12 baggr-0.6.4/baggr/R/prepare_ma.R | 82 +- baggr-0.6.4/baggr/R/print_baggr.R | 40 - baggr-0.6.4/baggr/R/prior_dist.R | 20 baggr-0.6.4/baggr/R/stanmodels.R | 43 - baggr-0.6.4/baggr/R/summarise_quantiles_data.R |only baggr-0.6.4/baggr/R/trt_effects.R | 187 +++- baggr-0.6.4/baggr/build/vignette.rds |binary baggr-0.6.4/baggr/configure |only baggr-0.6.4/baggr/configure.win |only baggr-0.6.4/baggr/data/chicks.rda |only baggr-0.6.4/baggr/data/data_spike.rda |only baggr-0.6.4/baggr/data/microcredit_simplified.rda |binary baggr-0.6.4/baggr/inst/doc/baggr.R | 22 baggr-0.6.4/baggr/inst/doc/baggr.Rmd | 54 - baggr-0.6.4/baggr/inst/doc/baggr.html | 312 ++++---- baggr-0.6.4/baggr/inst/doc/baggr_binary.R | 183 ++-- baggr-0.6.4/baggr/inst/doc/baggr_binary.Rmd | 291 ++++--- baggr-0.6.4/baggr/inst/doc/baggr_binary.html | 749 +++++++++++--------- baggr-0.6.4/baggr/inst/include/stan_meta_header.hpp |only baggr-0.6.4/baggr/inst/stan |only baggr-0.6.4/baggr/man/baggr-package.Rd | 7 baggr-0.6.4/baggr/man/baggr.Rd | 69 + baggr-0.6.4/baggr/man/baggr_compare.Rd | 66 - baggr-0.6.4/baggr/man/baggr_plot.Rd | 2 baggr-0.6.4/baggr/man/baggr_theme_set.Rd | 148 +-- baggr-0.6.4/baggr/man/binary_to_individual.Rd |only baggr-0.6.4/baggr/man/chicks.Rd |only baggr-0.6.4/baggr/man/convert_inputs.Rd | 134 +-- baggr-0.6.4/baggr/man/data_spike.Rd |only baggr-0.6.4/baggr/man/effect_draw.Rd | 51 + baggr-0.6.4/baggr/man/effect_plot.Rd | 21 baggr-0.6.4/baggr/man/fixed_effects.Rd | 66 - baggr-0.6.4/baggr/man/forest_plot.Rd | 102 +- baggr-0.6.4/baggr/man/get_n_samples.Rd | 38 - baggr-0.6.4/baggr/man/group_effects.Rd | 34 baggr-0.6.4/baggr/man/is.baggr_cv.Rd | 28 baggr-0.6.4/baggr/man/labbe.Rd |only baggr-0.6.4/baggr/man/loo_compare.Rd | 4 baggr-0.6.4/baggr/man/loocv.Rd | 25 baggr-0.6.4/baggr/man/microcredit.Rd | 4 baggr-0.6.4/baggr/man/microcredit_simplified.Rd | 8 baggr-0.6.4/baggr/man/mint.Rd | 52 - baggr-0.6.4/baggr/man/plot.baggr_compare.Rd | 28 baggr-0.6.4/baggr/man/plot_quantiles.Rd |only baggr-0.6.4/baggr/man/pooling.Rd | 63 + baggr-0.6.4/baggr/man/pp_check.baggr.Rd | 54 - baggr-0.6.4/baggr/man/predict.baggr.Rd | 52 - baggr-0.6.4/baggr/man/predict_mutau.Rd | 40 - baggr-0.6.4/baggr/man/predict_quantiles.Rd | 40 - baggr-0.6.4/baggr/man/predict_rubin.Rd | 40 - baggr-0.6.4/baggr/man/predict_unknown.Rd | 28 baggr-0.6.4/baggr/man/prepare_ma.Rd | 171 ++-- baggr-0.6.4/baggr/man/prepare_prior.Rd | 92 +- baggr-0.6.4/baggr/man/print.baggr.Rd | 56 - baggr-0.6.4/baggr/man/print.baggr_compare.Rd | 36 baggr-0.6.4/baggr/man/print.baggr_cv.Rd | 36 baggr-0.6.4/baggr/man/print.compare_baggr_cv.Rd | 36 baggr-0.6.4/baggr/man/print_dist.Rd |only baggr-0.6.4/baggr/man/priors.Rd | 4 baggr-0.6.4/baggr/man/random_effects.Rd |only baggr-0.6.4/baggr/man/rubin_data.Rd | 36 baggr-0.6.4/baggr/man/schools.Rd | 4 baggr-0.6.4/baggr/man/set_prior_val.Rd | 42 - baggr-0.6.4/baggr/man/stop_not_implemented.Rd | 22 baggr-0.6.4/baggr/man/summarise_quantiles_data.Rd |only baggr-0.6.4/baggr/man/treatment_effect.Rd | 56 - baggr-0.6.4/baggr/src/Makevars | 22 baggr-0.6.4/baggr/src/Makevars.win | 23 baggr-0.6.4/baggr/src/RcppExports.cpp |only baggr-0.6.4/baggr/src/stanExports_logit.cc |only baggr-0.6.4/baggr/src/stanExports_logit.h |only baggr-0.6.4/baggr/src/stanExports_mutau.cc |only baggr-0.6.4/baggr/src/stanExports_mutau.h |only baggr-0.6.4/baggr/src/stanExports_mutau_full.cc |only baggr-0.6.4/baggr/src/stanExports_mutau_full.h |only baggr-0.6.4/baggr/src/stanExports_rubin.cc |only baggr-0.6.4/baggr/src/stanExports_rubin.h |only baggr-0.6.4/baggr/src/stanExports_rubin_full.cc |only baggr-0.6.4/baggr/src/stanExports_rubin_full.h |only baggr-0.6.4/baggr/tests/testthat/Rplots.pdf |binary baggr-0.6.4/baggr/tests/testthat/test_8schools.R | 2 baggr-0.6.4/baggr/tests/testthat/test_binary.R | 114 +-- baggr-0.6.4/baggr/tests/testthat/test_full.R | 68 + baggr-0.6.4/baggr/tests/testthat/test_helpers.R | 87 ++ baggr-0.6.4/baggr/tests/testthat/test_loo.R | 11 baggr-0.6.4/baggr/tests/testthat/test_mutau.R | 17 baggr-0.6.4/baggr/tests/testthat/test_mutau_full.R |only baggr-0.6.4/baggr/tests/testthat/test_ordering.R | 4 baggr-0.6.4/baggr/tests/testthat/test_prior.R | 20 baggr-0.6.4/baggr/tests/testthat/test_rubin.R | 65 + baggr-0.6.4/baggr/vignettes/baggr.Rmd | 54 - baggr-0.6.4/baggr/vignettes/baggr.bib | 41 + baggr-0.6.4/baggr/vignettes/baggr_binary.Rmd | 291 ++++--- 122 files changed, 3771 insertions(+), 2497 deletions(-)
Title: Design of Experiments Suite: Generate and Evaluate Optimal
Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of blocked and split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible.
Author: Tyler Morgan-Wall [aut, cre],
George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between skpr versions 0.64.2 dated 2020-03-04 and 0.66.5 dated 2021-05-11
DESCRIPTION | 17 MD5 | 107 +- NAMESPACE | 6 R/RcppExports.R | 16 R/calc_interaction_degrees.R | 11 R/calculate_degrees_of_freedom.R | 3 R/effectpower.R | 12 R/eval_design.R | 18 R/eval_design_custom_mc.R | 7 R/eval_design_mc.R | 53 + R/eval_design_survival_mc.R | 2 R/gen_design.R | 398 ++++------ R/get_optimality.R | 10 R/methods.R | 39 - R/parallel_search_progress.R |only R/parameterpower.R | 12 R/plot_fds.R | 7 R/skprGUI.R | 465 +++++------- R/skprGUIserver.R | 271 ++++-- README.md | 207 +++-- inst/shiny/skprGUI/server.R | 571 ++++++-------- inst/shiny/skprGUI/ui.R | 758 +++++++++---------- man/aliasmodel.Rd | 34 man/blockingstructure.Rd | 34 man/calcblocksizes.Rd | 38 man/disallowed_combinations.Rd | 34 man/gen_anticoef.Rd | 42 - man/gen_design.Rd | 652 ++++++++-------- man/generate_noise_block.Rd | 34 man/get_optimality.Rd | 2 man/normalize_numeric_runmatrix.Rd | 34 man/permutations.Rd | 34 man/pipe.Rd | 14 man/plot_fds.Rd | 100 +- man/potential_permuted_factors.Rd | 34 man/print.skpr_eval_output.Rd | 7 man/priorlevels.Rd | 36 man/quad.Rd | 34 man/rearrange_formula_by_order.Rd | 34 man/reduceRunMatrix.Rd | 38 man/remove_skpr_blockcols.Rd | 34 man/skprGUI.Rd | 38 man/skprGUIbrowser.Rd | 28 man/skprGUIserver.Rd | 38 src/Makevars | 1 src/Makevars.win | 2 src/RcppExports.cpp | 55 + src/coord_exchange_functions.h |only src/exported_optimality.cpp | 2 src/genOptimalDesign.cpp | 1433 ------------------------------------- src/genOptimalDesignCoord.cpp |only src/genSplitPlotOptimalDesign.cpp |only src/getBlockedOptimalDesign.cpp |only src/nullify_alg.h | 2 src/optimalityfunctions.cpp | 2 tests/testthat/Rplots.pdf |binary tests/testthat/testExampleCode.R | 7 57 files changed, 2316 insertions(+), 3551 deletions(-)
Title: Using Percolation and Conductance to Find Information Flow
Certainty in a Direct Network
Description: To find the certainty of dominance interactions with indirect
interactions being considered.
Author: Kevin Fujii [aut],
Jian Jin [aut],
Jessica Vandeleest [aut, cre],
Aaron Shev [aut],
Brianne Beisner [aut],
Brenda McCowan [aut, cph],
Hsieh Fushing [aut, cph]
Maintainer: Jessica Vandeleest <vandelee@ucdavis.edu>
Diff between Perc versions 0.1.5 dated 2020-04-27 and 0.1.6 dated 2021-05-11
DESCRIPTION | 13 - MD5 | 18 - R/Perc.R | 2 build/vignette.rds |binary inst/doc/Perc.R | 42 +-- inst/doc/Perc.html | 458 +++++++++++++----------------------------- man/Perc.Rd | 2 man/sampleEdgelist.Rd | 6 man/sampleRawMatrix.Rd | 6 man/sampleWeightedEdgelist.Rd | 6 10 files changed, 197 insertions(+), 356 deletions(-)
Title: Simultaneous Confidence Intervals for Multinomial Proportions
According to the Method by Sison and Glaz
Description: An implementation of a method for building simultaneous confidence intervals for the probabilities of a multinomial distribution given a set of observations, proposed by Sison and Glaz in their paper:
Sison, C.P and J. Glaz. Simultaneous confidence intervals and sample size determination for multinomial proportions. Journal of the American Statistical Association, 90:366-369 (1995).
The method is an R translation of the SAS code implemented by May and Johnson in their paper:
May, W.L. and W.D. Johnson. Constructing two-sided simultaneous confidence intervals for multinomial proportions for small counts in a large number of cells. Journal of Statistical Software 5(6) (2000).
Paper and code available at <DOI:10.18637/jss.v005.i06>.
Author: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Maintainer: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Diff between MultinomialCI versions 1.1 dated 2019-09-07 and 1.2 dated 2021-05-11
DESCRIPTION | 14 +++--- MD5 | 8 +-- NAMESPACE | 4 - R/sison.R | 44 ++++++++++++++++++- man/multinomialCI.Rd | 114 +++++++++++++++++++++++---------------------------- 5 files changed, 108 insertions(+), 76 deletions(-)
Title: R Interface for the C Implementation of CEC Benchmark Functions
Description: Goal of this package is to provide access to benchmark functions defined for
the Special Session and Competition on Real-Parameter Single Objective Optimization in one place.
The package contains functions from following years: 2013, 2014, 2015,
2017, 2019, 2021 (<https://github.com/P-N-Suganthan>).
Implementations of CEC-2013 (Y. Gonzalez-Fernandez & M. Zambrano-Bigiarini) and CEC2017 (D. Jagodziński) are taken from existed R packages. Also,
the original C source code has been cleaned and reorganized for better readability.
Author: Eryk Warchulski [aut, cre],
Dariusz Jagodziński [cph],
Yasser Gonzalez-Fernandez [cph],
Mauricio Zambrano-Bigiarini [cph]
Maintainer: Eryk Warchulski <ewarchul@gmail.com>
Diff between cecs versions 0.2.0 dated 2021-04-25 and 0.2.1 dated 2021-05-11
DESCRIPTION | 6 +-- MD5 | 7 ++-- NEWS.md |only R/utils.R | 3 + README.md | 104 +++--------------------------------------------------------- 5 files changed, 15 insertions(+), 105 deletions(-)
Title: Weighted Mixed-Effects Models Using Multilevel Pseudo Maximum
Likelihood Estimation
Description: Run mixed-effects models that include weights at every level. The WeMix package fits a weighted mixed model, also known as a multilevel, mixed, or hierarchical linear model (HLM). The weights could be inverse selection probabilities, such as those developed for an education survey where schools are sampled probabilistically, and then students inside of those schools are sampled probabilistically. Although mixed-effects models are already available in R, WeMix is unique in implementing methods for mixed models using weights at multiple levels. Both linear and logit models are supported. Models may have up to three levels.
Author: Emmanuel Sikali [pdr],
Paul Bailey [aut, cre],
Claire Kelley [aut],
Trang Nguyen [aut],
Huade Huo [aut],
Eric Buehler [ctb],
Christian Kjeldsen [ctb]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between WeMix versions 3.1.6 dated 2020-12-08 and 3.1.7 dated 2021-05-11
DESCRIPTION | 31 ++++- MD5 | 16 +- R/adaptiveQuad.R | 13 +- R/helpers.R | 26 +++- build/vignette.rds |binary inst/NEWS.Rd | 8 + inst/doc/Introduction_to_Mixed_Effects_Models_With_WeMix.pdf |binary inst/doc/Weighted_Linear_Mixed_Effects_Models.pdf |binary tests/testthat/test-1-main.R | 59 +++++------ 9 files changed, 96 insertions(+), 57 deletions(-)
Title: Easily Access timsTOF Data
Description: Access 'timsTOF' mass spectrometry data, as described <https://sso.bruker.com/auth/realms/bruker/protocol/openid-connect/auth?client_id=aem-bruker.com&redirect_uri=https%3A%2F%2Fwww.bruker.com%2Fen.login.html%3FtargetUrl%3Dhttps%3A%2F%2Fwww.bruker.com%2Fen%2Fservices%2Fsoftware-downloads%2Fmass-spectrometry.html&response_type=id_token%20token&scope=openid%20profile&state=4f9d225e92f341cca3b03a55533dbd65&nonce=f550633b1e984ecfb07979ae6d9277b4&ui_locales=en> (after registering), using the 'OpenTIMS' C++ reader and save all into 'data.tables'.
Author: Mateusz Krzysztof Łącki [aut, cre, cph]
(<https://orcid.org/0000-0001-7415-4748>),
Michał Piotr Startek [aut, cph]
(<https://orcid.org/0000-0001-5227-3447>)
Maintainer: Mateusz Krzysztof Łącki <matteo.lacki@gmail.com>
Diff between timsr versions 0.0.2 dated 2021-05-04 and 0.0.3 dated 2021-05-11
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/timsr.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Fit a Spatial Occupancy Model via Gibbs Sampling
Description: Fit a spatial-temporal occupancy models using
a probit formulation instead of a traditional logit
model.
Author: Devin S. Johnson
Maintainer: Devin S. Johnson <devin.johnson@noaa.gov>
Diff between stocc versions 1.30 dated 2015-08-23 and 1.31 dated 2021-05-11
DESCRIPTION | 9 +++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 2 +- R/icar.Q.R | 11 +++++++++++ R/spatial.occupancy.R | 7 ++++--- R/stocc-package.R | 2 +- demo/simDataMCMC.R | 1 + man/habData.Rd | 18 +++++++++++------- man/icar.Q.Rd | 3 +-- man/make.so.data.Rd | 3 +-- man/occupancyData.Rd | 29 ++++++++++++++++------------- man/spatial.occupancy.Rd | 28 +++++++++++++++++----------- man/stocc-package.Rd | 7 +++---- man/visitData.Rd | 13 ++++++++----- 14 files changed, 93 insertions(+), 66 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>;
- net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>;
- measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>;
- ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>;
- partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Bruggemann, 2014) <DOI:10.1002/cem.2569>; (Rücker & Schwarzer, 2017) <DOI:10.1002/jrsm.1270>;
- split direct and indirect evidence to check consistency (Dias et al., 2010) <DOI:10.1002/sim.3767>, (Efthimiou et al., 2019) <DOI:10.1002/sim.8158>;
- league table with network meta-analysis results;
- additive network meta-analysis for combinations of treatments (Rücker et al., 2019) <DOI:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <DOI:10.1002/sim.8158>;
- 'comparison-adjusted' funnel plot (Chaimani & Salanti, 2012) <DOI:10.1002/jrsm.57>;
- automated drawing of network graphs described in Rücker & Schwarzer (2016) <DOI:10.1002/jrsm.1143>.
Author: Gerta Rücker [aut] (<https://orcid.org/0000-0002-2192-2560>),
Ulrike Krahn [aut],
Jochem König [aut] (<https://orcid.org/0000-0003-4683-0360>),
Orestis Efthimiou [aut] (<https://orcid.org/0000-0002-0955-7572>),
Guido Schwarzer [aut, cre] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 1.3-0 dated 2021-01-18 and 1.4-0 dated 2021-05-11
DESCRIPTION | 10 MD5 | 96 +- NAMESPACE | 4 NEWS.md | 91 + R/as.data.frame.netconnection.R |only R/as.data.frame.netmeta.R | 2 R/decomp.tau.R | 36 R/discomb.R | 207 +++- R/forest.netbind.R | 28 R/forest.netcomb.R | 4 R/forest.netmeta.R | 19 R/forest.netsplit.R | 2 R/multiarm.R | 4 R/netcomb.R | 2 R/netconnection.R | 187 +++ R/netgraph.netconnection.R | 21 R/netgraph.netmeta.R | 18 R/netheat.R | 41 R/netimpact.R | 12 R/netleague.R | 13 R/netmeasures.R | 48 - R/netmeta-internal.R | 46 R/netmeta-package.R | 6 R/netmeta.R | 347 ++++++- R/netsplit.R | 2 R/nma.additive.R | 3 R/nma.krahn.R | 11 R/nma.ruecker.R | 2 R/pairwise.R | 1767 ++++++++++++++++++++----------------- R/print.netmeta.R | 30 R/summary.netmeta.R | 14 man/as.data.frame.netconnection.Rd |only man/as.data.frame.netmeta.Rd | 2 man/discomb.Rd | 3 man/forest.netbind.Rd | 6 man/forest.netcomb.Rd | 4 man/forest.netmeta.Rd | 5 man/forest.netsplit.Rd | 2 man/netconnection.Rd | 7 man/netgraph.netconnection.Rd | 12 man/netgraph.netmeta.Rd | 4 man/netheat.Rd | 18 man/netimpact.Rd | 7 man/netleague.Rd | 12 man/netmeta-package.Rd | 4 man/netmeta.Rd | 51 - man/netsplit.Rd | 2 man/pairwise.Rd | 24 man/print.netmeta.Rd | 4 man/summary.netmeta.Rd | 4 50 files changed, 2181 insertions(+), 1063 deletions(-)
Title: Meta-Analysis of Diagnostic Accuracy Studies with Several
Cutpoints
Description: Provides methods by Steinhauser et al. (2016) <DOI:10.1186/s12874-016-0196-1> for meta-analysis of diagnostic accuracy studies with several cutpoints.
Author: Gerta Rücker [aut] (<https://orcid.org/0000-0002-2192-2560>),
Susanne Steinhauser [aut],
Srinath Kolampally [aut],
Guido Schwarzer [aut, cre] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between diagmeta versions 0.4-0 dated 2020-04-02 and 0.4-1 dated 2021-05-11
diagmeta-0.4-0/diagmeta/NEWS |only diagmeta-0.4-1/diagmeta/DESCRIPTION | 12 - diagmeta-0.4-1/diagmeta/MD5 | 16 +- diagmeta-0.4-1/diagmeta/NEWS.md |only diagmeta-0.4-1/diagmeta/R/diagmeta.R | 128 ++++++++++++++------- diagmeta-0.4-1/diagmeta/R/diagstats.R | 44 ++++--- diagmeta-0.4-1/diagmeta/R/plot.diagmeta.R | 8 - diagmeta-0.4-1/diagmeta/R/print.diagmeta.R | 2 diagmeta-0.4-1/diagmeta/R/print.summary.diagmeta.R | 2 diagmeta-0.4-1/diagmeta/man/diagmeta.Rd | 2 10 files changed, 138 insertions(+), 76 deletions(-)
Title: Helps You to Code Cleaner
Description: Check your R code for some of the most common
layout flaws. Many tried to teach us how to write code less dreadful,
be it implicitly as B. W. Kernighan and D. M. Ritchie (1988)
<ISBN:0-13-110362-8> in 'The C Programming Language' did, be it
explicitly as R.C. Martin (2008) <ISBN:0-13-235088-2> in 'Clean Code:
A Handbook of Agile Software Craftsmanship' did. So we should check
our code for files too long or wide, functions with too many lines,
too wide lines, too many arguments or too many levels of nesting.
Note: This is not a static code analyzer like pylint or the like.
Checkout <https://cran.r-project.org/package=lintr> instead.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between cleanr versions 1.3.1 dated 2020-11-20 and 1.3.2 dated 2021-05-11
DESCRIPTION | 9 -- MD5 | 48 ++++++----- NEWS.md | 4 R/checks.R | 6 - R/internals.R | 6 - R/options.R | 7 - R/utils.R | 67 +--------------- R/wrappers.R | 6 - build/cleanr.pdf |binary build/vignette.rds |binary inst/doc/cleanr_Introduction.html | 101 +++++++++---------------- inst/runit_tests/source/R_s4/AllConstructors.R | 2 inst/source/R/checks.R | 11 +- inst/source/R/internals.R | 6 - inst/source/R/options.R | 10 +- inst/source/R/utils.R | 6 - inst/source/R/wrappers.R | 26 +++--- inst/vignettes_code |only man/check_function_layout.Rd | 2 man/check_package.Rd | 2 man/function_checks.Rd | 2 man/get_cleanr_options.Rd | 3 man/is_not_false.Rd | 22 ----- man/load_internal_functions.Rd | 14 --- man/set_cleanr_options.Rd | 4 vignettes/sedscr |only 26 files changed, 142 insertions(+), 222 deletions(-)
Title: Calculate Power and Sample Size for Two Sample Mean Tests
Description: Power calculations are a critical component of any research study to determine the
minimum sample size necessary to detect differences between multiple groups. Here we
present an 'R' package, 'PASSED', that performs power and sample size calculations for
the test of two-sample means or ratios with data following beta,
gamma (Chang et al. (2011), <doi:10.1007/s00180-010-0209-1>), normal,
Poisson (Gu et al. (2008), <doi:10.1002/bimj.200710403>), binomial, geometric, and
negative binomial (Zhu and Lakkis (2014), <doi:10.1002/sim.5947>) distributions.
Author: Jinpu Li [aut, cre],
Ryan Knigge [aut],
Kaiyi Chen [aut],
Emily Leary [aut]
Maintainer: Jinpu Li <lijinp@health.missouri.edu>
Diff between PASSED versions 1.0-3 dated 2020-07-21 and 1.1-0 dated 2021-05-11
DESCRIPTION | 15 - MD5 | 32 +- NAMESPACE | 34 +- R/power_Beta.R | 556 ++++++++++++++++++++++-------------------- R/power_Binomial.R | 203 +++++++++------ R/power_Gamma.R | 240 +++++++++--------- R/power_Geometric.R | 174 +++++++------ R/power_NegativeBinomial.R | 175 +++++++------ R/power_Normal.R | 215 +++++++++------- R/power_Poisson.R | 144 ++++++---- man/power_Beta.Rd | 29 +- man/power_Binomial.Rd | 13 man/power_Gamma.Rd | 12 man/power_Geometric.Rd | 23 + man/power_NegativeBinomial.Rd | 24 + man/power_Normal.Rd | 18 - man/power_Poisson.Rd | 20 - 17 files changed, 1072 insertions(+), 855 deletions(-)
Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and
writing data between R and other statistical software packages like 'SPSS',
'SAS' or 'Stata', and working with labelled data. This includes easy ways
to get, set or change value and variable label attributes, to convert
labelled vectors into factors or numeric (and vice versa), or to deal with
multiple declared missing values.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
avid Ranzolin [ctb],
Jonathan De Troye [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjlabelled versions 1.1.7 dated 2020-09-24 and 1.1.8 dated 2021-05-11
DESCRIPTION | 14 MD5 | 86 +-- NEWS.md | 13 R/add_labels.R | 8 R/as_factor.R | 109 ++-- R/as_label.R | 2 R/as_labelled.R | 62 ++ R/as_numeric.R | 6 R/convert_case.R | 2 R/copy_labels.R | 4 R/drop_labels.R | 2 R/fill_labels.R | 10 R/get_label.R | 6 R/get_model_labels.R | 21 R/get_na.R | 17 R/get_values.R | 2 R/helpfunctions.R | 2 R/label_to_colnames.R | 14 R/read.R | 21 R/remove_all_labels.R | 2 R/remove_labels.R | 8 R/set_labels.R | 264 ++++++----- R/set_na.R | 186 ++++---- R/tidy_labels.R | 51 +- R/val_labels.R | 2 R/var_labels.R | 2 R/write.R | 4 R/zap_labels.R | 161 +++---- build/vignette.rds |binary inst/doc/intro_sjlabelled.html | 927 +++++++++++++++++++++-------------------- inst/doc/labelleddata.R | 4 inst/doc/labelleddata.Rmd | 4 inst/doc/labelleddata.html | 199 +++++--- inst/doc/quasiquotation.html | 439 ++++++++++--------- man/as_factor.Rd | 73 +-- man/as_labelled.Rd | 12 man/get_na.Rd | 15 man/label_to_colnames.Rd | 8 man/set_labels.Rd | 232 +++++----- man/set_na.Rd | 165 +++---- man/term_labels.Rd | 21 man/tidy_labels.Rd | 30 - man/zap_labels.Rd | 154 +++--- vignettes/labelleddata.Rmd | 4 44 files changed, 1818 insertions(+), 1550 deletions(-)
Title: Analysis of Single-Cell Chromatin Data
Description: A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2020) <doi:10.1101/2020.11.09.373613>.
Author: Tim Stuart [aut, cre] (<https://orcid.org/0000-0002-3044-0897>),
Avi Srivastava [aut] (<https://orcid.org/0000-0001-9798-2079>),
Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>),
Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)
Maintainer: Tim Stuart <tstuart@nygenome.org>
Diff between Signac versions 1.2.0 dated 2021-04-28 and 1.2.1 dated 2021-05-11
DESCRIPTION | 8 - MD5 | 27 +++--- NAMESPACE | 1 NEWS.md | 14 +++ R/fragments.R | 26 ++++++ R/objects.R | 4 R/preprocessing.R | 9 +- build/partial.rdb |binary inst/extdata/fragments_header.tsv.gz |only inst/extdata/fragments_header.tsv.gz.tbi |only man/head.Fragment.Rd |only src/filter.cpp | 24 ++++- src/group.cpp | 25 +++++- src/split.cpp | 23 ++++- src/validate.cpp | 24 +++++ tests/testthat/test_fragments.R | 128 +++++++++++++++++++++++++++++++ 16 files changed, 281 insertions(+), 32 deletions(-)
Title: Data from all Seasons of Survivor (US) TV Series in Tidy Format
Description: Several datasets which detail the results and events of each season of Survivor. This includes
details on the cast, voting history, immunity and reward challenges, jury votes and viewers. This data is
useful for practicing data wrangling, graph analytics and analysing how each season of Survivor played out.
Includes 'ggplot2' scales and colour palettes for visualisation.
Author: Daniel Oehm [aut, cre]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between survivoR versions 0.9.2 dated 2021-04-06 and 0.9.3 dated 2021-05-11
DESCRIPTION | 9 - MD5 | 37 ++++--- NEWS.md |only R/datasets.R | 104 +++++++++++++++++++- README.md | 237 ++++++++++++++++++++++++----------------------- data/castaways.rda |binary data/challenges.rda |only data/hidden-idols.rda |only data/immunity.rda |binary data/jury-votes.rda |binary data/rewards.rda |binary data/season-palettes.rda |binary data/season-summary.rda |binary data/tribe-colours.rda |binary data/tribe-mapping.rda |only data/viewers.rda |binary data/vote-history.rda |binary man/challenges.Rd |only man/hidden_idols.Rd |only man/immunity.Rd | 5 man/rewards.Rd | 3 man/season_summary.Rd | 4 man/tribe_mapping.Rd |only 23 files changed, 257 insertions(+), 142 deletions(-)
Title: Kernel Density Estimation for Heaped and Rounded Data
Description: In self-reported or anonymised data the user often encounters
heaped data, i.e. data which are rounded (to a possibly different degree
of coarseness). While this is mostly a minor problem in parametric density
estimation the bias can be very large for non-parametric methods such as kernel
density estimation. This package implements a partly Bayesian algorithm treating
the true unknown values as additional parameters and estimates the rounding
parameters to give a corrected kernel density estimate. It supports various
standard bandwidth selection methods. Varying rounding probabilities (depending
on the true value) and asymmetric rounding is estimable as well: Gross, M. and Rendtel, U. (2016) (<doi:10.1093/jssam/smw011>).
Additionally, bivariate non-parametric density estimation for rounded data, Gross, M. et al. (2016) (<doi:10.1111/rssa.12179>),
as well as data aggregated on areas is supported.
Author: Marcus Gross [aut, cre],
Kerstin Erfurth [ctb]
Maintainer: Marcus Gross <marcus.gross@inwt-statistics.de>
Diff between Kernelheaping versions 2.2.2 dated 2020-02-21 and 2.2.8 dated 2021-05-11
DESCRIPTION | 12 +-- MD5 | 24 +++---- NAMESPACE | 2 R/functions.R | 132 +++++++++++++++++++++++++++++------------ man/Kernelheaping.Rd | 1 man/createSim.Kernelheaping.Rd | 12 +++ man/dbivr.Rd | 10 ++- man/dclass.Rd | 24 ++++--- man/dheaping.Rd | 19 ++++- man/dshapebivr.Rd | 16 ++++ man/dshapebivrProp.Rd | 16 ++++ man/sim.Kernelheaping.Rd | 22 +++++- man/toOtherShape.Rd | 2 13 files changed, 210 insertions(+), 82 deletions(-)
Title: Create Interactive Chart with the JavaScript 'ApexCharts'
Library
Description: Provides an 'htmlwidgets' interface to 'apexcharts.js'.
'Apexcharts' is a modern JavaScript charting library to build interactive charts and visualizations with simple API.
'Apexcharts' examples and documentation are available here: <https://apexcharts.com/>.
Author: Victor Perrier [aut, cre],
Fanny Meyer [aut],
Juned Chhipa [cph] (apexcharts.js library),
Mike Bostock [cph] (d3.format library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between apexcharter versions 0.1.8 dated 2020-11-18 and 0.2.0 dated 2021-05-11
apexcharter-0.1.8/apexcharter/inst/example-brush |only apexcharter-0.1.8/apexcharter/inst/example-brush-proxy |only apexcharter-0.1.8/apexcharter/inst/example-spark |only apexcharter-0.1.8/apexcharter/inst/example-sync |only apexcharter-0.1.8/apexcharter/inst/examples-input |only apexcharter-0.1.8/apexcharter/inst/examples-proxy |only apexcharter-0.1.8/apexcharter/inst/htmlwidgets/lib |only apexcharter-0.2.0/apexcharter/DESCRIPTION | 12 apexcharter-0.2.0/apexcharter/MD5 | 353 +++++----- apexcharter-0.2.0/apexcharter/NAMESPACE | 27 apexcharter-0.2.0/apexcharter/NEWS.md | 11 apexcharter-0.2.0/apexcharter/R/apex-options.R | 7 apexcharter-0.2.0/apexcharter/R/apex-utils.R | 92 +- apexcharter-0.2.0/apexcharter/R/apex.R | 105 ++ apexcharter-0.2.0/apexcharter/R/apexcharter-package.R | 12 apexcharter-0.2.0/apexcharter/R/apexcharter.R | 16 apexcharter-0.2.0/apexcharter/R/colors.R | 6 apexcharter-0.2.0/apexcharter/R/data.R | 2 apexcharter-0.2.0/apexcharter/R/facets.R |only apexcharter-0.2.0/apexcharter/R/format.R | 4 apexcharter-0.2.0/apexcharter/R/grid.R |only apexcharter-0.2.0/apexcharter/R/mixed-charts.R | 13 apexcharter-0.2.0/apexcharter/R/onLoad.R | 8 apexcharter-0.2.0/apexcharter/R/parse-data.R | 10 apexcharter-0.2.0/apexcharter/R/proxy.R | 82 +- apexcharter-0.2.0/apexcharter/R/shiny-input.R | 15 apexcharter-0.2.0/apexcharter/R/spark-box.R | 8 apexcharter-0.2.0/apexcharter/R/utils.R | 62 + apexcharter-0.2.0/apexcharter/README.md | 13 apexcharter-0.2.0/apexcharter/build/vignette.rds |binary apexcharter-0.2.0/apexcharter/inst/doc/apexcharter.R | 36 - apexcharter-0.2.0/apexcharter/inst/doc/apexcharter.Rmd | 38 - apexcharter-0.2.0/apexcharter/inst/doc/apexcharter.html | 225 ++---- apexcharter-0.2.0/apexcharter/inst/doc/chart-options.R | 26 apexcharter-0.2.0/apexcharter/inst/doc/chart-options.Rmd | 26 apexcharter-0.2.0/apexcharter/inst/doc/chart-options.html | 194 ++--- apexcharter-0.2.0/apexcharter/inst/doc/facets.R |only apexcharter-0.2.0/apexcharter/inst/doc/facets.Rmd |only apexcharter-0.2.0/apexcharter/inst/doc/facets.html |only apexcharter-0.2.0/apexcharter/inst/doc/shiny-integration.R | 6 apexcharter-0.2.0/apexcharter/inst/doc/shiny-integration.Rmd | 4 apexcharter-0.2.0/apexcharter/inst/doc/shiny-integration.html | 111 +-- apexcharter-0.2.0/apexcharter/inst/doc/spark-box.R | 1 apexcharter-0.2.0/apexcharter/inst/doc/spark-box.Rmd | 1 apexcharter-0.2.0/apexcharter/inst/doc/spark-box.html | 95 -- apexcharter-0.2.0/apexcharter/inst/doc/sync-charts.R | 41 + apexcharter-0.2.0/apexcharter/inst/doc/sync-charts.Rmd | 25 apexcharter-0.2.0/apexcharter/inst/doc/sync-charts.html | 134 +-- apexcharter-0.2.0/apexcharter/inst/examples/brush |only apexcharter-0.2.0/apexcharter/inst/examples/brush-proxy |only apexcharter-0.2.0/apexcharter/inst/examples/input |only apexcharter-0.2.0/apexcharter/inst/examples/proxy |only apexcharter-0.2.0/apexcharter/inst/examples/spark |only apexcharter-0.2.0/apexcharter/inst/examples/sync |only apexcharter-0.2.0/apexcharter/inst/htmlwidgets/apexcharter.css | 65 + apexcharter-0.2.0/apexcharter/inst/htmlwidgets/apexcharter.js | 24 apexcharter-0.2.0/apexcharter/inst/htmlwidgets/apexcharter.yaml | 6 apexcharter-0.2.0/apexcharter/inst/htmlwidgets/assets |only apexcharter-0.2.0/apexcharter/man/apex-facets.Rd |only apexcharter-0.2.0/apexcharter/man/apex.Rd | 8 apexcharter-0.2.0/apexcharter/man/apex_grid.Rd |only apexcharter-0.2.0/apexcharter/man/apexcharter-exports.Rd | 2 apexcharter-0.2.0/apexcharter/man/apexcharter-shiny-facets.Rd |only apexcharter-0.2.0/apexcharter/man/apexcharter-shiny-grid.Rd |only apexcharter-0.2.0/apexcharter/man/ax_chart.Rd | 18 apexcharter-0.2.0/apexcharter/man/ax_colors.Rd | 10 apexcharter-0.2.0/apexcharter/man/ax_dataLabels.Rd | 5 apexcharter-0.2.0/apexcharter/man/ax_fill.Rd | 5 apexcharter-0.2.0/apexcharter/man/ax_grid.Rd | 9 apexcharter-0.2.0/apexcharter/man/ax_legend.Rd | 9 apexcharter-0.2.0/apexcharter/man/ax_plotOptions.Rd | 9 apexcharter-0.2.0/apexcharter/man/ax_proxy_options.Rd | 142 ++-- apexcharter-0.2.0/apexcharter/man/ax_proxy_series.Rd | 158 ++-- apexcharter-0.2.0/apexcharter/man/ax_responsive.Rd | 5 apexcharter-0.2.0/apexcharter/man/ax_states.Rd | 5 apexcharter-0.2.0/apexcharter/man/ax_theme.Rd | 13 apexcharter-0.2.0/apexcharter/man/ax_tooltip.Rd | 9 apexcharter-0.2.0/apexcharter/man/ax_xaxis.Rd | 13 apexcharter-0.2.0/apexcharter/man/ax_yaxis2.Rd | 5 apexcharter-0.2.0/apexcharter/man/bar_opts.Rd | 3 apexcharter-0.2.0/apexcharter/man/consumption.Rd | 2 apexcharter-0.2.0/apexcharter/man/pie_opts.Rd | 4 apexcharter-0.2.0/apexcharter/tests/testthat/test-annotations.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-apex-utils.R | 13 apexcharter-0.2.0/apexcharter/tests/testthat/test-apex.R | 44 + apexcharter-0.2.0/apexcharter/tests/testthat/test-colors.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-facets.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-format.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-grid.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-mixed-charts.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-parse-data.R | 4 apexcharter-0.2.0/apexcharter/tests/testthat/test-proxy.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-spark_box.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-tooltip.R |only apexcharter-0.2.0/apexcharter/vignettes/apexcharter.Rmd | 38 - apexcharter-0.2.0/apexcharter/vignettes/chart-options.Rmd | 26 apexcharter-0.2.0/apexcharter/vignettes/facets.Rmd |only apexcharter-0.2.0/apexcharter/vignettes/shiny-integration.Rmd | 4 apexcharter-0.2.0/apexcharter/vignettes/spark-box.Rmd | 1 apexcharter-0.2.0/apexcharter/vignettes/sync-charts.Rmd | 25 100 files changed, 1338 insertions(+), 1167 deletions(-)
Title: Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text
Shaping
Description: Provides access to the text shaping functionality in the 'HarfBuzz'
library and the bidirectional algorithm in the 'Fribidi' library.
'textshaping' is a low-level utility package mainly for graphic devices that
expands upon the font tool-set provided by the 'systemfonts' package.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between textshaping versions 0.3.3 dated 2021-03-16 and 0.3.4 dated 2021-05-11
DESCRIPTION | 7 +++---- MD5 | 9 +++++---- NEWS.md | 5 +++++ src/Makevars.ucrt |only src/Makevars.win | 2 +- src/utils.h | 30 +++++++++++++++--------------- 6 files changed, 29 insertions(+), 24 deletions(-)
Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font
handling varies between systems it is difficult to correctly locate
installed fonts across different operating systems. The 'systemfonts'
package provides bindings to the native libraries on Windows, macOS and
Linux for finding font files that can then be used further by e.g. graphic
devices. The main use is intended to be from compiled code but 'systemfonts'
also provides access from R.
Author: Thomas Lin Pedersen [aut, cre]
(<https://orcid.org/0000-0002-5147-4711>),
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
Devon Govett [aut] (Author of font-manager),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between systemfonts versions 1.0.1 dated 2021-02-09 and 1.0.2 dated 2021-05-11
DESCRIPTION | 7 +++---- MD5 | 13 +++++++------ NEWS.md | 5 +++++ inst/doc/c_interface.html | 9 ++++++++- src/Makevars.ucrt |only src/Makevars.win | 2 +- src/font_matching.cpp | 1 + src/ft_cache.cpp | 4 ++-- 8 files changed, 27 insertions(+), 14 deletions(-)
Title: Several Methods for Procedural Name Generation
Description: A small, dependency-free way to generate random names. Methods
provided include the adjective-surname approach of Docker containers
('<https://github.com/moby/moby/blob/master/pkg/namesgenerator/names-generator.go'),
and combinations of common English or Spanish words.
Author: Michael Mahoney [aut, cre] (<https://orcid.org/0000-0003-2402-304X>)
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between proceduralnames versions 0.1.1 dated 2021-01-07 and 0.1.2 dated 2021-05-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ README.md | 18 ++++++++++++------ 4 files changed, 23 insertions(+), 13 deletions(-)
More information about proceduralnames at CRAN
Permanent link
Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>),
Marcel Ramos [ctb, cre] (<https://orcid.org/0000-0002-3242-0582>)
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
Diff between BiocManager versions 1.30.14 dated 2021-05-10 and 1.30.15 dated 2021-05-11
DESCRIPTION | 6 MD5 | 20 NEWS | 9 R/available.R | 9 R/utilities.R | 10 R/valid.R | 4 build/vignette.rds |binary inst/doc/BiocManager.html | 944 +++++++++++++++++++------------------ man/available.Rd | 9 man/valid.Rd | 4 tests/testthat/test_repositories.R | 1 11 files changed, 546 insertions(+), 470 deletions(-)
Title: Spatial Analysis of Field Trials with Splines
Description: Analysis of field trial experiments by modelling spatial trends using two-dimensional Penalised spline (P-spline) models.
Author: Maria Xose Rodriguez-Alvarez [aut, cre],
Martin Boer [aut],
Paul Eilers [aut],
Fred van Eeuwijk [ctb]
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@bcamath.org>
Diff between SpATS versions 1.0-12 dated 2021-02-26 and 1.0-13 dated 2021-05-11
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 3 +++ R/PSANOVA.R | 11 ++++++----- R/SAP.R | 3 ++- R/SpATS.R | 5 +++-- R/construct.2d.pspline.R | 18 ++++++++++++++++-- R/construct.design.matrix.R | 4 ++-- R/construct.spatial.prediction.matrix.R | 5 +++++ R/obtain.spatialtrend.R | 26 +++++++++++++++++++++----- man/PSANOVA.Rd | 4 +++- man/SAP.Rd | 3 ++- man/SpATS-package.Rd | 4 ++-- 13 files changed, 81 insertions(+), 37 deletions(-)
Title: Shiny Matrix Input Field
Description: Implements a custom matrix input field.
Author: Andreas Neudecker
Maintainer: Andreas Neudecker <andreas.neudecker@inwt-statistics.de>
Diff between shinyMatrix versions 0.4.0 dated 2020-10-05 and 0.5.0 dated 2021-05-11
shinyMatrix-0.4.0/shinyMatrix/inst/appCopy |only shinyMatrix-0.4.0/shinyMatrix/inst/appCustom |only shinyMatrix-0.4.0/shinyMatrix/inst/appModal |only shinyMatrix-0.4.0/shinyMatrix/inst/www/matrixInput.css |only shinyMatrix-0.4.0/shinyMatrix/inst/www/matrixInput.js |only shinyMatrix-0.5.0/shinyMatrix/DESCRIPTION | 9 +- shinyMatrix-0.5.0/shinyMatrix/MD5 | 37 ++++----- shinyMatrix-0.5.0/shinyMatrix/NAMESPACE | 1 shinyMatrix-0.5.0/shinyMatrix/R/00-Namespace.R | 2 shinyMatrix-0.5.0/shinyMatrix/R/jsonToMatrix.R | 8 +- shinyMatrix-0.5.0/shinyMatrix/R/matrixInput.R | 64 +++++++++++----- shinyMatrix-0.5.0/shinyMatrix/README.md | 37 +++------ shinyMatrix-0.5.0/shinyMatrix/inst/app/ui.R | 4 - shinyMatrix-0.5.0/shinyMatrix/inst/appDelete |only shinyMatrix-0.5.0/shinyMatrix/inst/appDoubleHeader |only shinyMatrix-0.5.0/shinyMatrix/inst/appExtend/ui.R | 10 +- shinyMatrix-0.5.0/shinyMatrix/inst/appUpdate/server.R | 5 + shinyMatrix-0.5.0/shinyMatrix/inst/www/lodash.min.js |only shinyMatrix-0.5.0/shinyMatrix/inst/www/matrix-input.css |only shinyMatrix-0.5.0/shinyMatrix/inst/www/matrix-input.js |only shinyMatrix-0.5.0/shinyMatrix/inst/www/vue.js |only shinyMatrix-0.5.0/shinyMatrix/man/matrixInput.Rd | 15 ++- 22 files changed, 108 insertions(+), 84 deletions(-)
Title: Simulation of High-Dimensional Data and Parallelized Repeated
Penalized Regression
Description: Simulation of continuous, correlated high-dimensional data with
time to event or binary response, and parallelized functions for Lasso,
Ridge, and Elastic Net penalized regression with repeated starts and
two-dimensional tuning of the Elastic Net.
Author: Levi Waldron <lwaldron.research@gmail.com>
Maintainer: Levi Waldron <lwaldron.research@gmail.com>
Diff between pensim versions 1.3.2 dated 2020-04-20 and 1.3.3 dated 2021-05-11
pensim-1.3.2/pensim/NEWS.md |only pensim-1.3.3/pensim/DESCRIPTION | 8 pensim-1.3.3/pensim/MD5 | 7 pensim-1.3.3/pensim/README.md | 10 pensim-1.3.3/pensim/inst/doc/pensim.html | 435 +++++++++---------------------- 5 files changed, 142 insertions(+), 318 deletions(-)
Title: Visualization of a Correlation Matrix
Description: A graphical display of a correlation matrix or general matrix.
It also contains some algorithms to do matrix reordering. In addition,
corrplot is good at details, including choosing color, text labels,
color labels, layout, etc.
Author: Taiyun Wei [cre, aut],
Viliam Simko [aut],
Michael Levy [ctb],
Yihui Xie [ctb],
Yan Jin [ctb],
Jeff Zemla [ctb],
Moritz Freidank [ctb],
Jun Cai [ctb],
Tomas Protivinsky [ctb]
Maintainer: Taiyun Wei <weitaiyun@gmail.com>
Diff between corrplot versions 0.87 dated 2021-05-08 and 0.88 dated 2021-05-11
DESCRIPTION | 10 MD5 | 36 - R/corrMatOrder.R | 4 R/corrplot.R | 142 ++--- build/vignette.rds |binary inst/NEWS | 15 inst/doc/corrplot-intro.R | 119 +--- inst/doc/corrplot-intro.Rmd | 212 +++----- inst/doc/corrplot-intro.html | 911 +++++++++++++++--------------------- man/corrMatOrder.Rd | 8 man/corrRect.Rd | 14 man/corrRect.hclust.Rd | 14 man/corrplot.Rd | 50 + tests/testthat/test-corrplot.R | 6 vignettes/corrplot-intro.Rmd | 212 +++----- vignettes/example-corrMatOrder.R | 4 vignettes/example-corrRect.R | 14 vignettes/example-corrRect.hclust.R | 14 vignettes/example-corrplot.R | 32 + 19 files changed, 854 insertions(+), 963 deletions(-)
Title: Classical Age-Depth Modelling of Cores from Deposits
Description: Performs 'classical' age-depth modelling of dated sediment deposits - prior to applying more sophisticated techniques such as Bayesian age-depth modelling. Any radiocarbon dated depths are calibrated. Age-depth models are constructed by sampling repeatedly from the dated levels, each time drawing age-depth curves. Model types include linear interpolation, linear or polynomial regression, and a range of splines. See Blaauw (2010). <doi:10.1016/j.quageo.2010.01.002>.
Author: Maarten Blaauw [aut, cre],
J. Andres Christen [ctb],
Judith Esquivel Vazquez [ctb],
Simon Goring [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between clam versions 2.3.8 dated 2021-01-23 and 2.3.9 dated 2021-05-11
clam-2.3.8/clam/man/mix.calibrationcurves.Rd |only clam-2.3.9/clam/DESCRIPTION | 11 ++++--- clam-2.3.9/clam/MD5 | 15 ++++------ clam-2.3.9/clam/NAMESPACE | 6 ---- clam-2.3.9/clam/NEWS.md | 3 ++ clam-2.3.9/clam/R/calibrate.R | 39 --------------------------- clam-2.3.9/clam/R/clam.R | 5 +-- clam-2.3.9/clam/R/readwrite.R | 2 - clam-2.3.9/clam/build/partial.rdb |binary 9 files changed, 20 insertions(+), 61 deletions(-)
Title: Bayesian Estimation for Finite Mixture of Distributions
Description: Provides statistical tools for Bayesian estimation of mixture distributions, mainly a mixture of Gamma, Normal, and t-distributions. The package is implemented based on the Bayesian literature for the finite mixture of distributions, including Mohammadi and et al. (2013) <doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) <doi:10.1080/03610918.2011.588358>.
Author: Reza Mohammadi [aut, cre] (<https://orcid.org/0000-0001-9538-0648>)
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between bmixture versions 1.6 dated 2020-05-26 and 1.7 dated 2021-05-11
DESCRIPTION | 8 ++--- MD5 | 49 +++++++++++++++++----------------- NEWS.md | 8 ++++- R/bmixgamma.R | 63 +++++++++++++++++++++++--------------------- R/bmixnorm.R | 66 ++++++++++++++++++++++++----------------------- R/bmixnorm_bdmcmc.R | 49 +++++++++++++++++----------------- R/bmixt.R | 64 ++++++++++++++++++++++++--------------------- R/mixgamma.R | 35 ++++++++++++------------ R/mixnorm.R | 35 ++++++++++++------------ R/mixt.R | 37 ++++++++++++++------------ R/rdirichlet.R | 30 +++++++++++---------- README.md | 14 +++++---- build |only man/bmixgamma.Rd | 66 ++++++++++++++++++++++++++--------------------- man/bmixnorm.Rd | 58 ++++++++++++++++++++++------------------- man/bmixt.Rd | 63 ++++++++++++++++++++++++-------------------- man/bmixture-internal.Rd | 1 man/bmixture-package.Rd | 12 ++++---- man/galaxy.Rd | 60 +++++++++++++++++++++--------------------- man/mixgamma.Rd | 18 ++++++------ man/mixnorm.Rd | 19 +++++++------ man/mixt.Rd | 26 ++++++++++-------- man/print.bmixt.Rd | 3 +- man/rdirichlet.Rd | 6 ++-- man/summary.bmixnorm.Rd | 1 man/summary.bmixt.Rd | 1 26 files changed, 423 insertions(+), 369 deletions(-)
Title: Native R Kernel for the 'Jupyter Notebook'
Description: The R kernel for the 'Jupyter' environment executes R code which the front-end
('Jupyter Notebook' or other front-ends) submits to the kernel via the network.
Author: Thomas Kluyver [aut, cph],
Philipp Angerer [aut, cph, cre]
(<https://orcid.org/0000-0002-0369-2888>),
Jan Schulz [aut, cph],
Karthik Ram [aut, cph]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>
Diff between IRkernel versions 1.1.1 dated 2020-07-20 and 1.2 dated 2021-05-11
DESCRIPTION | 7 +-- MD5 | 20 ++++++---- R/completion.r | 2 - R/environment_shadow.r | 10 +++-- R/execution.r | 2 - R/kernel.r | 12 ++++-- README.md | 11 +++-- tests/testthat/__pycache__/test_ir.cpython-38.pyc |binary tests/testthat/__pycache__/test_ir.cpython-39.pyc |only tests/testthat/jkt/jupyter_kernel_test/__pycache__/__init__.cpython-39.pyc |only tests/testthat/jkt/jupyter_kernel_test/__pycache__/messagespec.cpython-39.pyc |only tests/testthat/jkt/jupyter_kernel_test/__pycache__/messagespec_common.cpython-39.pyc |only tests/testthat/test_ir.py | 3 + 13 files changed, 39 insertions(+), 28 deletions(-)
Title: Textual Statistics for the Quantitative Analysis of Textual Data
Description: Textual statistics functions formerly in the 'quanteda' package.
Textual statistics for characterizing and comparing textual data. Includes
functions for measuring term and document frequency, the co-occurrence of
words, similarity and distance between features and documents, feature entropy,
keyword occurrence, readability, and lexical diversity. These functions
extend the 'quanteda' package and are specially designed for sparse textual data.
Author: Kenneth Benoit [cre, aut, cph]
(<https://orcid.org/0000-0002-0797-564X>),
Kohei Watanabe [aut] (<https://orcid.org/0000-0001-6519-5265>),
Haiyan Wang [aut] (<https://orcid.org/0000-0003-4992-4311>),
Jiong Wei Lua [aut],
Jouni Kuha [aut] (<https://orcid.org/0000-0002-1156-8465>),
European Research Council [fnd] (ERC-2011-StG 283794-QUANTESS)
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda.textstats versions 0.94 dated 2021-04-06 and 0.94.1 dated 2021-05-11
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/textstat_simil.R | 17 +++++++++-------- R/textstat_summary.R | 15 ++++++++++++--- README.md | 2 +- build/partial.rdb |binary inst/WORDLIST | 1 + tests/testthat/test-textstat_proxy.R | 11 +++-------- 10 files changed, 44 insertions(+), 32 deletions(-)
More information about quanteda.textstats at CRAN
Permanent link
Title: Mail Merge Using R Markdown Documents and 'gmailr'
Description: Mail merge using markdown documents and gmail. With
this package you can parse markdown documents as the body of email,
and the 'yaml' header to specify the subject line of the email. Any
'{}' braces in the email will be encoded with 'glue::glue()'. You can
preview the email in the RStudio viewer pane, and send (draft) email
using 'gmailr'.
Author: Andrie de Vries [aut, cre]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between mailmerge versions 0.2.0 dated 2021-04-12 and 0.2.1 dated 2021-05-11
mailmerge-0.2.0/mailmerge/tests/testthat/test-mm_send_mail.R |only mailmerge-0.2.1/mailmerge/DESCRIPTION | 13 +- mailmerge-0.2.1/mailmerge/MD5 | 24 ++-- mailmerge-0.2.1/mailmerge/NEWS.md | 4 mailmerge-0.2.1/mailmerge/R/helpers.R | 60 +++++------ mailmerge-0.2.1/mailmerge/R/mail_merge.R | 33 ++++-- mailmerge-0.2.1/mailmerge/README.md | 14 ++ mailmerge-0.2.1/mailmerge/inst/WORDLIST | 3 mailmerge-0.2.1/mailmerge/inst/doc/introduction.R | 6 + mailmerge-0.2.1/mailmerge/inst/doc/introduction.html | 8 + mailmerge-0.2.1/mailmerge/man/fragments/intro_example.Rmd | 6 + mailmerge-0.2.1/mailmerge/man/mail_merge.Rd | 5 mailmerge-0.2.1/mailmerge/man/mailmerge-package.Rd | 1 mailmerge-0.2.1/mailmerge/tests/testthat/test-mail_merge.R |only 14 files changed, 119 insertions(+), 58 deletions(-)
Title: Mini Charts for Interactive Maps
Description: Add and modify small charts on an interactive map created with
package 'leaflet'. These charts can be used to represent at same time multiple
variables on a single map.
Author: Veronique Bachelier [aut, cre],
Jalal-Edine ZAWAM [aut],
Benoit Thieurmel [aut],
Francois Guillem [aut],
RTE [cph]
Maintainer: Veronique Bachelier <veronique.bachelier@rte-france.com>
Diff between leaflet.minicharts versions 0.6.0 dated 2019-11-27 and 0.6.2 dated 2021-05-11
DESCRIPTION | 8 MD5 | 36 NAMESPACE | 2 NEWS | 164 - R/add_flows.R | 18 R/add_minicharts.R | 21 R/data-doc.R | 2 README.md | 12 build/vignette.rds |binary inst/doc/introduction.Rmd | 368 +-- inst/doc/introduction.html | 4366 +---------------------------------------- inst/leaflet.minicharts.min.js | 30 man/addFlows.Rd | 269 +- man/addMinicharts.Rd | 438 ++-- man/d3.schemeCategory10.Rd | 44 man/eco2mix.Rd | 70 man/popupArgs.Rd | 92 man/syncWith.Rd | 92 vignettes/introduction.Rmd | 368 +-- 19 files changed, 1199 insertions(+), 5201 deletions(-)
More information about leaflet.minicharts at CRAN
Permanent link
Title: Dynamic Range Boxes
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>,
Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>,
Robert R. Junker <Robert.Junker@sbg.ac.at>,
Jonas Kuppler <Jonas.Kuppler@uni-duesseldorf.de>,
Arne Bathke <Arne.Bathke@sbg.ac.at>,
Judith H. Parkinson <judith.parkinson@sbg.ac.at>,
Raoul Kutil <Raoul_Hugo.Kutil@stud.sbg.ac.at>
Maintainer: Florian Griessenberger <florian.griessenberger@sbg.ac.at>
Diff between dynRB versions 0.15 dated 2018-12-18 and 0.16 dated 2021-05-11
DESCRIPTION | 10 MD5 | 24 - build/vignette.rds |binary inst/doc/TutorialdynRB.R | 18 + inst/doc/TutorialdynRB.html | 633 +++++++++++++++++++++++++++++++------------- man/dynRB-package.Rd | 7 man/dynRB_Pn.Rd | 8 man/dynRB_VPa.Rd | 8 man/dynRB_Vn.Rd | 8 man/finch.Rd | 4 man/finch2.Rd | 4 man/overview.Rd | 8 man/ranks_OV.Rd | 4 13 files changed, 504 insertions(+), 232 deletions(-)
Title: Chaos Game
Description: The main objective of the package is to enter a word of at least two letters based on which an Iterated Function System with Probabilities is constructed, and a two-dimensional fractal containing the chosen word infinitely often is generated via the Chaos Game. Additionally, the package allows to project the two-dimensional fractal on several three-dimensional surfaces and to transform the fractal into another fractal with uniform marginals.
Author: Florian Griessenberger [aut, cre],
Manuela Schreyer [aut],
Johannes Bartel [aut],
Wolfgang Trutschnig [aut]
Maintainer: Florian Griessenberger <florian.griessenberger@sbg.ac.at>
Diff between ChaosGame versions 1.0 dated 2021-03-01 and 1.1 dated 2021-05-11
DESCRIPTION | 11 +++++------ MD5 | 4 ++-- NAMESPACE | 8 +++++++- 3 files changed, 14 insertions(+), 9 deletions(-)
Title: Computes Proximity in Large Sparse Matrices
Description: Computes proximity between rows or columns of large matrices efficiently in C++.
Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries.
Among several built-in similarity/distance measures, computation of correlation,
cosine similarity and Euclidean distance is particularly fast.
Author: Kohei Watanabe [cre, aut, cph]
(<https://orcid.org/0000-0001-6519-5265>),
Robrecht Cannoodt [aut] (<https://orcid.org/0000-0003-3641-729X>)
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between proxyC versions 0.1.5 dated 2019-07-21 and 0.2.0 dated 2021-05-11
DESCRIPTION | 20 +++--- MD5 | 24 +++---- NEWS.md | 40 ++++++++---- R/RcppExports.R | 4 - R/proxy.R | 50 +++++++++------ man/colSds.Rd | 4 - man/simil.Rd | 48 +++++++++++--- src/RcppExports.cpp | 10 +-- src/linear.cpp | 7 +- src/pair.cpp | 142 ++++++++++++++++++++++++++------------------ tests/testthat/test-dist.R | 88 ++++++++++++++++++++------- tests/testthat/test-proxy.R | 95 +++++++++++++++++++---------- tests/testthat/test-simil.R | 23 +++---- 13 files changed, 357 insertions(+), 198 deletions(-)
Title: Relational Data Models
Description: Provides tools for working with multiple related
tables, stored as data frames or in a relational database. Multiple
tables (data and metadata) are stored in a compound object, which can
then be manipulated with a pipe-friendly syntax.
Author: Tobias Schieferdecker [aut],
Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Darko Bergant [aut],
Katharina Brunner [ctb],
James Wondrasek [ctb],
energie360° AG [fnd],
cynkra GmbH [fnd, cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between dm versions 0.2.0 dated 2021-05-03 and 0.2.1 dated 2021-05-11
dm-0.2.0/dm/man/dm_get_fk.Rd |only dm-0.2.1/dm/DESCRIPTION | 16 dm-0.2.1/dm/MD5 | 271 +++--- dm-0.2.1/dm/NAMESPACE | 14 dm-0.2.1/dm/NEWS.md | 25 dm-0.2.1/dm/R/aaa-dbplyr.R | 2 dm-0.2.1/dm/R/aaa-dplyr.R | 2 dm-0.2.1/dm/R/add-tbl.R | 24 dm-0.2.1/dm/R/bind.R | 2 dm-0.2.1/dm/R/data-model-helpers.R | 3 dm-0.2.1/dm/R/datamodelr-code.R | 5 dm-0.2.1/dm/R/db-helpers.R | 49 - dm-0.2.1/dm/R/db-interface.R | 3 dm-0.2.1/dm/R/disambiguate.R | 52 - dm-0.2.1/dm/R/dm-from-src.R | 1 dm-0.2.1/dm/R/dm.R | 209 +---- dm-0.2.1/dm/R/dplyr-src.R | 2 dm-0.2.1/dm/R/dplyr.R | 64 - dm-0.2.1/dm/R/draw-dm.R | 34 dm-0.2.1/dm/R/error-helpers.R | 17 dm-0.2.1/dm/R/examine-constraints.R | 14 dm-0.2.1/dm/R/filter-dm.R | 16 dm-0.2.1/dm/R/filter-helpers.R | 17 dm-0.2.1/dm/R/flatten.R | 6 dm-0.2.1/dm/R/foreign-keys.R | 406 ++++++---- dm-0.2.1/dm/R/global.R | 6 dm-0.2.1/dm/R/graph.R | 2 dm-0.2.1/dm/R/import.R | 5 dm-0.2.1/dm/R/keys.R | 2 dm-0.2.1/dm/R/learn.R | 26 dm-0.2.1/dm/R/nest.R | 9 dm-0.2.1/dm/R/nycflights13.R | 25 dm-0.2.1/dm/R/paste.R | 26 dm-0.2.1/dm/R/pkgdown.R | 4 dm-0.2.1/dm/R/primary-keys.R | 242 +++-- dm-0.2.1/dm/R/ptype.R | 2 dm-0.2.1/dm/R/rows-db.R | 9 dm-0.2.1/dm/R/select-tbl.R | 7 dm-0.2.1/dm/R/select.R | 6 dm-0.2.1/dm/R/table-surgery.R | 6 dm-0.2.1/dm/R/test-dm.R | 68 - dm-0.2.1/dm/R/tidyr.R | 8 dm-0.2.1/dm/R/tidyselect.R | 9 dm-0.2.1/dm/R/unnest.R |only dm-0.2.1/dm/R/upgrade.R |only dm-0.2.1/dm/R/utils.R | 4 dm-0.2.1/dm/R/validate.R |only dm-0.2.1/dm/R/zoom.R | 196 ++-- dm-0.2.1/dm/R/zzx-deprecated.R | 56 - dm-0.2.1/dm/R/zzz.R | 17 dm-0.2.1/dm/demo/berlin.R | 3 dm-0.2.1/dm/demo/nyc.R | 6 dm-0.2.1/dm/demo/seattle.R | 6 dm-0.2.1/dm/inst/doc/dm.html | 10 dm-0.2.1/dm/inst/doc/howto-dm-copy.R | 5 dm-0.2.1/dm/inst/doc/howto-dm-copy.Rmd | 7 dm-0.2.1/dm/inst/doc/howto-dm-copy.html | 18 dm-0.2.1/dm/inst/doc/howto-dm-db.html | 4 dm-0.2.1/dm/inst/doc/howto-dm-df.html | 4 dm-0.2.1/dm/inst/doc/howto-dm-rows.html | 4 dm-0.2.1/dm/inst/doc/howto-dm-theory.html | 38 dm-0.2.1/dm/inst/doc/tech-dm-cdm.html | 71 - dm-0.2.1/dm/inst/doc/tech-dm-class.R | 18 dm-0.2.1/dm/inst/doc/tech-dm-class.Rmd | 67 - dm-0.2.1/dm/inst/doc/tech-dm-class.html | 122 +-- dm-0.2.1/dm/inst/doc/tech-dm-draw.html | 4 dm-0.2.1/dm/inst/doc/tech-dm-filter.R | 3 dm-0.2.1/dm/inst/doc/tech-dm-filter.Rmd | 3 dm-0.2.1/dm/inst/doc/tech-dm-filter.html | 118 +- dm-0.2.1/dm/inst/doc/tech-dm-join.R | 3 dm-0.2.1/dm/inst/doc/tech-dm-join.Rmd | 3 dm-0.2.1/dm/inst/doc/tech-dm-join.html | 47 - dm-0.2.1/dm/inst/doc/tech-dm-low-level.html | 4 dm-0.2.1/dm/inst/doc/tech-dm-zoom.html | 68 - dm-0.2.1/dm/inst/extdata |only dm-0.2.1/dm/man/dm.Rd | 16 dm-0.2.1/dm/man/dm_add_fk.Rd | 89 -- dm-0.2.1/dm/man/dm_add_pk.Rd | 47 - dm-0.2.1/dm/man/dm_enum_fk_candidates.Rd | 3 dm-0.2.1/dm/man/dm_get_all_fks.Rd | 22 dm-0.2.1/dm/man/dm_get_all_pks.Rd | 18 dm-0.2.1/dm/man/dm_get_pk.Rd | 48 - dm-0.2.1/dm/man/dm_has_fk.Rd | 31 dm-0.2.1/dm/man/dm_has_pk.Rd | 2 dm-0.2.1/dm/man/dm_rm_fk.Rd |only dm-0.2.1/dm/man/dm_rm_pk.Rd |only dm-0.2.1/dm/man/dplyr_src.Rd | 2 dm-0.2.1/dm/man/enum_pk_candidates.Rd | 4 dm-0.2.1/dm/tests/testthat/_snaps/bind.md | 44 - dm-0.2.1/dm/tests/testthat/_snaps/dm.md | 34 dm-0.2.1/dm/tests/testthat/_snaps/dplyr.md | 389 +++++++++ dm-0.2.1/dm/tests/testthat/_snaps/draw-dm.md | 105 ++ dm-0.2.1/dm/tests/testthat/_snaps/draw-dm/dm-for-filter.svg |only dm-0.2.1/dm/tests/testthat/_snaps/draw-dm/nycflight-dm-copy.svg | 4 dm-0.2.1/dm/tests/testthat/_snaps/error-helpers.md | 11 dm-0.2.1/dm/tests/testthat/_snaps/examine-constraints.md | 8 dm-0.2.1/dm/tests/testthat/_snaps/filter-dm.md | 208 +++++ dm-0.2.1/dm/tests/testthat/_snaps/foreign-keys.md | 210 ++++- dm-0.2.1/dm/tests/testthat/_snaps/paste.md | 48 - dm-0.2.1/dm/tests/testthat/_snaps/primary-keys.md | 177 ++++ dm-0.2.1/dm/tests/testthat/_snaps/rows-dm.md | 348 ++++---- dm-0.2.1/dm/tests/testthat/_snaps/select-tbl.md | 4 dm-0.2.1/dm/tests/testthat/_snaps/select.md | 57 + dm-0.2.1/dm/tests/testthat/_snaps/tidyr.md | 196 ++++ dm-0.2.1/dm/tests/testthat/_snaps/zoom.md | 74 + dm-0.2.1/dm/tests/testthat/_snaps/zzx-deprecated.md |only dm-0.2.1/dm/tests/testthat/dm |only dm-0.2.1/dm/tests/testthat/helper-expectations.R | 15 dm-0.2.1/dm/tests/testthat/helper-print.R | 6 dm-0.2.1/dm/tests/testthat/helper-src.R | 140 +-- dm-0.2.1/dm/tests/testthat/helper-zoom.R | 16 dm-0.2.1/dm/tests/testthat/setup.R |only dm-0.2.1/dm/tests/testthat/test-db-interface.R | 7 dm-0.2.1/dm/tests/testthat/test-disambiguate.R | 4 dm-0.2.1/dm/tests/testthat/test-dm-from-src.R | 9 dm-0.2.1/dm/tests/testthat/test-dm.R | 223 ----- dm-0.2.1/dm/tests/testthat/test-dplyr-src.R |only dm-0.2.1/dm/tests/testthat/test-dplyr.R | 276 +++--- dm-0.2.1/dm/tests/testthat/test-draw-dm.R | 71 - dm-0.2.1/dm/tests/testthat/test-error-helpers.R | 4 dm-0.2.1/dm/tests/testthat/test-filter-dm.R | 53 - dm-0.2.1/dm/tests/testthat/test-flatten.R | 21 dm-0.2.1/dm/tests/testthat/test-foreign-keys.R | 158 ++- dm-0.2.1/dm/tests/testthat/test-learn.R | 66 - dm-0.2.1/dm/tests/testthat/test-nest.R | 12 dm-0.2.1/dm/tests/testthat/test-paste.R | 5 dm-0.2.1/dm/tests/testthat/test-primary-keys.R | 98 +- dm-0.2.1/dm/tests/testthat/test-rows-db.R | 2 dm-0.2.1/dm/tests/testthat/test-rows-dm.R | 36 dm-0.2.1/dm/tests/testthat/test-schema.R | 3 dm-0.2.1/dm/tests/testthat/test-select-tbl.R | 3 dm-0.2.1/dm/tests/testthat/test-select.R | 106 +- dm-0.2.1/dm/tests/testthat/test-table-surgery.R | 6 dm-0.2.1/dm/tests/testthat/test-tidyr.R | 57 - dm-0.2.1/dm/tests/testthat/test-upgrade.R |only dm-0.2.1/dm/tests/testthat/test-utils.R | 4 dm-0.2.1/dm/tests/testthat/test-validate.R |only dm-0.2.1/dm/tests/testthat/test-zoom.R | 47 - dm-0.2.1/dm/tests/testthat/test-zzx-deprecated.R | 145 +-- dm-0.2.1/dm/vignettes/howto-dm-copy.Rmd | 7 dm-0.2.1/dm/vignettes/tech-dm-class.Rmd | 67 - dm-0.2.1/dm/vignettes/tech-dm-filter.Rmd | 3 dm-0.2.1/dm/vignettes/tech-dm-join.Rmd | 3 143 files changed, 3836 insertions(+), 2661 deletions(-)
Title: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
Description: Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm from McCormick et al. (2016) <DOI:10.1080/01621459.2016.1152191>. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA4' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Author: Zehang Richard Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Richard Li <lizehang@gmail.com>
Diff between InSilicoVA versions 1.3.0 dated 2020-06-30 and 1.3.1 dated 2021-05-11
InSilicoVA-1.3.0/InSilicoVA/man/InsilicoVA-package.Rd |only InSilicoVA-1.3.0/InSilicoVA/tests/testthat/warnings.txt |only InSilicoVA-1.3.1/InSilicoVA/DESCRIPTION | 10 +- InSilicoVA-1.3.1/InSilicoVA/MD5 | 56 +++++------ InSilicoVA-1.3.1/InSilicoVA/NEWS.md | 5 - InSilicoVA-1.3.1/InSilicoVA/R/diag.r | 9 + InSilicoVA-1.3.1/InSilicoVA/R/get_indiv.r | 23 ++-- InSilicoVA-1.3.1/InSilicoVA/R/groupplot.r | 9 + InSilicoVA-1.3.1/InSilicoVA/R/indivplot.r | 9 + InSilicoVA-1.3.1/InSilicoVA/R/insilico_core.r | 4 InSilicoVA-1.3.1/InSilicoVA/R/insilico_standard.r | 6 - InSilicoVA-1.3.1/InSilicoVA/R/insilico_train.r | 2 InSilicoVA-1.3.1/InSilicoVA/R/plot.r | 9 + InSilicoVA-1.3.1/InSilicoVA/R/print_insilico.r | 9 + InSilicoVA-1.3.1/InSilicoVA/R/print_insilico_summary.r | 9 + InSilicoVA-1.3.1/InSilicoVA/R/report.r | 9 + InSilicoVA-1.3.1/InSilicoVA/man/csmf.diag.Rd | 19 ++-- InSilicoVA-1.3.1/InSilicoVA/man/extract.prob.Rd | 11 +- InSilicoVA-1.3.1/InSilicoVA/man/get.indiv.Rd | 19 ++-- InSilicoVA-1.3.1/InSilicoVA/man/indivplot.Rd | 31 ++++-- InSilicoVA-1.3.1/InSilicoVA/man/insilico.Rd | 57 ++++++++---- InSilicoVA-1.3.1/InSilicoVA/man/insilico.fit.Rd | 66 ++++++++++---- InSilicoVA-1.3.1/InSilicoVA/man/insilico.train.Rd | 57 ++++++++---- InSilicoVA-1.3.1/InSilicoVA/man/physician_debias.Rd | 12 ++ InSilicoVA-1.3.1/InSilicoVA/man/plot.insilico.Rd | 32 ++++-- InSilicoVA-1.3.1/InSilicoVA/man/print.insilico.Rd | 8 - InSilicoVA-1.3.1/InSilicoVA/man/print.insilico_summary.Rd | 8 - InSilicoVA-1.3.1/InSilicoVA/man/stackplot.Rd | 36 +++++-- InSilicoVA-1.3.1/InSilicoVA/man/summary.insilico.Rd | 19 ++-- InSilicoVA-1.3.1/InSilicoVA/man/updateIndiv.Rd | 8 - 30 files changed, 361 insertions(+), 191 deletions(-)
Title: Functions for Medical Statistics Book with some Demographic Data
Description: Several utility functions for the book entitled
"Practices of Medical and Health Data Analysis using R"
(Pearson Education Japan, 2007) with Japanese demographic
data and some demographic analysis related functions.
Author: Minato Nakazawa <minato-nakazawa@umin.net>
Maintainer: Minato Nakazawa <minato-nakazawa@umin.net>
Diff between fmsb versions 0.7.0 dated 2019-12-15 and 0.7.1 dated 2021-05-11
DESCRIPTION | 8 +++---- MD5 | 37 +++++++++++++++++++----------------- NAMESPACE | 3 +- NEWS | 6 +++++ R/demogjpn.R | 49 ++++++++++++++++++++++++++++-------------------- build |only man/CM.Rd | 4 --- man/CT.Rd | 3 -- man/Denny.Rd | 3 -- man/H27MPJ.Rd |only man/Hadwiger.Rd | 3 -- man/JASM.Rd | 5 ---- man/Jfert.Rd | 7 ++---- man/Jlife.Rd | 10 ++++----- man/Jpop.Rd | 6 ++--- man/Jpopl.Rd | 6 ++--- man/Jvital.Rd | 30 ++++++++++++++--------------- man/Jvital2013byPref.Rd | 4 +-- man/PrefYLL2015.Rd | 8 +++---- man/S60MPJ.Rd | 2 - tests |only 21 files changed, 102 insertions(+), 92 deletions(-)
Title: Biological Structure Analysis
Description: Utilities to process, organize and explore protein structure,
sequence and dynamics data. Features include the ability to read and write
structure, sequence and dynamic trajectory data, perform sequence and structure
database searches, data summaries, atom selection, alignment, superposition,
rigid core identification, clustering, torsion analysis, distance matrix
analysis, structure and sequence conservation analysis, normal mode analysis,
principal component analysis of heterogeneous structure data, and correlation
network analysis from normal mode and molecular dynamics data. In addition,
various utility functions are provided to enable the statistical and graphical
power of the R environment to work with biological sequence and structural data.
Please refer to the URLs below for more information.
Author: Barry Grant [aut, cre],
Xin-Qiu Yao [aut],
Lars Skjaerven [aut],
Julien Ide [aut]
Maintainer: Barry Grant <bjgrant@ucsd.edu>
Diff between bio3d versions 2.4-1 dated 2020-01-21 and 2.4-2 dated 2021-05-11
DESCRIPTION | 13 MD5 | 154 ++++----- NAMESPACE | 6 R/aanma.pdbs.R | 49 -- R/arg_filter.R |only R/blast.pdb.R | 23 + R/chain.pdb.R | 53 ++- R/cmap.pdb.R | 41 ++ R/cna.ensmb.R | 1 R/cnapath.R | 8 R/core.cmap.R | 34 -- R/dm.R | 40 ++ R/filter.dccm.R | 73 ++++ R/get.blast.R | 6 R/get.seq.R | 30 + R/hmmer.R | 17 - R/pb.R |only R/pca.array.R | 22 + R/pdb.annotate.R | 621 ++++++++++++++++++++++++++++--------- R/pdbs2pdb.R | 23 + R/plot.blast.R | 2 R/plot.cna.R | 37 ++ R/plot.dccm.R | 29 + R/pymol.pdbs.R | 33 + R/read.dcd.R | 10 R/summary.cnapath.R | 15 R/vmd.cna.R | 12 R/vmd.cnapath.R | 69 +++- README.md | 39 +- inst/doc/bio3d_vignettes.Rmd | 41 +- inst/doc/bio3d_vignettes.html | 30 - man/aa.index.Rd | 4 man/aa2index.Rd | 2 man/bio3d.package.Rd | 15 man/blast.pdb.Rd | 2 man/chain.pdb.Rd | 2 man/cmap.Rd | 8 man/cna.Rd | 13 man/cnapath.Rd | 17 - man/dm.Rd | 12 man/dssp.Rd | 4 man/filter.dccm.Rd | 12 man/fit.xyz.Rd | 10 man/get.seq.Rd | 2 man/hmmer.Rd | 2 man/identify.cna.Rd | 6 man/layout.cna.Rd | 4 man/mustang.Rd | 2 man/pca.array.Rd | 5 man/pdb.annotate.Rd | 25 - man/pdbs2pdb.Rd | 3 man/plot.cna.Rd | 8 man/print.cna.Rd | 4 man/pymol.Rd | 11 man/read.fasta.Rd | 2 man/read.ncdf.Rd | 6 man/seq2aln.Rd | 2 man/seqaln.Rd | 8 man/seqaln.pair.Rd | 2 man/uniprot.Rd | 2 man/vmd.cna.Rd | 14 man/write.fasta.Rd | 2 man/write.ncdf.Rd | 6 src/read_pdb.cpp | 14 tests/testthat/test-aanma.pdbs.R | 2 tests/testthat/test-clean.pdb.R | 18 - tests/testthat/test-cna.R | 6 tests/testthat/test-fitting.R | 10 tests/testthat/test-get.pdb.R | 8 tests/testthat/test-get.seq.R | 127 ++++++- tests/testthat/test-mol2.R | 12 tests/testthat/test-nma.R | 4 tests/testthat/test-pdb.annotate.R | 50 +- tests/testthat/test-pdbsplit.R | 15 tests/testthat/test-read.all.R | 4 tests/testthat/test-read.cif.R | 10 tests/testthat/test-read.pdb.R | 39 +- tests/testthat/test-seqaln.R | 4 vignettes/bio3d_vignettes.Rmd | 41 +- 79 files changed, 1493 insertions(+), 619 deletions(-)
Title: Simulating Spreading Activation in a Network
Description: The notion of spreading activation is a prevalent metaphor in the cognitive sciences. This package provides the tools for cognitive scientists and psychologists to conduct computer simulations that implement spreading activation in a network representation. The algorithmic method implemented in 'spreadr' subroutines follows the approach described in Vitevitch, Ercal, and Adagarla (2011, Frontiers), who viewed activation as a fixed cognitive resource that could spread among nodes that were connected to each other via edges or connections (i.e., a network). See Vitevitch, M. S., Ercal, G., & Adagarla, B. (2011). Simulating retrieval from a highly clustered network: Implications for spoken word recognition. Frontiers in Psychology, 2, 369. <doi:10.3389/fpsyg.2011.00369> and Siew, C. S. Q. (2019). spreadr: A R package to simulate spreading activation in a network. Behavior Research Methods, 51, 910-929. <doi: 10.3758/s13428-018-1186-5>.
Author: Cynthia Siew [aut, cre],
Dirk U. Wulff [ctb],
Ning Yuan Lee [ctb]
Maintainer: Cynthia Siew <cynsiewsq@gmail.com>
Diff between spreadr versions 0.1.0 dated 2018-11-19 and 0.2.0 dated 2021-05-11
spreadr-0.1.0/spreadr/R/spreadr_2.R |only spreadr-0.1.0/spreadr/R/zzz.R |only spreadr-0.1.0/spreadr/man/spreadr_2.Rd |only spreadr-0.2.0/spreadr/DESCRIPTION | 32 spreadr-0.2.0/spreadr/MD5 | 32 spreadr-0.2.0/spreadr/NAMESPACE | 10 spreadr-0.2.0/spreadr/NEWS.md |only spreadr-0.2.0/spreadr/R/data.R |only spreadr-0.2.0/spreadr/R/spreadr.R | 308 +- spreadr-0.2.0/spreadr/build/vignette.rds |binary spreadr-0.2.0/spreadr/data |only spreadr-0.2.0/spreadr/inst/doc/spreadr_vignette.R | 194 + spreadr-0.2.0/spreadr/inst/doc/spreadr_vignette.Rmd | 333 ++- spreadr-0.2.0/spreadr/inst/doc/spreadr_vignette.html | 2066 ++++++++++++++++--- spreadr-0.2.0/spreadr/man/pnet.Rd |only spreadr-0.2.0/spreadr/man/pnetm.Rd |only spreadr-0.2.0/spreadr/man/spreadr.Rd | 118 - spreadr-0.2.0/spreadr/src/RcppExports.cpp | 4 spreadr-0.2.0/spreadr/src/create_mat_t.cpp | 30 spreadr-0.2.0/spreadr/vignettes/sources.bib |only spreadr-0.2.0/spreadr/vignettes/spreadr_vignette.Rmd | 333 ++- 21 files changed, 2791 insertions(+), 669 deletions(-)
Title: Matching-Adjusted Indirect Comparison
Description: A generalised workflow for generation of subject weights to be
used in Matching-Adjusted Indirect Comparison (MAIC) per Signorovitch et
al (2012) <doi:10.1016/j.jval.2012.05.004>, Signorovitch et al (2010)
<doi:10.2165/11538370-000000000-00000>. In MAIC, unbiased
comparison between outcomes of two trials is facilitated by weighting the
subject-level outcomes of one trial with weights derived such that the
weighted aggregate measures of the prognostic or effect modifying variables
are equal to those of the sample in the comparator trial. The functions and
classes included in this package wrap and abstract the process demonstrated
in the UK National Institute for Health and Care Excellence Decision
Support Unit (NICE DSU)'s example (Phillippo et al, (2016) [see URL]),
providing a repeatable and easily specifiable workflow for producing
multiple comparison variable sets against a variety of target studies, with
preprocessing for a number of aggregate target forms (e.g. mean, median,
domain limits).
Author: Rob Young [aut, cre]
Maintainer: Rob Young <rob.young@heor.co.uk>
Diff between maic versions 0.1.2 dated 2020-04-30 and 0.1.3 dated 2021-05-11
DESCRIPTION | 11 MD5 | 24 NEWS.md | 43 R/examples/maic.example.R | 76 - R/examples/maic.weight.example.R | 58 - R/maic.R | 1799 ++++++++++++++++----------------- README.md | 214 +-- man/createMAICInput.Rd | 8 man/reportCovariates.Rd | 5 tests/testthat.R | 8 tests/testthat/test_maicInput.R | 864 +++++++-------- tests/testthat/test_maicWeighting.R | 599 +++++----- tests/testthat/test_reportCovariates.R | 268 ++-- 13 files changed, 1984 insertions(+), 1993 deletions(-)
Title: Colorblind-Friendly Color Maps for R
Description: Color maps designed to improve graph readability for readers with
common forms of color blindness and/or color vision deficiency. The color
maps are also perceptually-uniform, both in regular form and also when
converted to black-and-white for printing. This package also contains
'ggplot2' bindings for discrete and continuous color and fill scales. A lean
version of the package called 'viridisLite' that does not include the
'ggplot2' bindings can be found at
<https://cran.r-project.org/package=viridisLite>.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph],
Bob Rudis [ctb, cph],
Marco Sciaini [ctb, cph],
Antônio Pedro Camargo [ctb, cph],
Cédric Scherer [ctb, cph]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridis versions 0.6.0 dated 2021-04-15 and 0.6.1 dated 2021-05-11
DESCRIPTION | 9 +++--- MD5 | 16 ++++++---- NEWS.md | 17 ++++++++++- R/scales.R | 20 +++++++++++++ data |only inst/doc/intro-to-viridis.R | 15 +++++----- inst/doc/intro-to-viridis.Rmd | 15 +++++----- inst/doc/intro-to-viridis.html | 61 ++++++++++++++++++++--------------------- man/unemp.Rd |only vignettes/intro-to-viridis.Rmd | 15 +++++----- 10 files changed, 104 insertions(+), 64 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut] (<https://orcid.org/0000-0001-8538-6691>),
Melissa Hallow [aut],
Wenping Wang [aut, cre],
Zufar Mulyukov [ctb],
Alan Hindmarsh [ctb],
Awad H. Al-Mohy [ctb],
Matt Dowle [ctb],
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Arun Srinivasan [ctb],
Ernst Hairer [ctb],
Gerhard Wanner [ctb],
Goro Fuji [ctb],
Hadley Wickham [ctb],
Jack Dongarra [ctb],
Linda Petzold [ctb],
Martin Maechler [ctb],
Matteo Fasiolo [ctb],
Morwenn [ctb],
Nicholas J. Higham [ctb],
Roger B. Sidje [ctb],
Simon Frost [ctb],
Kevin Ushey [ctb],
Yu Feng [ctb]
Maintainer: Wenping Wang <wwang8198@gmail.com>
Diff between RxODE versions 1.0.8 dated 2021-04-10 and 1.0.9 dated 2021-05-11
RxODE-1.0.8/RxODE/inst/tools/r-stripper |only RxODE-1.0.9/RxODE/DESCRIPTION | 10 RxODE-1.0.9/RxODE/MD5 | 72 +++-- RxODE-1.0.9/RxODE/NEWS.md | 31 ++ RxODE-1.0.9/RxODE/R/RxODE_md5.R | 2 RxODE-1.0.9/RxODE/R/rxParams.R | 25 +- RxODE-1.0.9/RxODE/R/rxsolve.R | 73 +++-- RxODE-1.0.9/RxODE/build/partial.rdb |binary RxODE-1.0.9/RxODE/configure | 5 RxODE-1.0.9/RxODE/configure.win | 5 RxODE-1.0.9/RxODE/inst/doc/RxODE-syntax.html | 14 - RxODE-1.0.9/RxODE/inst/include/RxODE.h | 1 RxODE-1.0.9/RxODE/inst/tools/workaround.R |only RxODE-1.0.9/RxODE/inst/workaround.R |only RxODE-1.0.9/RxODE/src/Makevars.in | 2 RxODE-1.0.9/RxODE/src/cfode.c | 46 +-- RxODE-1.0.9/RxODE/src/cfode_static.c | 8 RxODE-1.0.9/RxODE/src/common.h | 2 RxODE-1.0.9/RxODE/src/corfailure.c | 16 - RxODE-1.0.9/RxODE/src/correction.c | 88 +++---- RxODE-1.0.9/RxODE/src/etTran.cpp | 12 RxODE-1.0.9/RxODE/src/intdy.c | 28 +- RxODE-1.0.9/RxODE/src/lsoda.c | 210 ++++++++--------- RxODE-1.0.9/RxODE/src/methodswitch.c | 64 ++--- RxODE-1.0.9/RxODE/src/ode.h | 4 RxODE-1.0.9/RxODE/src/orderswitch.c | 66 ++--- RxODE-1.0.9/RxODE/src/par_solve.cpp | 39 --- RxODE-1.0.9/RxODE/src/prja.c | 36 +- RxODE-1.0.9/RxODE/src/rxData.cpp | 146 ----------- RxODE-1.0.9/RxODE/src/rxData.h | 2 RxODE-1.0.9/RxODE/src/scaleh.c | 36 +- RxODE-1.0.9/RxODE/src/solsy.c | 12 RxODE-1.0.9/RxODE/src/stoda.c | 268 +++++++++++----------- RxODE-1.0.9/RxODE/src/strncmp.c |only RxODE-1.0.9/RxODE/src/strncmp.h |only RxODE-1.0.9/RxODE/tests/testthat/test-idFactor.R | 20 - RxODE-1.0.9/RxODE/tests/testthat/test-issue-410.R |only RxODE-1.0.9/RxODE/tests/testthat/test-pipeline.R | 156 ------------ RxODE-1.0.9/RxODE/tests/testthat/test-resample.R | 26 -- 39 files changed, 609 insertions(+), 916 deletions(-)
Title: Convert Plot to 'grob' or 'ggplot' Object
Description: Convert plot function call (using expression or formula) to 'grob' or 'ggplot' object that compatible to the 'grid' and 'ggplot2' ecosystem. With this package, we are able to e.g. using 'cowplot' to align plots produced by 'base' graphics, 'ComplexHeatmap', 'eulerr', 'grid', 'lattice', 'magick', 'pheatmap', 'vcd' etc. by converting them to 'ggplot' objects.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggplotify versions 0.0.6 dated 2021-04-22 and 0.0.7 dated 2021-05-11
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 4 ++++ R/as-grob.R | 9 +++++++++ inst/doc/ggplotify.html | 8 ++++---- man/as-grob.Rd | 3 +++ 7 files changed, 30 insertions(+), 13 deletions(-)
Title: Fetch 'Phylogenies' from Many Sources
Description: Includes methods for fetching 'phylogenies' from a variety
of sources, including the 'Phylomatic' web service
(<http://phylodiversity.net/phylomatic/>), and 'Phylocom'
(<https://github.com/phylocom/phylocom/>).
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between brranching versions 0.6.0 dated 2020-06-12 and 0.7.0 dated 2021-05-11
brranching-0.6.0/brranching/build |only brranching-0.6.0/brranching/inst/doc |only brranching-0.6.0/brranching/vignettes |only brranching-0.7.0/brranching/DESCRIPTION | 19 ++++------ brranching-0.7.0/brranching/MD5 | 12 ++---- brranching-0.7.0/brranching/NEWS.md | 8 ++++ brranching-0.7.0/brranching/README.md | 9 +--- brranching-0.7.0/brranching/tests/testthat/test-phylomatic_names.R | 15 ++----- 8 files changed, 28 insertions(+), 35 deletions(-)
Title: Interface to Bold Systems API
Description: A programmatic interface to the Web Service methods provided by
Bold Systems (<http://www.boldsystems.org/>) for genetic 'barcode' data.
Functions include methods for searching by sequences by taxonomic names,
ids, collectors, and institutions; as well as a function for searching
for specimens, and downloading trace files.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between bold versions 1.1.0 dated 2020-06-17 and 1.2.0 dated 2021-05-11
bold-1.1.0/bold/build |only bold-1.1.0/bold/inst |only bold-1.1.0/bold/vignettes |only bold-1.2.0/bold/DESCRIPTION | 14 +++++++------- bold-1.2.0/bold/LICENSE | 4 ++-- bold-1.2.0/bold/MD5 | 13 ++++--------- bold-1.2.0/bold/NEWS.md | 7 +++++++ bold-1.2.0/bold/README.md | 8 ++------ 8 files changed, 22 insertions(+), 24 deletions(-)
Title: Tools for Analysing and Visualising Workplace Analytics Data
Description: Opinionated functions that enable easier and faster
analysis of Workplace Analytics data. There are three main types of functions in 'wpa':
(i) Standard functions create a 'ggplot' visual or a summary table based on a specific
Workplace Analytics metric; (2) Report Generation functions generate HTML reports on
a specific analysis area, e.g. Collaboration; (3) Other miscellaneous functions cover
more specific applications (e.g. Subject Line text mining) of Workplace Analytics data.
This package adheres to 'tidyverse' principles and works well with the pipe syntax.
'wpa' is built with the beginner-to-intermediate R users in mind, and is optimised for
simplicity.
Author: Martin Chan [aut, cre],
Carlos Morales [aut],
Mark Powers [ctb],
Ainize Cidoncha [ctb],
Rosamary Ochoa Vargas [ctb],
Tannaz Sattari [ctb],
Lucas Hogner [ctb],
Jasminder Thind [ctb],
Simone Liebal [ctb],
Ellen Trinklein [ctb],
Microsoft Corporation [cph]
Maintainer: Martin Chan <martin.chan@microsoft.com>
Diff between wpa versions 1.4.3 dated 2021-04-06 and 1.5.0 dated 2021-05-11
wpa-1.4.3/wpa/data/datalist |only wpa-1.5.0/wpa/DESCRIPTION | 6 wpa-1.5.0/wpa/MD5 | 301 ++++++++++++------------- wpa-1.5.0/wpa/NAMESPACE | 1 wpa-1.5.0/wpa/NEWS.md | 11 wpa-1.5.0/wpa/R/IV_by_Period.R | 4 wpa-1.5.0/wpa/R/check_query.R | 75 +++++- wpa-1.5.0/wpa/R/collaboration_rank.R | 2 wpa-1.5.0/wpa/R/create_bar.R | 80 ++---- wpa-1.5.0/wpa/R/create_bar_asis.R | 12 wpa-1.5.0/wpa/R/create_boxplot.R | 4 wpa-1.5.0/wpa/R/create_dist.R | 194 +++++++++++++--- wpa-1.5.0/wpa/R/create_fizz.R | 32 ++ wpa-1.5.0/wpa/R/create_hist.R | 11 wpa-1.5.0/wpa/R/create_line.R | 59 ++-- wpa-1.5.0/wpa/R/create_period_scatter.R | 20 - wpa-1.5.0/wpa/R/create_rank.R | 5 wpa-1.5.0/wpa/R/create_scatter.R | 3 wpa-1.5.0/wpa/R/create_stacked.R | 156 ++++++++++-- wpa-1.5.0/wpa/R/create_trend.R | 21 + wpa-1.5.0/wpa/R/cut_hour.R | 63 ++++- wpa-1.5.0/wpa/R/export.R | 2 wpa-1.5.0/wpa/R/flag_ch_ratio.R | 2 wpa-1.5.0/wpa/R/flex_index.R | 7 wpa-1.5.0/wpa/R/generate_report.R | 2 wpa-1.5.0/wpa/R/globals.R | 10 wpa-1.5.0/wpa/R/hrvar_count_all.R | 5 wpa-1.5.0/wpa/R/hrvar_trend.R |only wpa-1.5.0/wpa/R/identify_nkw.R | 27 +- wpa-1.5.0/wpa/R/init.R | 2 wpa-1.5.0/wpa/R/meetingtype_dist_ca.R | 4 wpa-1.5.0/wpa/R/meetingtype_dist_mt.R | 4 wpa-1.5.0/wpa/R/mgrrel_matrix.R | 50 +--- wpa-1.5.0/wpa/R/network_describe.R | 2 wpa-1.5.0/wpa/R/one2one_freq.R | 106 +++++--- wpa-1.5.0/wpa/R/p_test.R | 2 wpa-1.5.0/wpa/R/period_change.R | 2 wpa-1.5.0/wpa/R/personas_hclust.R | 1 wpa-1.5.0/wpa/R/remove_outliers.R | 2 wpa-1.5.0/wpa/R/tm_cooc.R | 4 wpa-1.5.0/wpa/R/track_hr_change.R | 4 wpa-1.5.0/wpa/R/workpatterns_classify.R | 86 +++++-- wpa-1.5.0/wpa/R/workpatterns_classify_bw.R | 240 ++++++++++++++++++- wpa-1.5.0/wpa/R/workpatterns_classify_pav.R | 2 wpa-1.5.0/wpa/R/workpatterns_rank.R | 11 wpa-1.5.0/wpa/R/workpatterns_report.R | 46 +-- wpa-1.5.0/wpa/README.md | 3 wpa-1.5.0/wpa/build/vignette.rds |binary wpa-1.5.0/wpa/inst/doc/intro-to-wpa.Rmd | 2 wpa-1.5.0/wpa/inst/doc/intro-to-wpa.html | 57 ++-- wpa-1.5.0/wpa/man/IV_by_period.Rd | 5 wpa-1.5.0/wpa/man/afterhours_dist.Rd | 1 wpa-1.5.0/wpa/man/afterhours_fizz.Rd | 1 wpa-1.5.0/wpa/man/afterhours_line.Rd | 1 wpa-1.5.0/wpa/man/afterhours_rank.Rd | 1 wpa-1.5.0/wpa/man/afterhours_summary.Rd | 1 wpa-1.5.0/wpa/man/afterhours_trend.Rd | 4 wpa-1.5.0/wpa/man/check_query.Rd | 4 wpa-1.5.0/wpa/man/collaboration_area.Rd | 1 wpa-1.5.0/wpa/man/collaboration_dist.Rd | 1 wpa-1.5.0/wpa/man/collaboration_fizz.Rd | 1 wpa-1.5.0/wpa/man/collaboration_line.Rd | 1 wpa-1.5.0/wpa/man/collaboration_rank.Rd | 5 wpa-1.5.0/wpa/man/collaboration_sum.Rd | 1 wpa-1.5.0/wpa/man/collaboration_trend.Rd | 4 wpa-1.5.0/wpa/man/create_bar.Rd | 24 + wpa-1.5.0/wpa/man/create_bar_asis.Rd | 1 wpa-1.5.0/wpa/man/create_boxplot.Rd | 1 wpa-1.5.0/wpa/man/create_bubble.Rd | 1 wpa-1.5.0/wpa/man/create_dist.Rd | 40 +++ wpa-1.5.0/wpa/man/create_fizz.Rd | 1 wpa-1.5.0/wpa/man/create_line.Rd | 1 wpa-1.5.0/wpa/man/create_line_asis.Rd | 1 wpa-1.5.0/wpa/man/create_period_scatter.Rd | 1 wpa-1.5.0/wpa/man/create_rank.Rd | 8 wpa-1.5.0/wpa/man/create_sankey.Rd | 1 wpa-1.5.0/wpa/man/create_scatter.Rd | 1 wpa-1.5.0/wpa/man/create_stacked.Rd | 22 + wpa-1.5.0/wpa/man/create_trend.Rd | 10 wpa-1.5.0/wpa/man/cut_hour.Rd | 8 wpa-1.5.0/wpa/man/email_dist.Rd | 1 wpa-1.5.0/wpa/man/email_fizz.Rd | 1 wpa-1.5.0/wpa/man/email_line.Rd | 1 wpa-1.5.0/wpa/man/email_rank.Rd | 1 wpa-1.5.0/wpa/man/email_summary.Rd | 1 wpa-1.5.0/wpa/man/email_trend.Rd | 4 wpa-1.5.0/wpa/man/export.Rd | 3 wpa-1.5.0/wpa/man/external_network_plot.Rd | 1 wpa-1.5.0/wpa/man/extract_hr.Rd | 1 wpa-1.5.0/wpa/man/flag_ch_ratio.Rd | 3 wpa-1.5.0/wpa/man/flag_em_ratio.Rd | 1 wpa-1.5.0/wpa/man/flag_extreme.Rd | 1 wpa-1.5.0/wpa/man/flag_outlooktime.Rd | 1 wpa-1.5.0/wpa/man/flex_index.Rd | 7 wpa-1.5.0/wpa/man/generate_report.Rd | 3 wpa-1.5.0/wpa/man/hr_trend.Rd | 2 wpa-1.5.0/wpa/man/hrvar_count.Rd | 2 wpa-1.5.0/wpa/man/hrvar_count_all.Rd | 3 wpa-1.5.0/wpa/man/hrvar_trend.Rd |only wpa-1.5.0/wpa/man/identify_churn.Rd | 1 wpa-1.5.0/wpa/man/identify_holidayweeks.Rd | 1 wpa-1.5.0/wpa/man/identify_inactiveweeks.Rd | 1 wpa-1.5.0/wpa/man/identify_nkw.Rd | 15 - wpa-1.5.0/wpa/man/identify_outlier.Rd | 1 wpa-1.5.0/wpa/man/identify_privacythreshold.Rd | 1 wpa-1.5.0/wpa/man/identify_query.Rd | 1 wpa-1.5.0/wpa/man/identify_shifts.Rd | 1 wpa-1.5.0/wpa/man/identify_shifts_wp.Rd | 1 wpa-1.5.0/wpa/man/identify_tenure.Rd | 1 wpa-1.5.0/wpa/man/internal_network_plot.Rd | 1 wpa-1.5.0/wpa/man/keymetrics_scan.Rd | 1 wpa-1.5.0/wpa/man/meeting_dist.Rd | 1 wpa-1.5.0/wpa/man/meeting_fizz.Rd | 1 wpa-1.5.0/wpa/man/meeting_line.Rd | 1 wpa-1.5.0/wpa/man/meeting_quality.Rd | 1 wpa-1.5.0/wpa/man/meeting_rank.Rd | 1 wpa-1.5.0/wpa/man/meeting_summary.Rd | 1 wpa-1.5.0/wpa/man/meeting_trend.Rd | 4 wpa-1.5.0/wpa/man/meetingtype_dist.Rd | 1 wpa-1.5.0/wpa/man/meetingtype_dist_ca.Rd | 5 wpa-1.5.0/wpa/man/meetingtype_dist_mt.Rd | 5 wpa-1.5.0/wpa/man/meetingtype_summary.Rd | 1 wpa-1.5.0/wpa/man/mgrcoatt_dist.Rd | 1 wpa-1.5.0/wpa/man/mgrrel_matrix.Rd | 4 wpa-1.5.0/wpa/man/one2one_dist.Rd | 1 wpa-1.5.0/wpa/man/one2one_fizz.Rd | 1 wpa-1.5.0/wpa/man/one2one_freq.Rd | 25 +- wpa-1.5.0/wpa/man/one2one_line.Rd | 1 wpa-1.5.0/wpa/man/one2one_rank.Rd | 1 wpa-1.5.0/wpa/man/one2one_sum.Rd | 1 wpa-1.5.0/wpa/man/one2one_trend.Rd | 4 wpa-1.5.0/wpa/man/p_test.Rd | 3 wpa-1.5.0/wpa/man/period_change.Rd | 4 wpa-1.5.0/wpa/man/personas_hclust.Rd | 3 wpa-1.5.0/wpa/man/remove_outliers.Rd | 4 wpa-1.5.0/wpa/man/standardise_pq.Rd | 1 wpa-1.5.0/wpa/man/subject_validate.Rd | 1 wpa-1.5.0/wpa/man/subject_validate_report.Rd | 1 wpa-1.5.0/wpa/man/tm_cooc.Rd | 5 wpa-1.5.0/wpa/man/track_HR_change.Rd | 6 wpa-1.5.0/wpa/man/validation_report.Rd | 1 wpa-1.5.0/wpa/man/workloads_dist.Rd | 1 wpa-1.5.0/wpa/man/workloads_fizz.Rd | 1 wpa-1.5.0/wpa/man/workloads_line.Rd | 1 wpa-1.5.0/wpa/man/workloads_rank.Rd | 1 wpa-1.5.0/wpa/man/workloads_summary.Rd | 1 wpa-1.5.0/wpa/man/workloads_trend.Rd | 4 wpa-1.5.0/wpa/man/workpatterns_area.Rd | 1 wpa-1.5.0/wpa/man/workpatterns_classify.Rd | 84 +++++- wpa-1.5.0/wpa/man/workpatterns_classify_bw.Rd | 185 ++++++++------- wpa-1.5.0/wpa/man/workpatterns_classify_pav.Rd | 163 ++++++------- wpa-1.5.0/wpa/man/workpatterns_rank.Rd | 1 wpa-1.5.0/wpa/vignettes/intro-to-wpa.Rmd | 2 153 files changed, 1754 insertions(+), 742 deletions(-)
Title: Automated Spectral Deconvolution, Alignment, and Metabolite
Identification in GC/MS-Based Untargeted Metabolomics
Description: Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. Outputs a table with compound names, matching scores and the integrated area of the compound for each sample. Package implementation is described in Domingo-Almenara et al. (2016) <doi:10.1021/acs.analchem.6b02927>.
Author: Xavier Domingo-Almenara [aut, cre, cph], Jasen P. Finch [ctb], Sara Samino [aut], Maria Vinaixa [aut], Alexandre Perera [aut, ths], Jesus Brezmes [aut, ths], Oscar Yanes [aut, ths]
Maintainer: Xavier Domingo-Almenara <xavier.domingoa@eurecat.org>
Diff between erah versions 1.1.1 dated 2020-07-06 and 1.1.2 dated 2021-05-11
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/zzz.R | 28 ++++++---------------------- inst/NEWS | 4 ++++ inst/doc/eRahManual.pdf |binary 5 files changed, 19 insertions(+), 31 deletions(-)
Title: Competing Proximal Gradients Library
Description: Functions to generate ensembles of generalized linear models using
competing proximal gradients. The optimal sparsity and diversity
tuning parameters are selected via an alternating grid search.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Stefan Van Aelst <stefan.vanaelst@kuleuven.be>,
Ruben Zamar <ruben@stat.ubc.ca>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between CPGLIB versions 1.0.0 dated 2021-05-10 and 1.0.1 dated 2021-05-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 3 +++ src/CPGLIB.cpp | 1 - src/CV_CPGLIB.cpp | 10 +++++++--- 5 files changed, 18 insertions(+), 12 deletions(-)
Title: Turn Your Git Commit Messages into a HTML Book
Description: Read all commit messages of your local git repository and
sort them according to tags or specific text pattern into chapters of
a HTML book using 'bookdown'. The git history book presentation helps
organisms required to testify for every changes in their source code,
in relation to features requests.
Author: Sébastien Rochette [aut, cre] (<https://orcid.org/0000-0002-1565-9313>),
Cervan Girard [aut] (<https://orcid.org/0000-0002-4816-4624>),
ThinkR [cph],
Institut de Recherches Internationales Servier [spn]
Maintainer: Sébastien Rochette <sebastien@thinkr.fr>
Diff between gitdown versions 0.1.1 dated 2021-05-10 and 0.1.2 dated 2021-05-10
DESCRIPTION | 6 - MD5 | 20 +-- NEWS.md | 4 R/get_info_files.R | 10 + R/git_down.R | 12 +- README.md | 54 +++++----- inst/doc/ab-create-git_down.html | 32 +++--- man/create_vignette_last_modif.Rd | 10 + man/git_down.Rd | 12 +- tests/testthat/test-get_info_files.R | 47 ++++----- tests/testthat/test-git_down.R | 182 +++++++++++++++++------------------ 11 files changed, 210 insertions(+), 179 deletions(-)
Title: A Faster 'ARFF' File Reader and Writer
Description: Reads and writes 'ARFF' files. 'ARFF' (Attribute-Relation
File Format) files are like 'CSV' files, with a little bit of added
meta information in a header and standardized NA values. They are
quite often used for machine learning data sets and were introduced
for the 'WEKA' machine learning 'Java' toolbox. See
<https://waikato.github.io/weka-wiki/formats_and_processing/arff_stable/>
for further info on 'ARFF' and for
<http://www.cs.waikato.ac.nz/ml/weka/> for more info on 'WEKA'.
'farff' gets rid of the 'Java' dependency that 'RWeka' enforces, and
it is at least a faster reader (for bigger files). It uses 'readr' as
parser back-end for the data section of the 'ARFF' file. Consistency
with 'RWeka' is tested on 'Github' and 'Travis CI' with hundreds of
'ARFF' files from 'OpenML'.
Author: Marc Becker [cre, aut] (<https://orcid.org/0000-0002-8115-0400>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Jakob Bossek [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between farff versions 1.1 dated 2019-05-03 and 1.1.1 dated 2021-05-10
farff-1.1.1/farff/DESCRIPTION | 53 +++++++++++++++++++++++++++---------- farff-1.1.1/farff/MD5 | 14 ++------- farff-1.1.1/farff/NEWS.md | 3 ++ farff-1.1.1/farff/man/readARFF.Rd | 10 +++++- farff-1.1.1/farff/man/writeARFF.Rd | 9 ++++-- farff-1.1/farff/tests |only 6 files changed, 61 insertions(+), 28 deletions(-)
Title: Adaptive Gauss Hermite Quadrature for Bayesian Inference
Description: Adaptive Gauss Hermite Quadrature for Bayesian inference.
The AGHQ method for normalizing posterior distributions
and making Bayesian inferences based on them. Functions are provided for doing
quadrature and marginal Laplace approximations, and summary methods are provided
for making inferences based on the results.
See Stringer (2021). "Implementing Adaptive Quadrature for Bayesian Inference:
the aghq Package" <arXiv:2101.04468>.
Author: Alex Stringer
Maintainer: Alex Stringer <alex.stringer@mail.utoronto.ca>
Diff between aghq versions 0.1.0 dated 2021-01-18 and 0.2.0 dated 2021-05-10
aghq-0.1.0/aghq/R/utils-pipe.R |only aghq-0.1.0/aghq/man/pipe.Rd |only aghq-0.2.0/aghq/DESCRIPTION | 11 aghq-0.2.0/aghq/MD5 | 75 +- aghq-0.2.0/aghq/NAMESPACE | 18 aghq-0.2.0/aghq/NEWS.md |only aghq-0.2.0/aghq/R/00-misc-support-functions.R | 180 ++++++ aghq-0.2.0/aghq/R/01-optimization.R | 2 aghq-0.2.0/aghq/R/02-normalization.R | 20 aghq-0.2.0/aghq/R/03-summary-statistics.R | 323 +++++++++--- aghq-0.2.0/aghq/R/04-aghq.R | 287 +++++++++- aghq-0.2.0/aghq/README.md | 6 aghq-0.2.0/aghq/inst/doc/aghq.R | 28 - aghq-0.2.0/aghq/inst/doc/aghq.Rmd | 28 - aghq-0.2.0/aghq/inst/doc/aghq.html | 43 - aghq-0.2.0/aghq/man/aghq.Rd | 1 aghq-0.2.0/aghq/man/compute_moment.Rd | 13 aghq-0.2.0/aghq/man/compute_pdf_and_cdf.Rd | 17 aghq-0.2.0/aghq/man/compute_quantiles.Rd | 24 aghq-0.2.0/aghq/man/default_control.Rd |only aghq-0.2.0/aghq/man/default_control_marglaplace.Rd |only aghq-0.2.0/aghq/man/default_control_tmb.Rd |only aghq-0.2.0/aghq/man/laplace_approximation.Rd | 1 aghq-0.2.0/aghq/man/marginal_laplace.Rd | 38 + aghq-0.2.0/aghq/man/marginal_laplace_tmb.Rd |only aghq-0.2.0/aghq/man/marginal_posterior.Rd | 12 aghq-0.2.0/aghq/man/normalize_logpost.Rd | 14 aghq-0.2.0/aghq/man/optimize_theta.Rd | 1 aghq-0.2.0/aghq/man/plot.aghq.Rd | 2 aghq-0.2.0/aghq/man/print.aghq.Rd | 1 aghq-0.2.0/aghq/man/print.aghqsummary.Rd | 2 aghq-0.2.0/aghq/man/print.laplace.Rd | 1 aghq-0.2.0/aghq/man/print.laplacesummary.Rd | 2 aghq-0.2.0/aghq/man/sample_marginal.Rd | 108 +++- aghq-0.2.0/aghq/man/summary.aghq.Rd | 1 aghq-0.2.0/aghq/man/summary.laplace.Rd | 2 aghq-0.2.0/aghq/tests/testthat/setup-01-optimization.R | 169 ++++++ aghq-0.2.0/aghq/tests/testthat/test-01-optimization.R | 43 + aghq-0.2.0/aghq/tests/testthat/test-02-normalization.R | 121 ++++ aghq-0.2.0/aghq/tests/testthat/test-03-summary-statistics.R | 97 +++ aghq-0.2.0/aghq/tests/testthat/test-04-aghq.R | 53 + aghq-0.2.0/aghq/vignettes/aghq.Rmd | 28 - 42 files changed, 1518 insertions(+), 254 deletions(-)
Title: Use Interdependent Filters on Table Columns in Shiny Apps
Description: Allows to connect 'selectizeInputs' widgets as filters to a 'reactable' table.
As known from spreadsheet applications, column filters are interdependent, so each
filter only shows the values that are really available at the moment based on
the current selection in other filters. Filter values currently not available
(and also those being available) can be shown via popovers or tooltips.
Author: Joachim Zuckarelli [aut, cre] (<https://orcid.org/0000-0002-9280-3016>)
Maintainer: Joachim Zuckarelli <joachim@zuckarelli.de>
Diff between shinyfilter versions 0.1.0 dated 2020-12-02 and 0.1.1 dated 2021-05-10
DESCRIPTION | 6 - MD5 | 12 +-- NEWS.md | 9 ++ R/shinyfilter.r | 49 ++++++++++--- README.md | 71 +++++++++---------- man/update_filters.Rd | 6 - man/update_tooltips.Rd | 181 +++++++++++++++++++++++++------------------------ 7 files changed, 189 insertions(+), 145 deletions(-)
Title: Network Analysis of Dependencies of CRAN Packages
Description: The dependencies of CRAN packages can be analysed in a network fashion. For each package we can obtain the packages that it depends, imports, suggests, etc. By iterating this procedure over a number of packages, we can build, visualise, and analyse the dependency network, enabling us to have a bird's-eye view of the CRAN ecosystem. One aspect of interest is the number of reverse dependencies of the packages, or equivalently the in-degree distribution of the dependency network. This can be fitted by the power law and/or an extreme value mixture distribution <arXiv:2008.03073>, of which functions are provided.
Author: Clement Lee [aut, cre] (<https://orcid.org/0000-0003-1785-8671>)
Maintainer: Clement Lee <clement.lee.tm@outlook.com>
Diff between crandep versions 0.1.1 dated 2020-09-12 and 0.2.0 dated 2021-05-10
DESCRIPTION | 6 MD5 | 62 ++++---- NAMESPACE | 1 NEWS.md | 10 + R/RcppExports.R | 46 +++--- R/data.R | 2 R/get_dep.R | 3 R/graph.R | 14 + README.md | 144 ++++++++++---------- build/vignette.rds |binary inst/doc/cran.R | 53 +++---- inst/doc/cran.Rmd | 58 ++++---- inst/doc/cran.html | 302 +++++++++++++++++++----------------------- inst/doc/degree.R | 12 + inst/doc/degree.Rmd | 26 +++ inst/doc/degree.html | 73 ++++++---- inst/doc/introduction.html | 58 ++++---- man/Smix.Rd | 12 - man/Supp.Rd | 4 man/chi_citations.Rd | 3 man/cran_dependencies.Rd | 3 man/dmix.Rd | 16 +- man/dupp.Rd | 4 man/get_dep.Rd | 3 man/get_dep_all_packages.Rd | 3 man/get_dep_df.Rd | 3 man/get_graph_all_packages.Rd | 7 man/mcmc_mix.Rd | 6 src/RcppExports.cpp | 50 +++--- src/algo.cpp | 97 ++++++++----- vignettes/cran.Rmd | 58 ++++---- vignettes/degree.Rmd | 26 +++ 32 files changed, 652 insertions(+), 513 deletions(-)
Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation
(ODE) based models typically employed in quantitative pharmacology and
systems biology.
Author: Kyle T Baron [aut, cre] (<https://orcid.org/0000-0001-7252-5656>),
Bill Gillespie [ctb],
Charles Margossian [ctb],
Devin Pastoor [ctb],
Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>),
Dilawar Singh [ctb],
Felicien Le Louedec [ctb] (<https://orcid.org/0000-0003-3699-2729>),
Timothy Waterhouse [ctb] (<https://orcid.org/0000-0002-0954-9660>),
Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between mrgsolve versions 0.11.0 dated 2021-03-28 and 0.11.1 dated 2021-05-10
mrgsolve-0.11.0/mrgsolve/man/drop_re.Rd |only mrgsolve-0.11.1/mrgsolve/DESCRIPTION | 6 mrgsolve-0.11.1/mrgsolve/MD5 | 28 +-- mrgsolve-0.11.1/mrgsolve/NAMESPACE | 5 mrgsolve-0.11.1/mrgsolve/R/class_mrgmod.R | 2 mrgsolve-0.11.1/mrgsolve/R/matlist.R | 129 ++++++++---------- mrgsolve-0.11.1/mrgsolve/R/mrgsolve.R | 26 +++ mrgsolve-0.11.1/mrgsolve/R/utils.R | 2 mrgsolve-0.11.1/mrgsolve/inst/include/odeproblem.h | 1 mrgsolve-0.11.1/mrgsolve/man/matlist.Rd | 20 -- mrgsolve-0.11.1/mrgsolve/man/mrgsim.Rd | 6 mrgsolve-0.11.1/mrgsolve/man/zero_re.Rd |only mrgsolve-0.11.1/mrgsolve/src/devtran.cpp | 22 ++- mrgsolve-0.11.1/mrgsolve/src/odeproblem.cpp | 5 mrgsolve-0.11.1/mrgsolve/tests/testthat/test-mrgsim.R | 14 + mrgsolve-0.11.1/mrgsolve/tests/testthat/test-rename.R | 3 16 files changed, 152 insertions(+), 117 deletions(-)
Title: Rule- And Instance-Based Regression Modeling
Description: Regression modeling using rules with added instance-based corrections.
Author: Max Kuhn [aut, cre],
Steve Weston [ctb],
Chris Keefer [ctb],
Nathan Coulter [ctb],
Ross Quinlan [aut] (Author of imported C code),
Rulequest Research Pty Ltd. [cph] (Copyright holder of imported C code)
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between Cubist versions 0.2.3 dated 2020-01-10 and 0.2.40 dated 2021-05-10
DESCRIPTION | 16 MD5 | 32 - R/cubist.R | 12 R/makeDataFile.R | 3 R/makeNamesFile.R | 17 R/predict.cubist.R | 63 +- build/vignette.rds |binary inst/NEWS.Rd | 11 inst/doc/cubist.R | 101 +-- inst/doc/cubist.Rmd | 162 +---- inst/doc/cubist.html | 1475 +++++++++++++++++++++--------------------------- man/cubist.default.Rd | 2 man/dotplot.cubist.Rd | 6 man/predict.cubist.Rd | 10 man/summary.cubist.Rd | 38 - vignettes/cubist.Rmd | 162 +---- vignettes/extras |only vignettes/neighbors.gif |only 18 files changed, 947 insertions(+), 1163 deletions(-)
Title: Generate 'CodeMeta' Metadata for R Packages
Description: The 'Codemeta' Project defines a 'JSON-LD' format
for describing software metadata, as detailed at
<https://codemeta.github.io>. This package provides utilities to
generate, parse, and modify 'codemeta.json' files automatically for R
packages, as well as tools and examples for working with
'codemeta.json' 'JSON-LD' more generally.
Author: Carl Boettiger [aut, cre, cph]
(<https://orcid.org/0000-0002-1642-628X>),
Anna Krystalli [rev, ctb] (<https://orcid.org/0000-0002-2378-4915>),
Toph Allen [rev] (<https://orcid.org/0000-0003-4580-091X>),
Maëlle Salmon [ctb, aut] (<https://orcid.org/0000-0002-2815-0399>),
rOpenSci [fnd] (https://ropensci.org/),
Katrin Leinweber [ctb] (<https://orcid.org/0000-0001-5135-5758>),
Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>),
Arfon Smith [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Sebastian Meyer [ctb] (<https://orcid.org/0000-0002-1791-9449>),
Michael Rustler [ctb] (<https://orcid.org/0000-0003-0647-7726>),
Hauke Sonnenberg [ctb] (<https://orcid.org/0000-0001-9134-2871>),
Sebastian Kreutzer [ctb] (<https://orcid.org/0000-0002-0734-2199>),
Thierry Onkelinx [ctb] (<https://orcid.org/0000-0001-8804-4216>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between codemetar versions 0.1.9 dated 2020-07-18 and 0.3.0 dated 2021-05-10
DESCRIPTION | 27 MD5 | 74 - NEWS.md | 15 R/codemeta_description.R | 10 R/codemeta_readme.R | 5 R/extract_badges.R | 4 R/guess_github_metadata.R | 5 R/guess_other_metadata.R | 33 R/utils.R | 30 R/write_codemeta.R | 14 README.md | 669 ++------------ build/vignette.rds |binary inst/deprecated/test-crosswalk.R | 8 inst/doc/codemetar.R | 26 inst/doc/codemetar.Rmd | 6 inst/doc/codemetar.html | 1317 +++++++++++------------------ inst/examples/README_codemetar_good.md | 2 man/codemetar-package.Rd | 12 man/rmdhunks/example.Rmd | 33 man/rmdhunks/goals.Rmd | 2 man/rmdhunks/improvecodemetadata.Rmd | 10 man/rmdhunks/minimeta.Rmd | 2 man/write_codemeta.Rd | 32 tests/testthat/_snaps |only tests/testthat/test-codemeta_description.R | 6 tests/testthat/test-create_codemeta.R |only tests/testthat/test-extract_badges.R | 2 tests/testthat/test-frame.R | 4 tests/testthat/test-get_message.R | 2 tests/testthat/test-get_url.R | 2 tests/testthat/test-give_opinions.R | 8 tests/testthat/test-guess_metadata.R | 14 tests/testthat/test-parse_citation.R | 10 tests/testthat/test-parse_depends.R | 2 tests/testthat/test-parse_people.R | 2 tests/testthat/test-spdx_license.R | 2 tests/testthat/test-utils.R | 8 tests/testthat/test-write_codemeta.R | 58 - vignettes/codemetar.Rmd | 6 39 files changed, 869 insertions(+), 1593 deletions(-)
Title: Open Source OCR Engine
Description: Bindings to 'Tesseract' <https://opensource.google/projects/tesseract>:
a powerful optical character recognition (OCR) engine that supports over 100 languages.
The engine is highly configurable in order to tune the detection algorithms and
obtain the best possible results.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between tesseract versions 4.1 dated 2019-07-25 and 4.1.1 dated 2021-05-10
tesseract-4.1.1/tesseract/DESCRIPTION | 13 tesseract-4.1.1/tesseract/MD5 | 37 tesseract-4.1.1/tesseract/NEWS | 3 tesseract-4.1.1/tesseract/R/ocr.R | 1 tesseract-4.1.1/tesseract/R/onload.R | 4 tesseract-4.1.1/tesseract/R/tessdata.R | 10 tesseract-4.1.1/tesseract/build/vignette.rds |binary tesseract-4.1.1/tesseract/cleanup | 2 tesseract-4.1.1/tesseract/configure | 28 tesseract-4.1.1/tesseract/inst/doc/intro.R | 8 tesseract-4.1.1/tesseract/inst/doc/intro.Rmd | 2 tesseract-4.1.1/tesseract/inst/doc/intro.html | 1421 +------------------------- tesseract-4.1.1/tesseract/man/ocr.Rd | 6 tesseract-4.1.1/tesseract/man/tessdata.Rd | 14 tesseract-4.1.1/tesseract/man/tesseract.Rd | 14 tesseract-4.1.1/tesseract/src/Makevars.ucrt |only tesseract-4.1.1/tesseract/src/Makevars.win | 6 tesseract-4.1.1/tesseract/src/tesseract.cpp | 50 tesseract-4.1.1/tesseract/tools/test.cpp |only tesseract-4.1.1/tesseract/vignettes/intro.Rmd | 2 tesseract-4.1/tesseract/src/test.h |only 21 files changed, 185 insertions(+), 1436 deletions(-)
Title: Siena - Simulation Investigation for Empirical Network Analysis
Description: The main purpose of this package is to perform simulation-based
estimation of stochastic actor-oriented models for longitudinal network
data collected as panel data. Dependent variables can be single or
multivariate networks, which can be directed, non-directed, or two-mode;
and associated actor variables.
There are also functions for testing parameters and checking goodness of fit.
An overview of these models is given in Tom A.B. Snijders (2017), Stochastic
Actor-Oriented Models for Network Dynamics, Annual Review of Statistics and
Its Application, 4, 343-363 <doi: 10.1146/annurev-statistics-060116-054035>.
An extensive manual, scripts, and much further information is at the Siena
website <http://www.stats.ox.ac.uk/~snijders/siena/>.
Author: Tom A.B. Snijders [cre, aut] (<https://orcid.org/0000-0003-3157-4157>),
Ruth Ripley [aut],
Christian Steglich [aut, ctb] (<https://orcid.org/0000-0002-9097-0873>),
Johan Koskinen [aut, ctb] (<https://orcid.org/0000-0002-6860-325X>),
Nynke Niezink [aut, ctb],
Viviana Amati [aut, ctb] (<https://orcid.org/0000-0003-1190-1237>),
Christoph Stadtfeld [ctb] (<https://orcid.org/0000-0002-2704-2134>),
James Hollway [ctb] (IHEID, <https://orcid.org/0000-0002-8361-9647>),
Per Block [ctb],
Robert Krause [ctb],
Charlotte Greenan [ctb],
Josh Lospinoso [ctb],
Michael Schweinberger [ctb] (<https://orcid.org/0000-0003-3649-5386>),
Mark Huisman [ctb],
Krists Boitmanis [ctr],
Felix Schoenenberger [ctb],
Mark Ortmann [ctb],
Marion Hoffman [ctb],
Robert Hellpap [ctb],
Alvaro Uzaheta [ctb]
Maintainer: Tom A.B. Snijders <tom.snijders@nuffield.ox.ac.uk>
Diff between RSiena versions 1.2-23 dated 2020-01-12 and 1.3.0 dated 2021-05-10
RSiena-1.2-23/RSiena/ChangeLog |only RSiena-1.2-23/RSiena/inst/doc |only RSiena-1.2-23/RSiena/src/model/effects/generic/MixedInStarFunction.cpp |only RSiena-1.2-23/RSiena/src/model/effects/generic/MixedInStarFunction.h |only RSiena-1.2-23/RSiena/src/model/effects/generic/MixedOutStarFunction.cpp |only RSiena-1.2-23/RSiena/src/model/effects/generic/MixedOutStarFunction.h |only RSiena-1.2-23/RSiena/src/model/effects/generic/MixedTwoPathFunction.cpp |only RSiena-1.2-23/RSiena/src/model/effects/generic/MixedTwoPathFunction.h |only RSiena-1.3.0/RSiena/.Rinstignore | 23 RSiena-1.3.0/RSiena/DESCRIPTION | 81 RSiena-1.3.0/RSiena/LICENSE |only RSiena-1.3.0/RSiena/MD5 | 373 RSiena-1.3.0/RSiena/NAMESPACE | 154 RSiena-1.3.0/RSiena/NEWS.md |only RSiena-1.3.0/RSiena/R/RSienaRDocumentation.r | 584 - RSiena-1.3.0/RSiena/R/Sienatest.r | 912 - RSiena-1.3.0/RSiena/R/checkImpossibleChanges.r | 138 RSiena-1.3.0/RSiena/R/effects.r | 4318 ++++---- RSiena-1.3.0/RSiena/R/effectsDocumentation.r | 360 RSiena-1.3.0/RSiena/R/effectsMethods.r | 617 - RSiena-1.3.0/RSiena/R/getTargets.r | 278 RSiena-1.3.0/RSiena/R/globals.r | 421 RSiena-1.3.0/RSiena/R/initializeFRAN.r | 4832 ++++----- RSiena-1.3.0/RSiena/R/iwlsm.R | 894 - RSiena-1.3.0/RSiena/R/maxlike.r | 1688 +-- RSiena-1.3.0/RSiena/R/maxlikec.r | 486 RSiena-1.3.0/RSiena/R/maxlikecalc.r | 302 RSiena-1.3.0/RSiena/R/observationErrors.r | 406 RSiena-1.3.0/RSiena/R/phase1.r | 1207 +- RSiena-1.3.0/RSiena/R/phase2.r | 965 + RSiena-1.3.0/RSiena/R/phase3.r | 1844 +-- RSiena-1.3.0/RSiena/R/print01Report.r | 2738 ++--- RSiena-1.3.0/RSiena/R/print07Report.r | 556 - RSiena-1.3.0/RSiena/R/printDataReport.r | 673 - RSiena-1.3.0/RSiena/R/printInitialDescription.r | 1192 +- RSiena-1.3.0/RSiena/R/robmon.r | 830 - RSiena-1.3.0/RSiena/R/siena07.r | 1022 +- RSiena-1.3.0/RSiena/R/siena07gui.r | 207 RSiena-1.3.0/RSiena/R/siena08.r | 1842 ++- RSiena-1.3.0/RSiena/R/sienaDataCreate.r | 4991 +++++----- RSiena-1.3.0/RSiena/R/sienaGOF.r | 2861 ++--- RSiena-1.3.0/RSiena/R/sienaModelCreate.r | 407 RSiena-1.3.0/RSiena/R/sienaRI.r | 1468 +- RSiena-1.3.0/RSiena/R/sienaRIDynamics.r | 1050 +- RSiena-1.3.0/RSiena/R/sienaTimeTest.r | 2550 ++--- RSiena-1.3.0/RSiena/R/sienaeffects.r | 694 - RSiena-1.3.0/RSiena/R/sienaprint.r | 3463 +++--- RSiena-1.3.0/RSiena/R/sienatable.r | 1373 +- RSiena-1.3.0/RSiena/R/sienautils.r | 1138 +- RSiena-1.3.0/RSiena/R/simstatsc.r | 356 RSiena-1.3.0/RSiena/R/terminateFRAN.r | 80 RSiena-1.3.0/RSiena/R/zzz.R | 112 RSiena-1.3.0/RSiena/cleanup | 11 RSiena-1.3.0/RSiena/cleanup.win | 23 RSiena-1.3.0/RSiena/configure | 2144 ---- RSiena-1.3.0/RSiena/configure.ac | 366 RSiena-1.3.0/RSiena/configure.win | 56 RSiena-1.3.0/RSiena/data/allEffects.R | 6 RSiena-1.3.0/RSiena/data/allEffects.csv | 1089 +- RSiena-1.3.0/RSiena/inst/CITATION | 38 RSiena-1.3.0/RSiena/inst/examples/Sampson_t2.txt | 210 RSiena-1.3.0/RSiena/inst/examples/Sampson_t3.txt | 266 RSiena-1.3.0/RSiena/inst/examples/Sampson_t4.txt | 202 RSiena-1.3.0/RSiena/inst/examples/arclistdata.dat | 700 - RSiena-1.3.0/RSiena/inst/examples/vtextexoreal.dat | 64 RSiena-1.3.0/RSiena/inst/ilcampo.jpg |only RSiena-1.3.0/RSiena/inst/rsienalogo.png |only RSiena-1.3.0/RSiena/inst/scripts/RSienaSNADescriptives.R | 333 RSiena-1.3.0/RSiena/inst/scripts/Rscript01DataFormat.R | 893 - RSiena-1.3.0/RSiena/inst/scripts/Rscript02SienaVariableFormat.R | 941 - RSiena-1.3.0/RSiena/inst/scripts/Rscript03SienaRunModel.R | 753 - RSiena-1.3.0/RSiena/inst/scripts/Rscript04SienaBehaviour.R | 348 RSiena-1.3.0/RSiena/inst/sienascript | 1 RSiena-1.3.0/RSiena/inst/testdata |only RSiena-1.3.0/RSiena/man/RSiena-package.Rd | 222 RSiena-1.3.0/RSiena/man/Wald.Rd | 23 RSiena-1.3.0/RSiena/man/allEffects.Rd | 92 RSiena-1.3.0/RSiena/man/coCovar.Rd | 102 RSiena-1.3.0/RSiena/man/coDyadCovar.Rd | 80 RSiena-1.3.0/RSiena/man/edit.sienaEffects.Rd | 78 RSiena-1.3.0/RSiena/man/effectsDocumentation.Rd | 138 RSiena-1.3.0/RSiena/man/funnelPlot.Rd |only RSiena-1.3.0/RSiena/man/getEffects.Rd | 237 RSiena-1.3.0/RSiena/man/includeEffects.Rd | 189 RSiena-1.3.0/RSiena/man/includeGMoMStatistics.Rd |only RSiena-1.3.0/RSiena/man/includeInteraction.Rd | 258 RSiena-1.3.0/RSiena/man/includeTimeDummy.Rd | 264 RSiena-1.3.0/RSiena/man/iwlsm.Rd | 408 RSiena-1.3.0/RSiena/man/maxlikefn.Rd | 160 RSiena-1.3.0/RSiena/man/plot.sienaTimeTest.Rd | 178 RSiena-1.3.0/RSiena/man/print.sienaEffects.Rd | 135 RSiena-1.3.0/RSiena/man/print.sienaMeta.Rd | 265 RSiena-1.3.0/RSiena/man/print.sienaTest.Rd | 86 RSiena-1.3.0/RSiena/man/print01Report.Rd | 74 RSiena-1.3.0/RSiena/man/s50.Rd | 72 RSiena-1.3.0/RSiena/man/s501.Rd | 50 RSiena-1.3.0/RSiena/man/s502.Rd | 52 RSiena-1.3.0/RSiena/man/s503.Rd | 58 RSiena-1.3.0/RSiena/man/s50a.Rd | 64 RSiena-1.3.0/RSiena/man/s50s.Rd | 64 RSiena-1.3.0/RSiena/man/setEffect.Rd | 281 RSiena-1.3.0/RSiena/man/siena07.Rd | 675 - RSiena-1.3.0/RSiena/man/siena08.Rd | 320 RSiena-1.3.0/RSiena/man/sienaAlgorithmCreate.Rd | 17 RSiena-1.3.0/RSiena/man/sienaCompositionChange.Rd | 248 RSiena-1.3.0/RSiena/man/sienaDataConstraint.Rd | 100 RSiena-1.3.0/RSiena/man/sienaDataCreate.Rd | 137 RSiena-1.3.0/RSiena/man/sienaDependent.Rd | 230 RSiena-1.3.0/RSiena/man/sienaFit.Rd | 214 RSiena-1.3.0/RSiena/man/sienaGOF-auxiliary.Rd | 61 RSiena-1.3.0/RSiena/man/sienaGOF.Rd | 41 RSiena-1.3.0/RSiena/man/sienaGroupCreate.Rd | 294 RSiena-1.3.0/RSiena/man/sienaNodeSet.Rd | 82 RSiena-1.3.0/RSiena/man/sienaRI.Rd | 442 RSiena-1.3.0/RSiena/man/sienaTimeTest.Rd | 402 RSiena-1.3.0/RSiena/man/simstats0c.Rd | 254 RSiena-1.3.0/RSiena/man/summary.iwlsm.Rd | 208 RSiena-1.3.0/RSiena/man/tmp3.Rd | 50 RSiena-1.3.0/RSiena/man/tmp4.Rd | 50 RSiena-1.3.0/RSiena/man/updateTheta.Rd | 196 RSiena-1.3.0/RSiena/man/varCovar.Rd | 116 RSiena-1.3.0/RSiena/man/varDyadCovar.Rd | 108 RSiena-1.3.0/RSiena/man/xtable.Rd | 92 RSiena-1.3.0/RSiena/po/R-RSiena.pot | 1734 +-- RSiena-1.3.0/RSiena/src/model/EpochSimulation.cpp | 2 RSiena-1.3.0/RSiena/src/model/Model.cpp | 26 RSiena-1.3.0/RSiena/src/model/Model.h | 10 RSiena-1.3.0/RSiena/src/model/StatisticCalculator.cpp | 122 RSiena-1.3.0/RSiena/src/model/StatisticCalculator.h | 3 RSiena-1.3.0/RSiena/src/model/effects/AgreementTransitivityGMMEffect.h |only RSiena-1.3.0/RSiena/src/model/effects/AllEffects.h | 6 RSiena-1.3.0/RSiena/src/model/effects/AltersCovariateTotSimEffect.cpp | 3 RSiena-1.3.0/RSiena/src/model/effects/AverageAlterEffect.cpp | 16 RSiena-1.3.0/RSiena/src/model/effects/AverageAlterEffect.h | 2 RSiena-1.3.0/RSiena/src/model/effects/AverageInAlterEffect.cpp | 8 RSiena-1.3.0/RSiena/src/model/effects/BehaviorEffect.cpp | 16 RSiena-1.3.0/RSiena/src/model/effects/BehaviorEffect.h | 3 RSiena-1.3.0/RSiena/src/model/effects/ConstantEffect.cpp |only RSiena-1.3.0/RSiena/src/model/effects/ConstantEffect.h |only RSiena-1.3.0/RSiena/src/model/effects/CovariateDependentNetworkEffect.cpp | 94 RSiena-1.3.0/RSiena/src/model/effects/CovariateDependentNetworkEffect.h | 12 RSiena-1.3.0/RSiena/src/model/effects/CovariateSimilarityEffect.cpp | 4 RSiena-1.3.0/RSiena/src/model/effects/CovariateTransitiveTripletsEffect.cpp |only RSiena-1.3.0/RSiena/src/model/effects/CovariateTransitiveTripletsEffect.h |only RSiena-1.3.0/RSiena/src/model/effects/DoubleRecDegreeBehaviorEffect.cpp | 4 RSiena-1.3.0/RSiena/src/model/effects/EffectFactory.cpp | 402 RSiena-1.3.0/RSiena/src/model/effects/EffectFactory.h | 4 RSiena-1.3.0/RSiena/src/model/effects/HomCovariateTransitiveTripletsEffect.cpp | 52 RSiena-1.3.0/RSiena/src/model/effects/InteractionCovariateEffect.cpp | 4 RSiena-1.3.0/RSiena/src/model/effects/MaxAlterEffect.cpp | 14 RSiena-1.3.0/RSiena/src/model/effects/MaxAlterEffect.h | 1 RSiena-1.3.0/RSiena/src/model/effects/NetworkDependentBehaviorEffect.cpp | 145 RSiena-1.3.0/RSiena/src/model/effects/NetworkDependentBehaviorEffect.h | 14 RSiena-1.3.0/RSiena/src/model/effects/OutdegreeContinuousEffect.cpp | 6 RSiena-1.3.0/RSiena/src/model/effects/RealTransitivityGMMEffect.h |only RSiena-1.3.0/RSiena/src/model/effects/ReciprocityGMMEffect.h |only RSiena-1.3.0/RSiena/src/model/effects/SimilarityEffect.cpp | 245 RSiena-1.3.0/RSiena/src/model/effects/SimilarityEffect.h | 13 RSiena-1.3.0/RSiena/src/model/effects/SimilarityIndegreeEffect.cpp |only RSiena-1.3.0/RSiena/src/model/effects/SimilarityIndegreeEffect.h |only RSiena-1.3.0/RSiena/src/model/effects/SimilarityTransitiveTripletsEffect.cpp | 6 RSiena-1.3.0/RSiena/src/model/effects/SimilarityWEffect.cpp | 4 RSiena-1.3.0/RSiena/src/model/effects/generic/CovariateDistance2EgoAltSimNetworkFunction.h | 2 RSiena-1.3.0/RSiena/src/model/effects/generic/CovariateMixedNetworkAlterFunction.cpp | 2 RSiena-1.3.0/RSiena/src/model/effects/generic/CovariateMixedNetworkAlterFunction.h | 2 RSiena-1.3.0/RSiena/src/model/effects/generic/CovariateNetworkAlterFunction.cpp | 2 RSiena-1.3.0/RSiena/src/model/effects/generic/CovariateNetworkAlterFunction.h | 2 RSiena-1.3.0/RSiena/src/model/effects/generic/DyadicCovariateMixedNetworkAlterFunction.cpp |only RSiena-1.3.0/RSiena/src/model/effects/generic/DyadicCovariateMixedNetworkAlterFunction.h |only RSiena-1.3.0/RSiena/src/model/effects/generic/InStarFunction.cpp | 24 RSiena-1.3.0/RSiena/src/model/effects/generic/InStarFunction.h | 14 RSiena-1.3.0/RSiena/src/model/effects/generic/InStarsTimesDegreesFunction.cpp | 13 RSiena-1.3.0/RSiena/src/model/effects/generic/InStarsTimesDegreesFunction.h | 3 RSiena-1.3.0/RSiena/src/model/effects/generic/MixedTwoStepFunction.cpp |only RSiena-1.3.0/RSiena/src/model/effects/generic/MixedTwoStepFunction.h |only RSiena-1.3.0/RSiena/src/model/effects/generic/ReciprocatedTwoPathFunction.cpp | 27 RSiena-1.3.0/RSiena/src/model/effects/generic/ReciprocatedTwoPathFunction.h | 14 RSiena-1.3.0/RSiena/src/model/effects/generic/TwoStepFunction.cpp |only RSiena-1.3.0/RSiena/src/model/effects/generic/TwoStepFunction.h |only RSiena-1.3.0/RSiena/src/model/effects/generic/WeightedMixedTwoPathFunction.cpp |only RSiena-1.3.0/RSiena/src/model/effects/generic/WeightedMixedTwoPathFunction.h |only RSiena-1.3.0/RSiena/src/model/filters/DisjointFilter.cpp | 37 RSiena-1.3.0/RSiena/src/model/filters/DisjointFilter.h | 3 RSiena-1.3.0/RSiena/src/model/filters/HigherFilter.cpp | 36 RSiena-1.3.0/RSiena/src/model/filters/HigherFilter.h | 3 RSiena-1.3.0/RSiena/src/model/ml/Chain.cpp | 4 RSiena-1.3.0/RSiena/src/model/ml/MLSimulation.cpp | 4 RSiena-1.3.0/RSiena/src/model/ml/MLSimulation.h | 8 RSiena-1.3.0/RSiena/src/model/tables/MixedTwoPathTable.cpp | 21 RSiena-1.3.0/RSiena/src/model/tables/MixedTwoPathTable.h | 1 RSiena-1.3.0/RSiena/src/model/tables/TwoNetworkCache.cpp | 34 RSiena-1.3.0/RSiena/src/model/tables/TwoNetworkCache.h | 69 RSiena-1.3.0/RSiena/src/model/variables/BehaviorVariable.cpp | 14 RSiena-1.3.0/RSiena/src/model/variables/ContinuousVariable.cpp | 60 RSiena-1.3.0/RSiena/src/network/NetworkUtils.h | 4 RSiena-1.3.0/RSiena/src/network/OneModeNetwork.cpp | 9 RSiena-1.3.0/RSiena/src/network/OneModeNetwork.h | 2 RSiena-1.3.0/RSiena/src/network/UnionNeighborIterator.cpp |only RSiena-1.3.0/RSiena/src/network/UnionNeighborIterator.h |only RSiena-1.3.0/RSiena/src/siena07internals.cpp | 16 RSiena-1.3.0/RSiena/src/siena07models.cpp | 2 RSiena-1.3.0/RSiena/src/siena07setup.cpp | 1 RSiena-1.3.0/RSiena/src/sources.list | 2 RSiena-1.3.0/RSiena/tests/parallel.R | 308 RSiena-1.3.0/RSiena/tests/parallel.Rout.save | 1257 +- 205 files changed, 36123 insertions(+), 35749 deletions(-)
Title: Testing Neighbor Effects in Marker-Based Regressions
Description: To incorporate neighbor genotypic identity into genome-wide association studies, the package provides a set of functions for variation partitioning and association mapping. The theoretical background of the method is described in Sato et al. (2021) <doi:10.1038/s41437-020-00401-w>.
Author: Yasuhiro Sato [aut, cre] (<https://orcid.org/0000-0002-6466-723X>),
Eiji Yamamoto [aut],
Kentaro K. Shimizu [aut] (<https://orcid.org/0000-0002-6483-1781>),
Atsushi J. Nagano [aut] (<https://orcid.org/0000-0001-7891-5049>)
Maintainer: Yasuhiro Sato <sato.yasuhiro.36c@kyoto-u.jp>
Diff between rNeighborGWAS versions 1.2.3 dated 2021-04-07 and 1.2.4 dated 2021-05-10
DESCRIPTION | 6 +- MD5 | 4 - tests/testthat/test-neiGWAS.R | 114 +++++++++++++++++++++--------------------- 3 files changed, 62 insertions(+), 62 deletions(-)
Title: Create Colour Palettes Based on Famous Artworks from the
Rijksmuseum
Description: Create colour palettes based on famous paintings. Using the
function rijksPalette(), you can search for any painting in the collection
of the Dutch Rijksmuseum and generate a colour palette from it. This package
was developed using the fantastic Rijksmuseum API
<https://www.rijksmuseum.nl/api>.
Author: Erik-Jan van Kesteren [aut, cre]
Maintainer: Erik-Jan van Kesteren <e.vankesteren1@uu.nl>
Diff between rijkspalette versions 1.0.1 dated 2019-02-07 and 1.0.2 dated 2021-05-10
DESCRIPTION | 11 +++++------ MD5 | 6 +++--- R/helpers.R | 30 +++++++++++++++++++++++------- man/rijksQuery.Rd | 2 +- 4 files changed, 32 insertions(+), 17 deletions(-)
Title: Inbreeding-Purging Estimation in Pedigreed Populations
Description: Inbreeding-purging analysis of pedigreed populations, including the computation of the inbreeding coefficient, partial, ancestral and purged inbreeding coefficients, and measures of the opportunity of purging related to the individual reduction of inbreeding load.
In addition, functions to calculate the effective population size and other parameters relevant to population genetics are included.
Caballero A. and Toro M.A. (2000) <doi:10.1017/s0016672399004449>.
García-Dorado A., Wang J. and López-Cortegano E. (2016) <doi:10.1534/g3.116.032425>.
Gulisija D. and Crow J.F. (2007) <doi:10.1111/j.1558-5646.2007.00088.x>.
Gutiérrez J.P., Cervantes I., Goyache F. (2009) <doi:10.1111/j.1439-0388.2009.00810.x>.
López-Cortegano E., Bersabé D., Wang J., García-Dorado A. (2018) <doi:10.1038/s41437-017-0045-y>.
Author: Eugenio López-Cortegano [aut, cre]
Maintainer: Eugenio López-Cortegano <elcortegano@gmail.com>
Diff between purgeR versions 1.0 dated 2021-04-30 and 1.1 dated 2021-05-10
DESCRIPTION | 10 MD5 | 61 ++--- NEWS.md |only R/Nancestors.R | 3 R/RcppExports.R | 5 R/clean.R | 4 R/fitness.R | 6 R/generations.R | 3 R/inbreeding.R | 9 R/maternal.R | 3 R/partial.R | 2 R/rename.R | 11 inst/doc/ip.R | 86 +------ inst/doc/ip.Rmd | 84 +------ inst/doc/ip.html | 326 +++++++++++----------------- inst/doc/purgeR-tutorial.html | 12 - man/ancestors.Rd | 4 man/ip_F.Rd | 3 man/ip_Fa.Rd | 3 man/ip_Fij.Rd | 2 man/ip_g.Rd | 3 man/ped_clean.Rd | 4 man/ped_maternal.Rd | 3 man/ped_rename.Rd | 3 man/pop_t.Rd | 3 man/w_grandoffspring.Rd | 3 man/w_offspring.Rd | 3 src/RcppExports.cpp | 9 src/populationSize.cpp | 87 +++---- src/preProcessing.cpp | 1 tests/testthat/test_population_parameters.R | 9 vignettes/ip.Rmd | 84 +------ 32 files changed, 337 insertions(+), 512 deletions(-)
Title: Wrap Vectors in Markdown Formatting
Description: Ease the transition between R vectors and markdown
text. With 'gluedown' and 'rmarkdown', users can create traditional
vectors in R, glue those strings together with the markdown syntax,
and print those formatted vectors directly to the document. This
package primarily uses GitHub Flavored Markdown (GFM), an offshoot of
the unambiguous CommonMark specification by John MacFarlane (2019)
<https://spec.commonmark.org/>.
Author: Kiernan Nicholls [aut, cre]
Maintainer: Kiernan Nicholls <kiernann@protonmail.com>
Diff between gluedown versions 1.0.3 dated 2021-02-06 and 1.0.4 dated 2021-05-10
DESCRIPTION | 7 - MD5 | 22 +-- NEWS.md | 5 build/vignette.rds |binary inst/doc/github-spec.R | 43 ++++--- inst/doc/github-spec.Rmd | 35 +++--- inst/doc/github-spec.html | 211 +++++++++++++++++++------------------- inst/doc/literal-programming.R | 47 ++++++-- inst/doc/literal-programming.Rmd | 35 +++++- inst/doc/literal-programming.html | 16 ++ vignettes/github-spec.Rmd | 35 +++--- vignettes/literal-programming.Rmd | 35 +++++- 12 files changed, 304 insertions(+), 187 deletions(-)
Title: Some EM-Type Estimation Methods for the Heckman Selection Model
Description: Some EM-type algorithms to estimate parameters for the well-known Heckman selection model are provided in the package. Such algorithms are as follow: ECM(Expectation/Conditional Maximization), ECM(NR)(the Newton-Raphson method is adapted to the ECM) and ECME(Expectation/Conditional Maximization Either). Since the algorithms are based on the EM algorithm, they also have EM’s main advantages, namely, stability and ease of implementation. Further details and explanations of the algorithms can be found in Zhao et al. (2020) <doi: 10.1016/j.csda.2020.106930>.
Author: Kexuan Yang <717260446@qq.com>, Sang Kyu Lee <leesa111@msu.edu>, Jun Zhao <zhaojun2021@hotmail.com>, and Hyoung-Moon Kim <hmk966a@gmail.com >
Maintainer: Sang Kyu Lee <leesa111@msu.edu>
Diff between EMSS versions 1.0.2 dated 2020-08-28 and 1.1.0 dated 2021-05-10
DESCRIPTION | 13 MD5 | 11 NEWS.md |only R/EMSS.R | 953 ++++++++++++++++++++++++++++------------------------ man/EMSS.Rd | 2 man/summary.EMSS.Rd | 9 tests |only 7 files changed, 553 insertions(+), 435 deletions(-)
Title: Capture-Recapture Estimation using Bayesian Model Averaging
Description: Performs Bayesian model averaging for capture-recapture. This includes code to stratify records, check the strata for suitable overlap to be used for capture-recapture, and some functions to plot the estimated population size.
Author: James Johndrow [aut],
Kristian Lum [aut],
Patrick Ball [aut],
Olivier Binette [ctb, cre]
Maintainer: Olivier Binette <olivier.binette@gmail.com>
Diff between dga versions 2.0.0 dated 2021-05-04 and 2.0.1 dated 2021-05-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ src/utils.cpp | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It provides various routines for importing bibliographic data from 'SCOPUS' (<https://scopus.com>),
'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions'
(<https://www.dimensions.ai/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>),
and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut],
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 3.0.4 dated 2021-01-19 and 3.1.1 dated 2021-05-10
bibliometrix-3.0.4/bibliometrix/inst/logo |only bibliometrix-3.1.1/bibliometrix/DESCRIPTION | 21 bibliometrix-3.1.1/bibliometrix/MD5 | 91 bibliometrix-3.1.1/bibliometrix/NAMESPACE | 38 bibliometrix-3.1.1/bibliometrix/NEWS | 21 bibliometrix-3.1.1/bibliometrix/R/Hindex.R | 108 - bibliometrix-3.1.1/bibliometrix/R/authorProdOverTime.R | 39 bibliometrix-3.1.1/bibliometrix/R/biblioAnalysis.R | 6 bibliometrix-3.1.1/bibliometrix/R/biblioshiny.R | 55 bibliometrix-3.1.1/bibliometrix/R/bradford.R | 9 bibliometrix-3.1.1/bibliometrix/R/conceptualStructure.R | 80 bibliometrix-3.1.1/bibliometrix/R/convert2df.R | 16 bibliometrix-3.1.1/bibliometrix/R/countries.R | 30 bibliometrix-3.1.1/bibliometrix/R/couplingMap.R | 79 bibliometrix-3.1.1/bibliometrix/R/csvLens2df.R |only bibliometrix-3.1.1/bibliometrix/R/csvScopus2df.R | 14 bibliometrix-3.1.1/bibliometrix/R/dimensions2df.R | 12 bibliometrix-3.1.1/bibliometrix/R/fieldByYear.R | 131 - bibliometrix-3.1.1/bibliometrix/R/histPlot.R | 102 - bibliometrix-3.1.1/bibliometrix/R/logo.R |only bibliometrix-3.1.1/bibliometrix/R/mergeDbSources.R | 1 bibliometrix-3.1.1/bibliometrix/R/networkPlot.R | 62 bibliometrix-3.1.1/bibliometrix/R/plotThematicEvolution.R | 94 bibliometrix-3.1.1/bibliometrix/R/rpys.R | 9 bibliometrix-3.1.1/bibliometrix/R/splitCommunities.R |only bibliometrix-3.1.1/bibliometrix/R/tableTag.R | 9 bibliometrix-3.1.1/bibliometrix/R/termExtraction.R | 159 - bibliometrix-3.1.1/bibliometrix/R/thematicEvolution.R | 178 - bibliometrix-3.1.1/bibliometrix/R/thematicMap.R | 24 bibliometrix-3.1.1/bibliometrix/R/threeFieldsPlot.R | 90 bibliometrix-3.1.1/bibliometrix/R/zzz.R | 55 bibliometrix-3.1.1/bibliometrix/build/partial.rdb |binary bibliometrix-3.1.1/bibliometrix/data/logo.rda |only bibliometrix-3.1.1/bibliometrix/inst/biblioshiny/rsconnect/shinyapps.io/massimoaria/biblioshiny.dcf | 6 bibliometrix-3.1.1/bibliometrix/inst/biblioshiny/server.R | 931 ++++++--- bibliometrix-3.1.1/bibliometrix/inst/biblioshiny/ui.R | 954 ++++++---- bibliometrix-3.1.1/bibliometrix/man/Hindex.Rd | 8 bibliometrix-3.1.1/bibliometrix/man/biblioshiny.Rd | 9 bibliometrix-3.1.1/bibliometrix/man/conceptualStructure.Rd | 4 bibliometrix-3.1.1/bibliometrix/man/convert2df.Rd | 7 bibliometrix-3.1.1/bibliometrix/man/couplingMap.Rd | 8 bibliometrix-3.1.1/bibliometrix/man/fieldByYear.Rd | 11 bibliometrix-3.1.1/bibliometrix/man/logo.Rd |only bibliometrix-3.1.1/bibliometrix/man/networkPlot.Rd | 3 bibliometrix-3.1.1/bibliometrix/man/splitCommunities.Rd |only bibliometrix-3.1.1/bibliometrix/man/tableTag.Rd | 4 bibliometrix-3.1.1/bibliometrix/man/termExtraction.Rd | 16 bibliometrix-3.1.1/bibliometrix/man/thematicEvolution.Rd | 4 bibliometrix-3.1.1/bibliometrix/man/thematicMap.Rd | 4 bibliometrix-3.1.1/bibliometrix/man/threeFieldsPlot.Rd | 12 50 files changed, 2296 insertions(+), 1218 deletions(-)
Title: Access the 'City of Vancouver' Open Data API
Description: Wrapper around the 'City of Vancouver' Open Data API <https://opendata.vancouver.ca/api/v2/console> to simplify and standardize access to 'City of Vancouver' open data.
Functionality to list the data catalogue and access data and geographic records.
Author: Jens von Bergmann
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between VancouvR versions 0.1.2 dated 2021-01-13 and 0.1.3 dated 2021-05-10
DESCRIPTION | 9 +++---- MD5 | 18 +++++++-------- NEWS.md | 5 ++++ README.md | 3 -- build/vignette.rds |binary inst/doc/Demo.R | 2 - inst/doc/Demo.Rmd | 2 - inst/doc/Demo.html | 56 +++++++++++++++++++++++++------------------------ inst/doc/Isolines.html | 12 +++++++--- vignettes/Demo.Rmd | 2 - 10 files changed, 60 insertions(+), 49 deletions(-)
Title: Open Population Capture-Recapture
Description: Functions for non-spatial and spatial open-population capture-recapture analysis.
Author: Murray Efford [aut, cre] (<https://orcid.org/0000-0001-5231-5184>)
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between openCR versions 1.5.0 dated 2020-12-13 and 2.0.1 dated 2021-05-10
openCR-1.5.0/openCR/R/plotKernel.R |only openCR-1.5.0/openCR/man/plotKernel.Rd |only openCR-1.5.0/openCR/tests/testthat/test-initial.R.$$$ |only openCR-2.0.1/openCR/DESCRIPTION | 13 openCR-2.0.1/openCR/MD5 | 118 - openCR-2.0.1/openCR/NAMESPACE | 52 openCR-2.0.1/openCR/NEWS | 44 openCR-2.0.1/openCR/R/JS.counts.R | 64 openCR-2.0.1/openCR/R/LLsurface.openCR.R | 10 openCR-2.0.1/openCR/R/PCH1.R | 6 openCR-2.0.1/openCR/R/RcppExports.R | 12 openCR-2.0.1/openCR/R/derived.r | 557 +++--- openCR-2.0.1/openCR/R/getfn.R | 46 openCR-2.0.1/openCR/R/geth.R | 4 openCR-2.0.1/openCR/R/kappaloglik.R | 44 openCR-2.0.1/openCR/R/kernel.R | 571 +++++- openCR-2.0.1/openCR/R/loglik.R | 364 ++-- openCR-2.0.1/openCR/R/logliksecr.R | 551 +++--- openCR-2.0.1/openCR/R/m.array.R | 72 openCR-2.0.1/openCR/R/make.table.R | 35 openCR-2.0.1/openCR/R/methods.R | 94 - openCR-2.0.1/openCR/R/moving.fit.R | 3 openCR-2.0.1/openCR/R/onLoad.R | 18 openCR-2.0.1/openCR/R/openCR.design.R | 446 +++-- openCR-2.0.1/openCR/R/openCR.esa.r | 79 openCR-2.0.1/openCR/R/openCR.fit.R | 1513 +++++++++--------- openCR-2.0.1/openCR/R/openCR.make.newdata.R | 219 +- openCR-2.0.1/openCR/R/openCR.pdot.r | 37 openCR-2.0.1/openCR/R/plot.openCR.R | 34 openCR-2.0.1/openCR/R/posterior2.R | 18 openCR-2.0.1/openCR/R/predict.openCR.R | 314 ++- openCR-2.0.1/openCR/R/prwisecr.R | 13 openCR-2.0.1/openCR/R/stratify.R |only openCR-2.0.1/openCR/R/summary.openCR.R | 2 openCR-2.0.1/openCR/R/utility.R | 407 +++- openCR-2.0.1/openCR/build/partial.rdb |only openCR-2.0.1/openCR/build/vignette.rds |binary openCR-2.0.1/openCR/inst/doc/openCR-vignette.R | 196 ++ openCR-2.0.1/openCR/inst/doc/openCR-vignette.Rmd | 243 ++ openCR-2.0.1/openCR/inst/doc/openCR-vignette.pdf |binary openCR-2.0.1/openCR/man/derived.Rd | 5 openCR-2.0.1/openCR/man/fieldvoleCH.Rd | 2 openCR-2.0.1/openCR/man/kernel.Rd | 41 openCR-2.0.1/openCR/man/make.table.Rd | 7 openCR-2.0.1/openCR/man/matchscale.Rd |only openCR-2.0.1/openCR/man/openCR-internal.Rd | 8 openCR-2.0.1/openCR/man/openCR-package.Rd | 4 openCR-2.0.1/openCR/man/openCR.design.Rd | 6 openCR-2.0.1/openCR/man/openCR.fit.Rd | 58 openCR-2.0.1/openCR/man/openCR.make.newdata.Rd | 14 openCR-2.0.1/openCR/man/pkernel.Rd |only openCR-2.0.1/openCR/man/plot.openCR.Rd | 3 openCR-2.0.1/openCR/man/predict.openCR.Rd | 11 openCR-2.0.1/openCR/man/strata.Rd |only openCR-2.0.1/openCR/man/stratify.Rd |only openCR-2.0.1/openCR/man/utility.Rd | 8 openCR-2.0.1/openCR/src/PCH1.cpp | 15 openCR-2.0.1/openCR/src/RcppExports.cpp | 34 openCR-2.0.1/openCR/src/kernel.cpp |only openCR-2.0.1/openCR/src/makegk.cpp | 61 openCR-2.0.1/openCR/src/prwisecrparallel.cpp | 21 openCR-2.0.1/openCR/src/utils.cpp | 418 +--- openCR-2.0.1/openCR/src/utils.h | 10 openCR-2.0.1/openCR/tests/testthat/test-initial.R | 48 openCR-2.0.1/openCR/vignettes/openCR-vignette.Rmd | 243 ++ 65 files changed, 4431 insertions(+), 2785 deletions(-)
Title: Fast Extraction from Raster Datasets using Polygons
Description: Provides a replacement for the 'extract' function from the 'raster' package
that is suitable for extracting raster values using 'sf' polygons.
Author: Daniel Baston [aut, cre],
ISciences, LLC [cph]
Maintainer: Daniel Baston <dbaston@isciences.com>
Diff between exactextractr versions 0.6.0 dated 2021-04-17 and 0.6.1 dated 2021-05-10
DESCRIPTION | 8 MD5 | 33 +-- NEWS.md | 8 R/exact_extract.R | 12 + configure | 20 - configure.ac | 2 man/exact_extract.Rd | 24 ++ src/Makevars.ucrt |only src/coverage_fraction.cpp | 60 +++-- src/exact_extract.cpp | 282 ++++++++++++++------------ src/exactextract/src/exactextract.cpp | 1 src/exactextract/src/gdal_dataset_wrapper.cpp | 1 src/exactextract/src/geos_utils.cpp | 2 src/exactextract/src/raster.h | 42 ++- src/exactextract/src/weighted_quantiles.cpp | 2 src/exactextract/test/test_raster.cpp | 27 ++ src/resample.cpp | 78 ++++--- tests/testthat/test_exact_extract.R | 16 + 18 files changed, 384 insertions(+), 234 deletions(-)
Title: Interfaces for Loading Datasets
Description: Visual interface for loading datasets in RStudio from all installed (including unloaded) packages, also includes command line interfaces.
Author: Bastiaan quast [aut, cre]
Maintainer: Bastiaan quast <bquast@gmail.com>
Diff between datasets.load versions 1.4.0 dated 2020-04-27 and 1.6.0 dated 2021-05-10
DESCRIPTION | 11 ++++++----- MD5 | 12 +++++++----- NEWS.md | 13 ++++--------- R/datasets.R | 2 +- README.md | 5 +++-- man/datasets.Rd | 4 ++-- tests |only 7 files changed, 23 insertions(+), 24 deletions(-)
Title: Generation of Code Names for Organizations, People, Projects,
and Whatever Else
Description: This creates code names that a user can consider for their organizations, their projects, themselves, people
in their organizations or projects, or whatever else. The user can also supply a numeric seed (and even a character seed)
for maximum reproducibility. Use is simple and the code names produced come in various types too, contingent on what the
user may be desiring as a code name or nickname.
Author: Steve Miller [aut, cre] (<https://orcid.org/0000-0003-4072-6263>)
Maintainer: Steve Miller <steven.v.miller@gmail.com>
Diff between codename versions 0.1.0 dated 2021-04-14 and 0.2.0 dated 2021-05-10
DESCRIPTION | 6 +-- MD5 | 34 ++++++++++++---------- NAMESPACE | 2 + NEWS.md | 11 +++++++ R/codename.R | 15 ++++++++- R/codename_message.R |only R/data.R | 14 ++++----- R/variety_pack.R |only README.md | 73 ++++++++++++++++++++++++++++-------------------- data/animals.rda |binary data/gods.rda |binary man/adjectives.Rd | 2 - man/animals.Rd | 2 - man/codename_message.Rd |only man/gods.Rd | 2 - man/nouns.Rd | 2 - man/variety_pack.Rd |only man/wu_adjs.Rd | 2 - man/wu_nouns.Rd | 2 - man/xkcd_colors.Rd | 2 - 20 files changed, 105 insertions(+), 64 deletions(-)
Title: Breaks for Additive Season and Trend
Description: Decomposition of time series into
trend, seasonal, and remainder components with methods for detecting and
characterizing abrupt changes within the trend and seasonal components. 'BFAST'
can be used to analyze different types of satellite image time series and can
be applied to other disciplines dealing with seasonal or non-seasonal time
series, such as hydrology, climatology, and econometrics. The algorithm can be
extended to label detected changes with information on the parameters of the
fitted piecewise linear models. 'BFAST' monitoring functionality is described
in Verbesselt et al. (2010) <doi:10.1016/j.rse.2009.08.014>. 'BFAST monitor'
provides functionality to detect disturbance in near real-time based on 'BFAST'-
type models, and is described in Verbesselt et al. (2012) <doi:10.1016/j.rse.2012.02.022>.
'BFAST Lite' approach is a flexible approach that handles missing data
without interpolation, and will be described in an upcoming paper.
Furthermore, different models can now be used to fit the
time series data and detect structural changes (breaks).
Author: Jan Verbesselt [aut],
Dainius Masiliunas [aut, cre] (<https://orcid.org/0000-0001-5654-1277>),
Achim Zeileis [aut],
Rob Hyndman [ctb],
Marius Appel [aut],
Martin Jung [ctb],
Andrei Mirt [ctb] (<https://orcid.org/0000-0003-3654-2090>),
Paulo Negri Bernardino [ctb],
Dongdong Kong [ctb] (<https://orcid.org/0000-0003-1836-8172>)
Maintainer: Dainius Masiliunas <pastas4@gmail.com>
Diff between bfast versions 1.6.0 dated 2021-05-03 and 1.6.1 dated 2021-05-10
DESCRIPTION | 19 +++++++++++-------- MD5 | 8 ++++---- NEWS | 4 ++++ build/partial.rdb |binary src/bfastts.cpp | 8 ++++++-- 5 files changed, 25 insertions(+), 14 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut, cre],
Ian Cook [aut],
Jonathan Keane [aut],
Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>),
Jeroen Ooms [aut],
Javier Luraschi [ctb],
Jeffrey Wong [ctb],
Apache Arrow [aut, cph]
Maintainer: Neal Richardson <neal@ursalabs.org>
Diff between arrow versions 4.0.0 dated 2021-04-27 and 4.0.0.1 dated 2021-05-10
DESCRIPTION | 6 ++-- MD5 | 33 +++++++++++++------------ NEWS.md | 7 ++++- configure | 5 +++ configure.win | 2 - inst/build_arrow_static.sh | 7 +++-- inst/doc/arrow.Rmd | 2 - inst/doc/arrow.html | 2 - inst/doc/developing.Rmd | 25 ++++++++++--------- inst/doc/developing.html | 25 ++++++++++--------- src/Makevars.ucrt |only tests/testthat/helper-skip.R | 19 ++++++++++++++ tests/testthat/test-Array.R | 1 tests/testthat/test-arrow.R | 4 +++ tests/testthat/test-compute-aggregate.R | 12 +++++++-- tools/nixlibs.R | 41 +++++++++++++++++++------------- vignettes/arrow.Rmd | 2 - vignettes/developing.Rmd | 25 ++++++++++--------- 18 files changed, 137 insertions(+), 81 deletions(-)
Title: Raven Hydrological Modelling Framework R Support and Analysis
Description: Utilities for processing input and output files associated with the Raven Hydrological Modelling Framework. Includes various plotting functions, model diagnostics, reading output files into xts format, and support for writing Raven input files (rvt, rvh, rvc, etc.).
Author: Robert Chlumsky [cre, aut],
James Craig [ctb],
Genevieve Brown [ctb],
Leland Scantlebury [ctb],
Sarah Grass [ctb],
Simon Lin [ctb]
Maintainer: Robert Chlumsky <rchlumsk@uwaterloo.ca>
Diff between RavenR versions 2.0.1 dated 2020-11-19 and 2.0.9 dated 2021-05-10
RavenR-2.0.1/RavenR/man/rvn_col_transparent.Rd |only RavenR-2.0.1/RavenR/man/rvn_iscolour.Rd |only RavenR-2.0.9/RavenR/DESCRIPTION | 16 - RavenR-2.0.9/RavenR/MD5 | 122 ++++---- RavenR-2.0.9/RavenR/NAMESPACE | 24 + RavenR-2.0.9/RavenR/R/rvn_annual_quantiles.R | 7 RavenR-2.0.9/RavenR/R/rvn_annual_quantiles_plot.R | 4 RavenR-2.0.9/RavenR/R/rvn_custom_read.R | 30 +- RavenR-2.0.9/RavenR/R/rvn_forcings_read.R | 5 RavenR-2.0.9/RavenR/R/rvn_gen_gridweights.R | 262 ++++++++++++------ RavenR-2.0.9/RavenR/R/rvn_gridweights_write.R |only RavenR-2.0.9/RavenR/R/rvn_hyd_dygraph.R | 26 + RavenR-2.0.9/RavenR/R/rvn_hyd_extract.R | 88 ++---- RavenR-2.0.9/RavenR/R/rvn_hyd_plot.R | 56 +-- RavenR-2.0.9/RavenR/R/rvn_hyd_read.R | 12 RavenR-2.0.9/RavenR/R/rvn_netcdf_to_gridshp.R | 36 +- RavenR-2.0.9/RavenR/R/rvn_res_plot.R | 53 +-- RavenR-2.0.9/RavenR/R/rvn_res_read.R | 5 RavenR-2.0.9/RavenR/R/rvn_rvc_from_custom_output.R |only RavenR-2.0.9/RavenR/R/rvn_rvc_res.R | 2 RavenR-2.0.9/RavenR/R/rvn_rvc_write.R |only RavenR-2.0.9/RavenR/R/rvn_rvh_blankHRUdf.R | 2 RavenR-2.0.9/RavenR/R/rvn_rvh_blankSBdf.R | 2 RavenR-2.0.9/RavenR/R/rvn_rvh_cleanHRUs.R | 178 +++++++++--- RavenR-2.0.9/RavenR/R/rvn_rvh_read.R | 31 +- RavenR-2.0.9/RavenR/R/rvn_rvt_ECmet.R | 22 - RavenR-2.0.9/RavenR/R/rvn_rvt_obsfile_irregular.R |only RavenR-2.0.9/RavenR/R/rvn_rvt_obsweights.R | 4 RavenR-2.0.9/RavenR/R/rvn_rvt_read.R | 10 RavenR-2.0.9/RavenR/R/rvn_rvt_write.R | 6 RavenR-2.0.9/RavenR/R/rvn_rvt_wsc.R | 6 RavenR-2.0.9/RavenR/R/rvn_tidyhydat_sample.R | 2 RavenR-2.0.9/RavenR/R/rvn_utilities.R | 130 +++----- RavenR-2.0.9/RavenR/R/rvn_watershed_read.R | 5 RavenR-2.0.9/RavenR/R/rvn_watershedmeb_read.R | 5 RavenR-2.0.9/RavenR/R/rvn_weathercan_sample.R |only RavenR-2.0.9/RavenR/R/rvn_xts_plot.R |only RavenR-2.0.9/RavenR/README.md | 12 RavenR-2.0.9/RavenR/data/rvn_weathercan_sample.rda |only RavenR-2.0.9/RavenR/inst/extdata/GridWeights.rvt |only RavenR-2.0.9/RavenR/man/figures |only RavenR-2.0.9/RavenR/man/grapes-notin-grapes.Rd |only RavenR-2.0.9/RavenR/man/rvn_annual_quantiles.Rd | 7 RavenR-2.0.9/RavenR/man/rvn_annual_quantiles_plot.Rd | 4 RavenR-2.0.9/RavenR/man/rvn_custom_read.Rd | 5 RavenR-2.0.9/RavenR/man/rvn_forcings_read.Rd | 5 RavenR-2.0.9/RavenR/man/rvn_fortify_xts.Rd |only RavenR-2.0.9/RavenR/man/rvn_gen_gridweights.Rd | 40 +- RavenR-2.0.9/RavenR/man/rvn_gridweights_write.Rd |only RavenR-2.0.9/RavenR/man/rvn_hyd_dygraph.Rd | 12 RavenR-2.0.9/RavenR/man/rvn_hyd_extract.Rd | 8 RavenR-2.0.9/RavenR/man/rvn_hyd_plot.Rd | 4 RavenR-2.0.9/RavenR/man/rvn_hyd_read.Rd | 8 RavenR-2.0.9/RavenR/man/rvn_res_plot.Rd | 12 RavenR-2.0.9/RavenR/man/rvn_res_read.Rd | 5 RavenR-2.0.9/RavenR/man/rvn_rvc_from_custom_output.Rd |only RavenR-2.0.9/RavenR/man/rvn_rvc_write.Rd |only RavenR-2.0.9/RavenR/man/rvn_rvh_blankSBdf.Rd | 2 RavenR-2.0.9/RavenR/man/rvn_rvh_cleanhrus.Rd | 14 RavenR-2.0.9/RavenR/man/rvn_rvt_ECmet.Rd | 19 - RavenR-2.0.9/RavenR/man/rvn_rvt_obsfile_irregular.Rd |only RavenR-2.0.9/RavenR/man/rvn_rvt_read.Rd | 9 RavenR-2.0.9/RavenR/man/rvn_rvt_wsc.Rd | 6 RavenR-2.0.9/RavenR/man/rvn_tidyhydat_sample.Rd | 69 ++-- RavenR-2.0.9/RavenR/man/rvn_watershed_read.Rd | 5 RavenR-2.0.9/RavenR/man/rvn_watershedmeb_read.Rd | 5 RavenR-2.0.9/RavenR/man/rvn_weathercan_sample.Rd |only RavenR-2.0.9/RavenR/man/rvn_xts_plot.Rd |only 68 files changed, 863 insertions(+), 539 deletions(-)
Title: Bottom-Up Proteomics and LiP-MS Quality Control and Data
Analysis Tools
Description: Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
Author: Jan-Philipp Quast [aut, cre],
Dina Schuster [aut],
ETH Zurich [cph, fnd]
Maintainer: Jan-Philipp Quast <quast@imsb.biol.ethz.ch>
Diff between protti versions 0.1.0 dated 2021-04-23 and 0.1.1 dated 2021-05-10
DESCRIPTION | 10 MD5 | 62 ++--- NAMESPACE | 3 NEWS.md | 7 R/diff_abundance.R | 32 ++ R/fetch_chebi.R | 2 R/fetch_kegg.R | 14 + R/fetch_uniprot.R | 40 +++ R/fetch_uniprot_proteome.R | 22 +- R/try_query.R | 78 ++++--- README.md | 124 ++++++----- inst/doc/data_analysis_dose_response_workflow.R | 19 - inst/doc/data_analysis_dose_response_workflow.Rmd | 64 +---- inst/doc/data_analysis_dose_response_workflow.html | 46 +--- inst/doc/data_analysis_single_dose_treatment_workflow.Rmd | 66 +++--- inst/doc/data_analysis_single_dose_treatment_workflow.html | 68 +++--- inst/doc/input_preparation_workflow.Rmd | 42 +-- inst/doc/input_preparation_workflow.html | 30 +- inst/doc/quality_control_workflow.Rmd | 46 ++-- inst/doc/quality_control_workflow.html | 34 +-- man/diff_abundance.Rd | 4 man/fetch_chebi.Rd | 2 man/fetch_kegg.Rd | 4 man/fetch_uniprot_proteome.Rd | 10 man/try_query.Rd | 21 - tests/testthat/test-auxiliary_functions.R | 140 ++++++------- tests/testthat/test-qc_functions.R | 30 +- tests/testthat/test-workflow.R | 2 vignettes/data_analysis_dose_response_workflow.Rmd | 64 +---- vignettes/data_analysis_single_dose_treatment_workflow.Rmd | 66 +++--- vignettes/input_preparation_workflow.Rmd | 42 +-- vignettes/quality_control_workflow.Rmd | 46 ++-- 32 files changed, 624 insertions(+), 616 deletions(-)
Title: Subset- And Name-Aware Array Utility Functions
Description: Stacking arrays according to dimension names, subset-aware
splitting and mapping of functions, intersecting along arbitrary
dimensions, converting to and from data.frames, and many other helper
functions.
Author: Michael Schubert <mschu.dev@gmail.com>
Maintainer: Michael Schubert <mschu.dev@gmail.com>
Diff between narray versions 0.4.1 dated 2018-08-18 and 0.4.1.1 dated 2021-05-10
DESCRIPTION | 9 - MD5 | 12 - build/vignette.rds |binary inst/doc/narray.R | 16 +- inst/doc/narray.Rmd | 2 inst/doc/narray.html | 328 +++++++++++++++------------------------------------ vignettes/narray.Rmd | 2 7 files changed, 117 insertions(+), 252 deletions(-)
Title: Miscellaneous Useful Functions Including LaTeX Tables, Kalman
Filtering and Development Tools
Description: Implementing various things including functions for LaTeX tables,
the Kalman filter, web scraping, development tools, relative risk and odds
ratio.
Author: Benjamin M. Taylor
Maintainer: Benjamin M. Taylor <benjamin.taylor.software@gmail.com>
Diff between miscFuncs versions 1.5 dated 2021-05-06 and 1.5-1 dated 2021-05-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/roxtext.R | 14 +++++++------- inst/doc/miscFuncs.pdf |binary 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Good Regression
Description: Fit Good regression models to count data (Tur et al., 2021) <arXiv:2105.01557>. The package provides functions for model estimation and model prediction. Density, distribution function, quantile function and random generation for the Good distribution are also provided.
Author: Jordi Tur [aut, cre],
David Moriña [ctb],
Pere Puig [ctb],
Argimiro Arratia [ctb],
Alejandra Cabaña [ctb],
Amanda Fernández-Fontelo [aut]
Maintainer: Jordi Tur <jjtur@crm.cat>
Diff between good versions 1.0.0 dated 2021-05-06 and 1.0.1 dated 2021-05-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/glm.good.R | 6 +++--- man/glm.good.Rd | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Evidential Clustering
Description: Various clustering algorithms that produce a credal partition,
i.e., a set of Dempster-Shafer mass functions representing the membership of objects
to clusters. The mass functions quantify the cluster-membership uncertainty of the
objects. The algorithms are: Evidential c-Means, Relational Evidential c-Means,
Constrained Evidential c-Means, Evidential Clustering, Constrained Evidential
Clustering, Evidential K-nearest-neighbor-based Clustering, Bootstrap Model-Based
Evidential Clustering, Belief Peak Evidential Clustering, Neural-Network-based
Evidential Clustering.
Author: Thierry Denoeux
Maintainer: Thierry Denoeux <tdenoeux@utc.fr>
Diff between evclust versions 2.0.0 dated 2021-03-05 and 2.0.1 dated 2021-05-10
DESCRIPTION | 13 ++++++------- MD5 | 24 ++++++++++++------------ NEWS | 6 ++++-- R/bootclus.R | 6 +++--- R/delta_Bel.R | 3 ++- R/kcevclus.R | 8 +++----- build/vignette.rds |binary inst/doc/evclust_vignette.R | 2 +- inst/doc/evclust_vignette.Rnw | 3 ++- inst/doc/evclust_vignette.pdf |binary man/bootclus.Rd | 4 ++-- man/delta_Bel.Rd | 1 + vignettes/evclust_vignette.Rnw | 3 ++- 13 files changed, 38 insertions(+), 35 deletions(-)
Title: Estimation, Simulation and Reliability of Drifting Markov Models
Description: Performs the drifting Markov models (DMM) which are
non-homogeneous Markov models designed for modeling the heterogeneities of
sequences in a more flexible way than homogeneous Markov chains or even
hidden Markov models. In this context, we developed an R package dedicated to
the estimation, simulation and the exact computation of associated reliability
of drifting Markov models. The implemented methods are described in
Vergne, N. (2008), <doi:10.2202/1544-6115.1326> and
Barbu, V.S., Vergne, N. (2019) <doi:10.1007/s11009-018-9682-8> .
Author: Vlad Stefan Barbu [aut],
Geoffray Brelurut [ctb],
Annthomy Gilles [ctb],
Arnaud Lefebvre [ctb],
Corentin Lothode [aut],
Victor Mataigne [ctb],
Alexandre Seiller [aut],
Nicolas Vergne [aut, cre]
Maintainer: Nicolas Vergne <nicolas.vergne@univ-rouen.fr>
Diff between drimmR versions 1.0.0 dated 2021-03-22 and 1.0.1 dated 2021-05-10
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS.md | 4 ++++ build/partial.rdb |binary 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Accessing Statistics Canada Data Table and Vectors
Description: Searches for, accesses, and retrieves new-format and old-format Statistics Canada data
tables, as well as individual vectors, as tidy data frames. This package deals with encoding issues, allows for
bilingual English or French language data retrieval, and bundles convenience functions
to make it easier to work with retrieved table data. Optional caching features are provided.
Author: Jens von Bergmann [cre],
Dmitry Shkolnik [aut]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between cansim versions 0.3.6 dated 2021-05-08 and 0.3.7 dated 2021-05-10
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/cansim_sql.R | 4 ++-- README.md | 6 +++--- inst/doc/cansim.html | 4 ++-- inst/doc/working_with_large_tables.html | 10 +++++----- man/csv2sqlite.Rd | 4 ++-- 8 files changed, 31 insertions(+), 26 deletions(-)
Title: Search and Download Data from the Swiss Federal Statistical
Office (BFS)
Description: Search and download data from the Swiss Federal Statistical Office <https://www.bfs.admin.ch/>.
Author: Felix Luginbuhl [aut, cre]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between BFS versions 0.3.0 dated 2021-03-23 and 0.3.1 dated 2021-05-10
DESCRIPTION | 13 - MD5 | 11 NEWS.md | 9 R/bfs_get_catalog.R | 40 ++- R/main.R | 592 +++++++++++++++++++++------------------------------- R/utils.R |only README.md | 125 +++++----- 7 files changed, 352 insertions(+), 438 deletions(-)
Title: Access the 'Windsor.ai' API
Description: Collect multichannel marketing data from sources such as Google analytics, Facebook Ads, and many others using the 'Windsor.ai' API <https://www.windsor.ai/api-fields/>.
Author: Novica Nakov [aut, cre],
Windsor.ai [cph]
Maintainer: Novica Nakov <nnovica@gmail.com>
Diff between windsoraiR versions 0.1.1 dated 2021-04-28 and 0.1.2 dated 2021-05-10
DESCRIPTION | 7 ++-- MD5 | 15 +++++---- NEWS.md | 4 ++ R/data.R |only data |only inst/doc/basics.R | 13 +------- inst/doc/basics.Rmd | 15 ++------- inst/doc/basics.html | 78 +++++++++++++++++++++++++-------------------------- man/my_data.Rd |only vignettes/basics.Rmd | 15 ++------- 10 files changed, 67 insertions(+), 80 deletions(-)
Title: Statistical Modeling
Description: A collection of algorithms and functions to aid statistical modeling. Includes limiting dilution analysis (aka ELDA), growth curve comparisons, mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Also includes advanced generalized linear model functions including Tweedie and Digamma distributional families and a secure convergence algorithm.
Author: Gordon Smyth [cre, aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]
Maintainer: Gordon Smyth <smyth@wehi.edu.au>
Diff between statmod versions 1.4.35 dated 2020-10-19 and 1.4.36 dated 2021-05-10
DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- build |only man/elda.Rd | 2 +- man/gauss.quad.Rd | 4 +++- man/gauss.quad.prob.Rd | 5 ++++- man/glmgam.Rd | 2 +- man/glmnbfit.Rd | 2 +- man/glmscoretest.Rd | 2 +- man/qresiduals.Rd | 2 +- man/tweedie.Rd | 2 +- tests/statmod-Tests.R | 2 +- tests/statmod-Tests.Rout.save | 8 ++++---- 13 files changed, 34 insertions(+), 28 deletions(-)
Title: Simulation of Cohort Platform Trials for Combination Treatments
Description: A collection of functions dedicated to simulating staggered entry platform
trials whereby the treatment under investigation is a combination of two
active compounds. In order to obtain approval for this combination therapy,
superiority of the combination over the two active compounds and superiority
of the two active compounds over placebo need to be demonstrated.
A more detailed description of the design can be found in
Meyer et al. <arXiv:2103.09547>.
Author: Elias Laurin Meyer [aut, cre]
Maintainer: Elias Laurin Meyer <elias.meyer@meduniwien.ac.at>
Diff between CohortPlat versions 1.0.0 dated 2021-01-25 and 1.0.1 dated 2021-05-10
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CohortPlat-1.0.1/CohortPlat/vignettes/my-vignette_cache/html/unnamed-chunk-9_010d2232ecfa40c844f8592fe413348e.rdx |only 132 files changed, 132 insertions(+), 1505 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Description: State space modelling is an efficient and flexible framework for
statistical inference of a broad class of time series and other data. KFAS
includes computationally efficient functions for Kalman filtering, smoothing,
forecasting, and simulation of multivariate exponential family state space models,
with observations from Gaussian, Poisson, binomial, negative binomial, and gamma
distributions. See the paper by Helske (2017) <doi:10.18637/jss.v078.i10> for details.
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between KFAS versions 1.4.4 dated 2021-01-21 and 1.4.5 dated 2021-05-10
ChangeLog | 9 DESCRIPTION | 8 MD5 | 31 +-- NAMESPACE | 1 R/KFAS-package.R | 6 R/KFS.R | 3 R/SSMcycle.R | 4 R/SSModel.R | 2 R/logLik.SSModel.R | 5 R/zzz.R |only build/vignette.rds |binary inst/doc/KFAS.R | 526 ++++++++++++++++++++++++++--------------------------- inst/doc/KFAS.pdf |binary man/KFAS.Rd | 2 man/SSModel.Rd | 4 man/alcohol.Rd | 2 man/sexratio.Rd | 2 17 files changed, 314 insertions(+), 291 deletions(-)
Title: Taxonomic Standardization of Plant Species Names
Description: Automated standardization of taxonomic names and removal of orthographic errors in plant species names using 'The Plant List' website (www.theplantlist.org).
Author: Luis Cayuela, Ildefonso Macarro, Anke Stein, Jari Oksanen
Maintainer: Luis Cayuela <luis.cayuela@urjc.es>
Diff between Taxonstand versions 2.3 dated 2021-03-22 and 2.4 dated 2021-05-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/TPLck.R | 4 ++-- inst/NEWS.Rd | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Character String Processing Facilities
Description: A multitude of character string/text/natural language
processing tools: pattern searching (e.g., with 'Java'-like regular
expressions or the 'Unicode' collation algorithm), random string generation,
case mapping, string transliteration, concatenation, sorting, padding,
wrapping, Unicode normalisation, date-time formatting and parsing,
and many more. They are fast, consistent, convenient, and -
thanks to 'ICU' (International Components for Unicode) -
portable across all locales and platforms.
Author: Marek Gagolewski [aut, cre, cph] (<https://orcid.org/0000-0003-0637-6028>),
Bartek Tartanus [ctb],
and others (stringi source code);
IBM, Unicode, Inc. and others (ICU4C source code, Unicode Character Database)
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between stringi versions 1.5.3 dated 2020-09-09 and 1.6.1 dated 2021-05-10
stringi-1.5.3/stringi/src/icu61 |only stringi-1.5.3/stringi/src/icu61_common_c.txt |only stringi-1.5.3/stringi/src/icu61_common_cpp.txt |only stringi-1.5.3/stringi/src/icu61_i18n_c.txt |only stringi-1.5.3/stringi/src/icu61_i18n_cpp.txt |only stringi-1.5.3/stringi/src/icu61_stubdata_c.txt |only stringi-1.5.3/stringi/src/icu61_stubdata_cpp.txt |only stringi-1.6.1/stringi/DESCRIPTION | 22 stringi-1.6.1/stringi/INSTALL | 175 stringi-1.6.1/stringi/LICENSE | 7 stringi-1.6.1/stringi/MD5 | 2199 +++++----- stringi-1.6.1/stringi/NAMESPACE | 2 stringi-1.6.1/stringi/NEWS | 195 stringi-1.6.1/stringi/R/ICU_settings.R | 2 stringi-1.6.1/stringi/R/compare.R | 8 stringi-1.6.1/stringi/R/encoding.R | 4 stringi-1.6.1/stringi/R/encoding_conversion.R | 2 stringi-1.6.1/stringi/R/encoding_detection.R | 2 stringi-1.6.1/stringi/R/encoding_management.R | 2 stringi-1.6.1/stringi/R/escape.R | 5 stringi-1.6.1/stringi/R/files.R | 2 stringi-1.6.1/stringi/R/install.R | 126 stringi-1.6.1/stringi/R/internal_prepare_arg.R | 2 stringi-1.6.1/stringi/R/internal_test.R | 2 stringi-1.6.1/stringi/R/join.R | 2 stringi-1.6.1/stringi/R/length.R | 13 stringi-1.6.1/stringi/R/locale.R | 2 stringi-1.6.1/stringi/R/locale_management.R | 2 stringi-1.6.1/stringi/R/opts.R | 6 stringi-1.6.1/stringi/R/pad.R | 2 stringi-1.6.1/stringi/R/random.R | 2 stringi-1.6.1/stringi/R/reverse.R | 2 stringi-1.6.1/stringi/R/search.R | 2 stringi-1.6.1/stringi/R/search_count_4.R | 2 stringi-1.6.1/stringi/R/search_count_bound.R | 2 stringi-1.6.1/stringi/R/search_detect_4.R | 2 stringi-1.6.1/stringi/R/search_extract_4.R | 12 stringi-1.6.1/stringi/R/search_extract_bound.R | 2 stringi-1.6.1/stringi/R/search_locate_4.R | 9 stringi-1.6.1/stringi/R/search_locate_bound.R | 2 stringi-1.6.1/stringi/R/search_match_4.R | 2 stringi-1.6.1/stringi/R/search_replace_4.R | 10 stringi-1.6.1/stringi/R/search_split_4.R | 7 stringi-1.6.1/stringi/R/search_split_bound.R | 7 stringi-1.6.1/stringi/R/search_startsendswith_4.R | 2 stringi-1.6.1/stringi/R/search_subset_4.R | 2 stringi-1.6.1/stringi/R/sort.R | 89 stringi-1.6.1/stringi/R/stats.R | 2 stringi-1.6.1/stringi/R/stringi-package.R | 15 stringi-1.6.1/stringi/R/sub.R | 2 stringi-1.6.1/stringi/R/time_calendar.R | 2 stringi-1.6.1/stringi/R/time_format.R | 2 stringi-1.6.1/stringi/R/time_symbols.R | 2 stringi-1.6.1/stringi/R/time_zone.R | 2 stringi-1.6.1/stringi/R/todo_charclass.R | 2 stringi-1.6.1/stringi/R/todo_justify.R | 2 stringi-1.6.1/stringi/R/todo_rbnf.R | 2 stringi-1.6.1/stringi/R/todo_search_in.R | 2 stringi-1.6.1/stringi/R/todo_split.R | 2 stringi-1.6.1/stringi/R/trans_casemap.R | 20 stringi-1.6.1/stringi/R/trans_normalization.R | 2 stringi-1.6.1/stringi/R/trans_other.R | 2 stringi-1.6.1/stringi/R/trans_transliterate.R | 2 stringi-1.6.1/stringi/R/trim.R | 2 stringi-1.6.1/stringi/R/utils.R | 33 stringi-1.6.1/stringi/R/wrap.R | 3 stringi-1.6.1/stringi/cleanup | 2 stringi-1.6.1/stringi/configure | 1255 ++--- stringi-1.6.1/stringi/configure.ac | 1419 +++--- stringi-1.6.1/stringi/configure.win | 18 stringi-1.6.1/stringi/inst/AUTHORS | 85 stringi-1.6.1/stringi/inst/CITATION | 18 stringi-1.6.1/stringi/man/about_encoding.Rd | 2 stringi-1.6.1/stringi/man/about_locale.Rd | 1 stringi-1.6.1/stringi/man/about_search_boundaries.Rd | 1 stringi-1.6.1/stringi/man/about_search_coll.Rd | 1 stringi-1.6.1/stringi/man/about_stringi.Rd | 12 stringi-1.6.1/stringi/man/operator_compare.Rd | 1 stringi-1.6.1/stringi/man/operator_dollar.Rd | 13 stringi-1.6.1/stringi/man/stri_compare.Rd | 7 stringi-1.6.1/stringi/man/stri_count_boundaries.Rd | 1 stringi-1.6.1/stringi/man/stri_duplicated.Rd | 1 stringi-1.6.1/stringi/man/stri_enc_detect2.Rd | 1 stringi-1.6.1/stringi/man/stri_extract.Rd | 10 stringi-1.6.1/stringi/man/stri_extract_boundaries.Rd | 1 stringi-1.6.1/stringi/man/stri_locate.Rd | 7 stringi-1.6.1/stringi/man/stri_locate_boundaries.Rd | 1 stringi-1.6.1/stringi/man/stri_opts_brkiter.Rd | 4 stringi-1.6.1/stringi/man/stri_opts_collator.Rd | 1 stringi-1.6.1/stringi/man/stri_order.Rd | 9 stringi-1.6.1/stringi/man/stri_rank.Rd |only stringi-1.6.1/stringi/man/stri_replace.Rd | 8 stringi-1.6.1/stringi/man/stri_sort.Rd | 5 stringi-1.6.1/stringi/man/stri_sort_key.Rd | 16 stringi-1.6.1/stringi/man/stri_split.Rd | 5 stringi-1.6.1/stringi/man/stri_split_boundaries.Rd | 6 stringi-1.6.1/stringi/man/stri_trans_casemap.Rd | 13 stringi-1.6.1/stringi/man/stri_unescape_unicode.Rd | 3 stringi-1.6.1/stringi/man/stri_unique.Rd | 1 stringi-1.6.1/stringi/man/stri_width.Rd | 11 stringi-1.6.1/stringi/man/stri_wrap.Rd | 1 stringi-1.6.1/stringi/src/Makevars.in | 4 stringi-1.6.1/stringi/src/Makevars.win | 34 stringi-1.6.1/stringi/src/icu69 |only stringi-1.6.1/stringi/src/icu69_common_c.txt |only stringi-1.6.1/stringi/src/icu69_common_cpp.txt |only stringi-1.6.1/stringi/src/icu69_i18n_c.txt |only stringi-1.6.1/stringi/src/icu69_i18n_cpp.txt |only stringi-1.6.1/stringi/src/icu69_stubdata_c.txt |only stringi-1.6.1/stringi/src/icu69_stubdata_cpp.txt |only stringi-1.6.1/stringi/src/install.libs.R.in | 4 stringi-1.6.1/stringi/src/stri_ICU_settings.cpp | 2 stringi-1.6.1/stringi/src/stri_TODO_justify.cpp | 2 stringi-1.6.1/stringi/src/stri_TODO_splitpos.cpp | 2 stringi-1.6.1/stringi/src/stri_TODO_uchar.cpp | 2 stringi-1.6.1/stringi/src/stri_brkiter.cpp | 2 stringi-1.6.1/stringi/src/stri_brkiter.h | 2 stringi-1.6.1/stringi/src/stri_bytesearch_matcher.h | 2 stringi-1.6.1/stringi/src/stri_collator.cpp | 9 stringi-1.6.1/stringi/src/stri_common.cpp | 2 stringi-1.6.1/stringi/src/stri_compare.cpp | 2 stringi-1.6.1/stringi/src/stri_container_base.cpp | 2 stringi-1.6.1/stringi/src/stri_container_base.h | 2 stringi-1.6.1/stringi/src/stri_container_bytesearch.cpp | 2 stringi-1.6.1/stringi/src/stri_container_bytesearch.h | 2 stringi-1.6.1/stringi/src/stri_container_charclass.h | 2 stringi-1.6.1/stringi/src/stri_container_double.h | 2 stringi-1.6.1/stringi/src/stri_container_integer.h | 2 stringi-1.6.1/stringi/src/stri_container_listint.cpp | 2 stringi-1.6.1/stringi/src/stri_container_listint.h | 2 stringi-1.6.1/stringi/src/stri_container_listraw.cpp | 2 stringi-1.6.1/stringi/src/stri_container_listraw.h | 2 stringi-1.6.1/stringi/src/stri_container_listutf8.cpp | 2 stringi-1.6.1/stringi/src/stri_container_listutf8.h | 2 stringi-1.6.1/stringi/src/stri_container_logical.h | 2 stringi-1.6.1/stringi/src/stri_container_regex.cpp | 2 stringi-1.6.1/stringi/src/stri_container_regex.h | 2 stringi-1.6.1/stringi/src/stri_container_usearch.cpp | 8 stringi-1.6.1/stringi/src/stri_container_usearch.h | 2 stringi-1.6.1/stringi/src/stri_container_utf16.cpp | 2 stringi-1.6.1/stringi/src/stri_container_utf16.h | 2 stringi-1.6.1/stringi/src/stri_container_utf8.cpp | 2 stringi-1.6.1/stringi/src/stri_container_utf8.h | 2 stringi-1.6.1/stringi/src/stri_container_utf8_indexable.cpp | 2 stringi-1.6.1/stringi/src/stri_container_utf8_indexable.h | 2 stringi-1.6.1/stringi/src/stri_encoding_conversion.cpp | 2 stringi-1.6.1/stringi/src/stri_encoding_detection.cpp | 2 stringi-1.6.1/stringi/src/stri_encoding_management.cpp | 2 stringi-1.6.1/stringi/src/stri_escape.cpp | 2 stringi-1.6.1/stringi/src/stri_exception.cpp | 2 stringi-1.6.1/stringi/src/stri_exception.h | 2 stringi-1.6.1/stringi/src/stri_exports.h | 4 stringi-1.6.1/stringi/src/stri_external.h | 2 stringi-1.6.1/stringi/src/stri_interval.h | 2 stringi-1.6.1/stringi/src/stri_intvec.h | 2 stringi-1.6.1/stringi/src/stri_join.cpp | 2 stringi-1.6.1/stringi/src/stri_length.cpp | 87 stringi-1.6.1/stringi/src/stri_macros.h | 12 stringi-1.6.1/stringi/src/stri_messages.h | 2 stringi-1.6.1/stringi/src/stri_pad.cpp | 2 stringi-1.6.1/stringi/src/stri_prepare_arg.cpp | 10 stringi-1.6.1/stringi/src/stri_random.cpp | 2 stringi-1.6.1/stringi/src/stri_reverse.cpp | 2 stringi-1.6.1/stringi/src/stri_search_boundaries_count.cpp | 2 stringi-1.6.1/stringi/src/stri_search_boundaries_extract.cpp | 2 stringi-1.6.1/stringi/src/stri_search_boundaries_locate.cpp | 2 stringi-1.6.1/stringi/src/stri_search_boundaries_split.cpp | 2 stringi-1.6.1/stringi/src/stri_search_class_count.cpp | 2 stringi-1.6.1/stringi/src/stri_search_class_detect.cpp | 2 stringi-1.6.1/stringi/src/stri_search_class_extract.cpp | 2 stringi-1.6.1/stringi/src/stri_search_class_locate.cpp | 2 stringi-1.6.1/stringi/src/stri_search_class_replace.cpp | 2 stringi-1.6.1/stringi/src/stri_search_class_split.cpp | 2 stringi-1.6.1/stringi/src/stri_search_class_startsendswith.cpp | 2 stringi-1.6.1/stringi/src/stri_search_class_subset.cpp | 2 stringi-1.6.1/stringi/src/stri_search_class_trim.cpp | 2 stringi-1.6.1/stringi/src/stri_search_coll_count.cpp | 2 stringi-1.6.1/stringi/src/stri_search_coll_detect.cpp | 11 stringi-1.6.1/stringi/src/stri_search_coll_extract.cpp | 2 stringi-1.6.1/stringi/src/stri_search_coll_locate.cpp | 2 stringi-1.6.1/stringi/src/stri_search_coll_replace.cpp | 2 stringi-1.6.1/stringi/src/stri_search_coll_split.cpp | 2 stringi-1.6.1/stringi/src/stri_search_coll_startsendswith.cpp | 2 stringi-1.6.1/stringi/src/stri_search_coll_subset.cpp | 2 stringi-1.6.1/stringi/src/stri_search_common.cpp | 2 stringi-1.6.1/stringi/src/stri_search_fixed_count.cpp | 2 stringi-1.6.1/stringi/src/stri_search_fixed_detect.cpp | 2 stringi-1.6.1/stringi/src/stri_search_fixed_extract.cpp | 2 stringi-1.6.1/stringi/src/stri_search_fixed_locate.cpp | 2 stringi-1.6.1/stringi/src/stri_search_fixed_replace.cpp | 2 stringi-1.6.1/stringi/src/stri_search_fixed_split.cpp | 2 stringi-1.6.1/stringi/src/stri_search_fixed_startsendswith.cpp | 2 stringi-1.6.1/stringi/src/stri_search_fixed_subset.cpp | 2 stringi-1.6.1/stringi/src/stri_search_in.cpp | 2 stringi-1.6.1/stringi/src/stri_search_other_split.cpp | 2 stringi-1.6.1/stringi/src/stri_search_regex_count.cpp | 2 stringi-1.6.1/stringi/src/stri_search_regex_detect.cpp | 2 stringi-1.6.1/stringi/src/stri_search_regex_extract.cpp | 2 stringi-1.6.1/stringi/src/stri_search_regex_locate.cpp | 2 stringi-1.6.1/stringi/src/stri_search_regex_match.cpp | 2 stringi-1.6.1/stringi/src/stri_search_regex_replace.cpp | 2 stringi-1.6.1/stringi/src/stri_search_regex_split.cpp | 2 stringi-1.6.1/stringi/src/stri_search_regex_subset.cpp | 2 stringi-1.6.1/stringi/src/stri_sort.cpp | 142 stringi-1.6.1/stringi/src/stri_stats.cpp | 2 stringi-1.6.1/stringi/src/stri_string8.h | 2 stringi-1.6.1/stringi/src/stri_string8buf.h | 2 stringi-1.6.1/stringi/src/stri_stringi.cpp | 4 stringi-1.6.1/stringi/src/stri_stringi.h | 2 stringi-1.6.1/stringi/src/stri_sub.cpp | 2 stringi-1.6.1/stringi/src/stri_test.cpp | 2 stringi-1.6.1/stringi/src/stri_time_calendar.cpp | 2 stringi-1.6.1/stringi/src/stri_time_format.cpp | 2 stringi-1.6.1/stringi/src/stri_time_symbols.cpp | 2 stringi-1.6.1/stringi/src/stri_time_zone.cpp | 2 stringi-1.6.1/stringi/src/stri_trans_casemap.cpp | 84 stringi-1.6.1/stringi/src/stri_trans_normalization.cpp | 2 stringi-1.6.1/stringi/src/stri_trans_other.cpp | 2 stringi-1.6.1/stringi/src/stri_trans_transliterate.cpp | 2 stringi-1.6.1/stringi/src/stri_ucnv.cpp | 2 stringi-1.6.1/stringi/src/stri_ucnv.h | 2 stringi-1.6.1/stringi/src/stri_uloc.cpp | 2 stringi-1.6.1/stringi/src/stri_utils.cpp | 2 stringi-1.6.1/stringi/src/stri_wrap.cpp | 2 stringi-1.6.1/stringi/src/uconfig_local.h.in | 4 225 files changed, 3598 insertions(+), 3006 deletions(-)
Title: Find, Download and Process Sentinel-2 Data
Description: Functions to download Sentinel-2 optical images
and perform preliminary processing operations.
'sen2r' provides the instruments required to easily perform
(and eventually automate) the steps necessary to build a complete
Sentinel-2 processing chain.
A Graphical User Interface to facilitate data processing is also provided.
For additional documentation refer to the following article:
Ranghetti et al. (2020) <doi:10.1016/j.cageo.2020.104473>.
Author: Luigi Ranghetti [aut, cre] (<https://orcid.org/0000-0001-6207-5188>),
Lorenzo Busetto [aut] (<https://orcid.org/0000-0001-9634-6038>)
Maintainer: Luigi Ranghetti <luigi@ranghetti.info>
Diff between sen2r versions 1.4.3 dated 2021-05-04 and 1.4.4 dated 2021-05-10
DESCRIPTION | 6 +- MD5 | 74 ++++++++++++++-------------- NAMESPACE | 1 NEWS.md | 17 ++++++ R/s2_download.R | 32 +++++++++--- R/s2_list.R | 34 ++++++++----- R/s2_order.R | 16 ++++-- R/s2_tiles.R | 2 R/safe_is_online.R | 4 + R/safelist-class.R | 11 +++- R/scihub_login.R | 17 +++++- R/sen2r.R | 78 +++++++++++++++--------------- R/tiles_intersects.R | 2 build/partial.rdb |binary inst/WORDLIST | 1 man/s2_download.Rd | 5 + man/s2_list.Rd | 34 ++++++++----- man/s2_order.Rd | 4 + man/s2_tiles.Rd | 2 man/safe_is_online.Rd | 4 + man/safelist-class.Rd | 11 +++- man/scihub_login.Rd | 12 +++- man/sen2r.Rd | 78 +++++++++++++++--------------- man/tiles_intersects.Rd | 2 tests/testthat/setup-dependencies.R | 15 +++-- tests/testthat/test-s2_download.R | 1 tests/testthat/test-s2_list.R | 2 tests/testthat/test-s2_order.R | 1 tests/testthat/test-safelist-class.R | 1 tests/testthat/test-scihub_login.R | 1 tests/testthat/test-sen2cor.R | 4 - tests/testthat/test-sen2r-00_connection.R | 1 tests/testthat/test-sen2r-01_merge.R | 1 tests/testthat/test-sen2r-02_warp.R | 1 tests/testthat/test-sen2r-03_mask.R | 1 tests/testthat/test-sen2r-04_indices.R | 1 tests/testthat/test-sen2r-05_rgb.R | 1 tests/testthat/test-sen2r-06_ignorelist.R | 1 38 files changed, 305 insertions(+), 174 deletions(-)
Title: Geographic Information of Uruguay
Description: The toolbox have functions to load and process geographic information for Uruguay.
And extra-function to get address coordinates and orthophotos through the uruguayan 'IDE' API <https://www.gub.uy/infraestructura-datos-espaciales/tramites-y-servicios/servicios/servicio-direcciones-geograficas>.
Author: Richard Detomasi [aut, cre] (<https://orcid.org/0000-0002-6725-0261>),
Ministerio de Desarrollo Social, Uruguay (MIDES) [dtc],
Infraestrutura de Datos Espaciales, Uruguay (IDE) [dtc],
Servicio Geográfico Militar, Uruguay (SGM) [dtc],
Ministerio de Transporte y Obras Públicas, Uruguay (MTOP) [dtc],
Instituto Nacional de Estadística, Uruguay (INE) [dtc],
Instituto Geográfico Militar, Uruguay (IGM) [dtc],
Ministerio de Vivienda, Ordenamiento Territorial y Medio Ambiente,
Uruguay (MVOTMA) [dtc]
Maintainer: Richard Detomasi <richard.detomasi@gmail.com>
Diff between geouy versions 0.2.3 dated 2020-09-17 and 0.2.4 dated 2021-05-10
DESCRIPTION | 14 +-- MD5 | 40 +++++----- NAMESPACE | 25 ++++++ NEWS.md | 11 ++ R/data.R | 14 +++ R/geocode_ide_uy.R | 1 R/geouy.R | 2 R/load_geouy.R | 10 ++ R/plot_geouy.R | 6 - R/tiles_geouy.R |only R/utils.R | 2 README.md | 15 ++- data/metadata.rda |binary data/metadata_tables.rda |only inst/doc/geouy.Rmd | 2 inst/doc/geouy.html | 182 ++++++++++++++++++++++++++++------------------- man/is.uy5382.Rd | 2 man/loc_agr_ine.Rd | 67 ++++++++--------- man/metadata.Rd | 69 +++++++++-------- man/metadata_tables.Rd |only man/metadata_wms.Rd | 57 +++++++------- man/tiles_geouy.Rd |only vignettes/geouy.Rmd | 2 23 files changed, 314 insertions(+), 207 deletions(-)
Title: Visible Vowels: Visualization of Vowel Variation
Description: Visualizes vowel variation in f0, F1, F2, F3 and duration.
Author: Wilbert Heeringa, Hans Van de Velde
Maintainer: Wilbert Heeringa <wjheeringa@gmail.com>
Diff between visvow versions 1.3.0 dated 2021-05-06 and 1.3.1 dated 2021-05-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/visvow.R | 16 ++++++++-------- build/partial.rdb |binary 4 files changed, 14 insertions(+), 14 deletions(-)
Title: Super Learner Prediction
Description: Implements the super learner prediction method and contains a
library of prediction algorithms to be used in the super learner.
Author: Eric Polley [aut, cre],
Erin LeDell [aut],
Chris Kennedy [aut],
Sam Lendle [ctb],
Mark van der Laan [aut, ths]
Maintainer: Eric Polley <epolley@uchicago.edu>
Diff between SuperLearner versions 2.0-26 dated 2019-12-10 and 2.0-28 dated 2021-05-10
DESCRIPTION | 25 - MD5 | 104 ++--- NAMESPACE | 1 R/SL.gam.R | 4 R/SL.gbm.R | 8 R/SL.xgboost.R | 10 R/method.R | 21 - build/vignette.rds |binary inst/NEWS | 6 inst/doc/Guide-to-SuperLearner.R | 158 ++++---- inst/doc/Guide-to-SuperLearner.Rmd | 46 +- inst/doc/Guide-to-SuperLearner.html | 500 +++++++++++--------------- man/CV.SuperLearner.Rd | 4 man/CVFolds.Rd | 2 man/SL.biglasso.Rd | 10 man/SL.glmnet.Rd | 2 man/SL.ksvm.Rd | 5 man/SampleSplitSuperLearner.Rd | 4 man/SuperLearner.Rd | 6 man/listWrappers.Rd | 2 man/plot.CV.SuperLearner.Rd | 2 man/predict.superlearner.Rd | 2 man/recombineCVSL.Rd | 2 man/recombineSL.Rd | 2 man/summary.CV.SuperLearner.Rd | 2 man/write.SL.template.Rd | 2 man/write.method.template.Rd | 2 man/write.screen.template.Rd | 2 tests/testthat/test-SampleSplitSuperLearner.R | 23 - tests/testthat/test-SuperLearner.R | 7 tests/testthat/test-XGBoost.R | 18 tests/testthat/test-bartMachine.R | 24 - tests/testthat/test-biglasso.R | 12 tests/testthat/test-cforest.R | 30 - tests/testthat/test-createLearner.R | 10 tests/testthat/test-extraTrees.R | 80 ++-- tests/testthat/test-glm.R | 20 - tests/testthat/test-glmnet.R | 8 tests/testthat/test-kernelKnn.R | 7 tests/testthat/test-knn.R | 8 tests/testthat/test-ksvm.R | 12 tests/testthat/test-lda.R | 9 tests/testthat/test-lm.R | 20 - tests/testthat/test-methodCCLS.R | 22 - tests/testthat/test-methodCCnloglik.R | 15 tests/testthat/test-methods.R | 98 ++--- tests/testthat/test-qda.R | 10 tests/testthat/test-randomForest.R | 94 ++-- tests/testthat/test-ranger.R | 14 tests/testthat/test-speedglm.R | 12 tests/testthat/test-speedlm.R | 11 tests/testthat/test-summaryCVSuperLearner.R | 17 vignettes/Guide-to-SuperLearner.Rmd | 46 +- 53 files changed, 799 insertions(+), 762 deletions(-)
Title: The Exterior Calculus
Description: Provides functionality for working with tensors, alternating
tensors, wedge products, Stokes's theorem, and related concepts
from the exterior calculus. Functionality for Grassman algebra
is provided. The canonical reference would be:
M. Spivak (1965, ISBN:0-8053-9021-9) "Calculus on Manifolds".
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between stokes versions 1.0-7 dated 2021-04-27 and 1.0-8 dated 2021-05-10
stokes-1.0-7/stokes/inst/Alt.Rmd |only stokes-1.0-8/stokes/DESCRIPTION | 8 +-- stokes-1.0-8/stokes/MD5 | 29 +++++++----- stokes-1.0-8/stokes/R/mult.R | 18 +++---- stokes-1.0-8/stokes/build/partial.rdb |binary stokes-1.0-8/stokes/build/stokes.pdf |binary stokes-1.0-8/stokes/build/vignette.rds |binary stokes-1.0-8/stokes/inst/doc/Alt.R |only stokes-1.0-8/stokes/inst/doc/Alt.Rmd |only stokes-1.0-8/stokes/inst/doc/Alt.html |only stokes-1.0-8/stokes/inst/doc/inner.R |only stokes-1.0-8/stokes/inst/doc/inner.Rmd |only stokes-1.0-8/stokes/inst/doc/inner.html |only stokes-1.0-8/stokes/inst/doc/stokes.html | 60 +++++++------------------- stokes-1.0-8/stokes/man/Alt.Rd | 4 + stokes-1.0-8/stokes/man/consolidate.Rd | 20 ++------ stokes-1.0-8/stokes/man/inner.Rd | 21 ++++----- stokes-1.0-8/stokes/tests/testthat/test_alt.R | 19 ++++++-- stokes-1.0-8/stokes/vignettes/Alt.Rmd |only stokes-1.0-8/stokes/vignettes/inner.Rmd |only 20 files changed, 85 insertions(+), 94 deletions(-)
Title: Compute the Rectangular Statistical Cartogram
Description: Provides an interface and a C++ implementation of the RecMap MP2
construction heuristic (Panse C. (2018) <doi:10.18637/jss.v086.c01>).
This algorithm draws maps according to a given statistical value
(e.g., election results, population or epidemiological data).
The basic idea of the RecMap algorithm is that each map region
(e.g., different countries) is represented by a rectangle.
The area of each rectangle represents the statistical value given
as input (maintain zero cartographic error). Documentation about the usage
of the recmap algorithm is provided by a vignette included in this package.
Author: Christian Panse [aut, cre] (<https://orcid.org/0000-0003-1975-3064>)
Maintainer: Christian Panse <Christian.Panse@gmail.com>
Diff between recmap versions 1.0.7 dated 2020-02-20 and 1.0.9 dated 2021-05-10
DESCRIPTION | 19 ++--- MD5 | 30 ++++---- R/zzz.R | 1 README.md | 17 +++- build/partial.rdb |binary build/vignette.rds |binary data/jss2711.RData |binary inst/NEWS.Rd | 11 ++- inst/doc/recmap.html | 104 +++++++++++++++++++++--------- inst/include/recmap.h | 18 ++--- man/as.SpatialPolygonsDataFrame.recmap.Rd | 2 man/as.recmap.SpatialPolygonsDataFrame.Rd | 2 man/jss2711.Rd | 6 - man/recmap.Rd | 10 +- man/recmapGA.Rd | 2 src/Rrecmap.cpp | 1 16 files changed, 140 insertions(+), 83 deletions(-)
Title: Parse and Manipulate Research Patient Data Registry ('RPDR')
Text Queries
Description: Functions to load Research Patient Data Registry ('RPDR') text queries from Partners Healthcare institutions into R.
The package also provides helper functions to manipulate data and execute common procedures
such as finding the closest radiological exams considering a given timepoint. 'parseRPDR' currently supports
txt sources: "mrn", "con", "dem", "enc", "rdt", "lab", "med", "dia", "rfv", "car",
"dis", "end", "hnp", "opn", "pat", "prg", "pul", "rad" and "vis".
All functionalities are parallelized for fast and efficient analyses.
Author: Marton Kolossvary [aut, cre]
Maintainer: Marton Kolossvary <mkolossvary@mgh.harvard.edu>
Diff between parseRPDR versions 0.0.2 dated 2021-04-16 and 0.1.0 dated 2021-05-10
parseRPDR-0.0.2/parseRPDR/R/convert_rad.R |only parseRPDR-0.0.2/parseRPDR/R/load_rad.R |only parseRPDR-0.0.2/parseRPDR/man/convert_rad.Rd |only parseRPDR-0.0.2/parseRPDR/man/load_rad.Rd |only parseRPDR-0.1.0/parseRPDR/DESCRIPTION | 16 - parseRPDR-0.1.0/parseRPDR/MD5 | 68 +++-- parseRPDR-0.1.0/parseRPDR/NAMESPACE | 6 parseRPDR-0.1.0/parseRPDR/NEWS.md | 32 ++ parseRPDR-0.1.0/parseRPDR/R/convert_notes.R |only parseRPDR-0.1.0/parseRPDR/R/convert_rfv.R |only parseRPDR-0.1.0/parseRPDR/R/load_all.R | 69 ++++-- parseRPDR-0.1.0/parseRPDR/R/load_base.R | 4 parseRPDR-0.1.0/parseRPDR/R/load_con.R | 2 parseRPDR-0.1.0/parseRPDR/R/load_dem.R | 2 parseRPDR-0.1.0/parseRPDR/R/load_dia.R | 6 parseRPDR-0.1.0/parseRPDR/R/load_enc.R | 2 parseRPDR-0.1.0/parseRPDR/R/load_lab.R | 2 parseRPDR-0.1.0/parseRPDR/R/load_med.R | 4 parseRPDR-0.1.0/parseRPDR/R/load_mrn.R | 2 parseRPDR-0.1.0/parseRPDR/R/load_notes.R |only parseRPDR-0.1.0/parseRPDR/R/load_rdt.R | 4 parseRPDR-0.1.0/parseRPDR/R/load_rfv.R |only parseRPDR-0.1.0/parseRPDR/README.md | 17 - parseRPDR-0.1.0/parseRPDR/inst/doc/Using_parseRPDR.R | 17 + parseRPDR-0.1.0/parseRPDR/inst/doc/Using_parseRPDR.Rmd | 52 +++- parseRPDR-0.1.0/parseRPDR/inst/doc/Using_parseRPDR.html | 183 ++++++++-------- parseRPDR-0.1.0/parseRPDR/man/convert_notes.Rd |only parseRPDR-0.1.0/parseRPDR/man/convert_rfv.Rd |only parseRPDR-0.1.0/parseRPDR/man/load_all.Rd | 9 parseRPDR-0.1.0/parseRPDR/man/load_base.Rd | 2 parseRPDR-0.1.0/parseRPDR/man/load_con.Rd | 2 parseRPDR-0.1.0/parseRPDR/man/load_dem.Rd | 2 parseRPDR-0.1.0/parseRPDR/man/load_dia.Rd | 2 parseRPDR-0.1.0/parseRPDR/man/load_enc.Rd | 2 parseRPDR-0.1.0/parseRPDR/man/load_lab.Rd | 2 parseRPDR-0.1.0/parseRPDR/man/load_med.Rd | 2 parseRPDR-0.1.0/parseRPDR/man/load_mrn.Rd | 2 parseRPDR-0.1.0/parseRPDR/man/load_notes.Rd |only parseRPDR-0.1.0/parseRPDR/man/load_rdt.Rd | 2 parseRPDR-0.1.0/parseRPDR/man/load_rfv.Rd |only parseRPDR-0.1.0/parseRPDR/vignettes/Using_parseRPDR.Rmd | 52 +++- 41 files changed, 361 insertions(+), 206 deletions(-)
Title: Multimodal and Multilevel Network Analysis
Description: A set of tools that extend common social network analysis packages
for analysing multimodal and multilevel networks.
It includes functions for one- and two-mode (and sometimes three-mode)
centrality, centralization, clustering, and constraint,
as well as for one- and two-mode network regression and block-modelling.
All functions operate with matrices, edge lists,
and 'igraph', 'network'/'sna', and 'tidygraph' objects.
The package is released as a complement to
'Multimodal Political Networks' (2021, ISBN:9781108985000),
and includes various datasets used in the book.
Author: James Hollway [cph, cre, aut, ctb] (IHEID,
<https://orcid.org/0000-0002-8361-9647>)
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between migraph versions 0.6.3 dated 2021-04-26 and 0.6.5 dated 2021-05-10
migraph-0.6.3/migraph/R/data_elite_mex.R |only migraph-0.6.3/migraph/R/data_elite_usa_advice.R |only migraph-0.6.3/migraph/R/data_elite_usa_money.R |only migraph-0.6.5/migraph/DESCRIPTION | 14 - migraph-0.6.5/migraph/MD5 | 29 +- migraph-0.6.5/migraph/NAMESPACE | 12 migraph-0.6.5/migraph/NEWS.md | 31 ++ migraph-0.6.5/migraph/R/coercion.R | 4 migraph-0.6.5/migraph/R/data_elite.R |only migraph-0.6.5/migraph/R/plot.R | 170 +++++++++++++- migraph-0.6.5/migraph/R/project.R | 2 migraph-0.6.5/migraph/R/to.R |only migraph-0.6.5/migraph/man/mpn_elite_mex.Rd | 2 migraph-0.6.5/migraph/man/mpn_elite_usa_advice.Rd | 2 migraph-0.6.5/migraph/man/mpn_elite_usa_money.Rd | 2 migraph-0.6.5/migraph/man/plot_releases.Rd |only migraph-0.6.5/migraph/man/to.Rd |only migraph-0.6.5/migraph/tests/testthat/test-netlm.R | 2 migraph-0.6.5/migraph/tests/testthat/test-plot_releases.R |only migraph-0.6.5/migraph/tests/testthat/test-to.R |only 20 files changed, 239 insertions(+), 31 deletions(-)
Title: Interactive Statistical Data Visualization
Description: An extendable toolkit for interactive data visualization and exploration.
Author: Adrian Waddell [aut],
R. Wayne Oldford [aut, cre, ths],
Zehao Xu [ctb],
Martin Gauch [ctb]
Maintainer: R. Wayne Oldford <rwoldford@uwaterloo.ca>
Diff between loon versions 1.3.5 dated 2021-05-06 and 1.3.6 dated 2021-05-10
DESCRIPTION | 8 MD5 | 33 - R/l_bind.R | 8 R/l_isLoonWidget.R | 23 - R/loonGrob_l_facet_grid.R | 2 R/loonGrob_l_facet_wrap.R | 2 build/vignette.rds |binary inst/doc/introduction.html | 627 +++++++++++-------------------- inst/doc/logicalQueries.html | 339 ++++------------ inst/doc/savingLoonPlots.html | 382 +++++------------- inst/doc/teaching-example-smoothing.html | 558 +++++++++------------------ man/l_bind_context.Rd | 2 man/l_bind_glyph.Rd | 2 man/l_bind_layer.Rd | 2 man/l_bind_navigator.Rd | 2 man/l_isLoonWidget.Rd | 2 tests/testthat/test_facets.R | 10 tests/testthat/test_isLoonWidget.R |only 18 files changed, 683 insertions(+), 1319 deletions(-)
Title: API Client for Fantasy Football League Platforms
Description: Helps access various Fantasy Football APIs by handling
authentication and rate-limiting, forming appropriate calls, and
returning tidy dataframes which can be easily connected to other data
sources.
Author: Tan Ho [aut, cre],
Tony ElHabr [ctb],
Joe Sydlowski [ctb]
Maintainer: Tan Ho <tan@tanho.ca>
Diff between ffscrapr versions 1.4.1 dated 2021-04-18 and 1.4.2 dated 2021-05-10
DESCRIPTION | 6 MD5 | 250 ++++++++++++++++---------------- NEWS.md | 15 + R/0_generics.R | 34 ++-- R/0_helpers.R | 9 - R/0_utils.R | 2 R/1_import_dp.R | 6 R/1_import_nflfastr.R | 6 R/espn__helpers.R | 10 - R/espn_api.R | 10 - R/espn_connect.R | 2 R/espn_draft.R | 2 R/espn_draftpicks.R | 2 R/espn_franchises.R | 2 R/espn_league.R | 2 R/espn_players.R | 2 R/espn_playerscores.R | 2 R/espn_potentialpoints.R | 2 R/espn_rosters.R | 10 - R/espn_schedule.R | 2 R/espn_scoring.R | 2 R/espn_scoringhistory.R | 6 R/espn_standings.R | 2 R/espn_starterpositions.R | 2 R/espn_starters.R | 2 R/espn_transactions.R | 2 R/espn_userleagues.R | 2 R/flea_api.R | 4 R/flea_connect.R | 2 R/flea_draft.R | 2 R/flea_draftpicks.R | 2 R/flea_franchises.R | 2 R/flea_league.R | 2 R/flea_players.R | 2 R/flea_playerscores.R | 2 R/flea_rosters.R | 2 R/flea_schedule.R | 2 R/flea_scoring.R | 2 R/flea_scoringhistory.R | 18 +- R/flea_standings.R | 2 R/flea_starterpositions.R | 2 R/flea_starters.R | 2 R/flea_transactions.R | 2 R/flea_userleagues.R | 6 R/mfl_api.R | 6 R/mfl_connect.R | 4 R/mfl_draft.R | 2 R/mfl_draftpicks.R | 2 R/mfl_franchises.R | 2 R/mfl_league.R | 2 R/mfl_players.R | 21 +- R/mfl_playerscores.R | 2 R/mfl_rosters.R | 2 R/mfl_schedule.R | 2 R/mfl_scoring.R | 4 R/mfl_scoringhistory.R | 16 +- R/mfl_standings.R | 2 R/mfl_starterpositions.R | 2 R/mfl_starters.R | 2 R/mfl_transactions.R | 2 R/mfl_userleagues.R | 2 R/sleeper_api.R | 4 R/sleeper_connect.R | 2 R/sleeper_draft.R | 2 R/sleeper_draftpicks.R | 2 R/sleeper_franchises.R | 2 R/sleeper_league.R | 2 R/sleeper_players.R | 4 R/sleeper_playerscores.R | 2 R/sleeper_rosters.R | 2 R/sleeper_schedule.R | 2 R/sleeper_scoring.R | 2 R/sleeper_scoringhistory.R | 6 R/sleeper_standings.R | 2 R/sleeper_starterpositions.R | 2 R/sleeper_starters.R | 2 R/sleeper_transactions.R | 4 R/sleeper_userleagues.R | 6 README.md | 24 +-- inst/doc/espn_basics.R | 6 inst/doc/espn_basics.Rmd | 6 inst/doc/espn_basics.html | 6 inst/doc/espn_getendpoint.R | 6 inst/doc/espn_getendpoint.Rmd | 6 inst/doc/ffscrapr_scoringhistory.R | 4 inst/doc/ffscrapr_scoringhistory.Rmd | 4 inst/doc/fleaflicker_basics.R | 6 inst/doc/fleaflicker_basics.Rmd | 6 inst/doc/fleaflicker_getendpoint.R | 6 inst/doc/fleaflicker_getendpoint.Rmd | 6 inst/doc/mfl_basics.R | 6 inst/doc/mfl_basics.Rmd | 6 inst/doc/mfl_basics.html | 42 ++--- inst/doc/mfl_getendpoint.R | 6 inst/doc/mfl_getendpoint.Rmd | 6 inst/doc/sleeper_basics.R | 6 inst/doc/sleeper_basics.Rmd | 6 inst/doc/sleeper_basics.html | 34 ++-- inst/doc/sleeper_getendpoint.R | 6 inst/doc/sleeper_getendpoint.Rmd | 6 inst/doc/sleeper_getendpoint.html | 8 - man/dot-add_allplay.Rd | 4 man/ff_connect.Rd | 4 man/ff_draft.Rd | 2 man/ff_playerscores.Rd | 2 man/ff_rosters.Rd | 6 man/ff_transactions.Rd | 2 man/ff_userleagues.Rd | 4 man/fleaflicker_userleagues.Rd | 2 man/mfl_connect.Rd | 2 man/nflfastr_stat_mapping.Rd | 6 man/pipe.Rd | 2 man/release_bullets.Rd | 24 +-- man/sleeper_userleagues.Rd | 2 tests/testthat/setup.R | 6 tests/testthat/test-ff_rosters.R | 5 tests/testthat/test-ff_scoringhistory.R | 4 vignettes/espn_basics.Rmd | 6 vignettes/espn_getendpoint.Rmd | 6 vignettes/ffscrapr_scoringhistory.Rmd | 4 vignettes/fleaflicker_basics.Rmd | 6 vignettes/fleaflicker_getendpoint.Rmd | 6 vignettes/mfl_basics.Rmd | 6 vignettes/mfl_getendpoint.Rmd | 6 vignettes/sleeper_basics.Rmd | 6 vignettes/sleeper_getendpoint.Rmd | 6 126 files changed, 485 insertions(+), 435 deletions(-)
Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>),
Marcel Ramos [ctb, cre] (<https://orcid.org/0000-0002-3242-0582>)
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
Diff between BiocManager versions 1.30.13 dated 2021-05-07 and 1.30.14 dated 2021-05-10
DESCRIPTION | 6 MD5 | 18 NEWS | 11 R/inet.R | 20 R/install.R | 12 R/version.R | 30 - R/zzz.R | 16 build/vignette.rds |binary inst/doc/BiocManager.html | 944 +++++++++++++++++++----------------------- tests/testthat/test_version.R | 8 10 files changed, 506 insertions(+), 559 deletions(-)
Title: Clustering and Model Selection with the Integrated
Classification Likelihood
Description: An ensemble of algorithms that enable the clustering of networks and data matrix such as counts matrix with different type of generative models. Model selection and clustering is performed in combination by optimizing the Integrated Classification Likelihood (which is equivalent to minimizing the description length). Several models are available such as: Stochastic Block Model, degree corrected Stochastic Block Model, Mixtures of Multinomial, Latent Block Model. The optimization is performed thanks to a combination of greedy local search and a genetic algorithm (see <arXiv:2002:11577> for more details).
Author: Etienne Côme [aut, cre],
Nicolas Jouvin [aut]
Maintainer: Etienne Côme <etienne.come@univ-eiffel.fr>
Diff between greed versions 0.5.0 dated 2021-04-21 and 0.5.1 dated 2021-05-10
DESCRIPTION | 22 +-- MD5 | 152 ++++++++++++++---------- NAMESPACE | 5 NEWS.md |only R/RcppExports.R | 16 -- R/alg_classes.R | 33 ++++- R/cleanpath.R | 10 - R/coclust_dcsbm.R | 65 ++++++++-- R/data.R | 33 +++++ R/dcsbm.R | 82 +++++++++++-- R/diaggmm.R |only R/fit_classes.R | 3 R/gmm.R | 90 ++++++++++++-- R/misc.R | 8 + R/misssbm.R | 106 +++++++++++++++- R/mm.R | 53 ++++++++ R/multsbm.R | 55 ++++++++ R/mvmreg.R | 95 +++++++++++++-- R/plot.R | 90 ++++++++++++++ R/sbm.R | 56 ++++++++ README.md | 49 ++++--- build/vignette.rds |binary data/fashion.rda |only inst/doc/GMM.R |only inst/doc/GMM.Rmd |only inst/doc/GMM.html |only inst/doc/graph-clustering-with-sbm.html | 25 ++- man/co_dcsbm-class.Rd | 5 man/coef-co_dcsbm_fit-method.Rd |only man/coef-dcsbm_fit-method.Rd |only man/coef-diaggmm_fit-method.Rd |only man/coef-gmm_fit-method.Rd |only man/coef-misssbm_fit-method.Rd |only man/coef-mm_fit-method.Rd |only man/coef-multsbm_fit-method.Rd |only man/coef-mvmreg_fit-method.Rd |only man/coef-sbm_fit-method.Rd |only man/dcsbm-class.Rd | 6 man/dcsbm_fit-class.Rd | 6 man/diaggmm-class.Rd |only man/diaggmm_fit-class.Rd |only man/diaggmm_path-class.Rd |only man/fashion.Rd |only man/figures/cut-1.png |binary man/figures/future-1.png |binary man/figures/plot-1.png |binary man/figures/tree-1.png |binary man/gmm-class.Rd | 18 +- man/gmm_fit-class.Rd | 2 man/gmmpairs.Rd |only man/greed.Rd | 2 man/greed_cond.Rd | 2 man/icl_fit-class.Rd | 2 man/misssbm_fit-class.Rd | 2 man/misssbm_path-class.Rd | 18 ++ man/mvmreg-class.Rd | 17 ++ man/plot-diaggmm_path-missing-method.Rd |only man/plot-misssbm_fit-missing-method.Rd | 6 man/plot-misssbm_path-missing-method.Rd | 6 src/CoDcSbm.cpp | 19 ++- src/CoDcSbm.h | 3 src/DcSbm.cpp | 20 ++- src/DcSbm.h | 3 src/Fit.cpp | 52 +++++--- src/Gmm.cpp | 49 ++++--- src/Gmm.h | 2 src/IclModel.cpp | 13 -- src/IclModel.h | 6 src/MarSbm.cpp | 2 src/MarSbm.h | 2 src/MarSbmUndirected.cpp | 2 src/MarSbmUndirected.h | 2 src/MissSbm.cpp | 14 +- src/MissSbm.h | 2 src/Mm.cpp | 13 +- src/Mm.h | 2 src/MultSbm.cpp | 12 - src/MultSbm.h | 2 src/Mvmregcomp.cpp | 33 +++-- src/Mvmregcomp.h | 2 src/RcppExports.cpp | 67 ---------- src/Sbm.cpp | 9 - src/Sbm.h | 2 src/SphericalGmm.cpp |only src/SphericalGmm.h |only src/gicl_tools.cpp | 201 +++++++++++--------------------- src/gicl_tools.h | 27 ---- tests/testthat/test_diaggmm.R |only tests/testthat/test_mvmreg.R |only vignettes/GMM.Rmd |only 90 files changed, 1175 insertions(+), 526 deletions(-)
Title: An Interactive Editor for Viewing, Entering, Filtering & Editing
Data
Description: An interactive editor built on 'rhandsontable' to allow the
interactive viewing, entering, filtering and editing of data in R
<https://dillonhammill.github.io/DataEditR/>.
Author: Dillon Hammill [aut, cre] (<https://orcid.org/0000-0002-1407-7223>)
Maintainer: Dillon Hammill <Dillon.Hammill@anu.edu.au>
Diff between DataEditR versions 0.0.9 dated 2020-12-12 and 0.1.1 dated 2021-05-10
DESCRIPTION | 13 ++++++------- MD5 | 24 ++++++++++++------------ NEWS.md | 11 +++++++++++ R/dataEdit.R | 2 ++ R/dataFilter.R | 9 +++++---- R/dataInput.R | 8 ++++++-- R/dataSelect.R | 8 ++------ R/data_edit.R | 22 +++++++++++++--------- README.md | 19 +++++++++---------- man/dataEdit.Rd | 3 +++ man/dataFilter.Rd | 8 +++++--- man/dataInput.Rd | 6 +++++- man/dataSelect.Rd | 8 ++------ 13 files changed, 81 insertions(+), 60 deletions(-)
Title: Global Value Chains Tools
Description: Several tools for Global Value Chain ('GVC') analysis are
implemented.
Author: Bastiaan Quast [aut, cre],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between gvc versions 5.2.0 dated 2020-04-23 and 6.0.0 dated 2021-05-10
gvc-5.2.0/gvc/NEWS |only gvc-6.0.0/gvc/DESCRIPTION | 10 gvc-6.0.0/gvc/MD5 | 54 ++-- gvc-6.0.0/gvc/NEWS.md |only gvc-6.0.0/gvc/R/dfddva.R | 1 gvc-6.0.0/gvc/R/dfdfva.R | 1 gvc-6.0.0/gvc/R/downstream.R | 1 gvc-6.0.0/gvc/R/e2r.R | 1 gvc-6.0.0/gvc/R/ffddva.R | 1 gvc-6.0.0/gvc/R/i2e.R | 1 gvc-6.0.0/gvc/R/nrca.R | 1 gvc-6.0.0/gvc/R/upstream.R | 1 gvc-6.0.0/gvc/README.md | 46 +-- gvc-6.0.0/gvc/build/vignette.rds |binary gvc-6.0.0/gvc/inst/doc/gvc.R | 1 gvc-6.0.0/gvc/inst/doc/gvc.Rmd | 1 gvc-6.0.0/gvc/inst/doc/gvc.html | 364 ++++++++++++------------------- gvc-6.0.0/gvc/man/dfddva.Rd | 1 gvc-6.0.0/gvc/man/dfdfva.Rd | 1 gvc-6.0.0/gvc/man/downstream.Rd | 1 gvc-6.0.0/gvc/man/e2r.Rd | 1 gvc-6.0.0/gvc/man/ffddva.Rd | 1 gvc-6.0.0/gvc/man/i2e.Rd | 1 gvc-6.0.0/gvc/man/nrca.Rd | 1 gvc-6.0.0/gvc/man/upstream.Rd | 1 gvc-6.0.0/gvc/tests/testthat/test_e2r.R | 1 gvc-6.0.0/gvc/tests/testthat/test_i2e.R | 1 gvc-6.0.0/gvc/tests/testthat/test_nrca.R | 1 gvc-6.0.0/gvc/vignettes/gvc.Rmd | 1 29 files changed, 222 insertions(+), 274 deletions(-)
Title: Conditioned Latin Hypercube Sampling
Description: Conditioned Latin hypercube sampling, as published by Minasny and McBratney (2006) <DOI:10.1016/j.cageo.2005.12.009>. This method proposes to stratify sampling in presence of ancillary data. An extension of this method, which propose to associate a cost to each individual and take it into account during the optimisation process, is also proposed (Roudier et al., 2012, <DOI:10.1201/b12728>).
Author: Pierre Roudier [aut, cre],
Colby Brugnard [ctb],
Dylan Beaudette [ctb],
Benjamin Louis [ctb],
Kiri Daust [ctb],
David Clifford [ctb]
Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>
Diff between clhs versions 0.7-3 dated 2020-04-15 and 0.8.1 dated 2021-05-10
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Title: Base de Datos de Facil Acceso del Censo 2017 de Chile (2017
Chilean Census Easy Access Database)
Description: Provee un acceso conveniente a mas de 17 millones de registros
de la base de datos del Censo 2017. Los datos fueron importados desde
el DVD oficial del INE usando el Convertidor REDATAM creado por Pablo De
Grande. Esta paquete esta documentado intencionalmente en castellano
asciificado para que funcione sin problema en diferentes plataformas.
(Provides convenient access to more than 17 million records from the
Chilean Census 2017 database. The datasets were imported from the official
DVD provided by the Chilean National Bureau of Statistics by using the
REDATAM converter created by Pablo De Grande and in addition it includes the
maps accompanying these datasets.)
Author: Mauricio Vargas [aut, cre] (<https://orcid.org/0000-0003-1017-7574>),
Juan Correa [ctb],
Maria Paula Caldas [rev] (rOpenSci),
Frans van Dunee [rev] (rOpenSci),
Melina Vidoni [rev] (rOpenSci),
Constanza Manriquez [rev] (revision independiente de las vinietas),
Instituto Nacional de Estadisticas (INE) [dtc]
Maintainer: Mauricio Vargas <mvargas@dcc.uchile.cl>
Diff between censo2017 versions 0.4 dated 2021-02-06 and 0.5 dated 2021-05-10
DESCRIPTION | 32 ++ MD5 | 48 ++-- NEWS.md | 38 +-- R/censo2017-package.R |only R/connect.R | 331 +++++++++++++-------------- R/connection-pane.R | 172 +++++++------- R/download.R | 283 +++++++++++------------ R/remove.R | 33 +- R/schema.R | 431 ++++++++++++++++-------------------- R/utils.R | 75 +++--- R/zzz.R | 25 +- data/nivel_educacional_biobio.rda |binary inst/WORDLIST | 92 +++---- man/censo2017-package.Rd |only man/censo_bbdd.Rd | 60 ++--- man/censo_borrar_base.Rd | 32 +- man/censo_descargar_base.Rd | 48 +--- man/censo_desconectar_base.Rd | 28 +- man/censo_estado.Rd | 44 +-- man/censo_panel.Rd | 30 +- man/censo_tabla.Rd | 46 +-- man/nivel_educacional_biobio.Rd | 58 ++-- tests/testthat.R | 6 tests/testthat/test-01-download.R | 28 +- tests/testthat/test-02-tables.R | 64 ++--- tests/testthat/test-03-connection.R | 37 +-- 26 files changed, 1000 insertions(+), 1041 deletions(-)
Title: Read, Validate, Analyze, and Map Files in the General Transit
Feed Specification
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <http://gtfs.org/>.
Author: Flavio Poletti [aut],
Daniel Herszenhut [aut] (<https://orcid.org/0000-0001-8066-1105>),
Mark Padgham [aut],
Tom Buckley [aut, cre],
Danton Noriega-Goodwin [aut],
Angela Li [ctb],
Elaine McVey [ctb],
Charles Hans Thompson [ctb],
Michael Sumner [ctb],
Patrick Hausmann [ctb],
Bob Rudis [ctb],
James Lamb [ctb],
Alexandra Kapp [ctb],
Kearey Smith [ctb],
Dave Vautin [ctb],
Kyle Walker [ctb]
Maintainer: Tom Buckley <tom@tbuckl.com>
Diff between tidytransit versions 0.7.3 dated 2021-02-27 and 1.0.0 dated 2021-05-09
tidytransit-0.7.3/tidytransit/R/gtfstools-write_gtfs.R |only tidytransit-0.7.3/tidytransit/inst/doc/frequency.R |only tidytransit-0.7.3/tidytransit/inst/doc/frequency.Rmd |only tidytransit-0.7.3/tidytransit/inst/doc/frequency.html |only tidytransit-0.7.3/tidytransit/man/filter_feedlist.Rd |only tidytransit-0.7.3/tidytransit/man/filter_stop_times_by_hour.Rd |only tidytransit-0.7.3/tidytransit/man/get_feed.Rd |only tidytransit-0.7.3/tidytransit/man/get_route_frequency.Rd |only tidytransit-0.7.3/tidytransit/man/plot.gtfs.Rd |only tidytransit-0.7.3/tidytransit/man/set_date_service_table.Rd |only tidytransit-0.7.3/tidytransit/man/set_hms_times.Rd |only tidytransit-0.7.3/tidytransit/man/summary.gtfs.Rd |only tidytransit-0.7.3/tidytransit/vignettes/frequency.Rmd |only tidytransit-1.0.0/tidytransit/DESCRIPTION | 14 tidytransit-1.0.0/tidytransit/MD5 | 129 ++--- tidytransit-1.0.0/tidytransit/NAMESPACE | 16 tidytransit-1.0.0/tidytransit/R/frequencies.R | 141 +---- tidytransit-1.0.0/tidytransit/R/globals.R | 8 tidytransit-1.0.0/tidytransit/R/joins.R | 2 tidytransit-1.0.0/tidytransit/R/plot.R | 6 tidytransit-1.0.0/tidytransit/R/raptor.R | 26 - tidytransit-1.0.0/tidytransit/R/read_gtfs.R | 243 ---------- tidytransit-1.0.0/tidytransit/R/service.R | 25 - tidytransit-1.0.0/tidytransit/R/spatial.R | 31 - tidytransit-1.0.0/tidytransit/R/summary.R | 34 + tidytransit-1.0.0/tidytransit/R/time.R | 227 +++++---- tidytransit-1.0.0/tidytransit/R/transitfeeds.R | 109 ---- tidytransit-1.0.0/tidytransit/R/utils.R | 57 -- tidytransit-1.0.0/tidytransit/R/validate_gtfs.R | 70 -- tidytransit-1.0.0/tidytransit/build/vignette.rds |binary tidytransit-1.0.0/tidytransit/data/gtfs_duke.rda |binary tidytransit-1.0.0/tidytransit/inst/doc/introduction.Rmd | 1 tidytransit-1.0.0/tidytransit/inst/doc/introduction.html | 75 +-- tidytransit-1.0.0/tidytransit/inst/doc/servicepatterns.R | 20 tidytransit-1.0.0/tidytransit/inst/doc/servicepatterns.Rmd | 43 - tidytransit-1.0.0/tidytransit/inst/doc/servicepatterns.html | 28 - tidytransit-1.0.0/tidytransit/inst/doc/timetable.R | 36 - tidytransit-1.0.0/tidytransit/inst/doc/timetable.Rmd | 69 +- tidytransit-1.0.0/tidytransit/inst/doc/timetable.html | 219 ++++----- tidytransit-1.0.0/tidytransit/inst/extdata/sample-feed-plus.zip |binary tidytransit-1.0.0/tidytransit/man/convert_times_to_hms.Rd |only tidytransit-1.0.0/tidytransit/man/filter_stop_times.Rd | 4 tidytransit-1.0.0/tidytransit/man/get_route_geometry.Rd | 4 tidytransit-1.0.0/tidytransit/man/get_stop_frequency.Rd | 16 tidytransit-1.0.0/tidytransit/man/get_trip_geometry.Rd | 4 tidytransit-1.0.0/tidytransit/man/gtfs_as_sf.Rd | 7 tidytransit-1.0.0/tidytransit/man/gtfs_duke.Rd | 2 tidytransit-1.0.0/tidytransit/man/plot.tidygtfs.Rd |only tidytransit-1.0.0/tidytransit/man/print.tidygtfs.Rd |only tidytransit-1.0.0/tidytransit/man/read_gtfs.Rd | 17 tidytransit-1.0.0/tidytransit/man/service_by_dow.Rd | 4 tidytransit-1.0.0/tidytransit/man/set_dates_services.Rd |only tidytransit-1.0.0/tidytransit/man/set_servicepattern.Rd | 11 tidytransit-1.0.0/tidytransit/man/shapes_as_sf.Rd | 5 tidytransit-1.0.0/tidytransit/man/stops_as_sf.Rd | 5 tidytransit-1.0.0/tidytransit/man/summary.tidygtfs.Rd |only tidytransit-1.0.0/tidytransit/man/validate_gtfs.Rd | 8 tidytransit-1.0.0/tidytransit/man/write_gtfs.Rd | 7 tidytransit-1.0.0/tidytransit/tests/testthat/Rplots.pdf |binary tidytransit-1.0.0/tidytransit/tests/testthat/_test_tmp |only tidytransit-1.0.0/tidytransit/tests/testthat/test-headways.R | 33 - tidytransit-1.0.0/tidytransit/tests/testthat/test-raptor.R | 10 tidytransit-1.0.0/tidytransit/tests/testthat/test-read-gtfs.R | 27 - tidytransit-1.0.0/tidytransit/tests/testthat/test-service.R | 4 tidytransit-1.0.0/tidytransit/tests/testthat/test-spatial.R | 14 tidytransit-1.0.0/tidytransit/tests/testthat/test-time.R | 48 + tidytransit-1.0.0/tidytransit/tests/testthat/test-utils.R | 11 tidytransit-1.0.0/tidytransit/vignettes/introduction.Rmd | 1 tidytransit-1.0.0/tidytransit/vignettes/servicepatterns.Rmd | 43 - tidytransit-1.0.0/tidytransit/vignettes/timetable.Rmd | 69 +- 70 files changed, 793 insertions(+), 1190 deletions(-)
Title: Generalized Linear Models for Categorical Responses
Description: In statistical modeling, there is a wide variety of regression models for categorical dependent variables (nominal or ordinal data); yet, there is no software embracing all these models together in a uniform and generalized format. Following the methodology proposed by Peyhardi, Trottier, and Guédon (2015) <doi:10.1093/biomet/asv042>, we introduce 'GLMcat', an R package to estimate generalized linear models implemented under the unified specification (r, F, Z). Where r represents the ratio of probabilities (reference, cumulative, adjacent, or sequential), F the cumulative cdf function for the linkage, and Z, the design matrix.
Author: Lorena León [aut, cre],
Jean Peyhardi [aut],
Catherine Trottier [aut]
Maintainer: Lorena León <ylorenaleonv@gmail.com>
Diff between GLMcat versions 0.2.1 dated 2021-03-06 and 0.2.2 dated 2021-05-09
GLMcat-0.2.1/GLMcat/man/predict_glmcat.Rd |only GLMcat-0.2.1/GLMcat/src/distribution.cpp |only GLMcat-0.2.1/GLMcat/src/distribution.h |only GLMcat-0.2.2/GLMcat/DESCRIPTION | 12 GLMcat-0.2.2/GLMcat/MD5 | 80 +- GLMcat-0.2.2/GLMcat/NAMESPACE | 17 GLMcat-0.2.2/GLMcat/R/DisturbedDreamsDoc.R | 2 GLMcat-0.2.2/GLMcat/R/GLMcatMethods.R | 451 ++++++++++++++- GLMcat-0.2.2/GLMcat/R/RcppExports.R | 76 +- GLMcat-0.2.2/GLMcat/R/zzz.R | 18 GLMcat-0.2.2/GLMcat/README.md | 20 GLMcat-0.2.2/GLMcat/build/vignette.rds |binary GLMcat-0.2.2/GLMcat/inst/doc/Discrete_CM_examples.R | 17 GLMcat-0.2.2/GLMcat/inst/doc/Discrete_CM_examples.Rmd | 21 GLMcat-0.2.2/GLMcat/inst/doc/Discrete_CM_examples.pdf |binary GLMcat-0.2.2/GLMcat/inst/doc/GLMcat_tutorial.R | 44 - GLMcat-0.2.2/GLMcat/inst/doc/GLMcat_tutorial.Rmd | 74 +- GLMcat-0.2.2/GLMcat/inst/doc/GLMcat_tutorial.pdf |binary GLMcat-0.2.2/GLMcat/man/Discrete_CM.Rd | 34 - GLMcat-0.2.2/GLMcat/man/DisturbedDreams.Rd | 8 GLMcat-0.2.2/GLMcat/man/GLMcat.Rd | 38 - GLMcat-0.2.2/GLMcat/man/TravelChoice.Rd | 6 GLMcat-0.2.2/GLMcat/man/coef.Rd | 2 GLMcat-0.2.2/GLMcat/man/control.Rd |only GLMcat-0.2.2/GLMcat/man/logLik.Rd | 2 GLMcat-0.2.2/GLMcat/man/nobs_glmcat.Rd | 2 GLMcat-0.2.2/GLMcat/man/noncentralt.Rd |only GLMcat-0.2.2/GLMcat/man/predict.Rd |only GLMcat-0.2.2/GLMcat/man/step_glmcat.Rd |only GLMcat-0.2.2/GLMcat/man/student.Rd |only GLMcat-0.2.2/GLMcat/src/DiscreteCM.cpp | 322 ++++++++-- GLMcat-0.2.2/GLMcat/src/DiscreteCM.h | 4 GLMcat-0.2.2/GLMcat/src/GLMcat.cpp | 510 ++++++++++++----- GLMcat-0.2.2/GLMcat/src/RcppExports.cpp | 44 - GLMcat-0.2.2/GLMcat/src/adjacentR.cpp | 98 ++- GLMcat-0.2.2/GLMcat/src/adjacentR.h | 20 GLMcat-0.2.2/GLMcat/src/cdf.cpp |only GLMcat-0.2.2/GLMcat/src/cdf.h |only GLMcat-0.2.2/GLMcat/src/cumulativeR.cpp | 96 ++- GLMcat-0.2.2/GLMcat/src/cumulativeR.h | 20 GLMcat-0.2.2/GLMcat/src/reference.cpp | 83 ++ GLMcat-0.2.2/GLMcat/src/reference.h | 16 GLMcat-0.2.2/GLMcat/src/sequentialR.cpp | 101 ++- GLMcat-0.2.2/GLMcat/src/sequentialR.h | 52 - GLMcat-0.2.2/GLMcat/vignettes/Discrete_CM_examples.Rmd | 21 GLMcat-0.2.2/GLMcat/vignettes/GLMcat_tutorial.Rmd | 74 +- 46 files changed, 1752 insertions(+), 633 deletions(-)
Title: Global Value Chain Decomposition
Description: Three global value chain (GVC) decompositions are implemented.
The Leontief decomposition derives the value added origin of exports by
country and industry as in Hummels, Ishii and Yi (2001). The Koopman,
Wang and Wei (2014) decomposition splits country-level exports into 9
value added components, and the Wang, Wei and Zhu (2013) decomposition
splits bilateral exports into 16 value added components. Various GVC
indicators based on these decompositions are computed in the
complimentary 'gvc' package.
--- References: ---
Hummels, D., Ishii, J., & Yi, K. M. (2001). The nature and growth of
vertical specialization in world trade. Journal of international
Economics, 54(1), 75-96.
Koopman, R., Wang, Z., & Wei, S. J. (2014). Tracing value-added and double
counting in gross exports. American Economic Review, 104(2), 459-94.
Wang, Z., Wei, S. J., & Zhu, K. (2013). Quantifying international production
sharing at the bilateral and sector levels (No. w19677).
National Bureau of Economic Research.
Author: Bastiaan Quast [aut, cre],
Fei Wang [aut],
Victor Kummritz [aut],
Oliver Reiter [ctb],
Sebastian Krantz [ctb]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between decompr versions 4.5.0 dated 2016-08-17 and 6.0.0 dated 2021-05-09
decompr-4.5.0/decompr/man/countries.Rd |only decompr-4.5.0/decompr/man/decompr.Rd |only decompr-4.5.0/decompr/man/final.Rd |only decompr-4.5.0/decompr/man/industries.Rd |only decompr-4.5.0/decompr/man/inter.Rd |only decompr-4.5.0/decompr/man/out.Rd |only decompr-6.0.0/decompr/DESCRIPTION | 57 +- decompr-6.0.0/decompr/MD5 | 61 +- decompr-6.0.0/decompr/NAMESPACE | 7 decompr-6.0.0/decompr/NEWS | 6 decompr-6.0.0/decompr/R/decomp.R | 136 +---- decompr-6.0.0/decompr/R/decompr.R | 100 ++- decompr-6.0.0/decompr/R/kww.R |only decompr-6.0.0/decompr/R/leontief.R | 166 +++--- decompr-6.0.0/decompr/R/load_tables.R | 24 decompr-6.0.0/decompr/R/load_tables_vectors.R | 212 ++++---- decompr-6.0.0/decompr/R/wwz.R | 496 ++++++++++--------- decompr-6.0.0/decompr/README.md | 60 +- decompr-6.0.0/decompr/build/vignette.rds |binary decompr-6.0.0/decompr/data/leather.rda |binary decompr-6.0.0/decompr/inst/CITATION | 2 decompr-6.0.0/decompr/inst/doc/decompr.R | 32 - decompr-6.0.0/decompr/inst/doc/decompr.Rmd | 43 - decompr-6.0.0/decompr/inst/doc/decompr.html | 363 ++++++++----- decompr-6.0.0/decompr/inst/rstudio |only decompr-6.0.0/decompr/man/decomp.Rd | 115 ++-- decompr-6.0.0/decompr/man/decompr-package.Rd |only decompr-6.0.0/decompr/man/kww.Rd |only decompr-6.0.0/decompr/man/leather.Rd |only decompr-6.0.0/decompr/man/leontief.Rd | 56 +- decompr-6.0.0/decompr/man/load_tables.Rd | 10 decompr-6.0.0/decompr/man/load_tables_vectors.Rd | 83 ++- decompr-6.0.0/decompr/man/wwz.Rd | 62 +- decompr-6.0.0/decompr/man/wwz2kww.Rd |only decompr-6.0.0/decompr/src |only decompr-6.0.0/decompr/tests/testthat/test_leontief.R | 35 - decompr-6.0.0/decompr/tests/testthat/test_wwz.R | 53 +- decompr-6.0.0/decompr/vignettes/decompr.Rmd | 43 - 38 files changed, 1218 insertions(+), 1004 deletions(-)
Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: Provides functions for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
two public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' ('CTGOV', <https://clinicaltrials.gov/>) and
the 'ISRCTN' (<http://www.isrctn.com/>).
Trial information is downloaded, converted and stored in a database
('SQLite' or 'MongoDB', via 'nodbi').
Functions are provided to identify de-duplicated records,
to easily find and extract variables (fields) of interest even
from complex nesting as used by the registers, and
to update previous queries that users retrieved in a database.
The package can be used for meta analysis and trend-analysis of
the design and conduct as well as results of clinical trials.
Author: Ralf Herold [aut, cre] (<https://orcid.org/0000-0002-8148-6748>)
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.5.3 dated 2021-04-19 and 1.6.0 dated 2021-05-09
ctrdata-1.5.3/ctrdata/exec/xml2json.php |only ctrdata-1.5.3/ctrdata/exec/xml2json_euctrresults.php |only ctrdata-1.6.0/ctrdata/DESCRIPTION | 22 ctrdata-1.6.0/ctrdata/MD5 | 65 ctrdata-1.6.0/ctrdata/NAMESPACE | 1 ctrdata-1.6.0/ctrdata/NEWS.md | 22 ctrdata-1.6.0/ctrdata/R/main.R | 1357 +++++----- ctrdata-1.6.0/ctrdata/R/onload.R | 59 ctrdata-1.6.0/ctrdata/R/utils.R | 790 ++--- ctrdata-1.6.0/ctrdata/README.md | 168 - ctrdata-1.6.0/ctrdata/exec/ctgov2json.php |only ctrdata-1.6.0/ctrdata/exec/euctr2json.sh | 23 ctrdata-1.6.0/ctrdata/exec/euctr2json_results.php |only ctrdata-1.6.0/ctrdata/exec/isrctn2json.php |only ctrdata-1.6.0/ctrdata/inst/doc/ctrdata_analyse.pdf |binary ctrdata-1.6.0/ctrdata/inst/doc/ctrdata_install.pdf |binary ctrdata-1.6.0/ctrdata/inst/doc/ctrdata_retrieve.pdf |binary ctrdata-1.6.0/ctrdata/inst/image/README-ctrdata_results_neuroblastoma.png |binary ctrdata-1.6.0/ctrdata/inst/tinytest/ctrdata_euctr.R | 34 ctrdata-1.6.0/ctrdata/inst/tinytest/ctrdata_isrctn.R |only ctrdata-1.6.0/ctrdata/inst/tinytest/setup_ctrdata.R | 87 ctrdata-1.6.0/ctrdata/inst/tinytest/test_ctrdata_mongo_local_isrctn.R |only ctrdata-1.6.0/ctrdata/inst/tinytest/test_ctrdata_other_functions.R | 29 ctrdata-1.6.0/ctrdata/inst/tinytest/test_ctrdata_param_checks.R | 111 ctrdata-1.6.0/ctrdata/inst/tinytest/test_ctrdata_sqlite_isrctn.R |only ctrdata-1.6.0/ctrdata/man/checkBinary.Rd |only ctrdata-1.6.0/ctrdata/man/ctrConvertToJSON.Rd |only ctrdata-1.6.0/ctrdata/man/ctrLoadQueryIntoDb.Rd | 4 ctrdata-1.6.0/ctrdata/man/ctrLoadQueryIntoDbCtgov.Rd | 2 ctrdata-1.6.0/ctrdata/man/ctrLoadQueryIntoDbEuctr.Rd | 2 ctrdata-1.6.0/ctrdata/man/ctrLoadQueryIntoDbIsrctn.Rd |only ctrdata-1.6.0/ctrdata/man/ctrOpenSearchPagesInBrowser.Rd | 11 ctrdata-1.6.0/ctrdata/man/dbCTRUpdateQueryHistory.Rd | 2 ctrdata-1.6.0/ctrdata/man/dbFindIdsUniqueTrials.Rd | 9 ctrdata-1.6.0/ctrdata/vignettes/boxpep.png |binary ctrdata-1.6.0/ctrdata/vignettes/ctrdata_analyse.Rmd | 105 ctrdata-1.6.0/ctrdata/vignettes/ctrdata_install.Rmd | 26 ctrdata-1.6.0/ctrdata/vignettes/ctrdata_retrieve.Rmd | 66 ctrdata-1.6.0/ctrdata/vignettes/nb2.png |binary 39 files changed, 1589 insertions(+), 1406 deletions(-)
Title: R Tools for Helsinki Open Data
Description: Tools for accessing various open data sources in the Helsinki
region in Finland. Current data sources include
the Real Estate Department (<http://ptp.hel.fi/avoindata/>),
Service Map API (<http://api.hel.fi/servicemap/v2/>),
Linked Events API (<http://api.hel.fi/linkedevents/v1/>),
Helsinki Region Infoshare statistics API (<https://dev.hel.fi/stats/>).
Author: Juuso Parkkinen [aut, cre],
Joona Lehtomaki [aut],
Pyry Kantanen [aut],
Leo Lahti [aut] (<https://orcid.org/0000-0001-5537-637X>)
Maintainer: Juuso Parkkinen <juuso.parkkinen@iki.fi>
Diff between helsinki versions 0.9.29 dated 2017-02-18 and 1.0.1 dated 2021-05-09
helsinki-0.9.29/helsinki/inst/NEWS |only helsinki-0.9.29/helsinki/inst/doc/todo-datasets.Rmd |only helsinki-0.9.29/helsinki/inst/doc/todo-datasets.html |only helsinki-0.9.29/helsinki/man/get_hsy.Rd |only helsinki-0.9.29/helsinki/vignettes/helsinki_tutorial.md |only helsinki-0.9.29/helsinki/vignettes/todo-datasets.Rmd |only helsinki-1.0.1/helsinki/DESCRIPTION | 44 helsinki-1.0.1/helsinki/LICENSE | 4 helsinki-1.0.1/helsinki/MD5 | 64 helsinki-1.0.1/helsinki/NAMESPACE | 29 helsinki-1.0.1/helsinki/R/HKK.R | 15 helsinki-1.0.1/helsinki/R/HSY.R | 374 +---- helsinki-1.0.1/helsinki/R/firstlib.R | 6 helsinki-1.0.1/helsinki/R/get_city_map.R |only helsinki-1.0.1/helsinki/R/get_feature.R |only helsinki-1.0.1/helsinki/R/get_feature_list.R |only helsinki-1.0.1/helsinki/R/helsinki-deprecated.R |only helsinki-1.0.1/helsinki/R/helsinki-package.R | 6 helsinki-1.0.1/helsinki/R/regional_stats.R | 79 - helsinki-1.0.1/helsinki/R/services.R | 222 ++- helsinki-1.0.1/helsinki/R/to_sf.R |only helsinki-1.0.1/helsinki/R/wfs_api.R |only helsinki-1.0.1/helsinki/README.md | 87 + helsinki-1.0.1/helsinki/build/vignette.rds |binary helsinki-1.0.1/helsinki/inst/CITATION | 9 helsinki-1.0.1/helsinki/inst/doc/helsinki_tutorial.R | 159 +- helsinki-1.0.1/helsinki/inst/doc/helsinki_tutorial.Rmd | 256 ++- helsinki-1.0.1/helsinki/inst/doc/helsinki_tutorial.html | 987 ++++++++++----- helsinki-1.0.1/helsinki/man/aluejakokartat.Rd | 7 helsinki-1.0.1/helsinki/man/get_city_map.Rd |only helsinki-1.0.1/helsinki/man/get_feature.Rd |only helsinki-1.0.1/helsinki/man/get_feature_list.Rd |only helsinki-1.0.1/helsinki/man/get_hri_stats.Rd | 18 helsinki-1.0.1/helsinki/man/get_hsy-deprecated.Rd |only helsinki-1.0.1/helsinki/man/get_linkedevents.Rd | 47 helsinki-1.0.1/helsinki/man/get_rakennustietoruudukko.Rd |only helsinki-1.0.1/helsinki/man/get_servicemap.Rd | 61 helsinki-1.0.1/helsinki/man/get_vaestotietoruudukko.Rd |only helsinki-1.0.1/helsinki/man/helsinki-deprecated.Rd |only helsinki-1.0.1/helsinki/man/helsinki-package.Rd | 13 helsinki-1.0.1/helsinki/man/select_feature.Rd |only helsinki-1.0.1/helsinki/man/to_sf.Rd |only helsinki-1.0.1/helsinki/man/wfs_api.Rd |only helsinki-1.0.1/helsinki/vignettes/helsinki_tutorial.Rmd | 256 ++- 44 files changed, 1680 insertions(+), 1063 deletions(-)
Title: Full Reporting of Interaction Analyses
Description: Produces a publication-ready table that includes all effect estimates necessary for full reporting effect modification and interaction analysis as recommended by Knol and Vanderweele (2012) [<doi:10.1093/ije/dyr218>].
It also estimates confidence interval for the trio of additive interaction measures using the delta method (see Hosmer and Lemeshow (1992), [<doi:10.1097/00001648-199209000-00012>]), variance recovery method (see Zou (2008), [<doi:10.1093/aje/kwn104>]), or percentile bootstrapping (see Assmann et al. (1996), [<doi:10.1097/00001648-199605000-00012>]).
Author: Babatunde Alli
Maintainer: Babatunde Alli <babatunde.alli@mail.mcgill.ca>
Diff between interactionR versions 0.1.1 dated 2020-06-24 and 0.1.2 dated 2021-05-09
DESCRIPTION | 6 +++--- MD5 | 27 ++++++++++++++------------- NEWS.md | 13 +++++++++---- R/HDiscdata.R | 2 +- R/OCdata.R | 2 +- R/interactionR.R | 14 +++++++++++--- R/interactionR_boot.R | 11 +++++++++-- R/interactionR_delta.R | 11 +++++++++-- R/interactionR_mover.R | 11 +++++++++-- R/interactionR_table.R | 2 +- build |only man/HDiscdata.Rd | 2 +- man/OCdata.Rd | 2 +- man/interactionR.Rd | 2 +- man/interactionR_table.Rd | 2 +- 15 files changed, 71 insertions(+), 36 deletions(-)
Title: Slanted Matrices and Ordered Clustering
Description: Slanted matrices and ordered clustering for better visualization of similarity data.
Author: Oren Ben-Kiki [aut, cre],
Weizmann Institute of Science [cph]
Maintainer: Oren Ben-Kiki <oren@ben-kiki.org>
Diff between slanter versions 0.1-0 dated 2020-09-14 and 0.2-0 dated 2021-05-09
slanter-0.1-0/slanter/NEWS.md |only slanter-0.2-0/slanter/DESCRIPTION | 10 - slanter-0.2-0/slanter/MD5 | 28 ++-- slanter-0.2-0/slanter/NEWS |only slanter-0.2-0/slanter/R/slanter.R | 151 +++++++++++++++++--------- slanter-0.2-0/slanter/README.md | 12 +- slanter-0.2-0/slanter/build/vignette.rds |binary slanter-0.2-0/slanter/data/meristems.RData |binary slanter-0.2-0/slanter/inst/doc/meristems.R | 16 +- slanter-0.2-0/slanter/inst/doc/meristems.Rmd | 20 +-- slanter-0.2-0/slanter/inst/doc/meristems.html | 48 +++++--- slanter-0.2-0/slanter/man/oclust.Rd | 1 slanter-0.2-0/slanter/man/sheatmap.Rd | 48 ++++++-- slanter-0.2-0/slanter/man/slanted_orders.Rd | 13 +- slanter-0.2-0/slanter/man/slanted_reorder.Rd | 13 +- slanter-0.2-0/slanter/vignettes/meristems.Rmd | 20 +-- 16 files changed, 251 insertions(+), 129 deletions(-)
Title: Analyses of Protein Post-Translational Modifications
Description: Contains utilities for the analysis of post-translational modifications (PTMs) in proteins,
with particular emphasis on the sulfoxidation of methionine residues. Features include the ability to download,
filter and analyze data from the sulfoxidation database 'MetOSite', and integrate data from other main PTMs
(other databases). Utilities to search and characterize S-aromatic motifs in proteins are also provided.
In addition, functions to analyze sequence environments around modifiable residues in proteins can be found.
For instance, 'ptm' allows to search for amino acids either overrepresented or avoided around the modifiable
residues from the proteins of interest. Functions tailored to test statistical hypothesis related to
these differential sequence environments are also implemented. A number of utilities to assess the effect
of the modification/mutation of a given residue on the protein stability, have also been included in this package.
Further and detailed information regarding the methods in this package can be found in (Aledo (2020) <https://metositeptm.com>).
Author: Juan Carlos Aledo [au, cre]
Maintainer: Juan Carlos Aledo <caledo@uma.es>
Diff between ptm versions 0.2.2 dated 2020-12-16 and 0.2.3 dated 2021-05-09
ptm-0.2.2/ptm/R/dssp.R |only ptm-0.2.2/ptm/R/pdb_ancillary.R |only ptm-0.2.2/ptm/man/ball.Rd |only ptm-0.2.2/ptm/man/custom.aln.Rd |only ptm-0.2.2/ptm/man/dist2closest.Rd |only ptm-0.2.2/ptm/man/get.hssp.Rd |only ptm-0.2.2/ptm/man/gorilla.Rd |only ptm-0.2.2/ptm/man/list.hom.Rd |only ptm-0.2.2/ptm/man/parse.hssp.Rd |only ptm-0.2.2/ptm/man/pdb.pep.Rd |only ptm-0.2.2/ptm/man/pdb.res.Rd |only ptm-0.2.2/ptm/man/res.dist.Rd |only ptm-0.2.2/ptm/man/shannon.Rd |only ptm-0.2.2/ptm/man/site.type.Rd |only ptm-0.2.2/ptm/tests/testthat/Rplots.pdf |only ptm-0.2.2/ptm/tests/testthat/Zplot.png |only ptm-0.2.2/ptm/tests/testthat/myplot.png |only ptm-0.2.2/ptm/tests/testthat/pdb/1U8F.pdb |only ptm-0.2.2/ptm/tests/testthat/pdb/1b4i_MetO-Q29.pdb |only ptm-0.2.2/ptm/tests/testthat/pdb/1b4i_MetO-T29.pdb |only ptm-0.2.2/ptm/tests/testthat/pdb/1b4i_pSer15.pdb |only ptm-0.2.2/ptm/tests/testthat/pdb/1b4i_pSer8.pdb |only ptm-0.2.2/ptm/tests/testthat/pdb/1b4i_pThr21.pdb |only ptm-0.2.2/ptm/tests/testthat/pdb/1b4i_pThr23.pdb |only ptm-0.2.2/ptm/tests/testthat/pdb/1u8f.hssp |only ptm-0.2.2/ptm/tests/testthat/pdb/Rplots.pdf |only ptm-0.2.2/ptm/tests/testthat/plotptm_cache/scan_G3SB67.Rda |only ptm-0.2.2/ptm/tests/testthat/test_dssp.R |only ptm-0.2.2/ptm/tests/testthat/test_pdb_ancillary.R |only ptm-0.2.3/ptm/DESCRIPTION | 15 ptm-0.2.3/ptm/MD5 | 184 +- ptm-0.2.3/ptm/NAMESPACE | 32 ptm-0.2.3/ptm/R/aa.R | 164 +- ptm-0.2.3/ptm/R/abundance.R | 15 ptm-0.2.3/ptm/R/accdpx.R | 459 +++++ ptm-0.2.3/ptm/R/ddG.R | 320 +++ ptm-0.2.3/ptm/R/distances.R | 296 --- ptm-0.2.3/ptm/R/environment.R | 30 ptm-0.2.3/ptm/R/evolutionary.R | 1056 ------------- ptm-0.2.3/ptm/R/getseq.R | 974 ++++++++--- ptm-0.2.3/ptm/R/go.R | 326 ---- ptm-0.2.3/ptm/R/gracefully.R |only ptm-0.2.3/ptm/R/metosite.R | 63 ptm-0.2.3/ptm/R/ptmScan.R | 309 ++- ptm-0.2.3/ptm/R/ptmplot.R | 126 - ptm-0.2.3/ptm/R/saromatic.R | 46 ptm-0.2.3/ptm/R/sysdata.rda |binary ptm-0.2.3/ptm/data/hmeto.rda |binary ptm-0.2.3/ptm/man/aa.at.Rd | 3 ptm-0.2.3/ptm/man/aa.comp.Rd | 1 ptm-0.2.3/ptm/man/abundance.Rd | 4 ptm-0.2.3/ptm/man/acc.dssp.Rd | 3 ptm-0.2.3/ptm/man/compute.dssp.Rd | 4 ptm-0.2.3/ptm/man/dis.scan.Rd | 2 ptm-0.2.3/ptm/man/dpx.Rd | 3 ptm-0.2.3/ptm/man/env.extract.Rd | 2 ptm-0.2.3/ptm/man/foldx.mut.Rd | 2 ptm-0.2.3/ptm/man/get.seq.Rd | 2 ptm-0.2.3/ptm/man/gl.scan.Rd | 2 ptm-0.2.3/ptm/man/gracefully_fail.Rd |only ptm-0.2.3/ptm/man/id.mapping.Rd | 2 ptm-0.2.3/ptm/man/imutant.Rd | 2 ptm-0.2.3/ptm/man/is.at.Rd | 3 ptm-0.2.3/ptm/man/kegg.uniprot.Rd |only ptm-0.2.3/ptm/man/me.scan.Rd | 2 ptm-0.2.3/ptm/man/meto.list.Rd | 1 ptm-0.2.3/ptm/man/meto.scan.Rd | 2 ptm-0.2.3/ptm/man/meto.search.Rd | 1 ptm-0.2.3/ptm/man/mkdssp.Rd | 2 ptm-0.2.3/ptm/man/msa.Rd | 2 ptm-0.2.3/ptm/man/ni.scan.Rd | 2 ptm-0.2.3/ptm/man/pairwise.dist.Rd | 3 ptm-0.2.3/ptm/man/parse.dssp.Rd | 2 ptm-0.2.3/ptm/man/pdb.chain.Rd | 4 ptm-0.2.3/ptm/man/pdb.quaternary.Rd | 4 ptm-0.2.3/ptm/man/pdb.select.Rd | 2 ptm-0.2.3/ptm/man/pdb.seq.Rd | 4 ptm-0.2.3/ptm/man/pdb.uniprot.Rd |only ptm-0.2.3/ptm/man/pdb2uniprot.Rd | 4 ptm-0.2.3/ptm/man/prot2codon.Rd | 3 ptm-0.2.3/ptm/man/ptm.plot.Rd | 6 ptm-0.2.3/ptm/man/reg.scan.Rd | 2 ptm-0.2.3/ptm/man/renum.Rd | 1 ptm-0.2.3/ptm/man/renum.meto.Rd | 2 ptm-0.2.3/ptm/man/renum.pdb.Rd | 2 ptm-0.2.3/ptm/man/saro.dist.Rd | 2 ptm-0.2.3/ptm/man/saro.geometry.Rd | 1 ptm-0.2.3/ptm/man/search.go.Rd | 2 ptm-0.2.3/ptm/man/sni.scan.Rd | 2 ptm-0.2.3/ptm/man/species.mapping.Rd | 2 ptm-0.2.3/ptm/man/su.scan.Rd | 2 ptm-0.2.3/ptm/man/term.go.Rd | 2 ptm-0.2.3/ptm/man/ub.scan.Rd | 2 ptm-0.2.3/ptm/man/uniprot.kegg.Rd |only ptm-0.2.3/ptm/man/uniprot.pdb.Rd |only ptm-0.2.3/ptm/man/uniprot2pdb.Rd | 4 ptm-0.2.3/ptm/tests/testthat/go/id_set_dummy.txt |only ptm-0.2.3/ptm/tests/testthat/pdb/1u8f.pdb |only ptm-0.2.3/ptm/tests/testthat/plotptm_cache/scan_Q01196.Rda |binary ptm-0.2.3/ptm/tests/testthat/test_aa.R | 161 + ptm-0.2.3/ptm/tests/testthat/test_abundance.R | 62 ptm-0.2.3/ptm/tests/testthat/test_accdpx.R | 414 +++-- ptm-0.2.3/ptm/tests/testthat/test_ddG.R | 188 +- ptm-0.2.3/ptm/tests/testthat/test_distances.R | 229 -- ptm-0.2.3/ptm/tests/testthat/test_environment.R | 63 ptm-0.2.3/ptm/tests/testthat/test_evolutionary.R | 195 -- ptm-0.2.3/ptm/tests/testthat/test_getseq.R | 516 ++++-- ptm-0.2.3/ptm/tests/testthat/test_go.R | 231 +- ptm-0.2.3/ptm/tests/testthat/test_gracefully.R |only ptm-0.2.3/ptm/tests/testthat/test_metosite.R | 70 ptm-0.2.3/ptm/tests/testthat/test_ptmScan.R | 196 +- ptm-0.2.3/ptm/tests/testthat/test_saromatic.R | 18 112 files changed, 3512 insertions(+), 3351 deletions(-)
Title: Match One Sample using Two Criteria
Description: Multivariate matching in observational studies typically has two goals: 1. to construct
treated and control groups that have similar distribution of observed covariates and 2. to produce
matched pairs or sets that are homogeneous in a few priority variables. This packages implements a
network-flow-based method built around a tripartite graph that can simultaneously achieve both goals.
A detailed explanation of the workflow and numerous examples are given in the vignette.
Author: Bo Zhang [aut, cre]
Maintainer: Bo Zhang <bozhan@wharton.upenn.edu>
Diff between match2C versions 1.1.0 dated 2021-02-17 and 1.1.1 dated 2021-05-09
DESCRIPTION | 6 MD5 | 38 - NAMESPACE | 1 R/check_balance.R | 29 - R/construct_outcome.R | 12 R/create_list_from_mat.R | 15 R/create_list_from_scratch.R | 23 - R/force_control.R |only R/match_2C.R | 24 - R/match_2C_list.R | 4 inst/doc/tutorial.R | 154 +++++-- inst/doc/tutorial.Rmd | 259 +++++++++-- inst/doc/tutorial.html | 876 ++++++++++++++++++++++------------------ man/check_balance.Rd | 9 man/construct_outcome.Rd | 12 man/create_list_from_mat.Rd | 15 man/create_list_from_scratch.Rd | 22 - man/force_control.Rd |only man/match_2C.Rd | 16 man/match_2C_list.Rd | 4 vignettes/tutorial.Rmd | 259 +++++++++-- 21 files changed, 1192 insertions(+), 586 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data
management system with support for the Structured Query Language (SQL). This package includes all of
DuckDB and a R Database Interface (DBI) connector.
Author: Hannes Mühleisen [aut, cre] (<https://orcid.org/0000-0001-8552-0029>),
Mark Raasveldt [aut] (<https://orcid.org/0000-0001-5005-6844>),
DuckDB Contributors [aut],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrochers [cph],
Victor Zverovich [cph],
RAD Game Tools [cph],
Valve Software [cph],
Rich Geldreich [cph],
Tenacious Software LLC [cph],
The RE2 Authors [cph],
Google Inc. [cph],
Facebook Inc. [cph],
Steven G. Johnson [cph],
Jiahao Chen [cph],
Tony Kelman [cph],
Jonas Fonseca [cph],
Lukas Fittl [cph],
Salvatore Sanfilippo [cph],
Art.sy, Inc. [cph],
Oran Agra [cph],
Redis Labs, Inc. [cph],
Melissa O'Neill [cph],
PCG Project contributors [cph]
Maintainer: Hannes Mühleisen <hannes@cwi.nl>
Diff between duckdb versions 0.2.5 dated 2021-03-16 and 0.2.6 dated 2021-05-09
duckdb-0.2.5/duckdb/src/duckdb/src/function/aggregate/distributive/mode.cpp |only duckdb-0.2.5/duckdb/src/duckdb/src/include/duckdb/function/aggregate/t_digest.hpp |only duckdb-0.2.5/duckdb/src/duckdb/third_party/utf8proc/include/utf8proc_wrapper.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/common/bitstream.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/common/compiler.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/common/debug.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/common/error_private.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/common/fse.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/common/huf.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/common/mem.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/common/xxhash.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/common/zstd_errors.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/common/zstd_internal.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/compress/hist.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/compress/zstd_compress_internal.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/compress/zstd_compress_literals.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/compress/zstd_compress_sequences.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/compress/zstd_compress_superblock.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/compress/zstd_cwksp.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/compress/zstd_double_fast.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/compress/zstd_fast.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/compress/zstd_lazy.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/compress/zstd_ldm.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/compress/zstd_opt.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/decompress/zstd_ddict.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/decompress/zstd_decompress_block.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/decompress/zstd_decompress_internal.h |only duckdb-0.2.5/duckdb/src/duckdb/third_party/zstd/zstd.h |only duckdb-0.2.6/duckdb/DESCRIPTION | 29 duckdb-0.2.6/duckdb/MD5 | 917 duckdb-0.2.6/duckdb/R/Connection.R | 11 duckdb-0.2.6/duckdb/R/Driver.R | 13 duckdb-0.2.6/duckdb/R/Viewer.R |only duckdb-0.2.6/duckdb/inst |only duckdb-0.2.6/duckdb/src/Makevars | 2 duckdb-0.2.6/duckdb/src/duckdb/amalgamation-1.cpp | 10 duckdb-0.2.6/duckdb/src/duckdb/amalgamation-2.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/amalgamation-3.cpp | 10 duckdb-0.2.6/duckdb/src/duckdb/amalgamation-4.cpp | 10 duckdb-0.2.6/duckdb/src/duckdb/amalgamation-5.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/amalgamation-6.cpp | 10 duckdb-0.2.6/duckdb/src/duckdb/amalgamation-7.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/amalgamation-8.cpp | 8 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/column_reader.cpp | 149 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/boolean_column_reader.hpp |only duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/callback_column_reader.hpp |only duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/column_reader.hpp | 381 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/decimal_column_reader.hpp |only duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/list_column_reader.hpp |only duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/parquet_file_metadata_cache.hpp | 11 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/parquet_reader.hpp | 38 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/parquet_rle_bp_decoder.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/parquet_statistics.hpp | 7 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/parquet_timestamp.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/parquet_writer.hpp | 11 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/resizable_buffer.hpp | 19 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/string_column_reader.hpp |only duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/struct_column_reader.hpp |only duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/templated_column_reader.hpp |only duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/include/thrift_tools.hpp | 15 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/parquet-extension.cpp | 71 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/parquet_reader.cpp | 246 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/parquet_statistics.cpp | 13 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/parquet_timestamp.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/extension/parquet/parquet_writer.cpp | 37 duckdb-0.2.6/duckdb/src/duckdb/src/catalog/catalog_entry/index_catalog_entry.cpp | 7 duckdb-0.2.6/duckdb/src/duckdb/src/catalog/catalog_set.cpp | 18 duckdb-0.2.6/duckdb/src/duckdb/src/catalog/dependency_manager.cpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/common/allocator.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/common/bit_operations.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/common/cycle_counter.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/common/enums/expression_type.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/src/common/enums/logical_operator_type.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/common/enums/physical_operator_type.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/common/enums/statement_type.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/common/file_system.cpp | 23 duckdb-0.2.6/duckdb/src/duckdb/src/common/limits.cpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/common/operator/cast_operators.cpp | 186 duckdb-0.2.6/duckdb/src/duckdb/src/common/progress_bar.cpp | 7 duckdb-0.2.6/duckdb/src/duckdb/src/common/tree_renderer.cpp | 12 duckdb-0.2.6/duckdb/src/duckdb/src/common/types.cpp | 75 duckdb-0.2.6/duckdb/src/duckdb/src/common/types/chunk_collection.cpp | 12 duckdb-0.2.6/duckdb/src/duckdb/src/common/types/data_chunk.cpp | 110 duckdb-0.2.6/duckdb/src/duckdb/src/common/types/date.cpp | 36 duckdb-0.2.6/duckdb/src/duckdb/src/common/types/hash.cpp | 31 duckdb-0.2.6/duckdb/src/duckdb/src/common/types/hyperloglog.cpp | 32 duckdb-0.2.6/duckdb/src/duckdb/src/common/types/interval.cpp | 27 duckdb-0.2.6/duckdb/src/duckdb/src/common/types/row_data_collection.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/common/types/selection_vector.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/common/types/time.cpp | 18 duckdb-0.2.6/duckdb/src/duckdb/src/common/types/timestamp.cpp | 100 duckdb-0.2.6/duckdb/src/duckdb/src/common/types/validity_mask.cpp | 25 duckdb-0.2.6/duckdb/src/duckdb/src/common/types/value.cpp | 167 duckdb-0.2.6/duckdb/src/duckdb/src/common/types/vector.cpp | 210 duckdb-0.2.6/duckdb/src/duckdb/src/common/types/vector_buffer.cpp | 42 duckdb-0.2.6/duckdb/src/duckdb/src/common/vector_operations/vector_cast.cpp | 94 duckdb-0.2.6/duckdb/src/duckdb/src/common/vector_operations/vector_copy.cpp | 128 duckdb-0.2.6/duckdb/src/duckdb/src/execution/aggregate_hashtable.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/execution/expression_executor.cpp | 7 duckdb-0.2.6/duckdb/src/duckdb/src/execution/expression_executor/execute_case.cpp | 17 duckdb-0.2.6/duckdb/src/duckdb/src/execution/expression_executor/execute_comparison.cpp | 42 duckdb-0.2.6/duckdb/src/duckdb/src/execution/expression_executor/execute_function.cpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/execution/index/art/art.cpp | 11 duckdb-0.2.6/duckdb/src/duckdb/src/execution/index/art/art_key.cpp | 153 duckdb-0.2.6/duckdb/src/duckdb/src/execution/join_hashtable.cpp | 37 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/aggregate/physical_hash_aggregate.cpp | 59 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/aggregate/physical_perfecthash_aggregate.cpp | 34 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/aggregate/physical_simple_aggregate.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/aggregate/physical_window.cpp | 784 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/helper/physical_load.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/join/physical_blockwise_nl_join.cpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/join/physical_cross_product.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/join/physical_delim_join.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/join/physical_hash_join.cpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/join/physical_index_join.cpp | 9 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/join/physical_nested_loop_join.cpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/join/physical_piecewise_merge_join.cpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/order/physical_order.cpp | 1965 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/order/physical_top_n.cpp | 18 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/persistent/buffered_csv_reader.cpp | 55 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/persistent/physical_copy_to_file.cpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/persistent/physical_delete.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/persistent/physical_insert.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/persistent/physical_update.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/projection/physical_tableinout_function.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/projection/physical_unnest.cpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/scan/physical_table_scan.cpp | 10 duckdb-0.2.6/duckdb/src/duckdb/src/execution/operator/schema/physical_create_table_as.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/execution/partitionable_hashtable.cpp | 31 duckdb-0.2.6/duckdb/src/duckdb/src/execution/physical_plan/plan_aggregate.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/execution/physical_plan/plan_comparison_join.cpp | 22 duckdb-0.2.6/duckdb/src/duckdb/src/execution/physical_plan/plan_get.cpp | 13 duckdb-0.2.6/duckdb/src/duckdb/src/execution/physical_plan/plan_simple.cpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/execution/physical_plan/plan_window.cpp | 71 duckdb-0.2.6/duckdb/src/duckdb/src/execution/physical_plan_generator.cpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/execution/window_segment_tree.cpp | 11 duckdb-0.2.6/duckdb/src/duckdb/src/function/aggregate/distributive/count.cpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/function/aggregate/distributive_functions.cpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/function/aggregate/holistic/approximate_quantile.cpp | 14 duckdb-0.2.6/duckdb/src/duckdb/src/function/aggregate/holistic/mode.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/function/aggregate/holistic/quantile.cpp | 556 duckdb-0.2.6/duckdb/src/duckdb/src/function/aggregate/holistic/reservoir_quantile.cpp | 12 duckdb-0.2.6/duckdb/src/duckdb/src/function/aggregate/holistic_functions.cpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/function/aggregate/nested/histogram.cpp | 35 duckdb-0.2.6/duckdb/src/duckdb/src/function/aggregate/nested/list.cpp | 68 duckdb-0.2.6/duckdb/src/duckdb/src/function/cast_rules.cpp | 18 duckdb-0.2.6/duckdb/src/duckdb/src/function/pragma/pragma_functions.cpp | 10 duckdb-0.2.6/duckdb/src/duckdb/src/function/pragma/pragma_queries.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/date/date_part.cpp | 22 duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/date/date_trunc.cpp | 41 duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/date/strftime.cpp | 37 duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/nested/array_slice.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/nested/list_extract.cpp | 102 duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/nested/list_value.cpp | 21 duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/nested/struct_extract.cpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/nested_functions.cpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/operators/add.cpp | 9 duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/operators/arithmetic.cpp | 11 duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/operators/bitwise.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/sequence/currval.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/sequence/nextval.cpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/sequence_functions.cpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/string/contains.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/function/scalar/string/string_split.cpp | 75 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/arrow.cpp | 251 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/checkpoint.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/copy_csv.cpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/glob.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/information_schema/information_schema_columns.cpp | 13 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/information_schema/information_schema_schemata.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/information_schema/information_schema_tables.cpp | 11 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/pragma_detailed_profiling_output.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/function/table/pragma_last_profiling_output.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/function/table/range.cpp | 11 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/read_csv.cpp | 32 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/repeat.cpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/sqlite/pragma_collations.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/sqlite/pragma_database_list.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/sqlite/pragma_database_size.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/sqlite/pragma_functions.cpp | 26 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/sqlite/pragma_table_info.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/sqlite/sqlite_master.cpp | 12 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/sqlite_functions.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/summary.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/function/table/table_scan.cpp | 41 duckdb-0.2.6/duckdb/src/duckdb/src/function/table/version/pragma_version.cpp | 10 duckdb-0.2.6/duckdb/src/duckdb/src/function/udf_function.cpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb.h | 12 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/catalog/catalog.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/catalog/catalog_entry.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/catalog/catalog_entry/sequence_catalog_entry.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/catalog/catalog_set.hpp | 15 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/allocator.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/array.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/arrow.hpp | 5 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/atomic.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/bit_operations.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/constants.hpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/cycle_counter.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/deque.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/enums/expression_type.hpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/enums/logical_operator_type.hpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/enums/physical_operator_type.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/enums/relation_type.hpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/enums/statement_type.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/file_system.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/helper.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/mutex.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/operator/cast_operators.hpp | 152 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/operator/comparison_operators.hpp | 21 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/profiler.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/progress_bar.hpp | 20 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/serializer.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/single_thread_ptr.hpp | 43 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types.hpp | 230 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/cast_helpers.hpp | 6 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/chunk_collection.hpp | 15 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/data_chunk.hpp | 10 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/date.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/interval.hpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/null_value.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/row_data_collection.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/selection_vector.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/string_type.hpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/time.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/timestamp.hpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/validity_mask.hpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/value.hpp | 28 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/vector.hpp | 69 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/types/vector_buffer.hpp | 26 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/vector_operations/aggregate_executor.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/vector_operations/binary_executor.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/vector_operations/vector_operations.hpp | 20 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/winapi.hpp | 14 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/common/windows_undefs.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/executor.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/expression_executor.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/expression_executor_state.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/index/art/art_key.hpp | 31 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/join_hashtable.hpp | 5 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/operator/aggregate/physical_hash_aggregate.hpp | 6 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/operator/aggregate/physical_perfecthash_aggregate.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/operator/aggregate/physical_window.hpp | 7 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/operator/helper/physical_load.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/operator/join/physical_blockwise_nl_join.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/operator/join/physical_delim_join.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/operator/join/physical_hash_join.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/operator/join/physical_nested_loop_join.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/operator/join/physical_piecewise_merge_join.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/operator/order/physical_order.hpp | 42 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/operator/order/physical_top_n.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/operator/persistent/buffered_csv_reader.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/operator/persistent/physical_copy_to_file.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/operator/projection/physical_tableinout_function.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/partitionable_hashtable.hpp | 6 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/execution/physical_sink.hpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/function/aggregate/distributive_functions.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/function/aggregate/holistic_functions.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/function/function.hpp | 18 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/function/replacement_scan.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/function/scalar/nested_functions.hpp | 5 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/function/scalar/sequence_functions.hpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/function/scalar_function.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/function/table/list.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/function/table/sqlite_functions.hpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/function/table/summary.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/function/table/table_scan.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/function/table_function.hpp | 19 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/function/udf_function.hpp | 131 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/main/appender.hpp | 6 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/main/client_context.hpp | 14 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/main/config.hpp | 10 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/main/connection.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/main/loadable_extension.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/main/query_profiler.hpp | 45 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/main/relation.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/main/relation/create_view_relation.hpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/main/relation/query_relation.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/main/relation/table_function_relation.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parallel/concurrentqueue.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parallel/pipeline.hpp | 13 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parallel/task.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parallel/task_counter.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parallel/task_scheduler.hpp | 7 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parser/expression/cast_expression.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parser/expression/list.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parser/expression/operator_expression.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parser/expression/positional_reference_expression.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parser/parsed_data/load_info.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parser/statement/delete_statement.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parser/statement/list.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parser/statement/load_statement.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parser/tableref/table_function_ref.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parser/tokens.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/parser/transformer.hpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/planner/bind_context.hpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/planner/binder.hpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/planner/expression/bound_window_expression.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/planner/expression_binder.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/buffer/block_handle.hpp | 9 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/buffer_manager.hpp | 12 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/checkpoint/table_data_writer.hpp | 17 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/checkpoint/write_overflow_strings_to_disk.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/column_data.hpp | 79 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/data_table.hpp | 68 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/index.hpp | 5 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/numeric_segment.hpp | 67 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/object_cache.hpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/statistics/base_statistics.hpp | 7 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/statistics/numeric_statistics.hpp | 42 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/statistics/validity_statistics.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/storage_lock.hpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/string_segment.hpp | 101 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/table/append_state.hpp | 11 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/table/chunk_info.hpp | 15 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/table/column_segment.hpp | 19 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/table/persistent_segment.hpp | 20 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/table/persistent_table_data.hpp | 17 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/table/scan_state.hpp | 17 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/table/segment_base.hpp | 9 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/table/standard_column_data.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/table/transient_segment.hpp | 22 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/table/update_segment.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/table/validity_column_data.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/table/validity_segment.hpp |only duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/storage/uncompressed_segment.hpp | 58 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/transaction/transaction.hpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/transaction/transaction_manager.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/include/duckdb/transaction/update_info.hpp | 19 duckdb-0.2.6/duckdb/src/duckdb/src/main/appender.cpp | 15 duckdb-0.2.6/duckdb/src/duckdb/src/main/client_context.cpp | 24 duckdb-0.2.6/duckdb/src/duckdb/src/main/connection.cpp | 5 duckdb-0.2.6/duckdb/src/duckdb/src/main/database.cpp | 28 duckdb-0.2.6/duckdb/src/duckdb/src/main/duckdb-c.cpp | 33 duckdb-0.2.6/duckdb/src/duckdb/src/main/query_profiler.cpp | 14 duckdb-0.2.6/duckdb/src/duckdb/src/main/query_result.cpp | 52 duckdb-0.2.6/duckdb/src/duckdb/src/main/relation.cpp | 29 duckdb-0.2.6/duckdb/src/duckdb/src/main/relation/create_view_relation.cpp | 9 duckdb-0.2.6/duckdb/src/duckdb/src/main/relation/query_relation.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/main/relation/table_function_relation.cpp | 15 duckdb-0.2.6/duckdb/src/duckdb/src/optimizer/deliminator.cpp | 7 duckdb-0.2.6/duckdb/src/duckdb/src/optimizer/filter_combiner.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/src/optimizer/statistics/expression/propagate_cast.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/optimizer/statistics/expression/propagate_comparison.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/optimizer/statistics/expression/propagate_constant.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/optimizer/statistics/expression/propagate_operator.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/optimizer/statistics/operator/propagate_filter.cpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/optimizer/statistics/operator/propagate_join.cpp | 7 duckdb-0.2.6/duckdb/src/duckdb/src/parallel/executor.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/parallel/pipeline.cpp | 62 duckdb-0.2.6/duckdb/src/duckdb/src/parallel/task_scheduler.cpp | 16 duckdb-0.2.6/duckdb/src/duckdb/src/parser/expression/cast_expression.cpp | 17 duckdb-0.2.6/duckdb/src/duckdb/src/parser/expression/operator_expression.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/parser/expression/positional_reference_expression.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/parser/parsed_expression.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/src/parser/parsed_expression_iterator.cpp | 7 duckdb-0.2.6/duckdb/src/duckdb/src/parser/query_error_context.cpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/parser/statement/delete_statement.cpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/parser/statement/load_statement.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/parser/transform/expression/transform_array_access.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/parser/transform/expression/transform_cast.cpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/parser/transform/expression/transform_expression.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/parser/transform/expression/transform_function.cpp | 25 duckdb-0.2.6/duckdb/src/duckdb/src/parser/transform/expression/transform_positional_reference.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/parser/transform/statement/transform_create_table_as.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/parser/transform/statement/transform_delete.cpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/parser/transform/statement/transform_load.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/parser/transformer.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/planner/bind_context.cpp | 29 duckdb-0.2.6/duckdb/src/duckdb/src/planner/binder.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/planner/binder/expression/bind_cast_expression.cpp | 3 duckdb-0.2.6/duckdb/src/duckdb/src/planner/binder/expression/bind_comparison_expression.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/planner/binder/expression/bind_operator_expression.cpp | 25 duckdb-0.2.6/duckdb/src/duckdb/src/planner/binder/expression/bind_positional_reference_expression.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/planner/binder/statement/bind_delete.cpp | 27 duckdb-0.2.6/duckdb/src/duckdb/src/planner/binder/statement/bind_load.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/planner/binder/statement/bind_update.cpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/planner/binder/tableref/bind_basetableref.cpp | 23 duckdb-0.2.6/duckdb/src/duckdb/src/planner/binder/tableref/bind_table_function.cpp | 48 duckdb-0.2.6/duckdb/src/duckdb/src/planner/expression/bound_cast_expression.cpp | 20 duckdb-0.2.6/duckdb/src/duckdb/src/planner/expression/bound_window_expression.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/src/planner/expression_binder.cpp | 12 duckdb-0.2.6/duckdb/src/duckdb/src/planner/expression_iterator.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/src/planner/planner.cpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/storage/buffer_manager.cpp | 16 duckdb-0.2.6/duckdb/src/duckdb/src/storage/checkpoint/table_data_reader.cpp | 34 duckdb-0.2.6/duckdb/src/duckdb/src/storage/checkpoint/table_data_writer.cpp | 293 duckdb-0.2.6/duckdb/src/duckdb/src/storage/checkpoint/write_overflow_strings_to_disk.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/storage/column_data.cpp | 464 duckdb-0.2.6/duckdb/src/duckdb/src/storage/data_table.cpp | 225 duckdb-0.2.6/duckdb/src/duckdb/src/storage/index.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/storage/local_storage.cpp | 12 duckdb-0.2.6/duckdb/src/duckdb/src/storage/meta_block_reader.cpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/storage/meta_block_writer.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/storage/numeric_segment.cpp | 884 duckdb-0.2.6/duckdb/src/duckdb/src/storage/statistics/base_statistics.cpp | 51 duckdb-0.2.6/duckdb/src/duckdb/src/storage/statistics/numeric_statistics.cpp | 80 duckdb-0.2.6/duckdb/src/duckdb/src/storage/statistics/string_statistics.cpp | 13 duckdb-0.2.6/duckdb/src/duckdb/src/storage/statistics/validity_statistics.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/storage/storage_info.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/src/storage/string_segment.cpp | 506 duckdb-0.2.6/duckdb/src/duckdb/src/storage/table/morsel_info.cpp | 7 duckdb-0.2.6/duckdb/src/duckdb/src/storage/table/persistent_segment.cpp | 45 duckdb-0.2.6/duckdb/src/duckdb/src/storage/table/persistent_table_data.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/src/storage/table/standard_column_data.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/storage/table/transient_segment.cpp | 42 duckdb-0.2.6/duckdb/src/duckdb/src/storage/table/update_segment.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/storage/table/validity_column_data.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/storage/table/validity_segment.cpp |only duckdb-0.2.6/duckdb/src/duckdb/src/storage/uncompressed_segment.cpp | 215 duckdb-0.2.6/duckdb/src/duckdb/src/transaction/cleanup_state.cpp | 16 duckdb-0.2.6/duckdb/src/duckdb/src/transaction/commit_state.cpp | 25 duckdb-0.2.6/duckdb/src/duckdb/src/transaction/rollback_state.cpp | 1 duckdb-0.2.6/duckdb/src/duckdb/src/transaction/transaction.cpp | 8 duckdb-0.2.6/duckdb/src/duckdb/src/transaction/transaction_manager.cpp | 3 duckdb-0.2.6/duckdb/src/duckdb/third_party/concurrentqueue/blockingconcurrentqueue.h | 6 duckdb-0.2.6/duckdb/src/duckdb/third_party/concurrentqueue/concurrentqueue.h | 20 duckdb-0.2.6/duckdb/src/duckdb/third_party/concurrentqueue/lightweightsemaphore.h | 4 duckdb-0.2.6/duckdb/src/duckdb/third_party/fmt/include/fmt/printf.h | 4 duckdb-0.2.6/duckdb/src/duckdb/third_party/hyperloglog/hyperloglog.cpp | 23 duckdb-0.2.6/duckdb/src/duckdb/third_party/hyperloglog/hyperloglog.hpp | 12 duckdb-0.2.6/duckdb/src/duckdb/third_party/hyperloglog/sds.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/third_party/hyperloglog/sds.hpp | 5 duckdb-0.2.6/duckdb/src/duckdb/third_party/libpg_query/include/nodes/nodes.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/third_party/libpg_query/include/nodes/parsenodes.hpp | 11 duckdb-0.2.6/duckdb/src/duckdb/third_party/libpg_query/include/parser/gram.hpp | 240 duckdb-0.2.6/duckdb/src/duckdb/third_party/libpg_query/include/parser/kwlist.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/third_party/libpg_query/include/pg_definitions.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/third_party/libpg_query/src_backend_parser_gram.cpp |20128 +++++----- duckdb-0.2.6/duckdb/src/duckdb/third_party/libpg_query/src_backend_parser_scan.cpp | 832 duckdb-0.2.6/duckdb/src/duckdb/third_party/miniz/miniz.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/third_party/miniz/miniz.hpp | 4 duckdb-0.2.6/duckdb/src/duckdb/third_party/parquet/parquet_constants.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/third_party/parquet/parquet_constants.h | 2 duckdb-0.2.6/duckdb/src/duckdb/third_party/parquet/parquet_types.cpp | 1322 duckdb-0.2.6/duckdb/src/duckdb/third_party/parquet/parquet_types.h | 278 duckdb-0.2.6/duckdb/src/duckdb/third_party/pcg/pcg_random.hpp | 8 duckdb-0.2.6/duckdb/src/duckdb/third_party/re2/re2/stringpiece.h | 4 duckdb-0.2.6/duckdb/src/duckdb/third_party/snappy/snappy-stubs-internal.h | 6 duckdb-0.2.6/duckdb/src/duckdb/third_party/tdigest |only duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/TApplicationException.h | 6 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/TBase.h | 8 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/TLogging.h | 8 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/TToString.h | 4 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/Thrift.h | 10 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/protocol/TCompactProtocol.h | 8 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/protocol/TCompactProtocol.tcc | 4 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/protocol/TProtocol.cpp | 8 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/protocol/TProtocol.h | 10 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/protocol/TProtocolDecorator.h | 6 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/protocol/TProtocolException.h | 14 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/protocol/TProtocolTypes.h | 4 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/protocol/TVirtualProtocol.h | 12 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/thrift-config.h | 2 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/transport/TBufferTransports.cpp | 8 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/transport/TBufferTransports.h | 10 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/transport/TTransport.h | 10 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/transport/TTransportException.cpp | 8 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/transport/TTransportException.h | 18 duckdb-0.2.6/duckdb/src/duckdb/third_party/thrift/thrift/transport/TVirtualTransport.h | 8 duckdb-0.2.6/duckdb/src/duckdb/third_party/utf8proc/include/utf8proc_wrapper.hpp | 1 duckdb-0.2.6/duckdb/src/duckdb/third_party/utf8proc/utf8proc.cpp | 7 duckdb-0.2.6/duckdb/src/duckdb/third_party/utf8proc/utf8proc_wrapper.cpp | 23 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/common/entropy_common.cpp | 12 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/common/error_private.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/common/fse_decompress.cpp | 12 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/common/xxhash.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/common/zstd_common.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/compress/fse_compress.cpp | 18 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/compress/hist.cpp | 8 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/compress/huf_compress.cpp | 20 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/compress/zstd_compress.cpp | 30 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/compress/zstd_compress_literals.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/compress/zstd_compress_sequences.cpp | 2 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/compress/zstd_compress_superblock.cpp | 12 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/compress/zstd_double_fast.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/compress/zstd_fast.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/compress/zstd_lazy.cpp | 4 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/compress/zstd_ldm.cpp | 8 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/compress/zstd_opt.cpp | 6 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/decompress/huf_decompress.cpp | 14 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/decompress/zstd_ddict.cpp | 20 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/decompress/zstd_decompress.cpp | 24 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/decompress/zstd_decompress_block.cpp | 20 duckdb-0.2.6/duckdb/src/duckdb/third_party/zstd/include |only duckdb-0.2.6/duckdb/src/duckdbr.cpp | 181 duckdb-0.2.6/duckdb/tests/testthat/test_dbinfo.R |only duckdb-0.2.6/duckdb/tests/testthat/test_register_readonly.R |only duckdb-0.2.6/duckdb/tests/testthat/test_timezone.R | 9 490 files changed, 20402 insertions(+), 16957 deletions(-)
Title: Extension for 'DALEX' Package
Description: Provides wrapper of various machine learning models.
In applied machine learning, there
is a strong belief that we need to strike a balance
between interpretability and accuracy.
However, in field of the interpretable machine learning,
there are more and more new ideas for explaining black-box models,
that are implemented in 'R'.
'DALEXtra' creates 'DALEX' Biecek (2018) <arXiv:1806.08915> explainer for many type of models
including those created using 'python' 'scikit-learn' and 'keras' libraries, and 'java' 'h2o' library.
Important part of the package is Champion-Challenger analysis and innovative approach
to model performance across subsets of test data presented in Funnel Plot.
Third branch of 'DALEXtra' package is aspect importance analysis
that provides instance-level explanations for the groups of explanatory variables.
Author: Szymon Maksymiuk [aut, cre] (<https://orcid.org/0000-0002-3120-1601>),
Przemyslaw Biecek [aut] (<https://orcid.org/0000-0001-8423-1823>),
Anna Kozak [ctb],
Hubert Baniecki [ctb]
Maintainer: Szymon Maksymiuk <sz.maksymiuk@gmail.com>
Diff between DALEXtra versions 2.0 dated 2020-09-07 and 2.1.1 dated 2021-05-09
DESCRIPTION | 9 ++--- MD5 | 44 ++++++++++++------------- NEWS.md | 9 +++++ R/explain_h2o.R | 10 ++++- R/explain_keras.R | 3 + R/explain_mlr.R | 3 + R/explain_mlr3.R | 6 ++- R/explain_scikitlearn.R | 5 ++ R/explain_tidymodels.R | 6 ++- R/explain_xgboost.R | 3 + R/model_info.R | 12 +++++-- R/predict_surrogate.R | 7 ++-- R/yhat.R | 51 +++++++++++++++++++++++++++--- inst/CITATION | 11 ++++-- man/explain_h2o.Rd | 10 ++++- man/explain_keras.Rd | 3 + man/explain_mlr.Rd | 3 + man/explain_mlr3.Rd | 3 + man/explain_scikitlearn.Rd | 3 + man/explain_tidymodels.Rd | 3 + man/explain_xgboost.Rd | 3 + man/predict_surrogate.Rd | 4 +- tests/testthat/test_scikitlearn_explain.R | 17 ---------- 23 files changed, 158 insertions(+), 70 deletions(-)
Title: Matrix Completion via Iterative Soft-Thresholded SVD
Description: Iterative methods for matrix completion that use nuclear-norm regularization. There are two main approaches.The one approach uses iterative soft-thresholded svds to impute the missing values. The second approach uses alternating least squares. Both have an 'EM' flavor, in that at each iteration the matrix is completed with the current estimate. For large matrices there is a special sparse-matrix class named "Incomplete" that efficiently handles all computations. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank SVDs on large sparse centered matrices (i.e. principal components).
Author: Trevor Hastie <hastie@stanford.edu> and Rahul Mazumder <rahul.mazumder@gmail.com>
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between softImpute versions 1.4 dated 2015-04-07 and 1.4-1 dated 2021-05-09
DESCRIPTION | 12 MD5 | 25 - NAMESPACE | 2 build/vignette.rds |binary inst/doc/softImpute.R | 36 +- inst/doc/softImpute.Rmd | 4 inst/doc/softImpute.html | 665 ++++++++++++++++++++++++++--------------------- man/lambda0.Rd | 2 man/softImpute.Rd | 4 man/svd.als.Rd | 2 src/plusregC.f | 2 src/softImpute_init.c |only src/suvC.f | 2 vignettes/softImpute.Rmd | 4 14 files changed, 427 insertions(+), 333 deletions(-)
Title: Text Analysis with Emphasis on POS Tagging, Readability, and
Lexical Diversity
Description: A set of tools to analyze texts. Includes, amongst others, functions for
automatic language detection, hyphenation, several indices of lexical diversity
(e.g., type token ratio, HD-D/vocd-D, MTLD) and readability (e.g., Flesch,
SMOG, LIX, Dale-Chall). Basic import functions for language corpora are also
provided, to enable frequency analyses (supports Celex and Leipzig Corpora
Collection file formats) and measures like tf-idf. Note: For full functionality
a local installation of TreeTagger is recommended. It is also recommended to
not load this package directly, but by loading one of the available language
support packages from the 'l10n' repository
<https://undocumeantit.github.io/repos/l10n/>. 'koRpus' also includes a plugin
for the R GUI and IDE RKWard, providing graphical dialogs for its basic
features. The respective R package 'rkward' cannot be installed directly from a
repository, as it is a part of RKWard. To make full use of this feature, please
install RKWard from <https://rkward.kde.org> (plugins are detected
automatically). Due to some restrictions on CRAN, the full package sources are
only available from the project homepage. To ask for help, report bugs, request
features, or discuss the development of the package, please subscribe to the
koRpus-dev mailing list (<https://korpusml.reaktanz.de>).
Author: Meik Michalke [aut, cre],
Earl Brown [ctb],
Alberto Mirisola [ctb],
Alexandre Brulet [ctb],
Laura Hauser [ctb]
Maintainer: Meik Michalke <meik.michalke@hhu.de>
Diff between koRpus versions 0.13-5 dated 2021-02-02 and 0.13-6 dated 2021-05-09
ChangeLog | 23 ++++ DESCRIPTION | 8 - MD5 | 71 ++++++------ NAMESPACE | 1 R/01_class_02_kRp.TTR.R | 4 R/01_class_05_kRp.readability.R | 7 + R/02_method_readability.R | 136 +++++++++++++----------- R/02_method_show.kRp.readability.R | 12 ++ R/02_method_summary.kRp.readability.R | 11 + R/02_method_summary.kRp.text.R | 37 ++++++ R/02_method_tokenize.R | 16 -- R/02_method_treetag.R | 6 - R/guess.lang.R | 2 R/koRpus-internal.R | 36 ++++++ R/koRpus-internal.lexdiv.formulae.R | 7 - R/koRpus-internal.rdb.formulae.R | 40 ++++--- R/koRpus-internal.rdb.params.grades.R | 7 + R/koRpus-package.R | 4 R/readability.num.R | 3 R/wrapper_functions_readability.R | 36 ++++++ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 inst/NEWS.Rd | 32 +++++ inst/doc/koRpus_vignette.html | 72 +++++++----- inst/shiny/demo/ui.R | 1 man/guess.lang.Rd | 2 man/gutierrez.Rd |only man/kRp.TTR-class.Rd | 2 man/kRp.readability-class.Rd | 7 + man/koRpus-package.Rd | 4 man/readability-methods.Rd | 99 +++++++++-------- man/summary-methods.Rd | 10 + man/treetag-methods.Rd | 2 tests/testthat/sample_text_lexdiv_dput.txt | 2 tests/testthat/sample_text_readability_dput.txt | 31 ++--- tests/testthat/test_tokenizing_POS_tagging.R | 12 +- 37 files changed, 503 insertions(+), 244 deletions(-)
Title: SPRE Statistics for Exploring Heterogeneity in Meta-Analysis
Description: An implementation of SPRE (standardised predicted random-effects)
statistics in R to explore heterogeneity in genetic association meta-
analyses, as described by Magosi et al. (2019)
<doi:10.1093/bioinformatics/btz590>. SPRE statistics are precision
weighted residuals that indicate the direction and extent with which
individual study-effects in a meta-analysis deviate from the average
genetic effect. Overly influential positive outliers have the potential
to inflate average genetic effects in a meta-analysis whilst negative
outliers might lower or change the direction of effect. See the 'getspres'
website for documentation and examples
<https://magosil86.github.io/getspres/>.
Author: Lerato E Magosi [aut],
Jemma C Hopewell [aut],
Martin Farrall [aut],
Lerato E Magosi [cre]
Maintainer: Lerato E Magosi <magosil86@gmail.com>
Diff between getspres versions 0.1.1 dated 2020-03-31 and 0.2.0 dated 2021-05-09
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS.md | 7 +++++++ build/vignette.rds |binary inst/doc/getspres-tutorial.R | 2 +- man/getspres.Rd | 13 ++++++++++--- man/heartgenes214.Rd | 8 +++++--- man/plotspres.Rd | 25 +++++++++++++++++++------ 8 files changed, 54 insertions(+), 25 deletions(-)
Title: Quantifying Systematic Heterogeneity in Meta-Analysis
Description: Quantifying systematic heterogeneity in meta-analysis using R.
The M statistic aggregates heterogeneity information across multiple
variants to, identify systematic heterogeneity patterns and their direction
of effect in meta-analysis. It's primary use is to identify outlier studies,
which either show "null" effects or consistently show stronger or weaker
genetic effects than average across, the panel of variants examined in a
GWAS meta-analysis. In contrast to conventional heterogeneity metrics
(Q-statistic, I-squared and tau-squared) which measure random heterogeneity
at individual variants, M measures systematic (non-random)
heterogeneity across multiple independently associated variants. Systematic
heterogeneity can arise in a meta-analysis due to differences in the study
characteristics of participating studies. Some of the differences may
include: ancestry, allele frequencies, phenotype definition, age-of-disease
onset, family-history, gender, linkage disequilibrium and quality control
thresholds. See <https://magosil86.github.io/getmstatistic/> for statistical
statistical theory, documentation and examples.
Author: Lerato E Magosi [aut],
Jemma C Hopewell [aut],
Martin Farrall [aut],
Lerato E Magosi [cre]
Maintainer: Lerato E Magosi <magosil86@gmail.com>
Diff between getmstatistic versions 0.2.1 dated 2020-03-30 and 0.2.2 dated 2021-05-09
DESCRIPTION | 11 ++++++----- MD5 | 20 ++++++++++---------- NEWS.md | 6 +++++- build/vignette.rds |binary inst/doc/getmstatistic-tutorial.R | 2 +- inst/doc/getmstatistic-tutorial.Rmd | 8 ++++---- inst/doc/getmstatistic-tutorial.html | 8 ++++---- man/draw_table.Rd | 8 ++++---- man/getmstatistic.Rd | 19 ++++++++++++++----- man/heartgenes214.Rd | 8 +++++--- vignettes/getmstatistic-tutorial.Rmd | 8 ++++---- 11 files changed, 57 insertions(+), 41 deletions(-)
Title: Bias Corrected Bootstrap Confidence Intervals
Description: Computation of bootstrap confidence intervals in an almost automatic fashion as described in Efron and Narasimhan (2020, <doi:10.1080/10618600.2020.1714633>).
Author: Bradley Efron [aut],
Balasubramanian Narasimhan [aut, cre]
Maintainer: Balasubramanian Narasimhan <naras@stat.stanford.edu>
Diff between bcaboot versions 0.2-1 dated 2018-08-31 and 0.2-3 dated 2021-05-09
DESCRIPTION | 16 - MD5 | 26 +- build/vignette.rds |binary inst/doc/bcaboot.R | 71 ++--- inst/doc/bcaboot.Rmd | 24 + inst/doc/bcaboot.html | 622 ++++++++++++++++++++++++++------------------------ man/bcaboot.Rd | 1 man/bcajack.Rd | 16 + man/bcajack2.Rd | 17 + man/bcapar.Rd | 14 - man/bcaplot.Rd | 16 + man/diabetes.Rd | 6 vignettes/bcaboot.Rmd | 24 + vignettes/bcaboot.bib | 6 14 files changed, 484 insertions(+), 375 deletions(-)
Title: Joint Feature Screening via Sparse MLE
Description: Feature screening is a powerful tool in processing ultrahigh dimensional data. It attempts to screen out most irrelevant features in preparation for a more elaborate analysis. Xu and Chen (2014)<doi:10.1080/01621459.2013.879531> proposed an effective screening method SMLE, which naturally incorporates the joint effects among features in the screening process. This package provides an efficient implementation of SMLE-screening for high-dimensional linear, logistic, and Poisson models. The package also provides a function for conducting accurate post-screening feature selection based on an iterative hard-thresholding procedure and a user-specified selection criterion.
Author: Qianxiang Zang, Chen Xu, Kelly Burkett
Maintainer: Qianxiang Zang <qzang023@uottawa.ca>
Diff between SMLE versions 0.4.1 dated 2020-06-24 and 1.1.1 dated 2021-05-09
SMLE-0.4.1/SMLE/R/fits.R |only SMLE-0.4.1/SMLE/R/predict.smle.R |only SMLE-0.4.1/SMLE/R/print.sdata.R |only SMLE-0.4.1/SMLE/R/print.selection.R |only SMLE-0.4.1/SMLE/R/print.smle.R |only SMLE-0.4.1/SMLE/R/selection.R |only SMLE-0.4.1/SMLE/R/subfunctions.R |only SMLE-0.4.1/SMLE/README.md |only SMLE-0.4.1/SMLE/man/predict.smle.Rd |only SMLE-0.4.1/SMLE/man/print.sdata.Rd |only SMLE-0.4.1/SMLE/man/print.selection.Rd |only SMLE-0.4.1/SMLE/man/print.smle.Rd |only SMLE-1.1.1/SMLE/DESCRIPTION | 19 - SMLE-1.1.1/SMLE/MD5 | 56 +-- SMLE-1.1.1/SMLE/NAMESPACE | 21 - SMLE-1.1.1/SMLE/R/Gen_Data.R | 56 +-- SMLE-1.1.1/SMLE/R/SMLE.R | 549 +++++++++++++++++++++++++++++---- SMLE-1.1.1/SMLE/R/coef.R |only SMLE-1.1.1/SMLE/R/ctg_fit.R | 159 ++++++--- SMLE-1.1.1/SMLE/R/dummy.R | 9 SMLE-1.1.1/SMLE/R/ebicc.r | 20 - SMLE-1.1.1/SMLE/R/logLik.R |only SMLE-1.1.1/SMLE/R/plot.selection.R | 21 - SMLE-1.1.1/SMLE/R/plot.smle.R | 402 +++++++++--------------- SMLE-1.1.1/SMLE/R/predict.R |only SMLE-1.1.1/SMLE/R/print.R |only SMLE-1.1.1/SMLE/R/smle_select.R |only SMLE-1.1.1/SMLE/R/standardize.R | 6 SMLE-1.1.1/SMLE/R/summary.R |only SMLE-1.1.1/SMLE/R/ult.R |only SMLE-1.1.1/SMLE/man/Gen_Data.Rd | 16 SMLE-1.1.1/SMLE/man/SMLE-package.Rd | 13 SMLE-1.1.1/SMLE/man/SMLE.Rd | 423 +++++++++++++------------ SMLE-1.1.1/SMLE/man/coef.Rd |only SMLE-1.1.1/SMLE/man/logLik.Rd |only SMLE-1.1.1/SMLE/man/plot.selection.Rd | 4 SMLE-1.1.1/SMLE/man/plot.smle.Rd | 22 - SMLE-1.1.1/SMLE/man/predict.Rd |only SMLE-1.1.1/SMLE/man/print.Rd |only SMLE-1.1.1/SMLE/man/smle_select.Rd | 19 - SMLE-1.1.1/SMLE/man/summary.Rd |only 41 files changed, 1115 insertions(+), 700 deletions(-)
Title: Psychometric Meta-Analysis Toolkit
Description: Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more. Bugs can be reported to <https://github.com/psychmeta/psychmeta/issues> or <issues@psychmeta.com>.
Author: Jeffrey A. Dahlke [aut, cre],
Brenton M. Wiernik [aut],
Wesley Gardiner [ctb] (Unit tests),
Michael T. Brannick [ctb] (Testing),
Jack Kostal [ctb] (Code for reshape_mat2dat function),
Sean Potter [ctb] (Testing; Code for cumulative and leave1out plots),
John Sakaluk [ctb] (Code for funnel and forest plots),
Yuejia (Mandy) Teng [ctb] (Testing)
Maintainer: Jeffrey A. Dahlke <jdahlke@humrro.org>
Diff between psychmeta versions 2.5.0 dated 2021-05-02 and 2.5.1 dated 2021-05-08
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 21 +++++++++++++-------- R/ma_d_bb.R | 8 ++++---- R/ma_generic.R | 8 ++++---- R/ma_r.R | 8 ++++---- R/ma_r_bb.R | 8 ++++---- R/ma_r_ic.R | 20 ++++++++++---------- R/remove_dependency.R | 9 +++++---- R/wrangle_data.R | 4 ++-- build/partial.rdb |binary inst/doc/ma_r.html | 4 ++-- tests/testthat/test-ma_r.R | 32 ++++++++++++++++++++++++++++++-- 13 files changed, 94 insertions(+), 60 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 1.16.0 dated 2021-04-27 and 1.17.0 dated 2021-05-08
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Shadow-Test Approach to Computerized Adaptive Testing
Description: As an advanced approach to computerized adaptive testing (CAT),
shadow testing (van der Linden(2005) <doi:10.1007/0-387-29054-0>) dynamically
assembles entire shadow tests as a part of
selecting items throughout the testing process.
Selecting items from shadow tests guarantees the compliance of all content
constraints defined by the blueprint. 'RSCAT' is an R package for the
shadow-test approach to CAT. The objective of
'RSCAT' is twofold: 1) Enhancing the effectiveness of shadow-test CAT simulation;
2) Contributing to the academic and scientific community for CAT research.
Author: Bingnan Jiang [aut, cre],
ACT, Inc. [cph]
Maintainer: Bingnan Jiang <bnjiangece@gmail.com>
Diff between RSCAT versions 1.1.0 dated 2020-01-17 and 1.1.1 dated 2021-05-08
RSCAT-1.1.0/RSCAT/inst/java/RSCAT-1.1.0.jar |only RSCAT-1.1.0/RSCAT/java/src/main/java/org/act/cat |only RSCAT-1.1.0/RSCAT/java/src/main/java/org/act/mip |only RSCAT-1.1.0/RSCAT/java/src/main/java/org/act/sim |only RSCAT-1.1.0/RSCAT/java/src/main/java/org/act/sol |only RSCAT-1.1.0/RSCAT/java/src/main/java/org/act/testdef |only RSCAT-1.1.0/RSCAT/java/src/main/java/org/act/util |only RSCAT-1.1.0/RSCAT/java/src/test/java/org/act/sim |only RSCAT-1.1.1/RSCAT/DESCRIPTION | 8 RSCAT-1.1.1/RSCAT/MD5 | 171 +++++++++---------- RSCAT-1.1.1/RSCAT/R/runSim.R | 4 RSCAT-1.1.1/RSCAT/R/scoreMethodConfig.R | 10 - RSCAT-1.1.1/RSCAT/README.md | 16 - RSCAT-1.1.1/RSCAT/inst/java/RSCAT-1.1.1.jar |only RSCAT-1.1.1/RSCAT/java/pom.xml | 16 - RSCAT-1.1.1/RSCAT/java/src/main/java/org/act/rscat |only RSCAT-1.1.1/RSCAT/java/src/test/java/org/act/rscat |only RSCAT-1.1.1/RSCAT/man/launchApp.Rd | 30 +-- RSCAT-1.1.1/RSCAT/man/result2CSV.Rd | 32 +-- RSCAT-1.1.1/RSCAT/man/runSim.Rd | 2 RSCAT-1.1.1/RSCAT/man/scoreMethodConfig.Rd | 4 RSCAT-1.1.1/RSCAT/man/shinyAppUI.Rd | 28 +-- RSCAT-1.1.1/RSCAT/man/summary-SimResult-method.Rd | 28 +-- 23 files changed, 176 insertions(+), 173 deletions(-)
Title: Czech Interest Rates
Description: Interface to interest and foreign exchange rates published by the Czech National Bank.
Author: Jindra Lacko
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>
Diff between czechrates versions 0.1.10 dated 2020-08-26 and 0.2.0 dated 2021-05-08
DESCRIPTION | 13 - MD5 | 35 +-- NAMESPACE | 1 NEWS.md | 6 R/cnbfxrate.R |only R/czechrates.R | 7 R/ok_to_proceed.R |only R/pribor.R | 26 +- R/repo2w.R | 14 - README.md | 92 ++++++-- build/vignette.rds |binary inst/doc/vignette.R | 32 ++ inst/doc/vignette.Rmd | 60 ++++- inst/doc/vignette.html | 460 ++++++++++++++-------------------------- man/cnbfxrate.Rd |only man/czechrates-package.Rd | 2 man/ok_to_proceed.Rd |only tests/testthat/test-cnbfxrate.R |only tests/testthat/test-pribor.R | 5 tests/testthat/test-repo2w.R | 4 vignettes/vignette.Rmd | 60 ++++- 21 files changed, 435 insertions(+), 382 deletions(-)
Title: Analysis of Tidal Datasets
Description: Contains functions for analysis and summary of tidal datasets. Also provides access to tidal data collected by the National Oceanic and Atmospheric Administration's Center for Operational Oceanographic Products and Services and the Permanent Service for Mean Sea Level. For detailed description and application examples, see Hill, T.D. and S.C. Anisfeld (2021) <doi:10.6084/m9.figshare.14161202.v1> and Hill, T.D. and S.C. Anisfeld (2015) <doi:10.1016/j.ecss.2015.06.004>.
Author: Troy Hill [aut, cre] (<https://orcid.org/0000-0003-2980-4099>),
Shimon Anisfeld [ctb]
Maintainer: Troy Hill <Hill.Troy@gmail.com>
Diff between VulnToolkit versions 1.1.2 dated 2021-04-16 and 1.1.3 dated 2021-05-08
VulnToolkit-1.1.2/VulnToolkit/R/noaa_stations.R |only VulnToolkit-1.1.2/VulnToolkit/man/noaa.stations.Rd |only VulnToolkit-1.1.3/VulnToolkit/DESCRIPTION | 8 - VulnToolkit-1.1.3/VulnToolkit/MD5 | 70 +++++++----- VulnToolkit-1.1.3/VulnToolkit/NAMESPACE | 13 ++ VulnToolkit-1.1.3/VulnToolkit/NEWS | 9 + VulnToolkit-1.1.3/VulnToolkit/R/HL.r | 93 ++++++++++++++--- VulnToolkit-1.1.3/VulnToolkit/R/HL_plot.R | 38 +++++- VulnToolkit-1.1.3/VulnToolkit/R/dur_bias.R |only VulnToolkit-1.1.3/VulnToolkit/R/fldDurEvents.R | 3 VulnToolkit-1.1.3/VulnToolkit/R/fld_frq.R | 3 VulnToolkit-1.1.3/VulnToolkit/R/floodDepth.R | 2 VulnToolkit-1.1.3/VulnToolkit/R/form_no.R | 6 - VulnToolkit-1.1.3/VulnToolkit/R/harcon.R | 4 VulnToolkit-1.1.3/VulnToolkit/R/noaa.r | 5 VulnToolkit-1.1.3/VulnToolkit/R/noaaParameters.R | 2 VulnToolkit-1.1.3/VulnToolkit/R/noaa_datums.R | 6 - VulnToolkit-1.1.3/VulnToolkit/R/number_tides.R | 1 VulnToolkit-1.1.3/VulnToolkit/R/psmsl.R |only VulnToolkit-1.1.3/VulnToolkit/R/psmsl_stations.R |only VulnToolkit-1.1.3/VulnToolkit/build/vignette.rds |binary VulnToolkit-1.1.3/VulnToolkit/inst/doc/NOAA_PSMSL.R |only VulnToolkit-1.1.3/VulnToolkit/inst/doc/NOAA_PSMSL.Rmd |only VulnToolkit-1.1.3/VulnToolkit/inst/doc/NOAA_PSMSL.html |only VulnToolkit-1.1.3/VulnToolkit/inst/doc/Tidal_data.Rmd | 2 VulnToolkit-1.1.3/VulnToolkit/inst/doc/Tidal_data.html | 6 - VulnToolkit-1.1.3/VulnToolkit/man/HL.Rd | 49 +++++++- VulnToolkit-1.1.3/VulnToolkit/man/HL.plot.Rd | 39 ++++++- VulnToolkit-1.1.3/VulnToolkit/man/dur.bias.Rd |only VulnToolkit-1.1.3/VulnToolkit/man/dur.events.Rd | 3 VulnToolkit-1.1.3/VulnToolkit/man/fld.depth.Rd | 2 VulnToolkit-1.1.3/VulnToolkit/man/fld.frq.Rd | 3 VulnToolkit-1.1.3/VulnToolkit/man/form.no.Rd | 6 - VulnToolkit-1.1.3/VulnToolkit/man/harcon.Rd | 6 - VulnToolkit-1.1.3/VulnToolkit/man/noaa.Rd | 5 VulnToolkit-1.1.3/VulnToolkit/man/noaa.datums.Rd | 6 - VulnToolkit-1.1.3/VulnToolkit/man/noaa.parameters.Rd | 2 VulnToolkit-1.1.3/VulnToolkit/man/number.tides.Rd | 1 VulnToolkit-1.1.3/VulnToolkit/man/psmsl.Rd |only VulnToolkit-1.1.3/VulnToolkit/man/psmsl.stations.Rd |only VulnToolkit-1.1.3/VulnToolkit/vignettes/NOAA_PSMSL.Rmd |only VulnToolkit-1.1.3/VulnToolkit/vignettes/Tidal_data.Rmd | 2 42 files changed, 275 insertions(+), 120 deletions(-)
Title: Extending 'dendrogram' Functionality in R
Description: Offers a set of functions for extending
'dendrogram' objects in R, letting you visualize and compare trees of
'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different 'dendrograms' to one another.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Yoav Benjamini [ths],
Gavin Simpson [ctb],
Gregory Jefferis [aut, ctb] (imported code from his dendroextras
package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
The R Core Team [ctb] (Thanks for the Infastructure, and code in the
examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),
Andrie de Vries [ctb] (ggdendro author),
Zuguang Gu [ctb] (circlize author),
Cath [ctb] (https://github.com/CathG),
John Ma [ctb] (https://github.com/JohnMCMa),
Krzysiek G [ctb] (https://github.com/storaged),
Manuela Hummel [ctb] (https://github.com/hummelma),
Chase Clark [ctb] (https://github.com/chasemc),
Lucas Graybuck [ctb] (https://github.com/hypercompetent),
jdetribol [ctb] (https://github.com/jdetribol),
Ben Ho [ctb] (https://github.com/SplitInf),
Samuel Perreault [ctb] (https://github.com/samperochkin),
Christian Hennig [ctb] (http://www.homepages.ucl.ac.uk/~ucakche/),
David Bradley [ctb] (https://github.com/DBradley27),
Houyun Huang [ctb] (https://github.com/houyunhuang)
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between dendextend versions 1.14.0 dated 2020-08-26 and 1.15.1 dated 2021-05-08
ChangeLog | 1545 +++++++++++++++++++------------ DESCRIPTION | 8 MD5 | 35 NEWS | 15 NEWS.md | 10 R/colored_dots.R | 6 R/data.R | 6 R/get_subdendrograms.R | 44 README.md | 16 inst/doc/Cluster_Analysis.html | 663 ++++++------- inst/doc/FAQ.html | 593 ++++++----- inst/doc/Quick_Introduction.html | 123 +- inst/doc/dendextend.Rmd | 2 inst/doc/dendextend.html | 1335 +++++++++++++------------- man/colored_dots.Rd | 3 man/get_subdendrograms.Rd | 39 man/khan.Rd | 4 tests/testthat/test-get_subdendrograms.R |only vignettes/dendextend.Rmd | 2 19 files changed, 2550 insertions(+), 1899 deletions(-)
Title: Accessing Statistics Canada Data Table and Vectors
Description: Searches for, accesses, and retrieves new-format and old-format Statistics Canada data
tables, as well as individual vectors, as tidy data frames. This package deals with encoding issues, allows for
bilingual English or French language data retrieval, and bundles convenience functions
to make it easier to work with retrieved table data. Optional caching features are provided.
Author: Jens von Bergmann [cre],
Dmitry Shkolnik [aut]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between cansim versions 0.3.5 dated 2020-03-13 and 0.3.6 dated 2021-05-08
DESCRIPTION | 19 - LICENSE | 2 MD5 | 63 ++- NAMESPACE | 7 NEWS.md | 71 +--- R/cansim.R | 405 ++++++++++++++++++++--- R/cansim_helpers.R | 51 ++ R/cansim_sql.R |only R/cansim_tables_list.R | 98 +++-- R/cansim_vectors.R | 171 ++++++---- R/sysdata.rda |binary README.md | 21 - build/vignette.rds |binary inst/doc/cansim.R | 9 inst/doc/cansim.Rmd | 30 - inst/doc/cansim.html | 426 +++++++------------------ inst/doc/working_with_large_tables.R |only inst/doc/working_with_large_tables.Rmd |only inst/doc/working_with_large_tables.html |only man/collect_and_normalize.Rd |only man/create_index.Rd |only man/csv2sqlite.Rd |only man/disconnect_cansim_sqlite.Rd |only man/fold_in_metadata_for_columns.Rd |only man/get_cansim.Rd | 25 - man/get_cansim_changed_tables.Rd | 5 man/get_cansim_data_for_table_coord_periods.Rd | 17 man/get_cansim_ndm.Rd | 14 man/get_cansim_sqlite.Rd |only man/get_cansim_vector.Rd | 19 - man/get_cansim_vector_for_latest_periods.Rd | 20 + man/list_cansim_sqlite_cached_tables.Rd |only man/normalize_cansim_values.Rd | 5 man/parse_and_fold_in_metadata.Rd | 4 man/parse_metadata.Rd |only man/remove_cansim_sqlite_cached_table.Rd |only man/view_cansim_webpage.Rd | 5 vignettes/cansim.Rmd | 30 - vignettes/precompile.R |only vignettes/working_with_large_tables.Rmd |only 40 files changed, 919 insertions(+), 598 deletions(-)
Title: Using R to Install Stuff on Windows OS (Such As: R, 'Rtools',
'RStudio', 'Git', and More!)
Description: R is great for installing software. Through the 'installr'
package you can automate the updating of R (on Windows, using updateR())
and install new software. Software installation is initiated through a
GUI (just run installr()), or through functions such as: install.Rtools(),
install.pandoc(), install.git(), and many more. The updateR() command
performs the following: finding the latest R version, downloading it,
running the installer, deleting the installation file, copy and updating
old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Barry Rowlingson [ctb],
Boris Hejblum [ctb],
Dason [ctb],
Felix Schonbrodt [ctb],
G. Grothendieck [ctb],
GERGELY DAROCZI [ctb],
Heuristic Andrew [ctb],
James [ctb] (http://stackoverflow.com/users/269476/james),
Thomas Leeper [ctb] (http://thomasleeper.com/),
VitoshKa [ctb],
Yihui Xie [ctb] (http://yihui.name),
Michael Friendly [ctb] (http://datavis.ca/),
Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/),
Dieter Menne [ctb],
Tyler Hunt [ctb] (https://github.com/JackStat),
Takekatsu Hiramura [ctb] (https://github.com/hiratake55),
Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool),
Jonathan Godfrey [ctb] (https://github.com/ajrgodfrey),
Tom Allard [ctb],
ChingChuan Chen [ctb],
Jonathan Hill [ctb],
Chan-Yub Park [ctb] (https://github.com/mrchypark),
Gerhard Nachtmann [ctb],
Russ Hyde [ctb],
Lyndon D'Arcy [ctb] (https://github.com/logworthy),
Gerhard Burger [ctb] (https://github.com/burgerga),
Adrian Hordyk [ctb] (https://github.com/AdrianHordyk)
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between installr versions 0.22.0 dated 2019-08-02 and 0.23.2 dated 2021-05-08
ChangeLog | 305 ++ DESCRIPTION | 36 MD5 | 239 +- NAMESPACE | 215 - NEWS | 1739 +++++++------- NEWS.md | 1727 +++++++------- R/RStudio_CRAN_data.R | 1052 ++++---- R/create.global.library.R | 1109 ++++----- R/geo_functions.R | 474 +-- R/install.R | 3223 +++++++++++++-------------- R/install.inno.R | 110 R/installNodejs.R | 120 - R/installOpenJdk.R | 204 - R/installPython.R | 132 - R/installRtools.R |only R/installr-package.R | 71 R/is.x.R | 319 +- R/kill_pid.R | 566 ++-- R/os.manage.R | 526 ++-- R/rename_r_to_R.R | 222 - R/startup.R | 624 ++--- R/updateR.R | 1864 +++++++-------- R/xlsx2csv.R | 216 - R/zzz.R | 444 +-- README.md | 220 - TODO | 24 man/R_version_in_a_folder.Rd | 56 man/add.installr.GUI.Rd | 58 man/add_load_installr_on_startup_menu.Rd | 28 man/add_remove_installr_from_startup_menu.Rd | 28 man/add_to_.First_in_Rprofile.site.Rd | 74 man/ask.user.for.a.row.Rd | 84 man/ask.user.yn.question.Rd | 90 man/barplot_package_users_per_day.Rd | 98 man/browse.latest.R.NEWS.Rd | 49 man/check.for.updates.R.Rd | 73 man/check.integer.Rd | 76 man/checkMD5sums2.Rd | 72 man/copy.packages.between.libraries.Rd | 101 man/cranometer.Rd | 174 - man/create.global.library.Rd | 44 man/download_RStudio_CRAN_data.Rd | 119 man/fetch_tag_from_Rd.Rd | 102 man/file.name.from.url.Rd | 65 man/format_RStudio_CRAN_data.Rd | 102 man/freegeoip.Rd | 105 man/get.installed.R.folders.Rd | 77 man/get_Rscript_PID.Rd | 76 man/get_latest_r_version.Rd |only man/get_pid.Rd | 78 man/get_tasklist.Rd | 76 man/install.7zip.Rd | 97 man/install.CMake.Rd | 84 man/install.Cygwin.Rd | 66 man/install.FFmpeg.Rd | 71 man/install.GitHub.Rd | 73 man/install.GraphicsMagick.Rd | 74 man/install.ImageMagick.Rd | 73 man/install.LaTeX2RTF.Rd | 71 man/install.LyX.Rd | 83 man/install.MikTeX.Rd | 69 man/install.R.Rd | 106 man/install.RStudio.Rd | 68 man/install.Rdevel.Rd | 77 man/install.Rtools.Rd | 98 man/install.SWFTools.Rd | 75 man/install.Texmaker.Rd | 75 man/install.URL.Rd | 105 man/install.conda.Rd | 68 man/install.git.Rd | 66 man/install.inno.Rd | 74 man/install.java.Rd | 134 - man/install.nodejs.Rd | 76 man/install.notepadpp.Rd | 69 man/install.npptor.Rd | 70 man/install.packages.zip.Rd | 64 man/install.pandoc.Rd | 90 man/install.python.Rd | 81 man/installr-package.Rd | 27 man/installr.Rd | 62 man/is.RStudio.Rd | 50 man/is.Rgui.Rd | 56 man/is.empty.Rd | 106 man/is.exe.installed.Rd | 46 man/is.windows.Rd | 52 man/is.x64.Rd | 50 man/is_in_.First_in_Rprofile.site.Rd | 76 man/kill_all_Rscript_s.Rd | 90 man/kill_pid.Rd | 94 man/kill_process.Rd | 102 man/lineplot_package_downloads.Rd | 116 man/load_installr_on_startup.Rd | 56 man/most_downloaded_packages.Rd | 94 man/myip.Rd | 60 man/os.hibernate.Rd | 82 man/os.lock.Rd | 78 man/os.manage.Rd | 82 man/os.restart.Rd | 72 man/os.shutdown.Rd | 92 man/os.sleep.Rd | 82 man/package_authors.Rd | 145 - man/pkgDNLs_worldmapcolor.Rd | 100 man/read_RStudio_CRAN_data.Rd | 116 man/remove.installr.GUI.Rd | 46 man/remove_from_.First_in_Rprofile.site.Rd | 76 man/rename_r_to_R.Rd | 132 - man/require2.Rd | 66 man/restart_RGui.Rd | 48 man/rm_installr_from_startup.Rd | 58 man/source.https.Rd | 82 man/system.PATH.Rd | 44 man/turn.number.version.Rd | 46 man/turn.version.to.number.Rd | 44 man/turn.version.to.number1.Rd | 52 man/uninstall.R.Rd | 70 man/uninstall.packages.Rd | 74 man/up_folder.Rd | 50 man/updateR.Rd | 192 - man/xlsx2csv.Rd | 64 tests |only 120 files changed, 11727 insertions(+), 11246 deletions(-)
Title: Block Diagonal Extraction or Replacement
Description: Several tools for handling block-matrix diagonals and similar
constructs are implemented. Block-diagonal matrices can be extracted or removed
using two small functions implemented here. In addition, non-square matrices
are supported. Block diagonal matrices occur when two dimensions of a data set
are combined along one edge of a matrix. For example, trade-flow data in the
'decompr' and 'gvc' packages have each country-industry combination occur along
both edges of the matrix.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between diagonals versions 5.2.0 dated 2020-04-28 and 6.0.0 dated 2021-05-08
DESCRIPTION | 11 +- MD5 | 12 +- NEWS.md | 6 + README.md | 3 build/vignette.rds |binary inst/CITATION | 2 inst/doc/fatdiag.html | 236 ++++++-------------------------------------------- 7 files changed, 50 insertions(+), 220 deletions(-)
Title: Markov Chain-Based Cost-Optimal Control Charts
Description: Functions for cost-optimal control charts with a focus on health care applications. Compared to assumptions in traditional control chart theory, here, we allow random shift sizes, random repair and random sampling times. The package focuses on X-bar charts with a sample size of 1 (representing the monitoring of a single patient at a time). The methods are described in Zempleni et al. (2004) <doi:10.1002/asmb.521>, Dobi and Zempleni (2019) <doi:10.1002/qre.2518> and Dobi and Zempleni (2019) <http://ac.inf.elte.hu/Vol_049_2019/129_49.pdf>.
Author: Balazs Dobi & Andras Zempleni
Maintainer: Balazs Dobi <dobibalazs@inf.elte.hu>
Diff between Markovchart versions 2.0.0 dated 2021-04-23 and 2.0.1 dated 2021-05-08
Markovchart-2.0.0/Markovchart/R/Markovchart_functions_20210310.r |only Markovchart-2.0.1/Markovchart/DESCRIPTION | 6 +++--- Markovchart-2.0.1/Markovchart/MD5 | 8 ++++---- Markovchart-2.0.1/Markovchart/R/Markovchart_functions_20210502.r |only Markovchart-2.0.1/Markovchart/man/Markovstat.Rd | 2 +- Markovchart-2.0.1/Markovchart/man/plot.Markov_grid.Rd | 7 +++++-- 6 files changed, 13 insertions(+), 10 deletions(-)
Title: Desirable Dietary Pattern
Description: The desirable Dietary Pattern (DDP)/ PPH score
measures the variety of food consumption. The (weighted) score is calculated
based on the type of food. This package is intended to calculate
the DDP/ PPH score that is faster than traditional method via
a manual calculation by BKP (2017) <http://bkp.pertanian.go.id/storage/app/uploads/public/5bf/ca9/06b/5bfca906bc654274163456.pdf> and is simpler than the nutrition survey
<http://www.nutrisurvey.de>. The database to create weights and baseline values
is the Indonesia national survey in 2017.
Author: Weksi Budiaji [aut, cre]
Maintainer: Weksi Budiaji <budiaji@untirta.ac.id>
Diff between ddp versions 0.0.2 dated 2020-08-03 and 0.0.3 dated 2021-05-08
DESCRIPTION | 9 - MD5 | 17 +-- NAMESPACE | 3 NEWS.md |only R/valid.R |only build/vignette.rds |binary inst/doc/ddp.R | 5 inst/doc/ddp.Rmd | 12 ++ inst/doc/ddp.html | 278 +++++++++++++---------------------------------------- man/valid.Rd |only vignettes/ddp.Rmd | 12 ++ 11 files changed, 120 insertions(+), 216 deletions(-)
Title: Composite Grid Gaussian Processes
Description: Run computer experiments using the adaptive composite grid
algorithm with a Gaussian process model.
The algorithm works best when running an experiment that can evaluate thousands
of points from a deterministic computer simulation.
This package is an implementation of a forthcoming paper by Plumlee,
Erickson, Ankenman, et al. For a preprint of the paper,
contact the maintainer of this package.
Author: Collin Erickson [aut, cre],
Matthew Plumlee [aut]
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between CGGP versions 1.0.2 dated 2020-03-29 and 1.0.3 dated 2021-05-08
DESCRIPTION | 11 - MD5 | 16 - NEWS.md | 8 R/CGGP_calc_lS_cholS_valo_etc.R | 6 R/CGGP_corr_fs.R | 72 ++++--- R/CGGP_fastcalcassist_fs.R | 12 + build/vignette.rds |binary inst/doc/CGGP.html | 387 +++++++++++----------------------------- tests/testthat/testcorr.R | 139 ++++++++------ 9 files changed, 274 insertions(+), 377 deletions(-)
Title: Variable-Lag Time Series Causality Inference Framework
Description: A framework to infer causality on a pair of time series of real numbers based on variable-lag Granger causality and transfer entropy. Typically, Granger causality and transfer entropy have an assumption of a fixed and constant time delay between the cause and effect. However, for a non-stationary time series, this assumption is not true. For example, considering two time series of velocity of person A and person B where B follows A. At some time, B stops tying his shoes, then running to catch up A. The fixed-lag assumption is not true in this case. We propose a framework that allows variable-lags between cause and effect in Granger causality and transfer entropy to allow them to deal with variable-lag non-stationary time series. Please see Chainarong Amornbunchornvej, Elena Zheleva, and Tanya Berger-Wolf (2021) <doi:10.1145/3441452> when referring to this package in publications.
Author: Chainarong Amornbunchornvej [aut, cre]
(<https://orcid.org/0000-0003-3131-0370>)
Maintainer: Chainarong Amornbunchornvej <grandca@gmail.com>
Diff between VLTimeCausality versions 0.1.2 dated 2021-03-29 and 0.1.3 dated 2021-05-08
VLTimeCausality-0.1.2/VLTimeCausality/vignettes/VLTimeCausality_demo.nb.html |only VLTimeCausality-0.1.3/VLTimeCausality/DESCRIPTION | 8 VLTimeCausality-0.1.3/VLTimeCausality/MD5 | 39 +-- VLTimeCausality-0.1.3/VLTimeCausality/NEWS.md | 3 VLTimeCausality-0.1.3/VLTimeCausality/R/MultipleTSsimulation.R | 16 - VLTimeCausality-0.1.3/VLTimeCausality/R/multipleVLGranger.R | 8 VLTimeCausality-0.1.3/VLTimeCausality/R/multipleVLTransferEntropy.R | 10 VLTimeCausality-0.1.3/VLTimeCausality/README.md | 29 ++ VLTimeCausality-0.1.3/VLTimeCausality/build/vignette.rds |binary VLTimeCausality-0.1.3/VLTimeCausality/inst/CITATION | 17 - VLTimeCausality-0.1.3/VLTimeCausality/inst/doc/VLTimeCausality_demo.html | 6 VLTimeCausality-0.1.3/VLTimeCausality/man/GrangerFunc.Rd | 118 ++++----- VLTimeCausality-0.1.3/VLTimeCausality/man/MultipleSimulationVLtimeseries.Rd | 96 ++++---- VLTimeCausality-0.1.3/VLTimeCausality/man/SimpleSimulationVLtimeseries.Rd | 102 ++++---- VLTimeCausality-0.1.3/VLTimeCausality/man/VLGrangerFunc.Rd | 120 +++++----- VLTimeCausality-0.1.3/VLTimeCausality/man/VLTransferEntropy.Rd | 118 ++++----- VLTimeCausality-0.1.3/VLTimeCausality/man/checkMultipleSimulationVLtimeseries.Rd | 62 ++--- VLTimeCausality-0.1.3/VLTimeCausality/man/followingRelation.Rd | 84 +++---- VLTimeCausality-0.1.3/VLTimeCausality/man/multipleVLGrangerFunc.Rd | 102 ++++---- VLTimeCausality-0.1.3/VLTimeCausality/man/multipleVLTransferEntropy.Rd | 98 ++++---- VLTimeCausality-0.1.3/VLTimeCausality/man/plotTimeSeries.Rd | 60 ++--- 21 files changed, 562 insertions(+), 534 deletions(-)
More information about VLTimeCausality at CRAN
Permanent link
Title: Rare Variant Analysis and Genetic Simulations
Description: Rare variant association tests: burden tests (Bocher et al. 2019 <doi:10.1002/gepi.22210>) and the Sequence Kernel Association Test (Bocher et al. 2021 <doi:10.1038/s41431-020-00792-8>); and genetic simulations.
Author: Ozvan Bocher and Hervé Perdry
Maintainer: Ozvan Bocher <bocherozvan@gmail.com>
Diff between Ravages versions 0.1.3 dated 2021-04-08 and 0.1.4 dated 2021-05-08
DESCRIPTION | 8 ++--- MD5 | 40 ++++++++++++++--------------- NEWS | 3 ++ R/zzz.r | 4 +- inst/doc/Ravages_Simulations_vignette.html | 2 - inst/doc/Ravages_vignette.html | 10 +++---- man/SKAT.Rd | 4 +- man/burden.mlogit.Rd | 4 +- src/allelecounter.cpp | 1 src/allelecounter.h | 1 src/allelecounter2.cpp | 1 src/allelecounter2.h | 1 src/alleles_by_group.cpp | 1 src/count_alternative_alleles.cpp | 1 src/jaccard.cpp | 1 src/skat.cpp | 1 src/skatBootstrap.cpp | 1 src/sum_fst.cpp | 1 src/sum_fst1.cpp | 1 src/weighted_left_product.cpp | 1 src/weighted_left_product.h | 1 21 files changed, 39 insertions(+), 49 deletions(-)
Title: Useful Wrappers Around Commonly Used Functions
Description: The main functionalities of 'wrappedtools' are:
adding backticks to variable names; rounding to desired precision
with special case for p-values;
selecting columns based on pattern and storing their position, name,
and backticked name; computing and formatting of descriptive statistics
(e.g. mean±SD), comparing groups and creating publication-ready tables with
descriptive statics and p-values; creating specialized plots for correlation
or regression trees. Functions were mainly written for my own daily work or
teaching, but may be of use to others as well.
Author: Andreas Busjahn [cre, aut] (<https://orcid.org/0000-0001-9650-6919>)
Maintainer: Andreas Busjahn <andreas@busjahn.net>
Diff between wrappedtools versions 0.7.6 dated 2021-05-05 and 0.7.8 dated 2021-05-08
DESCRIPTION | 15 +++----- MD5 | 20 +++++----- NEWS.md | 8 ++++ R/pkgstart.R | 82 +++++++++++++++++++++++---------------------- R/tests.R | 4 +- README.md | 60 ++++++++++++++++++++++++++++---- inst/doc/wrappedtools.R | 11 ++++++ inst/doc/wrappedtools.Rmd | 23 ++++++++++++ inst/doc/wrappedtools.html | 45 ++++++++++++++++++++---- man/cortestR.Rd | 2 - vignettes/wrappedtools.Rmd | 23 ++++++++++++ 11 files changed, 217 insertions(+), 76 deletions(-)
Title: Fast Computation of some Matrices Useful in Statistics
Description: Small set of functions to fast computation of some matrices and operations
useful in statistics and econometrics. Currently, there are functions for efficient
computation of duplication, commutation and symmetrizer matrices with minimal storage
requirements. Some commonly used matrix decompositions (LU and LDL), basic matrix
operations (for instance, Hadamard, Kronecker products and the Sherman-Morrison formula)
and iterative solvers for linear systems are also available. In addition, the package
includes a number of common statistical procedures such as the sweep operator, weighted
mean and covariance matrix using an online algorithm, linear regression (using Cholesky,
QR, SVD, sweep operator and conjugate gradients methods), ridge regression (with optimal
selection of the ridge parameter considering the GCV procedure), functions to compute
the multivariate skewness, kurtosis, Mahalanobis distance (checking the positive
defineteness) and the Wilson-Hilferty transformation of chi squared variables. Furthermore,
the package provides interfaces to C code callable by another C code from other R packages.
Author: Felipe Osorio [aut, cre] (<https://orcid.org/0000-0002-4675-5201>),
Alonso Ogueda [aut]
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>
Diff between fastmatrix versions 0.3-81 dated 2021-02-05 and 0.3-819 dated 2021-05-08
fastmatrix-0.3-81/fastmatrix/R/cholesky.R |only fastmatrix-0.3-81/fastmatrix/R/geomean.R |only fastmatrix-0.3-81/fastmatrix/src/hadamard.f |only fastmatrix-0.3-819/fastmatrix/ChangeLog | 10 fastmatrix-0.3-819/fastmatrix/DESCRIPTION | 21 - fastmatrix-0.3-819/fastmatrix/MD5 | 65 ++- fastmatrix-0.3-819/fastmatrix/NAMESPACE | 14 fastmatrix-0.3-819/fastmatrix/R/asSymmetric.R |only fastmatrix-0.3-819/fastmatrix/R/cg.R |only fastmatrix-0.3-819/fastmatrix/R/hadamard.R | 16 fastmatrix-0.3-819/fastmatrix/R/jacobi.R |only fastmatrix-0.3-819/fastmatrix/R/ldl.R |only fastmatrix-0.3-819/fastmatrix/R/moments.R |only fastmatrix-0.3-819/fastmatrix/R/seidel.R |only fastmatrix-0.3-819/fastmatrix/R/whitening.R |only fastmatrix-0.3-819/fastmatrix/inst/CITATION | 4 fastmatrix-0.3-819/fastmatrix/inst/include/fastmatrix.h | 11 fastmatrix-0.3-819/fastmatrix/inst/include/fastmatrix_API.h | 134 ++++-- fastmatrix-0.3-819/fastmatrix/man/asSymmetric.Rd |only fastmatrix-0.3-819/fastmatrix/man/cg.Rd |only fastmatrix-0.3-819/fastmatrix/man/jacobi.Rd |only fastmatrix-0.3-819/fastmatrix/man/kurtosis.Rd | 10 fastmatrix-0.3-819/fastmatrix/man/ldl.Rd |only fastmatrix-0.3-819/fastmatrix/man/minkowski.Rd | 14 fastmatrix-0.3-819/fastmatrix/man/moments.Rd |only fastmatrix-0.3-819/fastmatrix/man/ols.Rd | 4 fastmatrix-0.3-819/fastmatrix/man/ols.fit-methods.Rd | 2 fastmatrix-0.3-819/fastmatrix/man/seidel.Rd |only fastmatrix-0.3-819/fastmatrix/man/whitening.Rd |only fastmatrix-0.3-819/fastmatrix/src/R_init_fastmatrix.c | 14 fastmatrix-0.3-819/fastmatrix/src/blas_1.c | 237 +++++++++++- fastmatrix-0.3-819/fastmatrix/src/brent.c | 4 fastmatrix-0.3-819/fastmatrix/src/cholesky.c | 2 fastmatrix-0.3-819/fastmatrix/src/cov.c | 10 fastmatrix-0.3-819/fastmatrix/src/fastmatrix.h | 37 + fastmatrix-0.3-819/fastmatrix/src/hadamard.c |only fastmatrix-0.3-819/fastmatrix/src/ldl_decomp.f |only fastmatrix-0.3-819/fastmatrix/src/linear_iterative.c |only fastmatrix-0.3-819/fastmatrix/src/norms.c | 2 fastmatrix-0.3-819/fastmatrix/src/ols.c | 71 ++- fastmatrix-0.3-819/fastmatrix/src/products.c | 6 fastmatrix-0.3-819/fastmatrix/src/ridge.c | 2 fastmatrix-0.3-819/fastmatrix/src/stats_API.c | 69 ++- fastmatrix-0.3-819/fastmatrix/src/whitening.c |only 44 files changed, 585 insertions(+), 174 deletions(-)
Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut],
Timo Bechger [aut],
Jesse Koops [aut, cre],
Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>
Diff between dexter versions 1.1.2 dated 2021-01-06 and 1.1.3 dated 2021-05-08
dexter-1.1.2/dexter/tests/testthat/test_interaction.R |only dexter-1.1.2/dexter/tests/testthat/test_oplike.r |only dexter-1.1.3/dexter/DESCRIPTION | 26 + dexter-1.1.3/dexter/MD5 | 75 ++--- dexter-1.1.3/dexter/NAMESPACE | 5 dexter-1.1.3/dexter/NEWS | 18 - dexter-1.1.3/dexter/R/RcppExports.R | 8 dexter-1.1.3/dexter/R/anon_plausible_values.R | 33 ++ dexter-1.1.3/dexter/R/data_selection.R | 3 dexter-1.1.3/dexter/R/database.R | 2 dexter-1.1.3/dexter/R/dexter.R | 6 dexter-1.1.3/dexter/R/enorm.R | 149 +++++++++- dexter-1.1.3/dexter/R/equating.R | 61 ++-- dexter-1.1.3/dexter/R/interaction_model.R | 36 +- dexter-1.1.3/dexter/R/misc.R | 85 +++++ dexter-1.1.3/dexter/R/plausible_values.R | 38 +- dexter-1.1.3/dexter/R/plots.R | 4 dexter-1.1.3/dexter/R/reparam.R | 10 dexter-1.1.3/dexter/R/resp_data.R | 4 dexter-1.1.3/dexter/R/suf_stats.R | 43 +- dexter-1.1.3/dexter/R/tia.R | 17 - dexter-1.1.3/dexter/README.md | 77 +++-- dexter-1.1.3/dexter/build/vignette.rds |binary dexter-1.1.3/dexter/inst/doc/DIF_vignette.html | 53 --- dexter-1.1.3/dexter/inst/doc/Equating.html | 57 --- dexter-1.1.3/dexter/inst/doc/Plausible_Values.html | 63 +--- dexter-1.1.3/dexter/inst/doc/Test_Individual_differences.html | 61 +--- dexter-1.1.3/dexter/inst/doc/dexter.R | 8 dexter-1.1.3/dexter/inst/doc/dexter.Rmd | 10 dexter-1.1.3/dexter/inst/doc/dexter.html | 145 ++++----- dexter-1.1.3/dexter/inst/doc/profile-plots.html | 44 -- dexter-1.1.3/dexter/man/dexter-package.Rd | 15 - dexter-1.1.3/dexter/man/fit_enorm.Rd | 5 dexter-1.1.3/dexter/man/latent_cor.Rd |only dexter-1.1.3/dexter/man/tia_tables.Rd | 4 dexter-1.1.3/dexter/src/RcppExports.cpp | 43 ++ dexter-1.1.3/dexter/src/roger.cpp | 107 ++++++- dexter-1.1.3/dexter/tests/testthat.R | 4 dexter-1.1.3/dexter/tests/testthat/test_ability.R | 40 -- dexter-1.1.3/dexter/vignettes/dexter.Rmd | 10 40 files changed, 838 insertions(+), 531 deletions(-)
Title: Analysis of Single-Cell Viral Growth Curves
Description: Aims to quantify time intensity data by using sigmoidal and
double sigmoidal curves. It fits straight lines, sigmoidal,
and double sigmoidal curves on to time vs intensity data.
Then all the fits are used to make decision on which model
best describes the data. This method was first developed
in the context of single-cell viral growth analysis (for
details, see Caglar et al. (2018) <doi:10.7717/peerj.4251>),
and the package name stands for "SIngle CEll Growth Analysis in R".
Author: M. Umut Caglar [aut],
Claus O. Wilke [aut, cre] (<https://orcid.org/0000-0002-7470-9261>)
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between sicegar versions 0.2.3 dated 2019-08-23 and 0.2.4 dated 2021-05-08
DESCRIPTION | 22 ++- MD5 | 47 ++++---- R/sicegar.R | 1 README.md | 6 - build/vignette.rds |binary inst/CITATION |only inst/doc/additional_parameters.R | 12 +- inst/doc/additional_parameters.html | 96 +++++++++++------ inst/doc/categorizing_fits.R | 14 +- inst/doc/categorizing_fits.html | 164 +++++++++++++++++------------ inst/doc/fitting_individual_models.R | 16 +- inst/doc/fitting_individual_models.html | 152 ++++++++++++++++----------- inst/doc/introduction.R | 14 +- inst/doc/introduction.html | 148 ++++++++++++++++---------- inst/doc/plotting_fitted_models.R | 6 - inst/doc/plotting_fitted_models.html | 180 ++++++++++++++++++-------------- man/categorize.Rd | 11 + man/doublesigmoidalFitFormula.Rd | 11 + man/doublesigmoidalFitFunction.Rd | 23 ++-- man/figureModelCurves.Rd | 14 +- man/fitAndCategorize.Rd | 46 ++++---- man/multipleFitFunction.Rd | 11 + man/preCategorize.Rd | 7 - man/sameSourceDataCheck.Rd | 3 man/sigmoidalFitFunction.Rd | 14 +- 25 files changed, 615 insertions(+), 403 deletions(-)
Title: WHOIS Server Querying
Description: Queries data from WHOIS servers.
Author: Brad Cable
Maintainer: Brad Cable <brad@bcable.net>
Diff between Rwhois versions 1.0.4 dated 2020-04-16 and 1.0.5 dated 2021-05-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/functions.R | 5 +++-- README.md | 2 +- 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Visualization of a Correlation Matrix
Description: A graphical display of a correlation matrix or general matrix.
It also contains some algorithms to do matrix reordering. In addition,
corrplot is good at details, including choosing color, text labels,
color labels, layout, etc.
Author: Taiyun Wei [cre, aut],
Viliam Simko [aut],
Michael Levy [ctb],
Yihui Xie [ctb],
Yan Jin [ctb],
Jeff Zemla [ctb],
Moritz Freidank [ctb],
Jun Cai [ctb],
Tomas Protivinsky [ctb]
Maintainer: Taiyun Wei <weitaiyun@gmail.com>
Diff between corrplot versions 0.84 dated 2017-10-16 and 0.87 dated 2021-05-08
DESCRIPTION | 24 LICENSE |only MD5 | 71 - NAMESPACE | 24 R/colorlegend.R | 210 +-- R/cor-mtest.R | 90 - R/corrMatOrder.R | 158 +- R/corrRect.R | 52 R/corrRect.hclust.R | 90 - R/corrplot-package.R | 86 - R/corrplot.R | 2015 ++++++++++++++++++------------------ R/corrplot.mixed.R | 161 +- build/vignette.rds |binary inst/CITATION | 48 inst/NEWS | 178 +-- inst/doc/corrplot-intro.R | 408 +++---- inst/doc/corrplot-intro.Rmd | 698 ++++++------ inst/doc/corrplot-intro.html | 1114 +++++++++---------- man/colorlegend.Rd | 152 +- man/cor.mtest.Rd | 68 - man/corrMatOrder.Rd | 157 +- man/corrRect.Rd | 120 +- man/corrRect.hclust.Rd | 141 +- man/corrplot-package.Rd | 80 - man/corrplot.Rd | 950 ++++++++-------- man/corrplot.mixed.Rd | 140 +- tests/testthat.R | 8 tests/testthat/test-colorlegend.R | 112 +- tests/testthat/test-cor-mtest.R | 50 tests/testthat/test-corrplot.R | 470 ++++---- vignettes/corrplot-intro.Rmd | 698 ++++++------ vignettes/example-colorlegend.R | 48 vignettes/example-corrMatOrder.R | 56 - vignettes/example-corrRect.R | 62 - vignettes/example-corrRect.hclust.R | 62 - vignettes/example-corrplot.R | 372 +++--- vignettes/example-corrplot.mixed.R | 26 37 files changed, 4662 insertions(+), 4537 deletions(-)
Title: Data Structures for Single Cell Data
Description: Defines S4 classes for single-cell genomic data and associated
information, such as dimensionality reduction embeddings, nearest-neighbor
graphs, and spatially-resolved coordinates. Provides data access methods and
R-native hooks to ensure the Seurat object is familiar to other R users. See
Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>,
Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>,
and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for
more details.
Author: Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>),
Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>),
Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>),
Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>),
Jeff Farrell [ctb],
Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>),
Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>),
Patrick Roelli [ctb],
Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)
Maintainer: Paul Hoffman <seurat@nygenome.org>
Diff between SeuratObject versions 4.0.0 dated 2021-01-15 and 4.0.1 dated 2021-05-08
SeuratObject-4.0.0/SeuratObject/README.md |only SeuratObject-4.0.1/SeuratObject/DESCRIPTION | 28 SeuratObject-4.0.1/SeuratObject/MD5 | 35 - SeuratObject-4.0.1/SeuratObject/NAMESPACE | 9 SeuratObject-4.0.1/SeuratObject/NEWS.md |only SeuratObject-4.0.1/SeuratObject/R/assay.R | 131 ---- SeuratObject-4.0.1/SeuratObject/R/generics.R | 17 SeuratObject-4.0.1/SeuratObject/R/seurat.R | 386 ++---------- SeuratObject-4.0.1/SeuratObject/R/utils.R | 90 +- SeuratObject-4.0.1/SeuratObject/R/zzz.R | 24 SeuratObject-4.0.1/SeuratObject/man/Assay-methods.Rd | 24 SeuratObject-4.0.1/SeuratObject/man/AttachDeps.Rd |only SeuratObject-4.0.1/SeuratObject/man/CellsByIdentities.Rd | 5 SeuratObject-4.0.1/SeuratObject/man/CreateAssayObject.Rd | 4 SeuratObject-4.0.1/SeuratObject/man/CreateSeuratObject.Rd | 5 SeuratObject-4.0.1/SeuratObject/man/IsMatrixEmpty.Rd |only SeuratObject-4.0.1/SeuratObject/man/Seurat-methods.Rd | 35 + SeuratObject-4.0.1/SeuratObject/man/SeuratObject-package.Rd | 8 SeuratObject-4.0.1/SeuratObject/man/Version.Rd |only SeuratObject-4.0.1/SeuratObject/man/WhichCells.Rd | 13 SeuratObject-4.0.1/SeuratObject/man/as.sparse.Rd | 5 21 files changed, 350 insertions(+), 469 deletions(-)
Title: Robust Estimation of the Proportion of Treatment Effect
Explained by Surrogate Marker Information
Description: Provides functions to estimate the proportion of treatment effect on the primary outcome that is explained by the treatment effect on the surrogate marker.
Author: Layla Parast
Maintainer: Layla Parast <parast@rand.org>
Diff between Rsurrogate versions 2.0 dated 2016-10-20 and 3.0 dated 2021-05-08
DESCRIPTION | 11 MD5 | 38 +- NAMESPACE | 5 R/Functions_Rsurrogate.R | 787 ++++++++++++++++++++++++++++++++++++++---- data/d_example_me.RData |only data/d_example_multiple.RData |only man/Aug.R.s.surv.estimate.Rd | 11 man/R.multiple.surv.Rd |only man/R.s.estimate.Rd | 12 man/R.s.estimate.me.Rd |only man/R.s.surv.estimate.Rd | 12 man/R.t.surv.estimate.Rd | 9 man/calculate.var.np.Rd |only man/censor.weight.Rd | 7 man/d_example_me.Rd |only man/d_example_multiple.Rd |only man/delta.multiple.surv.Rd |only man/delta.s.estimate.Rd | 2 man/delta.s.surv.estimate.Rd | 19 - man/delta.surv.estimate.Rd | 5 man/delta.t.surv.estimate.Rd | 9 man/fieller.calculate.me.Rd |only man/me.variance.estimate.Rd |only man/pred.smooth.Rd | 4 man/pred.smooth.surv.Rd | 16 25 files changed, 837 insertions(+), 110 deletions(-)
Title: General Resampling Infrastructure
Description: Classes and functions to create and summarize different types of resampling objects (e.g. bootstrap, cross-validation).
Author: Julia Silge [aut, cre] (<https://orcid.org/0000-0002-3671-836X>),
Fanny Chow [aut],
Max Kuhn [aut],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Julia Silge <julia.silge@rstudio.com>
Diff between rsample versions 0.0.9 dated 2021-02-17 and 0.1.0 dated 2021-05-08
rsample-0.0.9/rsample/vignettes/Applications/Nested_Resampling.Rmd |only rsample-0.1.0/rsample/DESCRIPTION | 19 +- rsample-0.1.0/rsample/LICENSE |only rsample-0.1.0/rsample/MD5 | 72 +++++----- rsample-0.1.0/rsample/NEWS.md | 16 ++ rsample-0.1.0/rsample/R/apparent.R | 9 - rsample-0.1.0/rsample/R/boot.R | 21 +- rsample-0.1.0/rsample/R/caret.R | 14 - rsample-0.1.0/rsample/R/gather.R | 20 ++ rsample-0.1.0/rsample/R/initial_split.R | 7 rsample-0.1.0/rsample/R/make_strata.R | 38 +++-- rsample-0.1.0/rsample/R/mc.R | 33 ++-- rsample-0.1.0/rsample/R/misc.R | 7 rsample-0.1.0/rsample/R/slide.R | 4 rsample-0.1.0/rsample/R/validation_split.R | 13 - rsample-0.1.0/rsample/R/vfold.R | 24 +-- rsample-0.1.0/rsample/build/vignette.rds |binary rsample-0.1.0/rsample/inst/doc/Working_with_rsets.html | 29 ++-- rsample-0.1.0/rsample/inst/doc/rsample.html | 1 rsample-0.1.0/rsample/man/bootstraps.Rd | 25 ++- rsample-0.1.0/rsample/man/figures/lifecycle-archived.svg |only rsample-0.1.0/rsample/man/figures/lifecycle-defunct.svg |only rsample-0.1.0/rsample/man/figures/lifecycle-deprecated.svg |only rsample-0.1.0/rsample/man/figures/lifecycle-experimental.svg |only rsample-0.1.0/rsample/man/figures/lifecycle-maturing.svg |only rsample-0.1.0/rsample/man/figures/lifecycle-questioning.svg |only rsample-0.1.0/rsample/man/figures/lifecycle-stable.svg |only rsample-0.1.0/rsample/man/figures/lifecycle-superseded.svg |only rsample-0.1.0/rsample/man/gather.rset.Rd | 16 ++ rsample-0.1.0/rsample/man/initial_split.Rd | 11 + rsample-0.1.0/rsample/man/make_strata.Rd | 4 rsample-0.1.0/rsample/man/mc_cv.Rd | 18 +- rsample-0.1.0/rsample/man/slide-resampling.Rd | 4 rsample-0.1.0/rsample/man/validation_split.Rd | 11 + rsample-0.1.0/rsample/man/vfold_cv.Rd | 17 +- rsample-0.1.0/rsample/tests/testthat/test_initial.R | 22 +++ rsample-0.1.0/rsample/tests/testthat/test_mc.R | 6 rsample-0.1.0/rsample/tests/testthat/test_strata.R | 42 +++++ rsample-0.1.0/rsample/tests/testthat/test_validation.R | 4 rsample-0.1.0/rsample/tests/testthat/test_vfold.R | 6 rsample-0.1.0/rsample/vignettes/Applications/Intervals.Rmd | 2 rsample-0.1.0/rsample/vignettes/Applications/Recipes_and_rsample.Rmd | 4 42 files changed, 350 insertions(+), 169 deletions(-)
Title: Factorization of Sparse Counts Matrices Through Poisson
Likelihood
Description: Creates a low-rank factorization of a sparse counts matrix by maximizing Poisson likelihood with l1/l2 regularization
with all non-negative latent factors (e.g. for recommender systems or topic modeling) (Cortes, (2018) <arXiv:1811.01908>).
Similar to hierarchical Poisson factorization, but follows an optimization-based approach with regularization instead of a
hierarchical structure, and is fit through gradient-based methods instead of variational inference.
Author: David Cortes [aut, cre, cph], Jean-Sebastien Roy [cph], Stephen Nash [cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between poismf versions 0.3.0 dated 2021-04-06 and 0.3.0-1 dated 2021-05-08
poismf-0.3.0-1/poismf/DESCRIPTION | 10 poismf-0.3.0-1/poismf/MD5 | 17 - poismf-0.3.0-1/poismf/NAMESPACE | 6 poismf-0.3.0-1/poismf/R/poismf.R | 395 +++++++------------------ poismf-0.3.0-1/poismf/configure | 18 - poismf-0.3.0-1/poismf/man/poismf.Rd | 25 - poismf-0.3.0-1/poismf/man/poismf_unsafe.Rd | 7 poismf-0.3.0-1/poismf/man/poisson.llk.Rd | 4 poismf-0.3.0-1/poismf/man/predict.poismf.Rd | 2 poismf-0.3.0/poismf/man/get.all.predictions.Rd |only 10 files changed, 164 insertions(+), 320 deletions(-)
Title: Computations over Distributed Data without Aggregation
Description: Implementing algorithms and fitting models when sites (possibly remote) share
computation summaries rather than actual data over HTTP with a master R process (using
'opencpu', for example). A stratified Cox model and a singular value decomposition are
provided. The former makes direct use of code from the R 'survival' package. (That is,
the underlying Cox model code is derived from that in the R 'survival' package.)
Sites may provide data via several means: CSV files, Redcap API, etc. An extensible
design allows for new methods to be added in the future and includes facilities
for local prototyping and testing. Web applications are provided (via 'shiny') for
the implemented methods to help in designing and deploying the computations.
Author: Balasubramanian Narasimhan [aut, cre],
Marina Bendersky [aut],
Sam Gross [aut],
Terry M. Therneau [ctb],
Thomas Lumley [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between distcomp versions 1.1 dated 2019-09-23 and 1.3-1 dated 2021-05-08
distcomp-1.1/distcomp/inst/doc_src/examples.md |only distcomp-1.1/distcomp/inst/ex/README.md |only distcomp-1.1/distcomp/inst/stuff |only distcomp-1.1/distcomp/man/createInstanceObject.Rd |only distcomp-1.3-1/distcomp/DESCRIPTION | 14 distcomp-1.3-1/distcomp/MD5 | 155 distcomp-1.3-1/distcomp/NAMESPACE | 26 distcomp-1.3-1/distcomp/NEWS.md |only distcomp-1.3-1/distcomp/R/coxstuff.R | 283 distcomp-1.3-1/distcomp/R/distcomp.R | 631 distcomp-1.3-1/distcomp/R/master.R |only distcomp-1.3-1/distcomp/R/ncp.R |only distcomp-1.3-1/distcomp/R/querycount.R |only distcomp-1.3-1/distcomp/R/survivalstuff.R | 25 distcomp-1.3-1/distcomp/R/svdstuff.R | 226 distcomp-1.3-1/distcomp/README.md | 31 distcomp-1.3-1/distcomp/build/vignette.rds |binary distcomp-1.3-1/distcomp/inst/doc/examples.html | 2681 ++- distcomp-1.3-1/distcomp/inst/doc/examples.pdf |binary distcomp-1.3-1/distcomp/inst/doc/prototyping.R | 38 distcomp-1.3-1/distcomp/inst/doc/prototyping.Rmd | 4 distcomp-1.3-1/distcomp/inst/doc/prototyping.html | 126 distcomp-1.3-1/distcomp/inst/doc_src/examples.Rmd | 107 distcomp-1.3-1/distcomp/inst/ex/README.Rmd | 17 distcomp-1.3-1/distcomp/inst/ex/README.html | 579 distcomp-1.3-1/distcomp/inst/ex/STCoxMaster.R | 12 distcomp-1.3-1/distcomp/inst/ex/STCoxMaster.RDS |only distcomp-1.3-1/distcomp/inst/ex/STCoxMaster.Rout | 45 distcomp-1.3-1/distcomp/inst/ex/STCoxSetup.Rout | 57 distcomp-1.3-1/distcomp/inst/ex/STCoxTest.rds |binary distcomp-1.3-1/distcomp/inst/ex/SVDMaster.R | 12 distcomp-1.3-1/distcomp/inst/ex/SVDMaster.RDS |only distcomp-1.3-1/distcomp/inst/ex/SVDMaster.Rout | 41 distcomp-1.3-1/distcomp/inst/ex/SVDSetup.Rout | 72 distcomp-1.3-1/distcomp/inst/ex/SVDTestDefn.rds |binary distcomp-1.3-1/distcomp/inst/ex/svd-example.R | 44 distcomp-1.3-1/distcomp/inst/ex/svd-example.Rout | 7916 ---------- distcomp-1.3-1/distcomp/inst/ex/uis-example.R | 15 distcomp-1.3-1/distcomp/inst/ex/uis-example.Rout | 173 distcomp-1.3-1/distcomp/inst/webApps/definitionApp/defineNewCoxModel/server.R | 1 distcomp-1.3-1/distcomp/inst/webApps/definitionApp/defineNewQueryCountModel |only distcomp-1.3-1/distcomp/inst/webApps/definitionApp/defineNewSVDModel/server.R | 1 distcomp-1.3-1/distcomp/inst/webApps/definitionApp/server.R | 4 distcomp-1.3-1/distcomp/inst/webApps/definitionApp/ui.R | 5 distcomp-1.3-1/distcomp/inst/webApps/setupMasterApp/server-working.R |only distcomp-1.3-1/distcomp/inst/webApps/setupMasterApp/server.R | 224 distcomp-1.3-1/distcomp/inst/webApps/setupMasterApp/ui-working.R |only distcomp-1.3-1/distcomp/inst/webApps/setupMasterApp/ui.R | 20 distcomp-1.3-1/distcomp/inst/webApps/setupNCPApp |only distcomp-1.3-1/distcomp/inst/webApps/setupWorkerApp/setupCoxWorker/server.R | 1 distcomp-1.3-1/distcomp/inst/webApps/setupWorkerApp/setupQueryCountWorker |only distcomp-1.3-1/distcomp/man/CoxMaster.Rd | 159 distcomp-1.3-1/distcomp/man/CoxWorker.Rd | 158 distcomp-1.3-1/distcomp/man/HEMaster.Rd |only distcomp-1.3-1/distcomp/man/HEQueryCountMaster.Rd |only distcomp-1.3-1/distcomp/man/HEQueryCountWorker.Rd |only distcomp-1.3-1/distcomp/man/NCP.Rd |only distcomp-1.3-1/distcomp/man/QueryCountMaster.Rd |only distcomp-1.3-1/distcomp/man/QueryCountWorker.Rd |only distcomp-1.3-1/distcomp/man/SVDMaster.Rd | 210 distcomp-1.3-1/distcomp/man/SVDWorker.Rd | 233 distcomp-1.3-1/distcomp/man/availableComputations.Rd | 2 distcomp-1.3-1/distcomp/man/createHEWorkerInstance.Rd |only distcomp-1.3-1/distcomp/man/createNCPInstance.Rd |only distcomp-1.3-1/distcomp/man/createWorkerInstance.Rd |only distcomp-1.3-1/distcomp/man/dccoxph.Rd | 22 distcomp-1.3-1/distcomp/man/defineNewComputation.Rd | 4 distcomp-1.3-1/distcomp/man/destroyInstanceObject.Rd | 2 distcomp-1.3-1/distcomp/man/distcomp.Rd | 5 distcomp-1.3-1/distcomp/man/distcompSetup.Rd | 22 distcomp-1.3-1/distcomp/man/executeHEMethod.Rd |only distcomp-1.3-1/distcomp/man/executeMethod.Rd | 16 distcomp-1.3-1/distcomp/man/generateId.Rd | 4 distcomp-1.3-1/distcomp/man/getComputationInfo.Rd | 2 distcomp-1.3-1/distcomp/man/getConfig.Rd | 2 distcomp-1.3-1/distcomp/man/makeDefinition.Rd | 2 distcomp-1.3-1/distcomp/man/makeHEMaster.Rd |only distcomp-1.3-1/distcomp/man/makeMaster.Rd | 16 distcomp-1.3-1/distcomp/man/makeNCP.Rd |only distcomp-1.3-1/distcomp/man/makeWorker.Rd | 22 distcomp-1.3-1/distcomp/man/resetComputationInfo.Rd | 2 distcomp-1.3-1/distcomp/man/runDistcompApp.Rd | 3 distcomp-1.3-1/distcomp/man/saveNewComputation.Rd | 6 distcomp-1.3-1/distcomp/man/saveNewNCP.Rd |only distcomp-1.3-1/distcomp/man/setComputationInfo.Rd | 2 distcomp-1.3-1/distcomp/man/setupMaster.Rd | 4 distcomp-1.3-1/distcomp/man/setupWorker.Rd | 4 distcomp-1.3-1/distcomp/man/uploadNewComputation.Rd | 4 distcomp-1.3-1/distcomp/man/uploadNewNCP.Rd |only distcomp-1.3-1/distcomp/man/writeCode.Rd | 17 distcomp-1.3-1/distcomp/vignettes/prototyping.Rmd | 4 91 files changed, 4677 insertions(+), 9836 deletions(-)
Title: A 'ggplot2' Implement of Venn Diagram
Description: Easy-to-use functions to generate 2-7 sets Venn plot in publication quality.
'ggVennDiagram' plot Venn using well-defined geometry dataset and 'ggplot2'. The shapes of 2-4 sets
Venn use circles and ellipses, while the shapes of 4-7 sets Venn use irregular polygons (4 has both forms), which
are developed and imported from another package 'venn', authored by Adrian Dusa. We provided internal functions to
integrate shape data with user provided sets data, and calculated the geometry of every regions/intersections
of them, then separately plot Venn in three components: set edges, set labels, and regions.
From version 1.0, it is possible to customize these components as you demand in ordinary 'ggplot2' grammar.
Author: Chun-Hui Gao [aut, cre] (<https://orcid.org/0000-0002-1445-7939>),
Guangchuang Yu [ctb] (<https://orcid.org/0000-0002-6485-8781>),
Adrian Dusa [ctb]
Maintainer: Chun-Hui Gao <gaospecial@gmail.com>
Diff between ggVennDiagram versions 1.0.7 dated 2021-04-28 and 1.1.0 dated 2021-05-07
DESCRIPTION | 20 +++- MD5 | 43 +++++---- NAMESPACE | 66 +++++++-------- NEWS.md | 13 ++- R/Construct.R | 4 R/ggVennDiagram.R | 130 ++++++++++++++++++++++++------ R/plot_shapes.R | 32 +++++-- R/process_data.R | 3 R/shape_generator.R | 6 + README.md | 17 +++ man/Venn-class.Rd | 4 man/ellipse.Rd | 4 man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-4-2.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/get_shape_data.Rd | 3 man/ggVennDiagram.Rd | 32 ++++++- man/plot_shapes.Rd | 10 ++ man/plot_venn.Rd | 43 +++++++-- man/vennplot-shapes.Rd |only 23 files changed, 311 insertions(+), 119 deletions(-)
Title: Apply Sojourn Methods for Processing ActiGraph Accelerometer
Data
Description: Provides a simple way for utilizing Sojourn methods for
accelerometer processing, as detailed in Lyden K, Keadle S,
Staudenmayer J, & Freedson P (2014) <doi:10.1249/MSS.0b013e3182a42a2d>,
Ellingson LD, Schwabacher IJ, Kim Y, Welk GJ, & Cook DB (2016)
<doi:10.1249/MSS.0000000000000915>, and Hibbing PR, Ellingson LD,
Dixon PM, & Welk GJ (2018) <doi:10.1249/MSS.0000000000001486>.
Author: Paul R. Hibbing [aut, cre],
Kate Lyden [aut],
Isaac J. Schwabacher [aut]
Maintainer: Paul R. Hibbing <paulhibbing@gmail.com>
Diff between Sojourn versions 1.0.2 dated 2021-04-12 and 1.1.0 dated 2021-05-07
Sojourn-1.0.2/Sojourn/R/RcppExports.R |only Sojourn-1.0.2/Sojourn/man/combine.sojourns.Rd |only Sojourn-1.1.0/Sojourn/DESCRIPTION | 14 Sojourn-1.1.0/Sojourn/MD5 | 46 - Sojourn-1.1.0/Sojourn/NAMESPACE | 2 Sojourn-1.1.0/Sojourn/NEWS.md | 5 Sojourn-1.1.0/Sojourn/R/SIP_Functions.R | 77 -- Sojourn-1.1.0/Sojourn/R/SIP_Soj_3x.R | 24 Sojourn-1.1.0/Sojourn/R/Sojourn.R | 6 Sojourn-1.1.0/Sojourn/R/Utils.R | 61 + Sojourn-1.1.0/Sojourn/R/combine_sojourns.R |only Sojourn-1.1.0/Sojourn/R/compute_bouts_info.R | 16 Sojourn-1.1.0/Sojourn/R/soj_1x_original.R | 20 Sojourn-1.1.0/Sojourn/R/soj_3x_original.R | 653 +++--------------- Sojourn-1.1.0/Sojourn/R/sysdata.rda |only Sojourn-1.1.0/Sojourn/R/youth_apply_sojourn.R | 31 Sojourn-1.1.0/Sojourn/R/youth_get_sojourns.R | 14 Sojourn-1.1.0/Sojourn/README.md | 3 Sojourn-1.1.0/Sojourn/man/apply_youth_sojourn.Rd | 21 Sojourn-1.1.0/Sojourn/man/combine_sojourns.Rd |only Sojourn-1.1.0/Sojourn/man/compute.bouts.info.Rd | 16 Sojourn-1.1.0/Sojourn/man/get_youth_sojourns.Rd | 2 Sojourn-1.1.0/Sojourn/man/prep_nnet_soj3x_original.Rd |only Sojourn-1.1.0/Sojourn/man/soj_1x_original.Rd | 6 Sojourn-1.1.0/Sojourn/man/soj_3x_original.Rd | 13 Sojourn-1.1.0/Sojourn/man/sojourn_3x_SIP.Rd | 4 Sojourn-1.1.0/Sojourn/tests/testthat/test_sojOutput.R | 7 27 files changed, 305 insertions(+), 736 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Lukas A. Widmer [aut],
Andrew Bean [aut],
Trustees of Columbia University [cph] (R/stanmodels.R, configure,
configure.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.6-5 dated 2020-05-07 and 0.7-0 dated 2021-05-07
DESCRIPTION | 15 MD5 | 70 + NAMESPACE | 14 R/OncoBayes2-package.R | 8 R/blrm_exnex.R | 16 R/blrm_formula_linear.R | 76 +- R/blrm_formula_saturating.R | 72 +- R/blrm_trial.R | 291 ++++++-- R/log_sum_exp.R |only R/plot_blrm.R |only R/predictive_interval.R | 8 R/summary.R | 256 ++++++- R/sysdata.rda |binary inst/NEWS | 12 inst/doc/OncoBayes2.pdf |binary inst/doc/introduction.R | 333 ++------- inst/doc/introduction.Rmd | 515 ++++++-------- inst/doc/introduction.html | 1058 ++++++++++++++++-------------- inst/sbc/calibration.md5 | 6 inst/sbc/make_reference_rankhist.R | 10 inst/sbc/sbc_example_models.R | 9 inst/sbc/sbc_report.R | 232 +----- inst/sbc/sbc_report.html |only inst/sbc/sbc_report_plots.R |only inst/sbc/sbc_tools.R | 13 man/blrm_formula_linear.Rd | 8 man/blrm_formula_saturating.Rd | 8 man/blrm_trial.Rd | 2 man/dot-marginSums.Rd |only man/dot-proportions.Rd |only man/dot-validate_group_stratum_nesting.Rd |only man/log_mean_exp.Rd |only man/log_sum_exp.Rd |only man/plot_blrm.Rd |only man/summary.blrm_trial.Rd | 14 man/summary.blrmfit.Rd | 29 tests/testthat/helper-plots.R |only tests/testthat/test-blrm_exnex.R | 94 ++ tests/testthat/test-blrm_trial.R | 350 +++++++++ tests/testthat/test-plots.R |only tools/build_ref_pdf.sh | 1 vignettes/introduction.Rmd | 515 ++++++-------- 42 files changed, 2318 insertions(+), 1717 deletions(-)
Title: Geospatial Queries Using 'PyMongo'
Description: Utilizes methods of the 'PyMongo' 'Python' library to initialize, insert and query 'GeoJson' data (see <https://github.com/mongodb/mongo-python-driver> for more information on 'PyMongo'). Furthermore, it allows the user to validate 'GeoJson' objects and to use the console for 'MongoDB' (bulk) commands. The 'reticulate' package provides the 'R' interface to 'Python' modules, classes and functions.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between GeoMongo versions 1.0.1 dated 2017-09-09 and 1.0.2 dated 2021-05-07
DESCRIPTION | 18 MD5 | 40 - NAMESPACE | 5 NEWS.md | 6 R/package.R | 35 - R/utils.R | 45 - README.md | 10 build/vignette.rds |binary inst/CITATION |only inst/doc/the_GeoMongo_package.R | 82 +- inst/doc/the_GeoMongo_package.Rmd | 4 inst/doc/the_GeoMongo_package.html | 1141 ++++++++++++++++++++++--------------- man/geomongo.Rd | 191 ++++-- man/json_schema_validator.Rd | 34 - man/mongodb_console.Rd | 4 tests |only vignettes/the_GeoMongo_package.Rmd | 4 17 files changed, 1011 insertions(+), 608 deletions(-)
Title: Generate Standardized Data
Description: Creates simulated data from structural equation models with standardized loading. Data generation methods are described in Schneider (2013) <doi:10.1177/0734282913478046>.
Author: W. Joel Schneider [aut, cre] (<https://orcid.org/0000-0002-8393-5316>)
Maintainer: W. Joel Schneider <w.joel.schneider@gmail.com>
Diff between simstandard versions 0.6.2 dated 2021-01-21 and 0.6.3 dated 2021-05-07
DESCRIPTION | 8 - MD5 | 28 ++--- NAMESPACE | 4 NEWS.md | 11 ++ R/main.R | 185 ++++++++++++++++++++++++++++++++-- README.md | 12 +- build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/simstandard_tutorial.html | 39 ++----- man/add_composite_scores.Rd | 12 ++ man/add_factor_scores.Rd | 3 man/get_factor_score_coefficients.Rd |only man/get_factor_score_validity.Rd |only man/get_factor_score_validity_se.Rd |only man/get_model_implied_correlations.Rd | 2 man/get_model_names.Rd |only tests/testthat/testthat.R | 20 +++ 17 files changed, 266 insertions(+), 59 deletions(-)
Title: Download, Compile and Link 'OpenBLAS' Library with R
Description: The 'ropenblas' package (<https://prdm0.github.io/ropenblas/>) is useful for users of any 'GNU/Linux' distribution. It will be possible to download, compile and link the 'OpenBLAS' library (<https://www.openblas.net/>) with the R language, always by the same procedure, regardless of the 'GNU/Linux' distribution used. With the 'ropenblas' package it is possible to download, compile and link the latest version of the 'OpenBLAS' library even the repositories of the 'GNU/Linux' distribution used do not include the latest versions of 'OpenBLAS'. If of interest, older versions of the 'OpenBLAS' library may be considered. Linking R with an optimized version of 'BLAS' (<http://www.netlib.org/blas/>) may improve the computational performance of R code. The 'OpenBLAS' library is an optimized implementation of 'BLAS' that can be easily linked to R with the 'ropenblas' package.
Author: Pedro Rafael D. Marinho [aut, cre]
(<https://orcid.org/0000-0003-1591-8300>)
Maintainer: Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>
Diff between ropenblas versions 0.2.9 dated 2021-02-16 and 0.2.10 dated 2021-05-07
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- NAMESPACE | 3 +++ NEWS.md | 8 +++++++- R/ropenblas.R | 30 ++++++++++++------------------ 5 files changed, 33 insertions(+), 29 deletions(-)
Title: Collecting Counter Strike Global Offensive Data
Description: An implementation of calls designed to collect and organize in an easy way the data from the Steam API specifically for the Counter-Strike Global Offensive Game (CS Go) <https://developer.valvesoftware.com/wiki/Steam_Web_API>.
Author: Adson Costanzi [aut, cre] (<https://orcid.org/0000-0002-5210-2952>),
Rodrigo Fontoura [aut] (<https://orcid.org/0000-0002-8156-3424>)
Maintainer: Adson Costanzi <adsoncostanzi32@gmail.com>
Diff between CSGo versions 0.5.2 dated 2021-03-27 and 0.6.7 dated 2021-05-07
CSGo-0.5.2/CSGo/data/suport.rda |only CSGo-0.5.2/CSGo/man/suport.Rd |only CSGo-0.6.7/CSGo/DESCRIPTION | 8 +-- CSGo-0.6.7/CSGo/MD5 | 43 +++++++++-------- CSGo-0.6.7/CSGo/R/csgo_api_profile.R | 23 +++++++-- CSGo-0.6.7/CSGo/R/data.R | 31 ++++++++++++ CSGo-0.6.7/CSGo/R/get_stats_friends.R | 75 +++++++++++++++---------------- CSGo-0.6.7/CSGo/R/get_stats_user.R | 14 +++-- CSGo-0.6.7/CSGo/R/globals.R | 2 CSGo-0.6.7/CSGo/README.md | 2 CSGo-0.6.7/CSGo/build/vignette.rds |binary CSGo-0.6.7/CSGo/data/map_pictures.rda |only CSGo-0.6.7/CSGo/data/support.rda |only CSGo-0.6.7/CSGo/data/weapon_pictures.rda |only CSGo-0.6.7/CSGo/inst/doc/auth.R | 6 +- CSGo-0.6.7/CSGo/inst/doc/auth.Rmd | 8 +-- CSGo-0.6.7/CSGo/inst/doc/auth.html | 18 +++++-- CSGo-0.6.7/CSGo/inst/doc/usecase.Rmd | 8 +-- CSGo-0.6.7/CSGo/inst/doc/usecase.html | 20 +++++--- CSGo-0.6.7/CSGo/man/csgo_api_profile.Rd | 13 ++++- CSGo-0.6.7/CSGo/man/get_stats_friends.Rd | 7 ++ CSGo-0.6.7/CSGo/man/map_pictures.Rd |only CSGo-0.6.7/CSGo/man/support.Rd |only CSGo-0.6.7/CSGo/man/weapon_pictures.Rd |only CSGo-0.6.7/CSGo/vignettes/auth.Rmd | 8 +-- CSGo-0.6.7/CSGo/vignettes/img/logo.png |only CSGo-0.6.7/CSGo/vignettes/usecase.Rmd | 8 +-- 27 files changed, 188 insertions(+), 106 deletions(-)
Title: Regularized Greedy Forest
Description: Regularized Greedy Forest wrapper of the 'Regularized Greedy Forest' <https://github.com/RGF-team/rgf/tree/master/python-package> 'python' package, which also includes a Multi-core implementation (FastRGF) <https://github.com/RGF-team/rgf/tree/master/FastRGF>.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>),
Ryosuke Fukatani [cph] (Author of the python wrapper of the
'Regularized Greedy Forest' machine learning algorithm),
Nikita Titov [cph] (Author of the python wrapper of the 'Regularized
Greedy Forest' machine learning algorithm),
Tong Zhang [cph] (Author of the 'Regularized Greedy Forest' and of the
Multi-core implementation of Regularized Greedy Forest machine
learning algorithm),
Rie Johnson [cph] (Author of the 'Regularized Greedy Forest' machine
learning algorithm)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between RGF versions 1.0.7 dated 2021-03-16 and 1.0.8 dated 2021-05-07
DESCRIPTION | 15 ++++----- MD5 | 39 ++++++++++++----------- NEWS.md | 9 +++++ R/FastRGF_Classifier.R | 8 ++-- R/FastRGF_Regressor.R | 4 +- R/RGF_Classifier.R | 4 +- R/RGF_Regressor.R | 4 +- R/TO_scipy_sparse.R | 4 +- R/mat_2scipy_sparse.R | 4 +- R/package.R | 62 +++++++------------------------------- inst/CITATION |only inst/doc/the_RGF_package.html | 4 +- man/FastRGF_Classifier.Rd | 8 ++-- man/FastRGF_Regressor.Rd | 4 +- man/RGF_Classifier.Rd | 4 +- man/RGF_Regressor.Rd | 4 +- man/TO_scipy_sparse.Rd | 4 +- man/mat_2scipy_sparse.Rd | 4 +- tests/testthat/helper-skip.R | 4 +- tests/testthat/setup.R | 4 +- tests/testthat/test-RGF_package.R | 19 ----------- 21 files changed, 83 insertions(+), 129 deletions(-)
Title: Probabilistic Sex Estimate using Logistic Regression, Based on
VISual Traits of the Human Os Coxae
Description: An R-Shiny application implementing a method of sexing the human os coxae based on logistic regressions and Bruzek's nonmetric traits <doi:10.1002/ajpa.23855>.
Author: Frédéric Santos [aut, cre] (<https://orcid.org/0000-0003-1445-3871>),
Élodie Bernardeau [ctb]
Maintainer: Frédéric Santos <frederic.santos@u-bordeaux.fr>
Diff between PELVIS versions 2.0.2 dated 2020-06-25 and 2.0.3 dated 2021-05-07
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NAMESPACE | 3 ++- NEWS.md | 5 +++++ build |only man/dataframe_sexing.Rd | 14 +++++++------- man/start_pelvis.Rd | 2 +- 7 files changed, 26 insertions(+), 19 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <arXiv:1103.3817> and
Tucker et al., 2014 <DOI:10.1016/j.csda.2012.12.001>). This framework
allows for elastic analysis of functional data through phase and
amplitude separation.
Author: J. Derek Tucker <jdtuck@sandia.gov>
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 1.9.4 dated 2020-10-09 and 1.9.6 dated 2021-05-07
fdasrvf-1.9.4/fdasrvf/R/srsf_to_f.R |only fdasrvf-1.9.4/fdasrvf/man/srsf_to_f.Rd |only fdasrvf-1.9.6/fdasrvf/DESCRIPTION | 11 fdasrvf-1.9.6/fdasrvf/MD5 | 202 - fdasrvf-1.9.6/fdasrvf/NAMESPACE | 205 - fdasrvf-1.9.6/fdasrvf/NEWS | 206 - fdasrvf-1.9.6/fdasrvf/R/AmplitudeBoxplot.R | 340 +- fdasrvf-1.9.6/fdasrvf/R/PhaseBoxplot.R | 360 +- fdasrvf-1.9.6/fdasrvf/R/SqrtMean.R | 130 fdasrvf-1.9.6/fdasrvf/R/SqrtMedian.R | 158 fdasrvf-1.9.6/fdasrvf/R/align_fPCA.R | 580 +-- fdasrvf-1.9.6/fdasrvf/R/bayesian_functions.R | 98 fdasrvf-1.9.6/fdasrvf/R/calc_shape_dist.R | 71 fdasrvf-1.9.6/fdasrvf/R/curve_functions.R | 1127 +++--- fdasrvf-1.9.6/fdasrvf/R/curve_geodesic.R | 96 fdasrvf-1.9.6/fdasrvf/R/curve_karcher_cov.R | 93 fdasrvf-1.9.6/fdasrvf/R/curve_karcher_mean.R | 284 + fdasrvf-1.9.6/fdasrvf/R/curve_pair_align.R | 73 fdasrvf-1.9.6/fdasrvf/R/curve_principal_directions.R | 191 - fdasrvf-1.9.6/fdasrvf/R/curve_srvf_align.R | 129 fdasrvf-1.9.6/fdasrvf/R/curve_to_q.R | 66 fdasrvf-1.9.6/fdasrvf/R/elastic.depth.R | 130 fdasrvf-1.9.6/fdasrvf/R/elastic.distance.R | 78 fdasrvf-1.9.6/fdasrvf/R/elastic_logistic.R | 238 - fdasrvf-1.9.6/fdasrvf/R/elastic_lpcr_regression.R | 152 fdasrvf-1.9.6/fdasrvf/R/elastic_mlogistic.R | 260 - fdasrvf-1.9.6/fdasrvf/R/elastic_mlpcr_regression.R | 170 - fdasrvf-1.9.6/fdasrvf/R/elastic_pcr_regression.R | 162 fdasrvf-1.9.6/fdasrvf/R/elastic_prediction.R | 228 - fdasrvf-1.9.6/fdasrvf/R/elastic_regression.R | 304 - fdasrvf-1.9.6/fdasrvf/R/f_to_srvf.R | 52 fdasrvf-1.9.6/fdasrvf/R/fdasrvf-package.r | 309 - fdasrvf-1.9.6/fdasrvf/R/function_group_warp_bayes.R | 302 - fdasrvf-1.9.6/fdasrvf/R/function_mean_bayes.R | 226 - fdasrvf-1.9.6/fdasrvf/R/gauss_model.R | 224 - fdasrvf-1.9.6/fdasrvf/R/geometry.R | 276 - fdasrvf-1.9.6/fdasrvf/R/gradient.R | 84 fdasrvf-1.9.6/fdasrvf/R/horizFPCA.R | 166 - fdasrvf-1.9.6/fdasrvf/R/image_funcs.R | 842 ++--- fdasrvf-1.9.6/fdasrvf/R/invertGamma.R | 50 fdasrvf-1.9.6/fdasrvf/R/joint_gauss_model.R | 142 fdasrvf-1.9.6/fdasrvf/R/jointfPCA.R | 306 - fdasrvf-1.9.6/fdasrvf/R/kmeans.R | 423 +- fdasrvf-1.9.6/fdasrvf/R/multiple_align_functions.R | 318 - fdasrvf-1.9.6/fdasrvf/R/optimum.reparam.R | 208 - fdasrvf-1.9.6/fdasrvf/R/outlier.detection.R | 80 fdasrvf-1.9.6/fdasrvf/R/pair_align_functions.R | 98 fdasrvf-1.9.6/fdasrvf/R/pair_align_functions_bayes.R | 342 +- fdasrvf-1.9.6/fdasrvf/R/pair_align_functions_expomap.R | 1610 ++++----- fdasrvf-1.9.6/fdasrvf/R/pair_align_image.R | 194 - fdasrvf-1.9.6/fdasrvf/R/plot.ampbox.R | 142 fdasrvf-1.9.6/fdasrvf/R/plot.fdakma.R | 58 fdasrvf-1.9.6/fdasrvf/R/plot.fdawarp.R | 68 fdasrvf-1.9.6/fdasrvf/R/plot.hfpca.R | 64 fdasrvf-1.9.6/fdasrvf/R/plot.jfpca.R | 90 fdasrvf-1.9.6/fdasrvf/R/plot.phbox.R | 138 fdasrvf-1.9.6/fdasrvf/R/plot.vfpca.R | 90 fdasrvf-1.9.6/fdasrvf/R/predict.lpcr.R | 292 - fdasrvf-1.9.6/fdasrvf/R/predict.mlpcr.R | 340 +- fdasrvf-1.9.6/fdasrvf/R/predict.pcr.R | 260 - fdasrvf-1.9.6/fdasrvf/R/q_to_curve.R | 55 fdasrvf-1.9.6/fdasrvf/R/regression_functions.R | 252 - fdasrvf-1.9.6/fdasrvf/R/reparam_curve.R | 284 - fdasrvf-1.9.6/fdasrvf/R/reparam_image.R | 180 - fdasrvf-1.9.6/fdasrvf/R/resamplecurve.R | 80 fdasrvf-1.9.6/fdasrvf/R/rgam.R | 116 fdasrvf-1.9.6/fdasrvf/R/sample_shapes.R | 136 fdasrvf-1.9.6/fdasrvf/R/smooth.data.R | 56 fdasrvf-1.9.6/fdasrvf/R/srvf_to_f.R |only fdasrvf-1.9.6/fdasrvf/R/summary.fdawarp.R | 28 fdasrvf-1.9.6/fdasrvf/R/time_warping.R | 544 +-- fdasrvf-1.9.6/fdasrvf/R/tolerance.R | 260 - fdasrvf-1.9.6/fdasrvf/R/utility_functions.R | 1644 +++++----- fdasrvf-1.9.6/fdasrvf/R/vertFPCA.R | 194 - fdasrvf-1.9.6/fdasrvf/R/warp_f_gamma.R | 58 fdasrvf-1.9.6/fdasrvf/R/warp_q_gamma.R | 68 fdasrvf-1.9.6/fdasrvf/README.md | 170 - fdasrvf-1.9.6/fdasrvf/man/beta.Rd | 34 fdasrvf-1.9.6/fdasrvf/man/calc_shape_dist.Rd | 12 fdasrvf-1.9.6/fdasrvf/man/curve_karcher_cov.Rd | 12 fdasrvf-1.9.6/fdasrvf/man/curve_karcher_mean.Rd | 95 fdasrvf-1.9.6/fdasrvf/man/curve_principal_directions.Rd | 23 fdasrvf-1.9.6/fdasrvf/man/curve_srvf_align.Rd | 14 fdasrvf-1.9.6/fdasrvf/man/curve_to_q.Rd | 2 fdasrvf-1.9.6/fdasrvf/man/elastic.depth.Rd | 66 fdasrvf-1.9.6/fdasrvf/man/f_to_srvf.Rd | 4 fdasrvf-1.9.6/fdasrvf/man/fdasrvf.Rd | 100 fdasrvf-1.9.6/fdasrvf/man/growth_vel.Rd | 32 fdasrvf-1.9.6/fdasrvf/man/im.Rd | 32 fdasrvf-1.9.6/fdasrvf/man/jointFPCA.Rd | 124 fdasrvf-1.9.6/fdasrvf/man/kmeans_align.Rd | 5 fdasrvf-1.9.6/fdasrvf/man/q_to_curve.Rd | 6 fdasrvf-1.9.6/fdasrvf/man/sample_shapes.Rd | 6 fdasrvf-1.9.6/fdasrvf/man/simu_data.Rd | 44 fdasrvf-1.9.6/fdasrvf/man/simu_warp.Rd | 44 fdasrvf-1.9.6/fdasrvf/man/simu_warp_median.Rd | 44 fdasrvf-1.9.6/fdasrvf/man/srvf_to_f.Rd |only fdasrvf-1.9.6/fdasrvf/man/toy_data.Rd | 38 fdasrvf-1.9.6/fdasrvf/man/toy_warp.Rd | 38 fdasrvf-1.9.6/fdasrvf/src/gropt/incl/DriverCpp.h | 2 fdasrvf-1.9.6/fdasrvf/src/gropt/incl/SphereTx.h | 2 fdasrvf-1.9.6/fdasrvf/tests/testthat.R | 16 fdasrvf-1.9.6/fdasrvf/tests/testthat/test_pair_align_functions_bayes.R | 40 fdasrvf-1.9.6/fdasrvf/tests/testthat/test_pair_align_functions_expomap.R | 226 - 104 files changed, 9684 insertions(+), 9438 deletions(-)
Title: Build Error Correction Models
Description: Functions for easy building of error correction models (ECM) for time series regression.
Author: Gaurav Bansal
Maintainer: Gaurav Bansal <gaurbans@gmail.com>
Diff between ecm versions 6.1.0 dated 2021-04-23 and 6.2.0 dated 2021-05-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/ecmave.R | 53 ++++++++++++++++++++++++++++++++++++++--------------- R/ecmaveback.r | 53 ++++++++++++++++++++++++++++++++++++++--------------- README.md | 4 ++-- 5 files changed, 85 insertions(+), 39 deletions(-)
Title: The Official SolveBio API Client
Description: R language bindings for SolveBio's API.
SolveBio is a biomedical knowledge hub that enables life science
organizations to collect and harmonize the complex, disparate
"multi-omic" data essential for today's R&D and BI needs.
For more information, visit <https://www.solvebio.com>.
Author: David Caplan
Maintainer: David Caplan <dcaplan@solvebio.com>
Diff between solvebio versions 2.10.1 dated 2021-03-10 and 2.11.0 dated 2021-05-07
DESCRIPTION | 8 +++--- MD5 | 19 ++++++++------- NEWS.md | 7 +++++ R/dataset.R | 17 ++++++-------- R/object.R | 8 +++--- R/utils.R | 53 ++++++++++++++++++++++++++++++++++++-------- README.md | 2 - man/Dataset.data.Rd | 4 --- man/Dataset.query.Rd | 10 +++++++- man/Object.data.Rd | 4 +-- tests/testthat/test_query.R |only 11 files changed, 90 insertions(+), 42 deletions(-)
Title: Software Option Settings Manager for R
Description: Provides option settings management that goes
beyond R's default 'options' function. With this package, users can define
their own option settings manager holding option names, default values and
(if so desired) ranges or sets of allowed option values that will be
automatically checked. Settings can then be retrieved, altered and reset
to defaults with ease. For R programmers and package developers it offers
cloning and merging functionality which allows for conveniently defining
global and local options, possibly in a multilevel options hierarchy. See
the package vignette for some examples concerning functions, S4 classes,
and reference classes. There are convenience functions to reset par()
and options() to their 'factory defaults'.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between settings versions 0.2.4 dated 2015-10-27 and 0.2.7 dated 2021-05-07
settings-0.2.4/settings/inst/doc/settings.R |only settings-0.2.4/settings/inst/doc/settings.Rmd |only settings-0.2.4/settings/inst/doc/settings.html |only settings-0.2.4/settings/tests/testthat |only settings-0.2.4/settings/tests/testthat.R |only settings-0.2.4/settings/vignettes/settings.Rmd |only settings-0.2.7/settings/DESCRIPTION | 10 +- settings-0.2.7/settings/MD5 | 47 +++++----- settings-0.2.7/settings/NAMESPACE | 2 settings-0.2.7/settings/NEWS | 6 + settings-0.2.7/settings/R/options.R | 40 ++++++-- settings-0.2.7/settings/build/vignette.rds |binary settings-0.2.7/settings/inst/doc/Introduction_to_settings.R |only settings-0.2.7/settings/inst/doc/Introduction_to_settings.Rmd |only settings-0.2.7/settings/inst/doc/Introduction_to_settings.html |only settings-0.2.7/settings/inst/doc/Validating_and_manipulating_option_values.R |only settings-0.2.7/settings/inst/doc/Validating_and_manipulating_option_values.Rmd |only settings-0.2.7/settings/inst/doc/Validating_and_manipulating_option_values.html |only settings-0.2.7/settings/inst/tinytest |only settings-0.2.7/settings/man/clone_and_merge.Rd | 6 - settings-0.2.7/settings/man/defaults.Rd | 3 settings-0.2.7/settings/man/inlist.Rd | 3 settings-0.2.7/settings/man/is_setting.Rd | 3 settings-0.2.7/settings/man/options_manager.Rd | 12 +- settings-0.2.7/settings/man/reset.Rd | 3 settings-0.2.7/settings/man/reset_options.Rd | 3 settings-0.2.7/settings/man/reset_par.Rd | 5 - settings-0.2.7/settings/man/settings.Rd | 8 - settings-0.2.7/settings/man/stop_if_reserved.Rd | 6 - settings-0.2.7/settings/tests/tinytest.R |only settings-0.2.7/settings/vignettes/Introduction_to_settings.Rmd |only settings-0.2.7/settings/vignettes/Validating_and_manipulating_option_values.Rmd |only 32 files changed, 93 insertions(+), 64 deletions(-)
Title: Non Metric Space (Approximate) Library
Description: A Non-Metric Space Library ('NMSLIB' <https://github.com/nmslib/nmslib>) wrapper, which according to the authors "is an efficient cross-platform similarity search library and a toolkit for evaluation of similarity search methods. The goal of the 'NMSLIB' <https://github.com/nmslib/nmslib> Library is to create an effective and comprehensive toolkit for searching in generic non-metric spaces. Being comprehensive is important, because no single method is likely to be sufficient in all cases. Also note that exact solutions are hardly efficient in high dimensions and/or non-metric spaces. Hence, the main focus is on approximate methods". The wrapper also includes Approximate Kernel k-Nearest-Neighbor functions based on the 'NMSLIB' <https://github.com/nmslib/nmslib> 'Python' Library.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>),
B. Naidan [cph] (Author of the Non-Metric Space Library (NMSLIB)),
L. Boytsov [cph] (Author of the Non-Metric Space Library (NMSLIB)),
Yu. Malkov [cph] (Author of the Non-Metric Space Library (NMSLIB)),
B. Frederickson [cph] (Author of the Non-Metric Space Library (NMSLIB)),
D. Novak [cph] (Author of the Non-Metric Space Library (NMSLIB))
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between nmslibR versions 1.0.4 dated 2020-03-08 and 1.0.5 dated 2021-05-07
nmslibR-1.0.4/nmslibR/R/zzz.R |only nmslibR-1.0.4/nmslibR/inst/COPYRIGHTS |only nmslibR-1.0.5/nmslibR/DESCRIPTION | 22 +- nmslibR-1.0.5/nmslibR/MD5 | 32 ++- nmslibR-1.0.5/nmslibR/NAMESPACE | 1 nmslibR-1.0.5/nmslibR/NEWS.md | 8 nmslibR-1.0.5/nmslibR/R/nmslib.R | 113 ++++++++----- nmslibR-1.0.5/nmslibR/R/package.R | 20 +- nmslibR-1.0.5/nmslibR/build/vignette.rds |binary nmslibR-1.0.5/nmslibR/inst/CITATION |only nmslibR-1.0.5/nmslibR/inst/doc/the_nmslibR_package.html | 30 +++ nmslibR-1.0.5/nmslibR/man/KernelKnnCV_nmslib.Rd | 2 nmslibR-1.0.5/nmslibR/man/KernelKnn_nmslib.Rd | 16 + nmslibR-1.0.5/nmslibR/man/NMSlib.Rd | 34 ++-- nmslibR-1.0.5/nmslibR/man/TO_scipy_sparse.Rd | 42 ++--- nmslibR-1.0.5/nmslibR/man/mat_2scipy_sparse.Rd | 20 +- nmslibR-1.0.5/nmslibR/tests/testthat/helper-init.R |only nmslibR-1.0.5/nmslibR/tests/testthat/helper-skip.R |only nmslibR-1.0.5/nmslibR/tests/testthat/setup.R |only nmslibR-1.0.5/nmslibR/tests/testthat/test-nmslibR_pkg.R | 130 ++-------------- 20 files changed, 225 insertions(+), 245 deletions(-)
Title: Subnational Data for the COVID-19 Outbreak
Description: An interface to subnational and national level COVID-19 data.
For all countries supported, this includes a daily time-series of
cases. Wherever available we also provide data on deaths,
hospitalisations, and tests. National level data is also supported
using a range of data sources as well as line list data and links to
intervention data sets.
Author: Sam Abbott [aut, cre] (<https://orcid.org/0000-0001-8057-8037>),
Katharine Sherratt [aut] (<https://orcid.org/0000-0003-2049-3423>),
Joe Palmer [aut],
Richard Martin-Nielsen [aut] (https://github.com/RichardMN),
Jonnie Bevan [aut],
Hamish Gibbs [aut] (<https://orcid.org/0000-0003-4413-453X>),
Sophie Meakin [ctb],
Joel Hellewell [ctb] (<https://orcid.org/0000-0003-2683-0849>),
Patrick Barks [ctb],
Paul Campbell [ctb],
Flavio Finger [ctb] (<https://orcid.org/0000-0002-8613-5170>),
Richard Boyes [ctb] (https://github.com/rboyes),
Hugo Gruson [ctb] (<https://orcid.org/0000-0002-4094-1476>),
Sebastian Funk [aut]
Maintainer: Sam Abbott <sam.abbott@lshtm.ac.uk>
Diff between covidregionaldata versions 0.9.0 dated 2021-04-24 and 0.9.1 dated 2021-05-07
DESCRIPTION | 14 MD5 | 173 ++++--- NAMESPACE | 6 NEWS.md | 23 R/Belgium.R | 1 R/Brazil.R | 1 R/Canada.R | 1 R/Colombia.R | 1 R/Cuba.R | 1 R/ECDC.R | 4 R/France.R | 1 R/Germany.R | 1 R/Google.R |only R/India.R | 1 R/Italy.R | 1 R/JHU.R |only R/Lithuania.R | 1 R/Mexico.R | 1 R/SouthAfrica.R | 1 R/UK.R | 87 +++ R/USA.R | 1 R/WHO.R | 8 R/datasets.R | 7 R/get_available_datasets.R | 15 R/get_national_data.R | 49 +- R/get_regional_data.R | 32 + R/processing.R | 66 ++ R/shared-methods.R | 251 ++++++++-- R/utils.R | 62 ++ README.md | 32 - build/vignette.rds |binary data/JHU_codes.rda |only inst/WORDLIST | 16 inst/doc/dataset-status.Rmd | 2 inst/doc/dataset-status.html | 215 +++++++++ inst/doc/quickstart.Rmd | 2 inst/doc/quickstart.html | 466 ++++++++++++++------ inst/doc/slowstart.Rmd | 4 inst/doc/slowstart.html | 301 ++++++++++-- man/Belgium.Rd | 20 man/Brazil.Rd | 20 man/Canada.Rd | 20 man/Colombia.Rd | 20 man/CountryDataClass.Rd | 39 + man/Cuba.Rd | 20 man/DataClass.Rd | 95 +++- man/ECDC.Rd | 11 man/France.Rd | 20 man/Germany.Rd | 20 man/Google.Rd |only man/India.Rd | 20 man/Italy.Rd | 20 man/JHU.Rd |only man/JHU_codes.Rd |only man/Lithuania.Rd | 20 man/Mexico.Rd | 20 man/SouthAfrica.Rd | 20 man/UK.Rd | 52 ++ man/USA.Rd | 20 man/WHO.Rd | 15 man/add_extra_na_cols.Rd | 8 man/calculate_columns_from_existing_data.Rd | 8 man/check_level.Rd |only man/complete_cumulative_columns.Rd | 8 man/download_excel.Rd |only man/fill_empty_dates_with_na.Rd | 8 man/get_available_datasets.Rd | 21 man/get_national_data.Rd | 57 ++ man/get_regional_data.Rd | 40 + man/glue_level.Rd |only man/initialise_dataclass.Rd | 62 ++ man/process_internal.Rd | 12 man/region_dispatch.Rd | 2 man/roxygen |only man/run_default_processing_fns.Rd |only man/run_optional_processing_fns.Rd |only man/set_negative_values_to_zero.Rd | 6 man/totalise_data.Rd | 6 tests/testthat/custom_data/Google_level_1.rds |only tests/testthat/custom_data/Google_level_2.rds |only tests/testthat/custom_data/Google_level_3.rds |only tests/testthat/custom_data/JHU_level_1.rds |only tests/testthat/custom_data/JHU_level_2.rds |only tests/testthat/custom_data/Mexico_level_1.rds |binary tests/testthat/custom_data/Mexico_level_2.rds |binary tests/testthat/custom_data/UK_level_1.rds |binary tests/testthat/custom_data/UK_level_2.rds |binary tests/testthat/custom_tests/test-regional-dataset.R | 10 tests/testthat/test-CountryDataClass.R | 1 tests/testthat/test-DataClass.R | 42 + tests/testthat/test-get_available_datasets.R | 4 tests/testthat/test-processing.R | 36 + tests/testthat/test-regional-datasets.R | 5 vignettes/dataset-status.Rmd | 2 vignettes/quickstart.Rmd | 2 vignettes/slowstart.Rmd | 4 96 files changed, 2176 insertions(+), 488 deletions(-)
More information about covidregionaldata at CRAN
Permanent link
Title: Multiple Testing Methods for Exploratory Research
Description: Provides an alternative approach to multiple testing
by calculating a simultaneous upper confidence bounds for the
number of true null hypotheses among any subset of the hypotheses of interest,
using the methods of Goeman and Solari (2011) <doi:10.1214/11-STS356>.
Author: Jelle Goeman, Aldo Solari, Rosa Meijer
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>
Diff between cherry versions 0.6-13 dated 2019-09-20 and 0.6-14 dated 2021-05-07
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 17 ++++++++--------- build/vignette.rds |binary inst/doc/cherry.pdf |binary 5 files changed, 17 insertions(+), 18 deletions(-)
Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>),
Marcel Ramos [ctb, cre] (<https://orcid.org/0000-0002-3242-0582>)
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
Diff between BiocManager versions 1.30.12 dated 2021-03-28 and 1.30.13 dated 2021-05-07
DESCRIPTION | 6 +- MD5 | 34 +++++++-------- NEWS | 22 +++++++++ R/available.R | 6 ++ R/inet.R | 7 +++ R/install.R | 64 ++++++++++++++++++++++------ R/repositories.R | 2 R/valid.R | 60 +++++++++++++++----------- R/version.R | 28 +++++++----- build/vignette.rds |binary inst/doc/BiocManager.Rmd | 8 +-- inst/doc/BiocManager.html | 83 +++++++++++++++++++++---------------- man/available.Rd | 6 ++ man/install.Rd | 9 +++- tests/testthat/test_install.R | 36 +++++++++++++++- tests/testthat/test_repositories.R | 2 tests/testthat/test_version.R | 8 ++- vignettes/BiocManager.Rmd | 8 +-- 18 files changed, 268 insertions(+), 121 deletions(-)
Title: Model Agnostic Instance Level Variable Attributions
Description: Model agnostic tool for decomposition of predictions from black boxes.
Supports additive attributions and attributions with interactions.
The Break Down Table shows contributions of every variable to a final prediction.
The Break Down Plot presents variable contributions in a concise graphical way.
This package works for classification and regression models.
It is an extension of the 'breakDown' package (Staniak and Biecek 2018) <doi:10.32614/RJ-2018-072>,
with new and faster strategies for orderings.
It supports interactions in explanations and has interactive visuals (implemented with 'D3.js' library).
The methodology behind is described in the 'iBreakDown' article (Gosiewska and Biecek 2019) <arXiv:1903.11420>
This package is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>),
Alicja Gosiewska [aut] (<https://orcid.org/0000-0001-6563-5742>),
Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>),
Adam Izdebski [aut],
Dariusz Komosinski [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between iBreakDown versions 1.3.1 dated 2020-07-29 and 2.0.1 dated 2021-05-07
iBreakDown-1.3.1/iBreakDown/inst/doc/vignette_iBreakDown_classification.R |only iBreakDown-1.3.1/iBreakDown/inst/doc/vignette_iBreakDown_classification.Rmd |only iBreakDown-1.3.1/iBreakDown/inst/doc/vignette_iBreakDown_classification.html |only iBreakDown-1.3.1/iBreakDown/inst/doc/vignette_iBreakDown_regression.R |only iBreakDown-1.3.1/iBreakDown/inst/doc/vignette_iBreakDown_regression.Rmd |only iBreakDown-1.3.1/iBreakDown/inst/doc/vignette_iBreakDown_regression.html |only iBreakDown-1.3.1/iBreakDown/vignettes/vignette_iBreakDown_classification.Rmd |only iBreakDown-1.3.1/iBreakDown/vignettes/vignette_iBreakDown_regression.Rmd |only iBreakDown-2.0.1/iBreakDown/DESCRIPTION | 7 iBreakDown-2.0.1/iBreakDown/MD5 | 70 ++--- iBreakDown-2.0.1/iBreakDown/NEWS.md | 5 iBreakDown-2.0.1/iBreakDown/R/break_down.R | 2 iBreakDown-2.0.1/iBreakDown/R/break_down_uncertainty.R | 10 iBreakDown-2.0.1/iBreakDown/R/describe_breakdown.R | 2 iBreakDown-2.0.1/iBreakDown/R/local_attributions.R | 2 iBreakDown-2.0.1/iBreakDown/R/local_interactions.R | 2 iBreakDown-2.0.1/iBreakDown/R/plotD3_break_down.R | 9 iBreakDown-2.0.1/iBreakDown/R/plotD3_shap.R | 9 iBreakDown-2.0.1/iBreakDown/R/plot_break_down.R | 9 iBreakDown-2.0.1/iBreakDown/R/plot_break_down_uncertainty.R | 2 iBreakDown-2.0.1/iBreakDown/R/print_break_down.R | 2 iBreakDown-2.0.1/iBreakDown/R/print_break_down_descriptions.R | 2 iBreakDown-2.0.1/iBreakDown/R/print_break_down_uncertainty.R | 2 iBreakDown-2.0.1/iBreakDown/build/vignette.rds |binary iBreakDown-2.0.1/iBreakDown/inst/d3js/breakDownD3.js | 8 iBreakDown-2.0.1/iBreakDown/inst/d3js/shapD3.js | 8 iBreakDown-2.0.1/iBreakDown/inst/doc/vignette_iBreakDown_description.html | 136 +++++++--- iBreakDown-2.0.1/iBreakDown/inst/doc/vignette_iBreakDown_titanic.html | 120 +++++++- iBreakDown-2.0.1/iBreakDown/man/break_down.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/break_down_uncertainty.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/describe.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/local_attributions.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/local_interactions.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/plot.break_down.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/plot.break_down_uncertainty.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/plotD3_break_down.Rd | 7 iBreakDown-2.0.1/iBreakDown/man/plotD3_shap.Rd | 7 iBreakDown-2.0.1/iBreakDown/man/print.break_down.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/print.break_down_description.Rd | 2 iBreakDown-2.0.1/iBreakDown/man/print.break_down_uncertainty.Rd | 2 40 files changed, 305 insertions(+), 136 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>,
@strengejacke),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>,
@Dom_Makowski),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>),
Mattan S. Ben-Shachar [aut, ctb]
(<https://orcid.org/0000-0002-4287-4801>),
Brenton M. Wiernik [aut] (<https://orcid.org/0000-0001-9560-6336>,
@bmwiernik)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between insight versions 0.13.2 dated 2021-04-01 and 0.14.0 dated 2021-05-07
DESCRIPTION | 17 MD5 | 253 ++- NAMESPACE | 111 - NEWS.md | 80 + R/check_if_installed.R |only R/clean_names.R | 2 R/clean_parameters.R | 13 R/compute_variances.R | 49 R/ellipsis_info.R | 41 R/export_table.R | 47 R/find_formula.R | 382 ++++-- R/find_interactions.R | 1 R/find_parameter_zi.R | 1 R/find_parameters.R | 51 R/find_parameters_bayesian.R | 139 +- R/find_parameters_emmeans.R | 3 R/find_parameters_gam.R | 21 R/find_parameters_mfx.R | 23 R/find_parameters_mixed.R | 13 R/find_predictors.R | 17 R/find_random.R | 2 R/find_random_slopes.R | 2 R/find_response.R | 60 R/find_smooth.R | 2 R/find_statistic.R | 243 --- R/find_terms.R | 26 R/find_variables.R | 15 R/find_weights.R | 2 R/format_message.R |only R/format_string.R |only R/format_table.R | 31 R/format_value.R | 36 R/get_auxiliary.R | 42 R/get_call.R | 12 R/get_data.R | 91 - R/get_deviance.R | 37 R/get_df.R | 118 + R/get_family.R | 2 R/get_loglikelihood.R | 23 R/get_modelmatrix.R |only R/get_parameters.R | 38 R/get_parameters_bayesian.R | 15 R/get_parameters_censored.R | 2 R/get_parameters_gam.R | 22 R/get_parameters_mfx.R | 1 R/get_parameters_mixed.R | 4 R/get_parameters_others.R | 53 R/get_parameters_zi.R | 1 R/get_predicted.R | 411 +++++- R/get_predicted_ci.R | 45 R/get_predicted_methods.R | 1 R/get_predictors.R | 2 R/get_priors.R | 67 - R/get_residuals.R | 16 R/get_response.R | 6 R/get_sigma.R | 169 ++ R/get_statistic.R | 204 ++- R/get_varcov.R | 44 R/get_weights.R | 9 R/helper_functions.R | 113 - R/is_model.R | 16 R/is_model_supported.R | 145 -- R/is_multivariate.R | 2 R/link_function.R | 12 R/link_inverse.R | 32 R/model_info.R | 67 - R/model_name.R | 2 R/n_obs.R | 39 R/n_parameters.R | 21 R/null_model.R | 3 R/print_parameters.R | 3 R/reshape_ci.R | 1 R/utils_get_data.R | 148 +- R/utils_model_info.R | 41 README.md | 35 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/WORDLIST | 48 inst/doc/display.html | 144 +- man/check_if_installed.Rd |only man/find_formula.Rd | 11 man/find_interactions.Rd | 8 man/find_parameters.BGGM.Rd | 268 ++-- man/find_parameters.averaging.Rd | 22 man/find_parameters.betamfx.Rd | 126 + man/find_parameters.gamlss.Rd | 112 - man/find_parameters.glmmTMB.Rd | 123 - man/find_parameters.zeroinfl.Rd | 22 man/find_predictors.Rd | 119 - man/find_terms.Rd | 4 man/find_variables.Rd | 169 +- man/format_message.Rd |only man/format_string.Rd |only man/get_auxiliary.Rd | 142 +- man/get_data.Rd | 248 +-- man/get_deviance.Rd | 9 man/get_df.Rd | 65 - man/get_loglikelihood.Rd | 4 man/get_modelmatrix.Rd |only man/get_parameters.BGGM.Rd | 349 ++--- man/get_parameters.betamfx.Rd | 80 - man/get_parameters.betareg.Rd | 15 man/get_parameters.gamm.Rd | 96 - man/get_parameters.glmm.Rd | 21 man/get_parameters.zeroinfl.Rd | 8 man/get_predicted.Rd | 93 + man/get_predicted_ci.Rd | 13 man/get_response.Rd | 4 man/get_sigma.Rd | 9 man/get_statistic.Rd | 14 man/get_varcov.Rd | 208 +-- man/model_info.Rd | 1 man/n_parameters.Rd | 8 tests/testthat.R | 41 tests/testthat/_snaps |only tests/testthat/test-GLMMadaptive.R | 6 tests/testthat/test-bigglm.R | 2 tests/testthat/test-brms.R | 6 tests/testthat/test-check_if_installed.R |only tests/testthat/test-coxme.R | 3 tests/testthat/test-coxph.R | 1 tests/testthat/test-export_table.R | 70 - tests/testthat/test-find_formula-data.R |only tests/testthat/test-formatting.R |only tests/testthat/test-gam.R | 2 tests/testthat/test-get_predicted.R | 37 tests/testthat/test-get_residuals.R | 3 tests/testthat/test-glmmTMB.R | 6 tests/testthat/test-mixed.R | 2 tests/testthat/test-mvrstanarm.R | 1965 +++++++++++++++---------------- tests/testthat/test-r3_4.R |only tests/testthat/test-survfit.R | 1 tests/testthat/test-survreg.R | 2 134 files changed, 4940 insertions(+), 3570 deletions(-)
Title: Plots of the Empirical Attainment Function
Description: Computation and visualization of the empirical attainment function (EAF) for the analysis of random sets in multi-criterion optimization. M. López-Ibáñez, L. Paquete, and T. Stützle (2010) <doi:10.1007/978-3-642-02538-9_9>.
Author: Manuel López-Ibáñez [aut, cre]
(<https://orcid.org/0000-0001-9974-1295>),
Marco Chiarandini [aut],
Carlos Fonseca [aut],
Luís Paquete [aut],
Thomas Stützle [aut],
Mickaël Binois [ctb]
Maintainer: Manuel López-Ibáñez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between eaf versions 2.0 dated 2021-02-08 and 2.1 dated 2021-05-07
DESCRIPTION | 6 +- MD5 | 43 +++++++++---------- NEWS.md | 23 +++++----- R/eaf.R | 82 ++++++++++++++++++++----------------- R/epsilon.R | 67 +++++++++++++++++++++--------- R/igd.R | 76 +++++++++++++++++++++++++--------- R/vorob.R | 4 - README.md | 14 +++--- build/partial.rdb |binary man/eafdiffplot.Rd | 2 man/eafplot.Rd | 12 ++--- man/eafs.Rd | 2 man/epsilon.Rd | 60 +++++++++++++++++++-------- man/igd.Rd | 75 +++++++++++++++++++++++++-------- src/Makevars.win | 4 - src/eaf/bit_array.h | 5 -- src/eaf/svn_version | 2 src/mo-tools/igd.c | 9 ---- src/mo-tools/igd.h | 67 +++++++++++++----------------- src/mo-tools/nondominated.c | 14 +++--- src/mo-tools/svn_version | 2 src/mo-tools/whv.c | 10 ++-- tests/testthat/test-eafplot-list.R |only 23 files changed, 354 insertions(+), 225 deletions(-)
Title: Create, Survey and Analyse Discrete Choice Experiments
Description: This app is intended to be a complete package for creating, surveying, and analysing discrete choice experiments. Although all these functionalities are available, the app can also be used only to obtain the design of a discrete choice experiment. Reference: Perez-Troncoso, D. (2021) <https://github.com/danielpereztr/DCEtool>.
Author: Daniel Perez Troncoso [aut, cre]
(<https://orcid.org/0000-0003-0091-8148>)
Maintainer: Daniel Perez Troncoso <danielperez@ugr.es>
Diff between DCEtool versions 0.0.1 dated 2021-04-21 and 0.1.1 dated 2021-05-07
DESCRIPTION | 8 ++-- MD5 | 13 +++---- NAMESPACE | 98 +++++++++++++++++++++++++++--------------------------- NEWS.md | 2 + R/app.r | 22 +++++++----- R/helpfiles |only build/partial.rdb |binary man/DCEtool.Rd | 2 + 8 files changed, 77 insertions(+), 68 deletions(-)
Title: An Implementation of Z-Curves
Description: An implementation of z-curves - a method for estimating expected discovery
and replicability rates on the bases of test-statistics of published studies. The package
provides functions for fitting the new density and EM version
(Bartoš & Schimmack, 2020, <doi:10.31234/osf.io/urgtn>) as well as the original density
z-curve (Brunner & Schimmack, 2020, <doi:10.15626/MP.2018.874>). Furthermore, the package
provides summarizing and plotting functions for the fitted z-curve objects. See the
aforementioned articles for more information about the z-curves, expected discovery
and replicability rates, validation studies, and limitations.
Author: František Bartoš [aut, cre],
Ulrich Schimmack [aut]
Maintainer: František Bartoš <f.bartos96@gmail.com>
Diff between zcurve versions 1.0.8 dated 2021-01-17 and 1.0.9 dated 2021-05-07
DESCRIPTION | 8 +-- MD5 | 21 +++++----- R/main.R | 3 - R/tools.R | 31 +++++++++------ R/zzz.R |only README.md | 63 +++++++++++++++++-------------- build/partial.rdb |binary inst/REFERENCES.bib | 6 +- man/figures/README-unnamed-chunk-6-1.png |binary man/power_to_z.Rd | 3 + man/z_to_power.Rd | 9 +++- man/zcurve-package.Rd | 2 12 files changed, 85 insertions(+), 61 deletions(-)
Title: Generate Treasury Total Returns from Yield Data
Description: Generate Total Returns (TR) from bond yield data with fixed maturity, e.g.
reported treasury yields. The generated TR series are very close to alternative series
that can be purchased (e.g. CRSP, Bloomberg), suggesting they are a high-quality
alternative for those, see Swinkels (2019) <doi:10.3390/data4030091>.
Author: Martin Geissmann [aut, cre]
Maintainer: Martin Geissmann <mg@econovo.ch>
Diff between treasuryTR versions 0.1.2 dated 2021-04-14 and 0.1.3 dated 2021-05-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/xts_to_tibble.R | 3 +++ inst/doc/treasuryTR.html | 40 ++++++++++++++++++++-------------------- man/xts_to_tibble.Rd | 3 +++ 5 files changed, 33 insertions(+), 27 deletions(-)
Title: Blind Source Separation for Multivariate Spatial Data
Description: Blind source separation for multivariate spatial data based on simultaneous/joint diagonalization of local covariance matrices. This package is an implementation of the methods described in Bachoc, Genton, Nordhausen, Ruiz-Gazen and Virta (2020) <doi:10.1093/biomet/asz079>.
Author: Christoph Muehlmann [aut, cre]
(<https://orcid.org/0000-0001-7330-8434>),
Klaus Nordhausen [aut] (<https://orcid.org/0000-0002-3758-8501>),
Joni Virta [aut] (<https://orcid.org/0000-0002-2150-2769>)
Maintainer: Christoph Muehlmann <christoph.muehlmann@tuwien.ac.at>
Diff between SpatialBSS versions 0.9-0 dated 2020-11-04 and 0.10-0 dated 2021-05-07
DESCRIPTION | 8 ++++---- MD5 | 30 ++++++++++++++++-------------- NAMESPACE | 2 +- R/sbss.R | 10 +++++++--- R/utils.R | 19 ++++++++++++------- build/partial.rdb |only build/vignette.rds |binary inst/ChangeLog.txt | 6 ++++++ inst/doc/SBSS.R | 11 ++++++++--- inst/doc/SBSS.Rmd | 27 ++++++++++++++++++++------- inst/doc/SBSS.html | 31 ++++++++++++++++++++++--------- man/SpatialBSS-package.Rd | 10 ++++++---- man/local_covariance_matrix.Rd | 15 +++++++++------ man/sbss.Rd | 20 ++++++++++++++------ man/spatial_kernel_matrix.Rd | 9 ++++++--- man/white_data.Rd |only vignettes/SBSS.Rmd | 27 ++++++++++++++++++++------- 17 files changed, 151 insertions(+), 74 deletions(-)
Title: Build Panel Data Sets from PSID Raw Data
Description: Makes it easy to build panel data in wide format from Panel Survey
of Income Dynamics ('PSID') delivered raw data. Downloads data directly from
the PSID server using the 'SAScii' package. 'psidR' takes care of merging
data from each wave onto a cross-period index file, so that individuals can be
followed over time. The user must specify which years they are interested in,
and the 'PSID' variable names (e.g. ER21003) for each year (they differ in each
year). The package offers helper functions to retrieve variable names from different
waves. There are different panel data designs and sample subsetting criteria
implemented ("SRC", "SEO", "immigrant" and "latino" samples).
Author: Florian Oswald
Maintainer: Florian Oswald <florian.oswald@gmail.com>
Diff between psidR versions 2.0 dated 2020-02-26 and 2.1 dated 2021-05-07
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS | 7 +++++++ R/build.panel.r | 32 +++++++++++++++++--------------- R/makeids.r | 20 ++++++++++---------- man/build.panel.Rd | 39 ++++++++++++++++++++++++++------------- man/get.psid.Rd | 2 +- man/getNamesPSID.Rd | 2 +- man/psidR.Rd | 1 - tests/testthat/test_testPSID.R | 4 ++-- 10 files changed, 78 insertions(+), 57 deletions(-)
Title: Miscellaneous Functions for Data Cleaning and Analysis
Description: Provides functions needed for data cleaning and
formatting and forms data cleaning and wrangling backend for the
following packages: 'ggstatsplot', 'pairwiseComparisons', and
'statsExpressions'.
Author: Indrajeet Patil [aut, cre, cph]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ipmisc versions 6.0.0 dated 2021-02-13 and 6.0.2 dated 2021-05-07
ipmisc-6.0.0/ipmisc/build |only ipmisc-6.0.0/ipmisc/man/figures |only ipmisc-6.0.2/ipmisc/DESCRIPTION | 12 ipmisc-6.0.2/ipmisc/LICENSE | 1348 +++++----- ipmisc-6.0.2/ipmisc/MD5 | 53 ipmisc-6.0.2/ipmisc/NAMESPACE | 80 ipmisc-6.0.2/ipmisc/NEWS.md | 204 - ipmisc-6.0.2/ipmisc/R/data.R | 126 ipmisc-6.0.2/ipmisc/R/format_num.R | 88 ipmisc-6.0.2/ipmisc/R/global_vars.R | 14 ipmisc-6.0.2/ipmisc/R/long_to_wide_converter.R | 218 - ipmisc-6.0.2/ipmisc/R/reexports.R | 98 ipmisc-6.0.2/ipmisc/R/stats_type_switch.R | 66 ipmisc-6.0.2/ipmisc/README.md | 154 - ipmisc-6.0.2/ipmisc/inst/WORDLIST | 49 ipmisc-6.0.2/ipmisc/man/format_num.Rd | 2 ipmisc-6.0.2/ipmisc/man/long_to_wide_converter.Rd | 163 - ipmisc-6.0.2/ipmisc/man/reexports.Rd | 65 ipmisc-6.0.2/ipmisc/man/stats_type_switch.Rd | 20 ipmisc-6.0.2/ipmisc/tests/spelling.R | 12 ipmisc-6.0.2/ipmisc/tests/testthat.R | 8 ipmisc-6.0.2/ipmisc/tests/testthat/_snaps/long_to_wide_converter.md | 280 +- ipmisc-6.0.2/ipmisc/tests/testthat/test-format_num.R | 64 ipmisc-6.0.2/ipmisc/tests/testthat/test-long_to_wide_converter.R | 338 +- ipmisc-6.0.2/ipmisc/tests/testthat/test-stats_type_switch.R | 34 25 files changed, 1768 insertions(+), 1728 deletions(-)
Title: Fuzzy String Matching
Description: Fuzzy string matching implementation of the 'fuzzywuzzy' <https://github.com/seatgeek/fuzzywuzzy> 'python' package. It uses the Levenshtein Distance <https://en.wikipedia.org/wiki/Levenshtein_distance> to calculate the differences between sequences.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>),
SeatGeek Inc [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between fuzzywuzzyR versions 1.0.3 dated 2018-02-26 and 1.0.4 dated 2021-05-07
DESCRIPTION | 17 MD5 | 32 NEWS.md | 5 R/fuzzy_w.R | 595 +++++++----- R/package.R | 39 README.md | 9 build/vignette.rds |binary inst/CITATION |only inst/doc/functionality_of_fuzzywuzzyR_package.R | 60 - inst/doc/functionality_of_fuzzywuzzyR_package.html | 804 +++++++++++------ man/FuzzExtract.Rd | 271 ++++- man/FuzzMatcher.Rd | 328 ++++++ man/FuzzUtils.Rd | 203 +++- man/GetCloseMatches.Rd | 20 man/SequenceMatcher.Rd | 129 ++ tests/testthat/helper-init.R |only tests/testthat/helper-skip.R |only tests/testthat/setup.R |only tests/testthat/test_package.R | 991 +++++++++++---------- 19 files changed, 2348 insertions(+), 1155 deletions(-)
Title: Co-Correspondence Analysis Methods
Description: Fits predictive and symmetric co-correspondence analysis (CoCA) models to relate one data matrix to another data matrix. More specifically, CoCA maximises the weighted covariance between the weighted averaged species scores of one community and the weighted averaged species scores of another community. CoCA attempts to find patterns that are common to both communities.
Author: Original Matlab routines by C.J.F. ter Braak and A.P. Schaffers. R port by Gavin L. Simpson.
Function simpls based on simpls.fit (package pls) by Ron Wehrens and Bjorn-Helge Mevik.
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between cocorresp versions 0.4-1 dated 2019-12-19 and 0.4-3 dated 2021-05-07
DESCRIPTION | 12 MD5 | 34 +- R/eigenvals.R | 3 R/print.crossval.R | 6 R/print.predcoca.R | 5 R/print.summary.crossval.R | 6 README.md | 24 - build/vignette.rds |binary data/beetles.rda |binary data/bryophyte.rda |binary data/plants.rda |binary data/vascular.rda |binary inst/ChangeLog | 16 inst/doc/cocorresp-intro.Rmd | 19 - inst/doc/cocorresp-intro.html | 578 ++++++++++++++++++++-------------- tests/Examples/cocorresp-Ex.Rout.save | 28 - tests/testthat/test-eigenvals.R | 9 vignettes/cocorresp-intro.Rmd | 19 - 18 files changed, 451 insertions(+), 308 deletions(-)
Title: Make 'ggplot2' and 'leaflet' Visualisation Easier
Description: Wrapper functions to make 'ggplot2' and 'leaflet' visualisation easier and prettier.
Author: David Hodge [aut, cre] (<https://orcid.org/0000-0002-3868-7501>),
Statistics New Zealand [cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between simplevis versions 3.0.0 dated 2021-04-30 and 3.1.0 dated 2021-05-07
simplevis-3.0.0/simplevis/R/plotly.R |only simplevis-3.0.0/simplevis/data/datalist |only simplevis-3.0.0/simplevis/data/example_stars.rda |only simplevis-3.0.0/simplevis/data/example_stars_2.rda |only simplevis-3.0.0/simplevis/man/example_stars.Rd |only simplevis-3.0.0/simplevis/man/example_stars_2.Rd |only simplevis-3.0.0/simplevis/man/plotly_legend_order.Rd |only simplevis-3.0.0/simplevis/man/plotly_legend_rev.Rd |only simplevis-3.1.0/simplevis/DESCRIPTION | 18 - simplevis-3.1.0/simplevis/MD5 | 92 ++++------ simplevis-3.1.0/simplevis/NAMESPACE | 12 - simplevis-3.1.0/simplevis/NEWS.md | 16 + simplevis-3.1.0/simplevis/R/data.R | 16 - simplevis-3.1.0/simplevis/R/ggplot_boxplot.R | 37 +--- simplevis-3.1.0/simplevis/R/ggplot_hbar.R | 81 +++----- simplevis-3.1.0/simplevis/R/ggplot_line.R | 24 +- simplevis-3.1.0/simplevis/R/ggplot_point.R | 24 +- simplevis-3.1.0/simplevis/R/ggplot_sf.R | 30 +-- simplevis-3.1.0/simplevis/R/ggplot_vbar.R | 34 +-- simplevis-3.1.0/simplevis/R/ggplotly.R |only simplevis-3.1.0/simplevis/R/imports.R | 16 - simplevis-3.1.0/simplevis/R/leaflet_basemap.R | 7 simplevis-3.1.0/simplevis/R/leaflet_sf.R | 59 +++--- simplevis-3.1.0/simplevis/R/other.R | 33 ++- simplevis-3.1.0/simplevis/inst/doc/simplevis.R | 18 - simplevis-3.1.0/simplevis/inst/doc/simplevis.Rmd | 20 +- simplevis-3.1.0/simplevis/inst/doc/simplevis.html | 76 ++++---- simplevis-3.1.0/simplevis/inst/shiny/template1/data/template1.zip |binary simplevis-3.1.0/simplevis/inst/shiny/template1/server.R | 1 simplevis-3.1.0/simplevis/inst/shiny/template2/data/template2.zip |binary simplevis-3.1.0/simplevis/inst/shiny/template2/server.R | 1 simplevis-3.1.0/simplevis/man/ggplot_boxplot.Rd | 7 simplevis-3.1.0/simplevis/man/ggplot_boxplot_col.Rd | 6 simplevis-3.1.0/simplevis/man/ggplot_boxplot_col_facet.Rd | 6 simplevis-3.1.0/simplevis/man/ggplot_hbar_col.Rd | 8 simplevis-3.1.0/simplevis/man/ggplot_hbar_col_facet.Rd | 6 simplevis-3.1.0/simplevis/man/ggplot_line_col.Rd | 8 simplevis-3.1.0/simplevis/man/ggplot_line_col_facet.Rd | 6 simplevis-3.1.0/simplevis/man/ggplot_point_col.Rd | 8 simplevis-3.1.0/simplevis/man/ggplot_point_col_facet.Rd | 6 simplevis-3.1.0/simplevis/man/ggplot_sf.Rd | 4 simplevis-3.1.0/simplevis/man/ggplot_sf_col.Rd | 8 simplevis-3.1.0/simplevis/man/ggplot_sf_col_facet.Rd | 8 simplevis-3.1.0/simplevis/man/ggplot_vbar_col.Rd | 8 simplevis-3.1.0/simplevis/man/ggplot_vbar_col_facet.Rd | 6 simplevis-3.1.0/simplevis/man/leaflet_basemap.Rd | 7 simplevis-3.1.0/simplevis/man/leaflet_sf.Rd | 4 simplevis-3.1.0/simplevis/man/leaflet_sf_col.Rd | 4 simplevis-3.1.0/simplevis/man/mutate_text.Rd | 4 simplevis-3.1.0/simplevis/man/plotly_camera.Rd | 9 simplevis-3.1.0/simplevis/man/plotly_col_legend.Rd |only simplevis-3.1.0/simplevis/vignettes/simplevis.Rmd | 20 +- 52 files changed, 349 insertions(+), 409 deletions(-)
Title: Gamma Lasso Regression
Description: The gamma lasso algorithm provides regularization paths corresponding to a range of non-convex cost functions between L0 and L1 norms. As much as possible, usage for this package is analogous to that for the glmnet package (which does the same thing for penalization between L1 and L2 norms). For details see: Taddy (2017 JCGS), 'One-Step Estimator Paths for Concave Regularization', <arXiv:1308.5623>.
Author: Matt Taddy <mataddy@gmail.com>
Maintainer: Matt Taddy <mataddy@gmail.com>
Diff between gamlr versions 1.13-6 dated 2020-06-08 and 1.13-7 dated 2021-05-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++++---- NAMESPACE | 4 ++-- R/cv.gamlr.R | 15 ++++++++++----- R/doubleML.R |only R/gamlr.R | 3 +-- R/naref.R |only man/doubleML.Rd |only man/naref.Rd |only 9 files changed, 25 insertions(+), 17 deletions(-)
Title: Analysis of Niche Evolution using Niche and Distribution Models
Description: Description: Tools for constructing niche models and analyzing patterns of niche evolution. Acts as an interface for many popular modeling algorithms, and allows users to conduct Monte Carlo tests to address basic questions in evolutionary ecology and biogeography. Warren, D.L., R.E. Glor, and M. Turelli (2008) <doi:10.1111/j.1558-5646.2008.00482.x> Glor, R.E., and D.L. Warren (2011) <doi:10.1111/j.1558-5646.2010.01177.x> Warren, D.L., R.E. Glor, and M. Turelli (2010) <doi:10.1111/j.1600-0587.2009.06142.x> Cardillo, M., and D.L. Warren (2016) <doi:10.1111/geb.12455> D.L. Warren, L.J. Beaumont, R. Dinnage, and J.B. Baumgartner (2019) <doi:10.1111/ecog.03900>.
Author: Dan Warren [aut, cre] (<https://orcid.org/0000-0002-8747-2451>),
Nick Matzke [ctb],
Marcel Cardillo [ctb],
John Baumgartner [ctb],
Linda Beaumont [ctb],
Nicholas Huron [ctb],
Marianna Simoes [ctb],
Teresa Iglesias [ctb],
Russell Dinnage [aut] (<https://orcid.org/0000-0003-0846-2819>)
Maintainer: Dan Warren <dan.l.warren@gmail.com>
Diff between ENMTools versions 1.0.3 dated 2021-04-02 and 1.0.4 dated 2021-05-07
DESCRIPTION | 8 ++-- MD5 | 70 ++++++++++++++++++++-------------------- NAMESPACE | 7 ++-- NEWS.md | 22 ++++++++++++ R/background.points.buffer.R | 14 ++------ R/background.raster.buffer.R | 17 ++------- R/background.shape.buffer.R | 9 ++--- R/check.bg.R | 61 +++++++++++++++++++++++++++++++--- R/check.env.R |only R/enmtools.bc.R | 30 ++++++++++------- R/enmtools.dm.R | 26 +++++++++----- R/enmtools.ecospat.bg.R | 1 R/enmtools.ecospat.id.R | 1 R/enmtools.gam.R | 30 ++++++++++------- R/enmtools.glm.R | 30 ++++++++++------- R/enmtools.maxent.R | 54 ++++++++++++++++++------------ R/enmtools.rf.R | 30 ++++++++++------- R/enmtools.rf.ranger.R | 32 ++++++++++-------- R/multistack.pca.R | 9 +---- R/package.depends.R | 4 +- R/zzz.R | 2 - man/background.points.buffer.Rd | 4 -- man/background.raster.buffer.Rd | 4 -- man/background.shape.buffer.Rd | 4 -- man/check.bg.Rd | 5 ++ man/check.env.Rd |only man/enmtools.bc.Rd | 6 +++ man/enmtools.dm.Rd | 6 +++ man/enmtools.ecospat.bg.Rd | 1 man/enmtools.ecospat.id.Rd | 1 man/enmtools.gam.Rd | 6 +++ man/enmtools.glm.Rd | 6 +++ man/enmtools.maxent.Rd | 6 +++ man/enmtools.rf.Rd | 6 +++ man/enmtools.rf.ranger.Rd | 6 +++ man/install.extras.Rd | 2 - man/multistack.pca.Rd | 9 +---- 37 files changed, 335 insertions(+), 194 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>),
Andrew Dunning [ctb] (<https://orcid.org/0000-0003-0464-5036>),
Atsushi Yasumoto [ctb, cph] (<https://orcid.org/0000-0002-8335-495X>,
Number sections Lua filter),
Barret Schloerke [ctb],
Carson Sievert [ctb] (<https://orcid.org/0000-0002-4958-2844>),
Christophe Dervieux [ctb],
Devon Ryan [ctb] (<https://orcid.org/0000-0002-8549-0971>),
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Jeff Allen [ctb],
JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>),
Malcolm Barrett [ctb],
Rob Hyndman [ctb],
Romain Lesur [ctb],
Roy Storey [ctb],
Ruben Arslan [ctb],
Sergio Oller [ctb],
RStudio, PBC [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/rmd/h/jqueryui-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Greg Franko [ctb, cph] (tocify library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library),
Dave Gandy [ctb, cph] (Font-Awesome),
Ben Sperry [ctb] (Ionicons),
Drifty [cph] (Ionicons),
Aidan Lister [ctb, cph] (jQuery StickyTabs),
Benct Philip Jonsson [ctb, cph] (pagebreak Lua filter),
Albert Krewinkel [ctb, cph] (pagebreak Lua filter)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 2.7 dated 2021-02-19 and 2.8 dated 2021-05-07
DESCRIPTION | 18 ++--- MD5 | 108 ++++++++++++++++--------------- NEWS.md | 39 ++++++++++- R/beamer_presentation.R | 4 - R/context_document.R | 2 R/html_document.R | 30 ++------ R/html_document_base.R | 64 +++++++++++++++++- R/html_vignette.R | 1 R/ioslides_presentation.R | 3 R/output_format.R | 39 ++++++++--- R/pandoc.R | 2 R/pdf_document.R | 6 - R/render.R | 54 ++++++++------- R/render_site.R | 16 ++-- R/shiny.R | 23 ++++-- R/shiny_prerendered.R | 44 +++++++++--- R/slidy_presentation.R | 1 R/tufte_handout.R | 24 ++---- R/util.R | 6 - README.md | 24 ++++-- build/vignette.rds |binary inst/doc/lua-filters.Rmd | 40 ++++++++++- inst/doc/lua-filters.html | 85 +++++++++++++++--------- inst/doc/rmarkdown.R | 13 +++ inst/doc/rmarkdown.Rmd | 66 ++++++++++++++---- inst/doc/rmarkdown.html | 46 +++++++++---- inst/rmarkdown/lua/latex-div.lua | 20 ++++- inst/rmarkdown/lua/number-sections.lua | 17 ++++ inst/rmarkdown/lua/pagebreak.lua | 17 ++++ inst/rmarkdown/lua/shared.lua |only inst/rmd/h/default.html | 11 ++- inst/rmd/h/navigation-1.1/codefolding.js | 17 ++++ inst/rmd/ioslides/default.html | 3 inst/rmd/slidy/default.html | 3 man/beamer_presentation.Rd | 4 - man/context_document.Rd | 2 man/figures |only man/html_document.Rd | 9 +- man/html_document_base.Rd | 6 + man/html_notebook.Rd | 5 + man/html_vignette.Rd | 2 man/ioslides_presentation.Rd | 2 man/pandoc_args.Rd | 2 man/pandoc_options.Rd | 2 man/pdf_document.Rd | 4 - man/render.Rd | 5 + man/render_site.Rd | 16 ++-- man/slidy_presentation.Rd | 2 man/tufte_handout.Rd | 19 ----- tests/testthat/_snaps/lua-filters.md |only tests/testthat/helpers.R | 30 +++++++- tests/testthat/test-lua-filters.R | 49 ++++++++++++-- tests/testthat/test-output_format.R | 8 ++ tests/testthat/test-shiny.R | 15 +++- tests/testthat/test-shiny_prerendered.R |only vignettes/lua-filters.Rmd | 40 ++++++++++- vignettes/rmarkdown.Rmd | 66 ++++++++++++++---- 57 files changed, 817 insertions(+), 317 deletions(-)