Title: Functional Analysis of Phenotypic Growth Data to Smooth and
Extract Traits
Description: Assists in the plotting and functional smoothing of traits
measured over time and the extraction of features from these traits,
implementing the SET (Smoothing and Extraction of Traits) method
described in Brien et al. (2020) Plant Methods, 16. Smoothing of
growth trends for individual plants using natural cubic smoothing
splines or P-splines is available for removing transient effects and
segmented smoothing is available to deal with discontinuities in
growth trends. There are graphical tools for assessing the adequacy
of trait smoothing, both when using this and other packages, such as
those that fit nonlinear growth models. A range of per-unit (plant,
pot, plot) growth traits or features can be extracted from the
data, including single time points, interval growth rates and other
growth statistics, such as maximum growth or days to maximum growth.
The package also has tools adapted to inputting data from
high-throughput phenotyping facilities, such from a Lemna-Tec
Scananalyzer 3D ( [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between growthPheno versions 2.1.23 dated 2023-10-24 and 2.1.24 dated 2024-02-28
DESCRIPTION | 9 MD5 | 30 R/dataLongi_v9.r | 32 R/traitSmooth.r | 22 build/partial.rdb |binary build/vignette.rds |binary inst/News.Rd | 5 inst/doc/Rice.pdf |binary inst/doc/Tomato.pdf |binary inst/doc/growthPheno-manual.pdf |binary man/args4chosen_plot.Rd | 4 man/plotAnom.Rd | 20 man/plotProfiles.Rd | 18 tests/testthat/testProbeSmooths.r | 1260 +++++++++++++++++++------------------ tests/testthat/testTraitWrappers.r | 17 tests/testthat/testexampleData.r | 36 - 16 files changed, 776 insertions(+), 677 deletions(-)
Title: Data and Code for Financial Accounting Research
Description: Handy functions and data to support a course book for accounting research.
Gow, Ian and Tongqing Ding (2022) 'Accounting Research: An Introductory Course' <https://iangow.github.io/far_book/>.
Author: Ian Gow [aut, cre]
Maintainer: Ian Gow <iandgow@gmail.com>
Diff between farr versions 0.2.39 dated 2023-12-13 and 0.3.0 dated 2024-02-28
DESCRIPTION | 9 +++-- MD5 | 26 +++++++++------- NAMESPACE | 1 NEWS.md | 7 ++++ R/data.R | 15 +++++++-- R/get_annc_dates.R | 2 - R/get_event_cum_rets.R | 42 ++++++++++++++++++++------ R/get_event_cum_rets_mth.R | 41 ++++++++++++++++++------- R/get_event_rets.R | 72 ++++++++++++++++++++++++++++++--------------- R/get_trading_dates.R | 7 +++- R/system_time.R |only data/camp_attendance.rda |only data/test_scores.rda |binary man/camp_attendance.Rd |only man/system_time.Rd |only man/test_scores.Rd | 4 -- 16 files changed, 156 insertions(+), 70 deletions(-)
Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Description: Implements spatial and spatiotemporal GLMMs (Generalized Linear
Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial
Differential Equation) Gaussian Markov random field approximation to
Gaussian random fields. One common application is for spatially explicit
species distribution models (SDMs).
See Anderson et al. (2022) <doi:10.1101/2022.03.24.485545>.
Author: Sean C. Anderson [aut, cre] ,
Eric J. Ward [aut] ,
Philina A. English [aut] ,
Lewis A. K. Barnett [aut] ,
James T. Thorson [aut, cph] ,
Joe Watson [ctb] ,
Julia Indivero [ctb] ,
Jillian C. Dunic [ctb] ,
Cole C. Monnahan [ctb, cph] ,
Mollie Brooks [ct [...truncated...]
Maintainer: Sean C. Anderson <sean@seananderson.ca>
Diff between sdmTMB versions 0.4.2 dated 2024-01-17 and 0.4.3 dated 2024-02-28
DESCRIPTION | 8 - MD5 | 42 +++++----- NEWS.md | 29 +++++++ R/check.R | 107 +++++++++++++++----------- R/cross-val.R | 6 - R/families.R | 134 +++++++++++++++++---------------- R/fit.R | 51 ++++++------ R/index.R | 2 R/predict.R | 11 ++ R/utils.R | 10 -- inst/CITATION | 5 - man/families.Rd | 33 +++++--- man/sanity.Rd | 6 + man/sdmTMB.Rd | 18 ++-- man/sdmTMB_cv.Rd | 6 - tests/testthat/Rplots.pdf |binary tests/testthat/test-2-fit-less-basic.R | 12 ++ tests/testthat/test-5-residuals.R | 100 ++++++++++++++---------- tests/testthat/test-cross-validation.R | 2 tests/testthat/test-delta.R | 8 - tests/testthat/test-dharma.R | 2 tests/testthat/test-extra-time.R | 66 ++++++++++++++++ 22 files changed, 419 insertions(+), 239 deletions(-)
Title: Semi-Automatic Reporting of Ordinary Surveys
Description: Produces highly customized reports, primarily intended for survey
research. Building on 'Quarto' (<https://quarto.org>), it generates draft
chapters of all specified dependent/independent variables, which can be
further edited by hand, containing figures, tables and analyses (currently
only uni-/bivariate tests of equivalent means/proportions). The feature
'mesos'-reports offer tailor-made batch report production where e.g. an
institution can compare itself to all other participants. Publication tools
are also included, such as password generation for 'mesos'-report sections
on a 'Quarto' Website.
Author: Stephan Daus [aut, cre, cph] ,
Nordic Institute for The Studies of Innovation, Research and Education
[fnd],
Kristiania University College [fnd]
Maintainer: Stephan Daus <stephus.daus@gmail.com>
Diff between saros versions 1.0.1 dated 2024-01-26 and 1.0.4 dated 2024-02-28
DESCRIPTION | 8 MD5 | 158 - NEWS.md | 16 R/add_attributes_unfinished.R | 4 R/add_caption_attribute.R | 4 R/add_section_heading_line.R | 2 R/argument_validation_and_insertion.R | 354 +-- R/attach_indep.R | 2 R/cat_freq_plot_html.R | 493 ++-- R/cat_prop_plot_html.R | 94 R/cat_table.R | 12 R/checks.R | 20 R/chr_table.R | 2 R/colour.R | 546 ++-- R/crosstable3.R | 6 R/data_overview.R | 1048 ++++----- R/default_draft_report_arguments_in_yaml.R | 90 R/draft_report.R | 1853 +++++++--------- R/embed_cat_freq_plot_docx.R | 478 ++-- R/embed_cat_prop_plot_docx.R | 250 +- R/filename_sanitizer.R | 44 R/gen_heading_line.R | 2 R/gen_inner_section.R | 22 R/gen_micro.R | 34 R/gen_qmd_chapters.R | 10 R/gen_qmd_index.R | 126 - R/gen_within_chapter_structure.R | 8 R/globals.R | 78 R/handpick.R | 58 R/insert_obj_in_qmd.R | 6 R/insert_qmd_tablet_tailored_order.R | 8 R/int_plot.R | 492 ++-- R/log_unused_variables.R | 32 R/make_filename_prefix.R | 2 R/prep_cat_freq_plot_docx.R | 478 ++-- R/prep_cat_prop_plot_docx.R | 194 - R/process_yaml.R | 12 R/qualtrics.R | 41 R/remove_empty_col_for_mesos_group.R | 4 R/remove_label_part.R | 68 R/rename_by_labels.R | 214 - R/render.R | 420 +-- R/render_full_reports.R | 270 +- R/replace_stata_labels.R | 2 R/setup_access_restrictions.R | 616 ++--- R/summarize_data.R | 85 R/update_dots.R | 80 R/utils.R | 908 +++---- R/utils_labels.R | 444 +-- R/utils_qmd.R | 22 inst/WORDLIST | 2 man/attach_qualtrics_labels.Rd | 54 man/draft_report.Rd | 1409 ++++++------ man/embed_cat_freq_plot.Rd | 142 - man/embed_cat_freq_plot_docx.Rd | 230 - man/embed_cat_prop_plot.Rd | 140 - man/embed_cat_prop_plot_docx.Rd | 152 - man/gen_qmd_index.Rd | 78 man/handpick.Rd | 48 man/list_available_element_types.Rd | 38 man/omitted_recoder_df.Rd | 214 - man/prep_cat_freq_plot_docx.Rd | 112 man/prep_cat_prop_plot_docx.Rd | 86 man/prepare_safe_render.Rd | 86 man/read_default_draft_report_args.Rd | 42 man/refine_chapter_overview.Rd | 130 - man/render_full_reports.Rd | 86 man/sanitize_labels.Rd | 3 man/setup_access_restrictions.Rd | 99 man/write_default_draft_report_args.Rd | 40 tests/spelling.Rout.save |only tests/testthat.R | 8 tests/testthat/test-argument_validation_and_insertion.R | 136 - tests/testthat/test-draft_report.R | 79 tests/testthat/test-gen_qmd_index.R | 110 tests/testthat/test-rename_by_labels.R | 34 tests/testthat/test-setup_access_restrictions.R |only tests/testthat/test-summarize_data.R | 767 +++--- tests/testthat/test-ungroup_data.R | 18 tests/testthat/test-utils.R | 18 tests/testthat/test_omitted_recoder.R | 138 - 81 files changed, 7406 insertions(+), 7313 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] ,
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 1.0.4 dated 2024-02-21 and 1.0.5 dated 2024-02-28
renv-1.0.4/renv/inst/repos/src/contrib/renv_1.0.4.tar.gz |only renv-1.0.5/renv/DESCRIPTION | 6 - renv-1.0.5/renv/MD5 | 42 ++++---- renv-1.0.5/renv/NEWS.md | 12 ++ renv-1.0.5/renv/R/abi.R | 74 ++++++++++++++- renv-1.0.5/renv/R/activate.R | 2 renv-1.0.5/renv/R/cache.R | 12 +- renv-1.0.5/renv/R/install.R | 21 +++- renv-1.0.5/renv/inst/doc/ci.Rmd | 2 renv-1.0.5/renv/inst/doc/ci.html | 2 renv-1.0.5/renv/inst/doc/package-install.Rmd | 6 - renv-1.0.5/renv/inst/doc/package-install.html | 7 - renv-1.0.5/renv/inst/doc/profiles.Rmd | 2 renv-1.0.5/renv/inst/doc/profiles.html | 2 renv-1.0.5/renv/inst/repos/src/contrib/PACKAGES | 4 renv-1.0.5/renv/inst/repos/src/contrib/PACKAGES.gz |binary renv-1.0.5/renv/inst/repos/src/contrib/PACKAGES.rds |binary renv-1.0.5/renv/inst/repos/src/contrib/renv_1.0.5.tar.gz |only renv-1.0.5/renv/man/activate.Rd | 2 renv-1.0.5/renv/tests/testthat/test-install.R | 15 ++- renv-1.0.5/renv/vignettes/ci.Rmd | 2 renv-1.0.5/renv/vignettes/package-install.Rmd | 6 - renv-1.0.5/renv/vignettes/profiles.Rmd | 2 23 files changed, 166 insertions(+), 55 deletions(-)
Title: A Common API to Clustering
Description: A common interface to specifying clustering models, in the
same style as 'parsnip'. Creates unified interface across different
functions and computational engines.
Author: Emil Hvitfeldt [aut, cre] ,
Kelly Bodwin [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between tidyclust versions 0.2.0 dated 2023-09-25 and 0.2.1 dated 2024-02-28
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/metric-aaa.R | 3 ++- R/tune_cluster.R | 21 ++++++++++++++++----- README.md | 24 ++++++++++++------------ 6 files changed, 42 insertions(+), 26 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. 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>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] ,
Saket Choudhary [ctb] ,
Charlotte Darby [ctb] ,
Jeff Farrell [ctb],
Isabella Grabski [ctb] ,
Christoph Hafemeister [ctb] ,
Yuhan Hao [ctb] ,
Austin Hartman [ctb] ,
Paul Hoffman [ctb] ,
Jaison Jain [ctb] ,
Longda Jiang [ctb] ,
Ma [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between Seurat versions 5.0.1 dated 2023-11-17 and 5.0.2 dated 2024-02-28
Seurat-5.0.1/Seurat/build/partial.rdb |only Seurat-5.0.2/Seurat/DESCRIPTION | 10 Seurat-5.0.2/Seurat/MD5 | 53 +- Seurat-5.0.2/Seurat/NEWS.md | 9 Seurat-5.0.2/Seurat/R/differential_expression.R | 207 +++------- Seurat-5.0.2/Seurat/R/integration5.R | 4 Seurat-5.0.2/Seurat/R/mixscape.R | 10 Seurat-5.0.2/Seurat/R/objects.R | 4 Seurat-5.0.2/Seurat/R/preprocessing.R | 13 Seurat-5.0.2/Seurat/R/preprocessing5.R | 34 + Seurat-5.0.2/Seurat/R/utilities.R | 15 Seurat-5.0.2/Seurat/build/Seurat.pdf |binary Seurat-5.0.2/Seurat/build/stage23.rdb |only Seurat-5.0.2/Seurat/man/DEenrichRPlot.Rd | 2 Seurat-5.0.2/Seurat/man/FindAllMarkers.Rd | 19 Seurat-5.0.2/Seurat/man/FindConservedMarkers.Rd | 4 Seurat-5.0.2/Seurat/man/FindMarkers.Rd | 100 +--- Seurat-5.0.2/Seurat/man/MixscapeHeatmap.Rd | 2 Seurat-5.0.2/Seurat/man/MixscapeLDA.Rd | 2 Seurat-5.0.2/Seurat/man/PrepLDA.Rd | 2 Seurat-5.0.2/Seurat/man/SCTransform.Rd | 7 Seurat-5.0.2/Seurat/man/reexports.Rd | 15 Seurat-5.0.2/Seurat/src/RcppExports.cpp | 2 Seurat-5.0.2/Seurat/tests/testthat/test_differential_expression.R | 25 + Seurat-5.0.2/Seurat/tests/testthat/test_dimensional_reduction.R | 3 Seurat-5.0.2/Seurat/tests/testthat/test_integratedata.R | 97 ---- Seurat-5.0.2/Seurat/tests/testthat/test_integration5.R |only Seurat-5.0.2/Seurat/tests/testthat/test_preprocessing.R | 64 +++ Seurat-5.0.2/Seurat/tests/testthat/test_utilities.R | 31 + 29 files changed, 356 insertions(+), 378 deletions(-)
Title: Conducting Maximum Likelihood Estimation with Truncated
Mortality Data
Description: Estimates hazard ratios and mortality differentials for
doubly-truncated data without population denominators. This method is
described in Goldstein et al. (2023) <doi:10.1007/s11113-023-09785-z>.
Author: Casey Breen [aut] ,
Maria Osborne [aut, cre],
Joshua R. Goldstein [aut]
Maintainer: Maria Osborne <mariaosborne@berkeley.edu>
Diff between gompertztrunc versions 0.1.1 dated 2022-12-23 and 0.1.2 dated 2024-02-28
gompertztrunc-0.1.1/gompertztrunc/data/datalist |only gompertztrunc-0.1.2/gompertztrunc/DESCRIPTION | 18 gompertztrunc-0.1.2/gompertztrunc/MD5 | 21 gompertztrunc-0.1.2/gompertztrunc/NEWS.md | 3 gompertztrunc-0.1.2/gompertztrunc/R/gompertz_mle.R | 38 gompertztrunc-0.1.2/gompertztrunc/build/partial.rdb |binary gompertztrunc-0.1.2/gompertztrunc/build/vignette.rds |binary gompertztrunc-0.1.2/gompertztrunc/inst/doc/gompertztrunc_vignette.R | 12 gompertztrunc-0.1.2/gompertztrunc/inst/doc/gompertztrunc_vignette.Rmd | 8 gompertztrunc-0.1.2/gompertztrunc/inst/doc/gompertztrunc_vignette.html | 1019 ++++++---- gompertztrunc-0.1.2/gompertztrunc/man/gompertz_mle.Rd | 7 gompertztrunc-0.1.2/gompertztrunc/vignettes/gompertztrunc_vignette.Rmd | 8 12 files changed, 728 insertions(+), 406 deletions(-)
Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the
OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped
to the Observational Medical Outcomes Partnership (OMOP) common data model.
New users and prevalent users cohorts can be generated and their
characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [ctb] ,
Xintong Li [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between DrugUtilisation versions 0.5.0 dated 2024-02-10 and 0.5.1 dated 2024-02-28
DESCRIPTION | 6 MD5 | 68 +- NAMESPACE | 2 R/cohortUtilities.R | 46 - R/generateAtcCohortSet.R |only R/generateDrugUtilisationCohortSet.R | 4 R/generateIngredientCohortSet.R |only R/mockDrugUtilisation.R | 2 R/pattern.R | 8 R/readConceptList.R | 362 +++++------ R/summariseTreatment.R | 1 R/utils-pipe.R | 28 README.md | 325 +++++----- build/vignette.rds |binary inst/doc/a01_introCreateCohort.R | 18 inst/doc/a01_introCreateCohort.Rmd | 678 ++++++++++----------- inst/doc/a01_introCreateCohort.html | 114 +-- inst/doc/a02_scalingOfInstantiateCohorts.html | 4 inst/doc/a03_addIndications-example.R | 2 inst/doc/a03_addIndications-example.Rmd | 2 inst/doc/a03_addIndications-example.html | 42 - inst/doc/a04_addDrugInfo.html | 160 ++-- inst/doc/a05_treatmentDiscontinuation.html | 4 inst/doc/a06_treatmentSummary.R | 18 inst/doc/a06_treatmentSummary.Rmd | 18 inst/doc/a06_treatmentSummary.html | 70 +- inst/doc/a07_characteriseACohort.html | 4 inst/doc/routePatternDose.html | 68 +- man/generateAtcCohortSet.Rd |only man/generateDrugUtilisationCohortSet.Rd | 4 man/generateIngredientCohortSet.Rd |only tests/testthat/test-generateConceptCohortSet.R | 28 tests/testthat/test-generatedAtcCohortSet.R |only tests/testthat/test-generatedIngredientCohortSet.R |only tests/testthat/test-readConceptList.R | 28 vignettes/a01_introCreateCohort.Rmd | 678 ++++++++++----------- vignettes/a03_addIndications-example.Rmd | 2 vignettes/a06_treatmentSummary.Rmd | 18 38 files changed, 1433 insertions(+), 1379 deletions(-)
More information about DrugUtilisation at CRAN
Permanent link
Title: Simulate Temporally Autocorrelated Populations
Description: Temporally autocorrelated populations are correlated in their vital rates (growth, death, etc.) from year to year. It is very common for populations, whether they be bacteria, plants, or humans, to be temporally autocorrelated. This poses a challenge for stochastic population modeling, because a temporally correlated population will behave differently from an uncorrelated one.
This package provides tools for simulating populations with white noise (no temporal autocorrelation), red noise (positive temporal autocorrelation), and blue noise (negative temporal autocorrelation). The algebraic formulation for autocorrelated noise comes from Ruokolainen et al. (2009) <doi:10.1016/j.tree.2009.04.009>. Models for unstructured populations and for structured populations (matrix models) are available.
Author: July Pilowsky [aut, cre]
Maintainer: July Pilowsky <pilowskyj@caryinstitute.org>
Diff between colorednoise versions 1.1.1 dated 2023-09-22 and 1.1.2 dated 2024-02-28
colorednoise-1.1.1/colorednoise/R/colorednoise.R |only colorednoise-1.1.1/colorednoise/man/colorednoise.Rd |only colorednoise-1.1.2/colorednoise/DESCRIPTION | 10 colorednoise-1.1.2/colorednoise/MD5 | 53 colorednoise-1.1.2/colorednoise/NAMESPACE | 38 colorednoise-1.1.2/colorednoise/NEWS.md | 75 colorednoise-1.1.2/colorednoise/R/RcppExports.R | 310 +- colorednoise-1.1.2/colorednoise/R/colorednoise-package.R |only colorednoise-1.1.2/colorednoise/R/simulate_populations.R | 502 ++-- colorednoise-1.1.2/colorednoise/R/utils.R | 54 colorednoise-1.1.2/colorednoise/README.md | 126 - colorednoise-1.1.2/colorednoise/build/partial.rdb |only colorednoise-1.1.2/colorednoise/build/vignette.rds |binary colorednoise-1.1.2/colorednoise/inst/doc/noise.R | 196 - colorednoise-1.1.2/colorednoise/inst/doc/noise.Rmd | 340 +- colorednoise-1.1.2/colorednoise/inst/doc/noise.html | 1167 +++++----- colorednoise-1.1.2/colorednoise/man/autocorr_sim.Rd | 138 - colorednoise-1.1.2/colorednoise/man/autocorrelation.Rd | 54 colorednoise-1.1.2/colorednoise/man/colored_multi_rnorm.Rd | 72 colorednoise-1.1.2/colorednoise/man/colored_noise.Rd | 64 colorednoise-1.1.2/colorednoise/man/colorednoise-package.Rd |only colorednoise-1.1.2/colorednoise/man/cor2cov.Rd | 50 colorednoise-1.1.2/colorednoise/man/matrix_model.Rd | 156 - colorednoise-1.1.2/colorednoise/man/multi_rnorm.Rd | 56 colorednoise-1.1.2/colorednoise/man/stdev_transform.Rd | 68 colorednoise-1.1.2/colorednoise/man/unstructured_pop.Rd | 138 - colorednoise-1.1.2/colorednoise/tests/testthat.R | 8 colorednoise-1.1.2/colorednoise/tests/testthat/test_noise.R | 88 colorednoise-1.1.2/colorednoise/tests/testthat/test_simulations.R | 90 colorednoise-1.1.2/colorednoise/vignettes/noise.Rmd | 340 +- 30 files changed, 2112 insertions(+), 2081 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb]
Maintainer: Samuel Marsh <samuel.marsh@childrens.harvard.edu>
Diff between scCustomize versions 2.1.1 dated 2024-02-24 and 2.1.2 dated 2024-02-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 14 ++++++++++++++ R/Nebulosa_Plotting.R | 14 ++++++++++++-- man/Plot_Density_Custom.Rd | 2 +- man/Plot_Density_Joint_Only.Rd | 2 +- 6 files changed, 37 insertions(+), 13 deletions(-)
Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
Description: R and 'Eigen' integration using 'Rcpp'.
'Eigen' is a C++ template library for linear algebra: matrices, vectors,
numerical solvers and related algorithms. It supports dense and sparse
matrices on integer, floating point and complex numbers, decompositions of
such matrices, and solutions of linear systems. Its performance on many
algorithms is comparable with some of the best implementations based on
'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header
files from the 'Eigen' C++ template library. Thus users do not need to
install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1,
'Eigen' is licensed under the Mozilla Public License (version 2); earlier
version were licensed under the GNU LGPL version 3 or later. 'RcppEigen'
(the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL
version 2 or later, as is the rest of 'Rcpp'.
Author: Douglas Bates, Dirk Eddelbuettel, Romain Francois, and Yixuan Qiu;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppEigen versions 0.3.3.9.4 dated 2023-11-02 and 0.3.4.0.0 dated 2024-02-28
RcppEigen-0.3.3.9.4/RcppEigen/inst/include/Eigen/src/Core/arch/CUDA/Half.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/Eigen/src/Core/arch/CUDA/MathFunctions.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/Eigen/src/Core/arch/CUDA/PacketMath.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/Eigen/src/Core/arch/CUDA/PacketMathHalf.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/Eigen/src/Core/arch/CUDA/TypeCasting.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/Eigen/src/Geometry/arch/Geometry_SSE.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/Eigen/src/LU/arch/Inverse_SSE.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSycl.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclConvertToDeviceExpression.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclExprConstructor.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclExtractAccessor.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclExtractFunctors.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclLeafCount.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclPlaceHolderExpr.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclRun.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorSyclTuple.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/ThreadPool/SimpleThreadPool.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/util/EmulateCXX11Meta.h |only RcppEigen-0.3.3.9.4/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/arch/CUDA |only RcppEigen-0.3.4.0.0/RcppEigen/ChangeLog | 18 RcppEigen-0.3.4.0.0/RcppEigen/DESCRIPTION | 8 RcppEigen-0.3.4.0.0/RcppEigen/MD5 | 812 - RcppEigen-0.3.4.0.0/RcppEigen/inst/NEWS.Rd | 10 RcppEigen-0.3.4.0.0/RcppEigen/inst/doc/RcppEigen-Introduction.pdf |binary RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/Cholesky | 1 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/CholmodSupport | 1 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/Core | 378 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/Eigenvalues | 1 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/Geometry | 9 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/Householder | 1 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/Jacobi | 1 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/KLUSupport |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/LU | 7 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/OrderingMethods | 3 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/PaStiXSupport | 1 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/QR | 1 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/QtAlignedMalloc | 1 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/SVD | 1 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/Sparse | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/SparseCholesky | 8 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/SparseLU | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Cholesky/LDLT.h | 69 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Cholesky/LLT.h | 62 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h | 141 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/ArithmeticSequence.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Array.h | 110 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/ArrayBase.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/ArrayWrapper.h | 42 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Assign.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/AssignEvaluator.h | 175 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Assign_MKL.h | 20 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/BandMatrix.h | 32 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Block.h | 116 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/BooleanRedux.h | 60 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/CommaInitializer.h | 10 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/CoreEvaluators.h | 597 - RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/CoreIterators.h | 5 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/CwiseBinaryOp.h | 43 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/CwiseNullaryOp.h | 171 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/CwiseUnaryOp.h | 12 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/CwiseUnaryView.h | 22 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/DenseBase.h | 167 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/DenseCoeffsBase.h | 46 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/DenseStorage.h | 218 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Diagonal.h | 44 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/DiagonalMatrix.h | 52 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/DiagonalProduct.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Dot.h | 20 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/EigenBase.h | 19 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/ForceAlignedAccess.h | 12 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Fuzzy.h | 6 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/GeneralProduct.h | 30 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/GenericPacketMath.h | 744 + RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/GlobalFunctions.h | 73 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/IO.h | 47 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/IndexedView.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Inverse.h | 19 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Map.h | 14 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/MapBase.h | 8 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/MathFunctions.h | 876 + RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/MathFunctionsImpl.h | 137 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Matrix.h | 156 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/MatrixBase.h | 21 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/NestByValue.h | 75 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/NoAlias.h | 7 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/NumTraits.h | 127 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/PartialReduxEvaluator.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/PermutationMatrix.h | 6 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/PlainObjectBase.h | 199 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Product.h | 57 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/ProductEvaluators.h | 325 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Random.h | 38 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Redux.h | 350 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Ref.h | 139 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Replicate.h | 16 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Reshaped.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/ReturnByValue.h | 12 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Reverse.h | 30 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Select.h | 14 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/SelfAdjointView.h | 53 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Solve.h | 28 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/SolveTriangular.h | 26 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/SolverBase.h | 44 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/StableNorm.h | 170 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/StlIterators.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Stride.h | 13 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Swap.h | 9 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Transpose.h | 113 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Transpositions.h | 34 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/TriangularMatrix.h | 160 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/VectorBlock.h | 10 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/VectorwiseOp.h | 229 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/Visitor.h | 166 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX/Complex.h | 179 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX/MathFunctions.h | 467 - RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX/PacketMath.h | 1247 ++ RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX/TypeCasting.h | 66 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX512/Complex.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX512/MathFunctions.h | 397 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX512/PacketMath.h | 1508 ++- RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AVX512/TypeCasting.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/Complex.h | 317 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/MathFunctions.h | 270 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/MatrixProduct.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/PacketMath.h | 2344 ++++- RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/CUDA/Complex.h | 315 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/Default/BFloat16.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/Default/ConjHelper.h | 116 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/Default/GenericPacketMathFunctions.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/Default/GenericPacketMathFunctionsFwd.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/Default/Half.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/Default/Settings.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/Default/TypeCasting.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/GPU |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/HIP |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/MSA |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/Complex.h | 536 - RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/GeneralBlockPanelKernel.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/MathFunctions.h | 122 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/PacketMath.h | 4639 +++++++++- RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/TypeCasting.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/Complex.h | 238 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/MathFunctions.h | 495 - RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/PacketMath.h | 1192 +- RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/TypeCasting.h | 65 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/SVE |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/SYCL |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/ZVector/Complex.h | 395 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/ZVector/MathFunctions.h | 106 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/arch/ZVector/PacketMath.h | 883 + RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/functors/AssignmentFunctors.h | 13 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/functors/BinaryFunctors.h | 158 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/functors/NullaryFunctors.h | 61 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/functors/StlFunctors.h | 34 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/functors/UnaryFunctors.h | 369 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralBlockPanelKernel.h | 1652 ++- RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrix.h | 36 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h | 8 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixVector.h | 895 - RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/Parallelizer.h | 32 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointMatrixMatrix.h | 29 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h | 14 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointProduct.h | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointRank2Update.h | 9 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/TriangularMatrixMatrix.h | 6 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/TriangularSolverMatrix.h | 8 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/products/TriangularSolverVector.h | 23 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/BlasUtil.h | 332 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/ConfigureVectorization.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/Constants.h | 34 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/DisableStupidWarnings.h | 19 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/ForwardDeclarations.h | 32 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/IndexedViewHelper.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/IntegralConstant.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/MKL_support.h | 9 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/Macros.h | 911 + RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/Memory.h | 274 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/Meta.h | 458 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/ReshapedHelper.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/StaticAssert.h | 13 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/SymbolicIndex.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Core/util/XprHelper.h | 78 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/ComplexEigenSolver.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/ComplexSchur.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/EigenSolver.h | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/HessenbergDecomposition.h | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/RealQZ.h | 15 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/RealSchur.h | 15 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h | 117 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Eigenvalues/Tridiagonalization.h | 35 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/AlignedBox.h | 104 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/AngleAxis.h | 8 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/EulerAngles.h | 6 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/Homogeneous.h | 26 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/Hyperplane.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/OrthoMethods.h | 5 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/ParametrizedLine.h | 41 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/Quaternion.h | 66 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/Rotation2D.h | 6 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/Scaling.h | 26 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/Transform.h | 151 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/Translation.h | 12 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Geometry/arch/Geometry_SIMD.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Householder/BlockHouseholder.h | 11 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Householder/Householder.h | 12 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Householder/HouseholderSequence.h | 173 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h | 30 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h | 30 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h | 27 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h | 88 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h | 111 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h | 90 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h | 22 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h | 20 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/Jacobi/Jacobi.h | 41 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/KLUSupport |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/LU/Determinant.h | 54 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/LU/FullPivLU.h | 72 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/LU/InverseImpl.h | 33 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/LU/PartialPivLU.h | 124 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/LU/arch/InverseSize4.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/OrderingMethods/Amd.h | 24 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/OrderingMethods/Eigen_Colamd.h | 582 - RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/OrderingMethods/Ordering.h | 16 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/PaStiXSupport/PaStiXSupport.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/PardisoSupport/PardisoSupport.h | 19 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/QR/ColPivHouseholderQR.h | 61 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/QR/CompleteOrthogonalDecomposition.h | 127 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/QR/FullPivHouseholderQR.h | 81 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/QR/HouseholderQR.h | 71 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h | 28 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SVD/BDCSVD.h | 187 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SVD/JacobiSVD.h | 36 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SVD/SVDBase.h | 103 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SVD/UpperBidiagonalization.h | 6 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCholesky/SimplicialCholesky.h | 24 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h | 47 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/CompressedStorage.h | 16 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h | 12 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseAssign.h | 108 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseBlock.h | 82 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseCompressedBase.h | 51 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseCwiseBinaryOp.h | 26 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseCwiseUnaryOp.h | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseDenseProduct.h | 38 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseMatrix.h | 134 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseMatrixBase.h | 17 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseProduct.h | 14 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseRef.h | 14 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseSelfAdjointView.h | 3 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseUtil.h | 8 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseCore/SparseVector.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU.h | 170 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_Memory.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h | 78 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_column_dfs.h | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_gemm_kernel.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseLU/SparseLU_panel_bmod.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SparseQR/SparseQR.h | 25 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/StlSupport/StdDeque.h | 16 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/StlSupport/StdList.h | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/StlSupport/StdVector.h | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/SuperLUSupport/SuperLUSupport.h | 14 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/UmfPackSupport/UmfPackSupport.h | 214 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/misc/lapacke.h | 9 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/ArrayCwiseBinaryOps.h | 28 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/ArrayCwiseUnaryOps.h | 166 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/BlockMethods.h | 926 + RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/CommonCwiseUnaryOps.h | 14 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/IndexedViewMethods.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/MatrixCwiseBinaryOps.h | 8 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/MatrixCwiseUnaryOps.h | 10 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/Eigen/src/plugins/ReshapedMethods.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/AdolcForward | 5 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/AlignedVector3 | 12 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/ArpackSupport | 9 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/AutoDiff | 6 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/BVH | 6 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/Tensor | 77 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/TensorSymmetry | 6 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/ThreadPool | 21 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/README.md | 371 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/Tensor.h | 29 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h | 78 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h | 94 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h | 268 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h | 767 + RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h | 278 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h | 84 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h | 623 + RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h | 41 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h | 1393 --- RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h | 238 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h | 1578 ++- RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h | 269 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h | 190 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h | 10 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h | 90 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h | 69 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceCuda.h | 337 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceDefault.h | 33 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceGpu.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceSycl.h | 1070 ++ RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceThreadPool.h | 347 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDimensions.h | 162 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorEvalTo.h | 111 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h | 634 + RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h | 695 + RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorExpr.h | 23 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorFFT.h | 86 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorFixedSize.h | 34 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorForcedEval.h | 190 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorForwardDeclarations.h | 90 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorFunctors.h | 191 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorGenerator.h | 149 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaDefines.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaUndefines.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorImagePatch.h | 164 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorIndexList.h | 203 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorInflation.h | 28 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorInitializer.h | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorIntDiv.h | 28 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorLayoutSwap.h | 71 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorMacros.h | 52 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorMap.h | 114 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorMeta.h | 129 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorMorphing.h | 568 - RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorPadding.h | 375 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorPatch.h | 32 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorRandom.h | 198 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h | 383 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorReductionCuda.h | 750 - RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorReductionGpu.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorReductionSycl.h | 746 + RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorRef.h | 37 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorReverse.h | 263 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorScan.h | 423 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorScanSycl.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorShuffling.h | 325 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorStorage.h | 27 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorStriding.h | 78 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorTrace.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorTraits.h | 44 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorUInt128.h | 1 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorVolumePatch.h | 103 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/TensorSymmetry/util/TemplateGroupTheory.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/ThreadPool/Barrier.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/ThreadPool/EventCount.h | 196 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/ThreadPool/NonBlockingThreadPool.h | 398 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/ThreadPool/RunQueue.h | 98 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/ThreadPool/ThreadCancel.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/ThreadPool/ThreadEnvironment.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/ThreadPool/ThreadLocal.h | 289 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/ThreadPool/ThreadPoolInterface.h | 15 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/ThreadPool/ThreadYield.h | 1 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/util/CXX11Meta.h | 93 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/util/CXX11Workarounds.h | 8 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/util/EmulateArray.h | 54 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/CXX11/src/util/MaxSizeVector.h | 51 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/EulerAngles | 8 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/FFT | 12 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/IterativeSolvers | 21 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/LevenbergMarquardt | 16 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/MPRealSupport | 6 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/MatrixFunctions | 10 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/MoreVectorization | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/NonLinearOptimization | 44 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/NumericalDiff | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/OpenGLSupport | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/Polynomials | 9 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/Skyline | 6 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/SparseExtra | 1 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/SpecialFunctions | 46 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/Splines | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/AutoDiff/AutoDiffScalar.h | 80 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/BVH/KdBVH.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/Eigenvalues/ArpackSelfAdjointEigenSolver.h | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/EulerAngles/EulerAngles.h | 261 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/EulerAngles/EulerSystem.h | 197 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/FFT/ei_fftw_impl.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/FFT/ei_kissfft_impl.h | 55 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h | 10 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/DGMRES.h | 63 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/GMRES.h | 36 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/IterationController.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/MINRES.h | 38 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/Scaling.h | 6 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/LevenbergMarquardt/LMqrsolv.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h | 6 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h | 5 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h | 29 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h | 20 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h | 20 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h | 12 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h | 6 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/r1updt.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/Polynomials/Companion.h | 51 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h | 4 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/Skyline/SkylineMatrix.h | 18 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h | 10 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/Skyline/SkylineStorage.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h | 8 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SparseExtra/MarketIO.h | 93 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h | 130 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SparseExtra/RandomSetter.h | 54 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsArrayAPI.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsBFloat16.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsFunctors.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsHalf.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsImpl.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsPacketMath.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h | 55 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h | 140 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h | 11 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h | 1048 +- RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h | 23 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/arch/AVX |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/arch/AVX512 |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/arch/GPU |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/SpecialFunctions/arch/NEON |only RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/Splines/Spline.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/Splines/SplineFitting.h | 11 RcppEigen-0.3.4.0.0/RcppEigen/inst/include/unsupported/Eigen/src/Splines/SplineFwd.h | 2 RcppEigen-0.3.4.0.0/RcppEigen/src/fastLm.cpp | 4 439 files changed, 37246 insertions(+), 17358 deletions(-)
Title: Generate Personality Insights Sunburst Diagrams
Description: Generates Personality Insights sunburst diagrams based on
'IBM Watson' Personality Insights service output.
Author: Colin Gillespie [aut, cre],
Steph Locke [aut] ,
IBM [cph] ,
Hendrik Feddersen [fnd] ,
Kent Russell [aut],
Maelle Salmon [ctb] ,
Jumping Rivers [fnd]
Maintainer: Colin Gillespie <colin@jumpingrivers.com>
Diff between ibmsunburst versions 0.1.3 dated 2023-10-30 and 0.1.4 dated 2024-02-28
DESCRIPTION | 12 ++++---- MD5 | 8 ++--- NEWS.md | 4 ++ build/vignette.rds |binary inst/doc/ibmsunburst.html | 64 +++++++++++++++++++++++----------------------- 5 files changed, 46 insertions(+), 42 deletions(-)
Title: Modules to Import and Manipulate Data in 'Shiny'
Description: 'Shiny' modules to import data into an application or 'addin'
from various sources, and to manipulate them after that.
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
Samra Goumri [aut],
Zauad Shahreer Abeer [aut],
Eduard Szoecs [ctb]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between datamods versions 1.4.4 dated 2024-02-08 and 1.4.5 dated 2024-02-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/edit-data.R | 2 ++ man/select-group.Rd | 2 +- 5 files changed, 16 insertions(+), 8 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] ,
Mike Bostock [cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between apexcharter versions 0.4.1 dated 2023-06-14 and 0.4.2 dated 2024-02-28
DESCRIPTION | 8 MD5 | 28 +- NAMESPACE | 1 NEWS.md | 7 R/apex.R | 5 R/data.R | 2 build/vignette.rds |binary inst/doc/apexcharter.R | 6 inst/doc/apexcharter.Rmd | 7 inst/doc/apexcharter.html | 380 ++++++++++++++-------------- inst/htmlwidgets/apexcharter.js | 2 inst/htmlwidgets/apexcharter.js.LICENSE.txt | 4 man/apexcharter-package.Rd | 10 man/unhcr_ts.Rd | 2 vignettes/apexcharter.Rmd | 7 15 files changed, 254 insertions(+), 215 deletions(-)
Title: Diversity-Interactions (DI) Models
Description: The 'DImodels' package is suitable for analysing data from biodiversity and ecosystem function studies using the Diversity-Interactions (DI) modelling approach introduced by Kirwan et al. (2009) <doi:10.1890/08-1684.1>. Suitable data will contain proportions for each species and a community-level response variable, and may also include additional factors, such as blocks or treatments. The package can perform data manipulation tasks, such as computing pairwise interactions (the DI_data() function), can perform an automated model selection process (the autoDI() function) and has the flexibility to fit a wide range of user-defined DI models (the DI() function).
Author: Rafael de Andrade Moral [aut, cre],
John Connolly [aut],
Rishabh Vishwakarma [ctb],
Caroline Brophy [aut]
Maintainer: Rafael de Andrade Moral <rafael.deandrademoral@mu.ie>
Diff between DImodels versions 1.3.1 dated 2024-01-24 and 1.3.2 dated 2024-02-28
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/DI_internal.R | 35 ++++++++++++++++++++++------------- R/predictDI.R | 20 ++++++++------------ build/partial.rdb |binary tests/testthat/test-DI.R | 10 +++++++++- tests/testthat/test-predictDI.R | 11 ++++------- 7 files changed, 53 insertions(+), 43 deletions(-)
Title: Probability Computations on Pedigrees
Description: An implementation of the Elston-Stewart algorithm for
calculating pedigree likelihoods given genetic marker data (Elston and
Stewart (1971) <doi:10.1159/000152448>). The standard algorithm is
extended to allow inbred founders. 'pedprobr' is part of the 'ped
suite', a collection of packages for pedigree analysis in R. In
particular, 'pedprobr' depends on 'pedtools' for pedigree
manipulations and 'pedmut' for mutation modelling. For more
information, see 'Pedigree Analysis in R' (Vigeland, 2021,
ISBN:9780128244302).
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedprobr versions 0.8.0 dated 2023-04-13 and 0.9.2 dated 2024-02-28
pedprobr-0.8.0/pedprobr/R/likelihood-startdata.R |only pedprobr-0.9.2/pedprobr/DESCRIPTION | 8 pedprobr-0.9.2/pedprobr/MD5 | 53 - pedprobr-0.9.2/pedprobr/NEWS.md | 14 pedprobr-0.9.2/pedprobr/R/buildGenolist.R | 17 pedprobr-0.9.2/pedprobr/R/genoCombinations.R | 5 pedprobr-0.9.2/pedprobr/R/informative.R | 5 pedprobr-0.9.2/pedprobr/R/likelihood.R | 42 - pedprobr-0.9.2/pedprobr/R/likelihood2.R | 22 pedprobr-0.9.2/pedprobr/R/merlin.R | 6 pedprobr-0.9.2/pedprobr/R/oneMarkerDistribution.R | 11 pedprobr-0.9.2/pedprobr/R/peel.R | 359 +++------- pedprobr-0.9.2/pedprobr/R/setMutationModel.R | 12 pedprobr-0.9.2/pedprobr/R/startdata.R |only pedprobr-0.9.2/pedprobr/R/twoMarkerDistribution.R | 27 pedprobr-0.9.2/pedprobr/R/utils.R | 20 pedprobr-0.9.2/pedprobr/build/partial.rdb |binary pedprobr-0.9.2/pedprobr/inst |only pedprobr-0.9.2/pedprobr/man/HWprob.Rd | 56 - pedprobr-0.9.2/pedprobr/man/likelihood.Rd | 349 ++++----- pedprobr-0.9.2/pedprobr/man/merlin.Rd | 344 ++++----- pedprobr-0.9.2/pedprobr/man/oneMarkerDistribution.Rd | 4 pedprobr-0.9.2/pedprobr/man/setMutationModel.Rd | 148 ++-- pedprobr-0.9.2/pedprobr/man/twoMarkerDistribution.Rd | 149 ++-- pedprobr-0.9.2/pedprobr/tests/testthat/test-inbred-founders.R | 1 pedprobr-0.9.2/pedprobr/tests/testthat/test-likelihood-linked.R | 14 pedprobr-0.9.2/pedprobr/tests/testthat/test-likelihood.R | 4 pedprobr-0.9.2/pedprobr/tests/testthat/test-merlin.R | 28 pedprobr-0.9.2/pedprobr/tests/testthat/test-twoMarkerDist.R | 17 29 files changed, 833 insertions(+), 882 deletions(-)
Title: Tagging and Validating Epidemiological Data
Description: Provides tools to help storing and handling case line list data. The 'linelist' class adds a tagging system to classical 'data.frame' objects to identify key epidemiological data such as dates of symptom onset, epidemiological case definition, age, gender or disease outcome. Once tagged, these variables can be seamlessly used in downstream analyses, making data pipelines more robust and reliable.
Author: Hugo Gruson [aut, cre] ,
Thibaut Jombart [aut, ccp],
Tim Taylor [ctb],
Chris Hartgerink [rev]
Maintainer: Hugo Gruson <hugo@data.org>
Diff between linelist versions 1.0.0 dated 2023-10-19 and 1.1.0 dated 2024-02-28
linelist-1.0.0/linelist/R/linelist.R |only linelist-1.0.0/linelist/R/validate_type.R |only linelist-1.0.0/linelist/man/linelist.Rd |only linelist-1.0.0/linelist/tests/testthat/test-tag_variable.R |only linelist-1.0.0/linelist/tests/testthat/test-validate_type.R |only linelist-1.1.0/linelist/DESCRIPTION | 33 linelist-1.1.0/linelist/LICENSE | 2 linelist-1.1.0/linelist/MD5 | 139 +-- linelist-1.1.0/linelist/NAMESPACE | 4 linelist-1.1.0/linelist/NEWS.md | 137 +++ linelist-1.1.0/linelist/R/custom_assertions.R | 1 linelist-1.1.0/linelist/R/drop_linelist.R | 2 linelist-1.1.0/linelist/R/linelist-package.R |only linelist-1.1.0/linelist/R/lost_tags_action.R | 10 linelist-1.1.0/linelist/R/make_linelist.R | 68 + linelist-1.1.0/linelist/R/names.R | 2 linelist-1.1.0/linelist/R/print.linelist.R | 2 linelist-1.1.0/linelist/R/prune_tags.R | 10 linelist-1.1.0/linelist/R/restore_tags.R | 2 linelist-1.1.0/linelist/R/select_tags.R | 2 linelist-1.1.0/linelist/R/set_tags.R | 22 linelist-1.1.0/linelist/R/square_bracket.R | 27 linelist-1.1.0/linelist/R/tag_variable.R | 53 - linelist-1.1.0/linelist/R/tags.R | 2 linelist-1.1.0/linelist/R/tags_defaults.R | 22 linelist-1.1.0/linelist/R/tags_df.R | 2 linelist-1.1.0/linelist/R/tags_names.R | 2 linelist-1.1.0/linelist/R/tags_types.R | 8 linelist-1.1.0/linelist/R/validate_linelist.R | 2 linelist-1.1.0/linelist/R/validate_tags.R | 2 linelist-1.1.0/linelist/R/validate_types.R | 42 - linelist-1.1.0/linelist/build/vignette.rds |binary linelist-1.1.0/linelist/inst/WORDLIST |only linelist-1.1.0/linelist/inst/doc/compat-dplyr.Rmd | 2 linelist-1.1.0/linelist/inst/doc/compat-dplyr.html | 26 linelist-1.1.0/linelist/inst/doc/design-principles.R |only linelist-1.1.0/linelist/inst/doc/design-principles.Rmd |only linelist-1.1.0/linelist/inst/doc/design-principles.html |only linelist-1.1.0/linelist/inst/doc/linelist.R | 22 linelist-1.1.0/linelist/inst/doc/linelist.Rmd | 70 - linelist-1.1.0/linelist/inst/doc/linelist.html | 408 ++++------ linelist-1.1.0/linelist/man/figures/README-unnamed-chunk-8-1.png |binary linelist-1.1.0/linelist/man/figures/lifecycle-archived.svg |only linelist-1.1.0/linelist/man/figures/lifecycle-defunct.svg |only linelist-1.1.0/linelist/man/figures/lifecycle-deprecated.svg |only linelist-1.1.0/linelist/man/figures/lifecycle-experimental.svg |only linelist-1.1.0/linelist/man/figures/lifecycle-maturing.svg |only linelist-1.1.0/linelist/man/figures/lifecycle-questioning.svg |only linelist-1.1.0/linelist/man/figures/lifecycle-soft-deprecated.svg |only linelist-1.1.0/linelist/man/figures/lifecycle-stable.svg |only linelist-1.1.0/linelist/man/figures/lifecycle-superseded.svg |only linelist-1.1.0/linelist/man/linelist-package.Rd |only linelist-1.1.0/linelist/man/lost_tags_action.Rd | 12 linelist-1.1.0/linelist/man/make_linelist.Rd | 37 linelist-1.1.0/linelist/man/names-set-.linelist.Rd | 3 linelist-1.1.0/linelist/man/print.linelist.Rd | 3 linelist-1.1.0/linelist/man/select_tags.Rd | 3 linelist-1.1.0/linelist/man/set_tags.Rd | 15 linelist-1.1.0/linelist/man/sub_linelist.Rd | 16 linelist-1.1.0/linelist/man/tags.Rd | 3 linelist-1.1.0/linelist/man/tags_defaults.Rd | 3 linelist-1.1.0/linelist/man/tags_df.Rd | 3 linelist-1.1.0/linelist/man/tags_names.Rd | 3 linelist-1.1.0/linelist/man/tags_types.Rd | 13 linelist-1.1.0/linelist/man/validate_linelist.Rd | 3 linelist-1.1.0/linelist/man/validate_tags.Rd | 3 linelist-1.1.0/linelist/man/validate_types.Rd | 3 linelist-1.1.0/linelist/tests/spelling.R |only linelist-1.1.0/linelist/tests/testthat.R | 12 linelist-1.1.0/linelist/tests/testthat/_snaps/deprecated.md | 128 +++ linelist-1.1.0/linelist/tests/testthat/_snaps/validate_types.md |only linelist-1.1.0/linelist/tests/testthat/helper-state.R |only linelist-1.1.0/linelist/tests/testthat/test-deprecated.R | 14 linelist-1.1.0/linelist/tests/testthat/test-make_linelist.R | 19 linelist-1.1.0/linelist/tests/testthat/test-prune_tags.R | 7 linelist-1.1.0/linelist/tests/testthat/test-square_bracket.R | 34 linelist-1.1.0/linelist/tests/testthat/test-tag_variables.R |only linelist-1.1.0/linelist/tests/testthat/test-validate_linelist.R | 8 linelist-1.1.0/linelist/tests/testthat/test-validate_types.R | 55 - linelist-1.1.0/linelist/tests/testthat/test_set_tags.R | 6 linelist-1.1.0/linelist/vignettes/compat-dplyr.Rmd | 2 linelist-1.1.0/linelist/vignettes/design-principles.Rmd |only linelist-1.1.0/linelist/vignettes/linelist.Rmd | 70 - 83 files changed, 921 insertions(+), 683 deletions(-)
Title: Carbon-Related Assessment of Silvicultural Concepts
Description: A simulation model and accompanying functions that support
assessing silvicultural concepts on the forest estate level with a focus on
the CO2 uptake by wood growth and CO2 emissions by forest operations. For
achieving this, a virtual forest estate area is split into the areas covered
by typical phases of the silvicultural concept of interest. Given initial
area shares of these phases, the dynamics of these areas is simulated. The
typical carbon stocks and flows which are known for all phases are
attributed post-hoc to the areas and upscaled to the estate level. CO2
emissions by forest operations are estimated based on the amounts and
dimensions of the harvested timber. Probabilities of damage events are taken
into account.
Author: Peter Biber [aut, cre, cph] ,
Stefano Grigolato [ctb] ,
Julia Schmucker [ctb] ,
Enno Uhl [ctb] ,
Hans Pretzsch [ctb]
Maintainer: Peter Biber <p.biber@tum.de>
Diff between care4cmodel versions 1.0.0 dated 2023-11-16 and 1.0.1 dated 2024-02-28
care4cmodel-1.0.0/care4cmodel/man/figures/README-pressure-1.png |only care4cmodel-1.0.1/care4cmodel/DESCRIPTION | 10 ++--- care4cmodel-1.0.1/care4cmodel/MD5 | 19 ++++------ care4cmodel-1.0.1/care4cmodel/NEWS.md | 7 +++ care4cmodel-1.0.1/care4cmodel/R/area_evaluation.R | 5 +- care4cmodel-1.0.1/care4cmodel/README.md | 5 ++ care4cmodel-1.0.1/care4cmodel/build/partial.rdb |binary care4cmodel-1.0.1/care4cmodel/inst/doc/getting-started-with-care4cmodel.html | 8 ++-- care4cmodel-1.0.1/care4cmodel/man/figures/README-example-1.png |binary care4cmodel-1.0.1/care4cmodel/man/figures/README-example-2.png |binary care4cmodel-1.0.1/care4cmodel/man/figures/README-example-3.png |binary 11 files changed, 32 insertions(+), 22 deletions(-)
Title: Harmonised Index of Consumer Prices
Description: The Harmonised Index of Consumer Prices (HICP) is the key economic figure to measure inflation in the euro area.
The methodology underlying the HICP is documented in the HICP Methodological Manual (<https://ec.europa.eu/eurostat/web/products-manuals-and-guidelines/w/ks-gq-24-003>).
Based on the manual, this package provides functions to access and work with HICP data from Eurostat's public database (<https://ec.europa.eu/eurostat/data/database>).
Author: Sebastian Weinand [aut, cre]
Maintainer: Sebastian Weinand <sebastian.weinand@ec.europa.eu>
Diff between hicp versions 0.4.1 dated 2024-02-04 and 0.4.2 dated 2024-02-28
hicp-0.4.1/hicp/tests/testthat/test-input.checks.R |only hicp-0.4.2/hicp/DESCRIPTION | 8 hicp-0.4.2/hicp/MD5 | 50 ++-- hicp-0.4.2/hicp/NEWS.md | 7 hicp-0.4.2/hicp/R/chaining.R | 6 hicp-0.4.2/hicp/R/coicop.bundles.r | 10 hicp-0.4.2/hicp/R/coicop.relatives.r | 6 hicp-0.4.2/hicp/R/coicop.tree.R | 6 hicp-0.4.2/hicp/R/hicp.data.r | 11 - hicp-0.4.2/hicp/R/index.aggregation.r | 28 +- hicp-0.4.2/hicp/R/linking.r | 11 - hicp-0.4.2/hicp/R/rates.r | 19 - hicp-0.4.2/hicp/README.md | 2 hicp-0.4.2/hicp/inst/doc/hicp_intro.Rmd | 4 hicp-0.4.2/hicp/inst/doc/hicp_intro.html | 223 ++++++++++----------- hicp-0.4.2/hicp/man/chaining.Rd | 19 + hicp-0.4.2/hicp/man/coicop.relatives.Rd | 10 hicp-0.4.2/hicp/man/coicop.tree.Rd | 10 hicp-0.4.2/hicp/man/hicp.data.Rd | 7 hicp-0.4.2/hicp/man/index.aggregation.Rd | 12 - hicp-0.4.2/hicp/man/linking.Rd | 4 hicp-0.4.2/hicp/man/rates.Rd | 13 - hicp-0.4.2/hicp/tests/testthat/test_chaining.R | 16 - hicp-0.4.2/hicp/tests/testthat/test_input.checks.R |only hicp-0.4.2/hicp/tests/testthat/test_linking.r | 7 hicp-0.4.2/hicp/vignettes/hicp_intro.Rmd | 4 hicp-0.4.2/hicp/vignettes/references.bib | 10 27 files changed, 262 insertions(+), 241 deletions(-)
Title: Intraclass Correlation Coefficient for Count Data
Description: Estimates the intraclass correlation coefficient (ICC) for count data to assess repeatability (intra-methods concordance) and concordance (between-method concordance). In the concordance setting, the ICC is equivalent to the concordance correlation coefficient estimated by variance components. The ICC is estimated using the estimates from generalized linear mixed models. The within-subjects distributions considered are: Poisson; Negative Binomial with additive and proportional extradispersion; Zero-Inflated Poisson; and Zero-Inflated Negative Binomial with additive and proportional extradispersion. The statistical methodology used to estimate the ICC with count data can be found in Carrasco (2010) <doi:10.1111/j.1541-0420.2009.01335.x>.
Author: Josep L. Carrasco <jlcarrasco@ub.edu>
Maintainer: Josep L. Carrasco <jlcarrasco@ub.edu>
Diff between iccCounts versions 1.1.1 dated 2022-06-09 and 1.1.2 dated 2024-02-28
iccCounts-1.1.1/iccCounts/vignettes/examples_1_0_1.R.RData |only iccCounts-1.1.2/iccCounts/DESCRIPTION | 8 iccCounts-1.1.2/iccCounts/MD5 | 13 iccCounts-1.1.2/iccCounts/build/vignette.rds |binary iccCounts-1.1.2/iccCounts/inst/doc/iccCounts_examples.R | 14 iccCounts-1.1.2/iccCounts/inst/doc/iccCounts_examples.Rmd | 15 iccCounts-1.1.2/iccCounts/inst/doc/iccCounts_examples.html | 396 ++++++------- iccCounts-1.1.2/iccCounts/vignettes/iccCounts_examples.Rmd | 15 8 files changed, 240 insertions(+), 221 deletions(-)
Title: Genotyping Triploids (or Diploids) from Luminescence Data
Description: Genotyping of triploid individuals from luminescence data (marker probeset A and B). Works also for diploids.
Two main functions: Run_Clustering() that regroups individuals with a same genotype based on proximity and
Run_Genotyping() that assigns a genotype to each cluster. For Shiny interface use: launch_GenoShiny().
Author: Julien Roche [aut, cre],
Florence Phocas [aut],
Mathieu Besson [aut],
Pierre Patrice [aut],
Marc Vandeputte [aut],
Francois Allal [aut],
Pierrick Haffray [aut]
Maintainer: Julien Roche <jjm.roche@gmail.com>
Diff between GenoTriplo versions 1.0.3 dated 2023-10-03 and 1.0.4 dated 2024-02-28
DESCRIPTION | 6 MD5 | 8 R/App_GenoTriploShiny.R | 2060 +++++++++++++++++++++--------------------- R/function_GenoTot_pop_same.R | 62 + R/function_create_dataset.R | 55 - 5 files changed, 1123 insertions(+), 1068 deletions(-)
Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions.
Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc.
Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM)
for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates).
Other functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc.
Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large dat [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrMisc versions 1.14.1 dated 2024-02-13 and 1.14.2 dated 2024-02-28
DESCRIPTION | 8 MD5 | 14 R/htmlSpecCharConv.R | 16 R/packageDownloadStat.R | 69 +-- inst/doc/wrMiscVignette1.html | 66 +-- inst/extdata/rpackagesMicro.html | 858 +++++++++++++-------------------------- man/htmlSpecCharConv.Rd | 9 man/packageDownloadStat.Rd | 8 8 files changed, 405 insertions(+), 643 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [ctb],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oehlschlaegel [ctb, cph],
Suman Rakshit [ctb], [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.2-8 dated 2024-01-26 and 3.2-9 dated 2024-02-28
DESCRIPTION | 8 MD5 | 76 +++--- NAMESPACE | 7 NEWS | 25 ++ R/affine.R | 4 R/areadiff.R | 4 R/boundingbox.R | 14 - R/clickpoly.R | 6 R/diagram.R | 6 R/disc.R | 6 R/flipxy.R | 4 R/infline.R | 14 - R/morphology.R | 2 R/nncross.R | 15 - R/periodify.R | 8 R/plot.anylist.R | 4 R/plot.im.R | 12 - R/plot.owin.R | 10 R/plot.psp.R | 4 R/polygood.R | 4 R/ppx.R | 4 R/psp.R | 6 R/randomseg.R | 4 R/rescue.rectangle.R | 6 R/ripras.R | 4 R/setcov.R | 4 R/simplepanel.R | 12 - R/symbolmap.R | 90 ++++++- R/tess.R | 6 R/texture.R | 14 - R/window.R | 491 +++++++++++++++++++++--------------------- R/wingeom.R | 33 +- inst/doc/packagesizes.txt | 1 man/as.colourmap.Rd | 9 man/nncross.Rd | 4 man/spatstat.geom-internal.Rd | 13 + man/symbolmap.Rd | 2 src/nndistX.h | 8 src/nndistance.c | 8 39 files changed, 549 insertions(+), 403 deletions(-)
Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating
grouped date classes. This package is part of the RECON
(<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between grates versions 1.1.0 dated 2023-06-08 and 1.1.1 dated 2024-02-28
DESCRIPTION | 9 MD5 | 52 ++-- NEWS.md | 9 R/accessors.R | 4 R/defunct.R | 2 R/epiweek.R | 70 ++---- R/isoweek.R | 71 +++--- R/month.R | 56 ++-- R/period.R | 52 ++-- R/scale-epiweek.R | 28 +- R/scale-isoweek.R | 28 +- R/scale-month.R | 38 ++- R/scale-period.R | 34 ++ R/scale-year.R | 30 +- R/scale-yearmonth.R | 29 +- R/scale-yearquarter.R | 28 +- R/scale-yearweek.R | 31 ++ R/utils-general.R | 6 R/year.R | 35 +-- R/yearmonth.R | 70 +++--- R/yearquarter.R | 76 +++--- R/yearweek.R | 91 +++---- build/vignette.rds |binary inst/doc/grates.R | 4 inst/doc/grates.Rmd | 2 inst/doc/grates.html | 574 +++++++++++++++++++++++++------------------------- vignettes/grates.Rmd | 2 27 files changed, 774 insertions(+), 657 deletions(-)
Title: Graph Signal Processing
Description: Provides the standard operations for signal processing on graphs:
graph Fourier transform, spectral graph wavelet transform,
visualization tools. It also implements a data driven method
for graph signal denoising/regression, for details see
De Loynes, Navarro, Olivier (2019) <arxiv:1906.01882>.
The package also provides an interface to the SuiteSparse Matrix Collection,
<https://sparse.tamu.edu/>, a large and widely used set of sparse matrix
benchmarks collected from a wide range of applications.
Author: Basile de Loynes [aut] ,
Fabien Navarro [aut, cre] ,
Baptiste Olivier [aut]
Maintainer: Fabien Navarro <fabien.navarro@math.cnrs.fr>
Diff between gasper versions 1.1.5 dated 2023-10-26 and 1.1.6 dated 2024-02-28
DESCRIPTION | 8 - MD5 | 107 ++++++++++----------- NEWS.md | 9 + R/GVN.R | 4 R/LD_SUREthresh.R | 39 +++++++ R/SURE_MSEthresh.R | 49 +++++++++ R/SUREthresh.R | 34 +----- R/SuiteSparseData.R |only R/analysis.R | 4 R/betathresh.R | 2 R/download_graph.R | 51 ++++++---- R/eigensort.R | 6 - R/forward_gft.R | 22 +++- R/forward_sgwt.R | 4 R/get_graph_info.R | 17 ++- R/grid1.R | 2 R/inverse_gft.R | 17 +++ R/inverse_sgwt.R | 2 R/localize_sgwt.R | 16 +-- R/minnesota.R | 3 R/pittsburgh.R | 7 - R/plot_signal.R | 33 +++++- R/randsignal.R | 10 + R/smoothmodulus.R | 7 - R/spectral_coords.R | 14 ++ data/SuiteSparseData.rda |only data/grid1.rda |binary data/minnesota.rda |binary inst/doc/gasper_vignette.R | 125 ++++++++++++++++++++---- inst/doc/gasper_vignette.pdf |binary inst/doc/gasper_vignette.rmd | 214 +++++++++++++++++++++++++++++++++++------- man/GVN.Rd | 4 man/LD_SUREthresh.Rd | 40 +++++++ man/SURE_MSEthresh.Rd | 50 +++++++++ man/SUREthresh.Rd | 19 ++- man/SuiteSparseData.Rd |only man/analysis.Rd | 4 man/betathresh.Rd | 2 man/download_graph.Rd | 15 +- man/eigensort.Rd | 4 man/forward_gft.Rd | 23 +++- man/forward_sgwt.Rd | 4 man/get_graph_info.Rd | 6 - man/grid1.Rd | 2 man/inverse_gft.Rd | 18 +++ man/inverse_sgwt.Rd | 2 man/localize_sgwt.Rd | 16 +-- man/minnesota.Rd | 3 man/pittsburgh.Rd | 7 - man/plot_signal.Rd | 10 + man/randsignal.Rd | 7 + man/smoothmodulus.Rd | 9 + man/spectral_coords.Rd | 13 ++ vignettes/gasper_vignette.rmd | 214 +++++++++++++++++++++++++++++++++++------- vignettes/references.bib | 44 ++++++++ vignettes/template-latex.tex | 2 56 files changed, 1027 insertions(+), 297 deletions(-)
Title: Using CF-Compliant Calendars with Climate Projection Data
Description: Support for all calendars as specified in the Climate and Forecast
(CF) Metadata Conventions for climate and forecasting data. The CF Metadata
Conventions is widely used for distributing files with climate observations
or projections, including the Coupled Model Intercomparison Project (CMIP)
data used by climate change scientists and the Intergovernmental Panel on
Climate Change (IPCC). This package specifically allows the user to work
with any of the CF-compliant calendars (many of which are not compliant with
POSIXt). The CF time coordinate is formally defined in the CF Metadata
Conventions document available at <https://cfconventions.org/Data/cf-conventions/cf-conventions-1.10/cf-conventions.html#time-coordinate>.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between CFtime versions 1.2.0 dated 2023-11-02 and 1.3.0 dated 2024-02-28
DESCRIPTION | 6 LICENSE | 2 MD5 | 58 ++--- NAMESPACE | 2 NEWS.md | 18 + R/CFdatum.R | 40 ++- R/CFfactor.R | 110 +++++----- R/CFformat.R | 27 +- R/CFparse.R | 8 R/CFtime.R | 375 +++++++++++++++++++++--------------- R/CFutils.R | 46 ++-- R/zzz.R | 2 README.md | 27 +- TODO | 9 build/vignette.rds |binary inst/doc/CFtime.R | 3 inst/doc/CFtime.Rmd | 45 +++- inst/doc/CFtime.html | 83 +++++-- inst/doc/Processing.Rmd | 7 inst/doc/Processing.html | 10 man/CFproperties.Rd | 21 +- man/CFsubset.Rd |only man/CFtime-class.Rd | 4 man/CFtimestamp.Rd | 2 man/plus-CFtime-CFtime-method.Rd | 29 +- tests/testthat/test-CFformat.R | 213 ++++++++++++++------ tests/testthat/test-CFtime.R | 77 ++++++- tests/testthat/test-functions.R |only tests/testthat/test-parse_deparse.R | 29 ++ vignettes/CFtime.Rmd | 45 +++- vignettes/Processing.Rmd | 7 31 files changed, 849 insertions(+), 456 deletions(-)
Title: Generates Polygon Straight Skeletons and 3D Bevels
Description: Generates polygon straight skeletons and 3D models.
Provides functions to create and visualize interior polygon offsets,
3D beveled polygons, and 3D roof models.
Author: Tyler Morgan-Wall [aut, cph, cre]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between raybevel versions 0.1.1 dated 2024-02-26 and 0.1.2 dated 2024-02-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/convert_ss_to_polygons_rcpp.cpp | 24 ++++++++++++------------ src/generate_offset_links_nodes_rcpp.cpp | 8 ++++---- src/rayskeleton.cpp | 10 +++++----- 5 files changed, 28 insertions(+), 28 deletions(-)
Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code, automated
reporting or use an easy to remember set of tidy functions for low
code exploratory data analysis.
Author: Roland Krasser [aut, cre]
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between explore versions 1.1.1 dated 2024-02-10 and 1.2.0 dated 2024-02-28
DESCRIPTION | 14 +- MD5 | 100 ++++++++------ NAMESPACE | 12 + NEWS.md | 23 +++ R/create-data.R | 65 ++++++++- R/drop.R |only R/explain-xgboost.R |only R/explain.R | 14 +- R/tools.R | 76 +++++++++++ README.md | 3 build/vignette.rds |binary inst/doc/abtest.html | 4 inst/doc/clean-drop.R |only inst/doc/clean-drop.Rmd |only inst/doc/clean-drop.html |only inst/doc/data.R | 4 inst/doc/data.Rmd | 43 +++--- inst/doc/data.html | 255 +++++++++++++++++++------------------- inst/doc/describe.html | 4 inst/doc/explain.R | 19 ++ inst/doc/explain.Rmd | 41 +++++- inst/doc/explain.html | 102 +++++++++++---- inst/doc/explore.R | 12 + inst/doc/explore.Rmd | 58 ++++++-- inst/doc/explore.html | 208 ++++++++++++++++++------------ inst/doc/explore_mtcars.html | 4 inst/doc/explore_penguins.html | 4 inst/doc/explore_titanic.html | 4 inst/doc/predict.Rmd | 1 inst/doc/predict.html | 5 inst/doc/report-target.html | 4 inst/doc/report-targetpct.html | 4 inst/doc/report.html | 4 inst/doc/tips-tricks.R | 38 ----- inst/doc/tips-tricks.Rmd | 54 +------- inst/doc/tips-tricks.html | 135 ++------------------ man/check_vec_low_variance.Rd |only man/create_data_empty.Rd | 4 man/create_data_esoteric.Rd |only man/drop_obs_if.Rd |only man/drop_obs_with_na.Rd |only man/drop_var_by_names.Rd |only man/drop_var_low_variance.Rd |only man/drop_var_no_variance.Rd |only man/drop_var_not_numeric.Rd |only man/drop_var_with_na.Rd |only man/explain_forest.Rd | 1 man/explain_xgboost.Rd |only man/log_info_if.Rd |only man/mix_color.Rd |only man/predict_target.Rd | 3 man/show_color.Rd |only tests/testthat/test-create-data.R | 32 ++++ tests/testthat/test-drop.R |only tests/testthat/test-tools.R | 31 ++++ vignettes/clean-drop.Rmd |only vignettes/data.Rmd | 43 +++--- vignettes/explain.Rmd | 41 +++++- vignettes/explore.Rmd | 58 ++++++-- vignettes/predict.Rmd | 1 vignettes/tips-tricks.Rmd | 54 +------- 61 files changed, 956 insertions(+), 626 deletions(-)
Title: Import Professional Baseball Data from 'Retrosheet'
Description: A collection of tools to import and structure the (currently) single-season
event, game-log, roster, and schedule data available from <https://www.retrosheet.org>.
In particular, the event (a.k.a. play-by-play) files can be especially difficult to parse.
This package does the parsing on those files, returning the requested data in the most
practical R structure to use for sabermetric or other analyses.
Author: Colin Douglas [aut, cre, cph],
Richard Scriven [aut, cph]
Maintainer: Colin Douglas <colin@douglas.science>
Diff between retrosheet versions 1.1.5 dated 2023-07-07 and 1.1.6 dated 2024-02-28
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/getPartialGamelog.R | 6 ++---- R/getRetrosheet.R | 4 ++-- README.md | 4 ++-- man/getPartialGamelog.Rd | 6 ++---- tests/testthat/test-getRetrosheet.R | 7 ++++--- tests/testthat/test-get_retrosheet.R | 7 ++++--- 9 files changed, 33 insertions(+), 30 deletions(-)
Title: Tools for Modeling Rate-Dependent Hysteretic Processes and
Ellipses
Description: Fit, summarize and plot sinusoidal hysteretic processes using:
two-step simple harmonic least squares, ellipse-specific non-linear least
squares, the direct method, geometric least squares or linear least squares. See
Yang, F and A. Parkhurst, "Efficient Estimation of Elliptical Hysteresis with
Application to the Characterization of Heat Stress" <DOI:10.1007/s13253-015-0213-6>.
Author: Spencer Maynes, Fan Yang, and Anne Parkhurst
Maintainer: Spencer Maynes <smaynes89@gmail.com>
Diff between hysteresis versions 2.7 dated 2021-05-14 and 2.7.2 dated 2024-02-28
hysteresis-2.7.2/hysteresis/DESCRIPTION | 14 hysteresis-2.7.2/hysteresis/MD5 | 358 +++--- hysteresis-2.7.2/hysteresis/NAMESPACE | 186 +-- hysteresis-2.7.2/hysteresis/NEWS | 18 hysteresis-2.7.2/hysteresis/R/coef.ellipsefit.R | 2 hysteresis-2.7.2/hysteresis/R/coef.ellipsefitlist.R | 2 hysteresis-2.7.2/hysteresis/R/coef.ellipsesummary.R | 2 hysteresis-2.7.2/hysteresis/R/coef.ellipsesummarylist.R | 2 hysteresis-2.7.2/hysteresis/R/coef.fittedloop.R | 2 hysteresis-2.7.2/hysteresis/R/coef.fittedlooplist.R | 2 hysteresis-2.7.2/hysteresis/R/coef.fittedlooplist2r.R | 2 hysteresis-2.7.2/hysteresis/R/coef.loop2r.R | 2 hysteresis-2.7.2/hysteresis/R/coef.loop2rsummary.R | 2 hysteresis-2.7.2/hysteresis/R/coef.loopsummary.R | 2 hysteresis-2.7.2/hysteresis/R/coef.loopsummarylist.R | 2 hysteresis-2.7.2/hysteresis/R/coef.loopsummarylist2r.R | 2 hysteresis-2.7.2/hysteresis/R/delta.error.R | 192 +-- hysteresis-2.7.2/hysteresis/R/delta.error.loop.R | 130 +- hysteresis-2.7.2/hysteresis/R/delta.error.loop2r.R | 162 +-- hysteresis-2.7.2/hysteresis/R/derived.1.r | 14 hysteresis-2.7.2/hysteresis/R/derived.2.r | 16 hysteresis-2.7.2/hysteresis/R/derived.amps.R | 18 hysteresis-2.7.2/hysteresis/R/derived.focus.r | 16 hysteresis-2.7.2/hysteresis/R/direct.R | 112 +- hysteresis-2.7.2/hysteresis/R/direct_renorm.R | 116 +- hysteresis-2.7.2/hysteresis/R/directboot.R | 60 - hysteresis-2.7.2/hysteresis/R/directsummary.R | 130 +- hysteresis-2.7.2/hysteresis/R/ellipsespot.R | 10 hysteresis-2.7.2/hysteresis/R/fel.R | 192 +-- hysteresis-2.7.2/hysteresis/R/fel.direct.R | 48 hysteresis-2.7.2/hysteresis/R/fel.direct2harmonic.R | 102 - hysteresis-2.7.2/hysteresis/R/fel.geometric.R | 92 - hysteresis-2.7.2/hysteresis/R/fel.harmonic2.R | 70 - hysteresis-2.7.2/hysteresis/R/fel.lm.R | 96 - hysteresis-2.7.2/hysteresis/R/fel.nls.R | 106 +- hysteresis-2.7.2/hysteresis/R/fel.repeated.R | 48 hysteresis-2.7.2/hysteresis/R/felReflect.R | 10 hysteresis-2.7.2/hysteresis/R/fitstatistics.R | 34 hysteresis-2.7.2/hysteresis/R/fitted.ellipsefit.R | 6 hysteresis-2.7.2/hysteresis/R/fitted.ellipsefitlist.R | 24 hysteresis-2.7.2/hysteresis/R/fitted.ellipsesummary.R | 6 hysteresis-2.7.2/hysteresis/R/fitted.ellipsesummarylist.R | 26 hysteresis-2.7.2/hysteresis/R/fitted.fittedloop.R | 6 hysteresis-2.7.2/hysteresis/R/fitted.fittedlooplist.R | 26 hysteresis-2.7.2/hysteresis/R/fitted.fittedlooplist2r.R | 26 hysteresis-2.7.2/hysteresis/R/fitted.loop2r.R | 6 hysteresis-2.7.2/hysteresis/R/fitted.loop2rsummary.R | 8 hysteresis-2.7.2/hysteresis/R/fitted.loopsummary.R | 8 hysteresis-2.7.2/hysteresis/R/fitted.loopsummarylist.R | 54 - hysteresis-2.7.2/hysteresis/R/floop.R | 284 ++--- hysteresis-2.7.2/hysteresis/R/floop.repeated.R | 48 hysteresis-2.7.2/hysteresis/R/floop2r.R | 310 ++--- hysteresis-2.7.2/hysteresis/R/floop2r.repeated.R | 48 hysteresis-2.7.2/hysteresis/R/floopCauchyLoss.R | 40 hysteresis-2.7.2/hysteresis/R/floopCauchyLoss2r.R | 42 hysteresis-2.7.2/hysteresis/R/floopReflect.R | 10 hysteresis-2.7.2/hysteresis/R/geom_ellipse.R | 58 - hysteresis-2.7.2/hysteresis/R/geom_step.R | 62 - hysteresis-2.7.2/hysteresis/R/geometric_distance.R | 48 hysteresis-2.7.2/hysteresis/R/geometricboot.R | 104 - hysteresis-2.7.2/hysteresis/R/geometricbootwrapper.R | 18 hysteresis-2.7.2/hysteresis/R/geometricsummary.R | 134 +- hysteresis-2.7.2/hysteresis/R/halir.R | 30 hysteresis-2.7.2/hysteresis/R/harmonic2boot.R | 84 - hysteresis-2.7.2/hysteresis/R/harmonic2summary.R | 124 +- hysteresis-2.7.2/hysteresis/R/harmonic2summaryEBS.r | 236 ++-- hysteresis-2.7.2/hysteresis/R/harmonicOptPoint.R | 62 - hysteresis-2.7.2/hysteresis/R/harmonicspot.R | 10 hysteresis-2.7.2/hysteresis/R/internal.1.r | 16 hysteresis-2.7.2/hysteresis/R/internal.2.r | 16 hysteresis-2.7.2/hysteresis/R/internal.3.r | 12 hysteresis-2.7.2/hysteresis/R/lmboot.R | 116 +- hysteresis-2.7.2/hysteresis/R/lmbootwrapper.R | 18 hysteresis-2.7.2/hysteresis/R/lmsummary.R | 130 +- hysteresis-2.7.2/hysteresis/R/loopboot.R | 110 +- hysteresis-2.7.2/hysteresis/R/loopbootgeom.R | 130 +- hysteresis-2.7.2/hysteresis/R/m_ellipse.R | 32 hysteresis-2.7.2/hysteresis/R/mel.r | 22 hysteresis-2.7.2/hysteresis/R/mel1.r | 28 hysteresis-2.7.2/hysteresis/R/mel2.r | 26 hysteresis-2.7.2/hysteresis/R/mel3.R | 30 hysteresis-2.7.2/hysteresis/R/mel4.R | 68 - hysteresis-2.7.2/hysteresis/R/mloop.r | 52 hysteresis-2.7.2/hysteresis/R/mloop2r.R | 66 - hysteresis-2.7.2/hysteresis/R/nlsboot.R | 116 +- hysteresis-2.7.2/hysteresis/R/nlsbootwrapper.R | 16 hysteresis-2.7.2/hysteresis/R/nlssummary.R | 134 +- hysteresis-2.7.2/hysteresis/R/plot.ellipsefit.R | 196 +-- hysteresis-2.7.2/hysteresis/R/plot.ellipsefitlist.R | 20 hysteresis-2.7.2/hysteresis/R/plot.ellipsesummary.R | 170 +-- hysteresis-2.7.2/hysteresis/R/plot.ellipsesummarylist.R | 20 hysteresis-2.7.2/hysteresis/R/plot.fittedloop.R | 144 +- hysteresis-2.7.2/hysteresis/R/plot.fittedlooplist.R | 42 hysteresis-2.7.2/hysteresis/R/plot.loop2r.R | 118 +- hysteresis-2.7.2/hysteresis/R/plot.loop2rsummary.R | 122 +- hysteresis-2.7.2/hysteresis/R/plot.loopsummary.R | 140 +- hysteresis-2.7.2/hysteresis/R/plot.loopsummarylist.R | 42 hysteresis-2.7.2/hysteresis/R/print.ellipsefit.R | 34 hysteresis-2.7.2/hysteresis/R/print.ellipsefitlist.R | 18 hysteresis-2.7.2/hysteresis/R/print.ellipsemake.r | 8 hysteresis-2.7.2/hysteresis/R/print.ellipsesummary.r | 62 - hysteresis-2.7.2/hysteresis/R/print.ellipsesummarylist.R | 76 - hysteresis-2.7.2/hysteresis/R/print.fittedloop.R | 12 hysteresis-2.7.2/hysteresis/R/print.fittedlooplist.R | 38 hysteresis-2.7.2/hysteresis/R/print.loop2r.R | 14 hysteresis-2.7.2/hysteresis/R/print.loop2rsummary.R | 18 hysteresis-2.7.2/hysteresis/R/print.loopsummary.R | 18 hysteresis-2.7.2/hysteresis/R/print.loopsummarylist.R | 120 +- hysteresis-2.7.2/hysteresis/R/renorm_ellipse.R | 34 hysteresis-2.7.2/hysteresis/R/residuals.ellipsefit.R | 16 hysteresis-2.7.2/hysteresis/R/residuals.ellipsefitlist.R | 36 hysteresis-2.7.2/hysteresis/R/residuals.ellipsesummary.R | 14 hysteresis-2.7.2/hysteresis/R/residuals.ellipsesummarylist.R | 30 hysteresis-2.7.2/hysteresis/R/residuals.fittedloop.R | 14 hysteresis-2.7.2/hysteresis/R/residuals.fittedlooplist.R | 62 - hysteresis-2.7.2/hysteresis/R/residuals.loop2r.R | 14 hysteresis-2.7.2/hysteresis/R/residuals.loop2rsummary.R | 14 hysteresis-2.7.2/hysteresis/R/residuals.loopsummary.R | 14 hysteresis-2.7.2/hysteresis/R/residuals.loopsummarylist.R | 62 - hysteresis-2.7.2/hysteresis/R/rstudent.ellipsefit.R | 30 hysteresis-2.7.2/hysteresis/R/rstudent.ellipsefitlist.R | 28 hysteresis-2.7.2/hysteresis/R/rstudent.ellipsesummary.R | 30 hysteresis-2.7.2/hysteresis/R/rstudent.ellipsesummarylist.R | 28 hysteresis-2.7.2/hysteresis/R/rstudent.fittedloop.R | 34 hysteresis-2.7.2/hysteresis/R/rstudent.fittedlooplist.R | 54 - hysteresis-2.7.2/hysteresis/R/rstudent.loop2r.R | 44 hysteresis-2.7.2/hysteresis/R/rstudent.loop2rsummary.R | 44 hysteresis-2.7.2/hysteresis/R/rstudent.loopsummary.R | 34 hysteresis-2.7.2/hysteresis/R/rstudent.loopsummarylist.R | 56 - hysteresis-2.7.2/hysteresis/R/sandwich.error.R | 24 hysteresis-2.7.2/hysteresis/R/splitloopboot.R | 124 +- hysteresis-2.7.2/hysteresis/R/splitloopbootgeom.R | 140 +- hysteresis-2.7.2/hysteresis/R/summary.ellipsefit.R | 46 hysteresis-2.7.2/hysteresis/R/summary.ellipsefitlist.R | 120 +- hysteresis-2.7.2/hysteresis/R/summary.fittedloop.R | 104 - hysteresis-2.7.2/hysteresis/R/summary.fittedlooplist.R | 82 - hysteresis-2.7.2/hysteresis/R/summary.fittedlooplist2r.R | 82 - hysteresis-2.7.2/hysteresis/R/summary.loop2r.R | 108 +- hysteresis-2.7.2/hysteresis/R/tprofile.error.R | 12 hysteresis-2.7.2/hysteresis/README.md | 8 hysteresis-2.7.2/hysteresis/build/vignette.rds |binary hysteresis-2.7.2/hysteresis/inst/doc/index.Rmd | 548 +++++----- hysteresis-2.7.2/hysteresis/inst/doc/index.html | 573 ++++------- hysteresis-2.7.2/hysteresis/man/EllipseData.Rd | 98 - hysteresis-2.7.2/hysteresis/man/HysteresisData.Rd | 96 - hysteresis-2.7.2/hysteresis/man/fel.Rd | 231 ++-- hysteresis-2.7.2/hysteresis/man/fel.repeated.Rd | 212 ++-- hysteresis-2.7.2/hysteresis/man/floop.Rd | 278 ++--- hysteresis-2.7.2/hysteresis/man/floop.repeated.Rd | 242 ++-- hysteresis-2.7.2/hysteresis/man/floopReflect.Rd | 82 - hysteresis-2.7.2/hysteresis/man/hysteresis-package.Rd | 7 hysteresis-2.7.2/hysteresis/man/loop.parameters.Rd | 208 +-- hysteresis-2.7.2/hysteresis/man/mel.rd | 284 ++--- hysteresis-2.7.2/hysteresis/man/mloop.Rd | 202 +-- hysteresis-2.7.2/hysteresis/man/plot.fittedloop.Rd | 216 ++-- hysteresis-2.7.2/hysteresis/man/residuals.fittedloop.Rd | 278 ++--- hysteresis-2.7.2/hysteresis/man/summary.fittedloop.Rd | 214 ++-- hysteresis-2.7.2/hysteresis/vignettes/index.Rmd | 548 +++++----- hysteresis-2.7/hysteresis/vignettes/boottest-1.png |only hysteresis-2.7/hysteresis/vignettes/boottest.png |only hysteresis-2.7/hysteresis/vignettes/bx-1.png |only hysteresis-2.7/hysteresis/vignettes/bx-2.png |only hysteresis-2.7/hysteresis/vignettes/bx-3.png |only hysteresis-2.7/hysteresis/vignettes/bx1.png |only hysteresis-2.7/hysteresis/vignettes/bx2.png |only hysteresis-2.7/hysteresis/vignettes/bx3.png |only hysteresis-2.7/hysteresis/vignettes/by-1.png |only hysteresis-2.7/hysteresis/vignettes/by-2.png |only hysteresis-2.7/hysteresis/vignettes/by-3.png |only hysteresis-2.7/hysteresis/vignettes/by1.png |only hysteresis-2.7/hysteresis/vignettes/by2.png |only hysteresis-2.7/hysteresis/vignettes/by3.png |only hysteresis-2.7/hysteresis/vignettes/geometric-1.png |only hysteresis-2.7/hysteresis/vignettes/geometric.png |only hysteresis-2.7/hysteresis/vignettes/mandn-1.png |only hysteresis-2.7/hysteresis/vignettes/mandn.png |only hysteresis-2.7/hysteresis/vignettes/moremandn-1.png |only hysteresis-2.7/hysteresis/vignettes/moremandn.png |only hysteresis-2.7/hysteresis/vignettes/multiple-1.png |only hysteresis-2.7/hysteresis/vignettes/multiple-2.png |only hysteresis-2.7/hysteresis/vignettes/multiple-3.png |only hysteresis-2.7/hysteresis/vignettes/multiple1.png |only hysteresis-2.7/hysteresis/vignettes/multiple2.png |only hysteresis-2.7/hysteresis/vignettes/multiple3.png |only hysteresis-2.7/hysteresis/vignettes/retention-1.png |only hysteresis-2.7/hysteresis/vignettes/retention-2.png |only hysteresis-2.7/hysteresis/vignettes/retention-3.png |only hysteresis-2.7/hysteresis/vignettes/retention1.png |only hysteresis-2.7/hysteresis/vignettes/retention2.png |only hysteresis-2.7/hysteresis/vignettes/retention3.png |only hysteresis-2.7/hysteresis/vignettes/tests-1.png |only hysteresis-2.7/hysteresis/vignettes/tests.png |only hysteresis-2.7/hysteresis/vignettes/unnamed-chunk-1-1.png |only hysteresis-2.7/hysteresis/vignettes/unnamed-chunk-1.png |only hysteresis-2.7/hysteresis/vignettes/unnamed-chunk-2-1.png |only hysteresis-2.7/hysteresis/vignettes/unnamed-chunk-2.png |only hysteresis-2.7/hysteresis/vignettes/unnamed-chunk-6-1.png |only hysteresis-2.7/hysteresis/vignettes/unnamed-chunk-6.png |only hysteresis-2.7/hysteresis/vignettes/unnamed-chunk-7-1.png |only hysteresis-2.7/hysteresis/vignettes/unnamed-chunk-7.png |only hysteresis-2.7/hysteresis/vignettes/unnamed-chunk-9-1.png |only hysteresis-2.7/hysteresis/vignettes/unnamed-chunk-9.png |only 202 files changed, 6286 insertions(+), 6465 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.2.9 dated 2024-02-19 and 1.3.0 dated 2024-02-28
DESCRIPTION | 8 MD5 | 68 +- R/GPModel.R | 2 R/gpb.cv.R | 10 R/gpboost.R | 47 - configure.ac | 2 man/GPModel_shared_params.Rd | 2 man/fit.GPModel.Rd | 2 man/fit.Rd | 2 man/fitGPModel.Rd | 2 man/gpb.cv.Rd | 47 - man/gpb.grid.search.tune.parameters.Rd | 24 man/gpb.train.Rd | 35 - man/gpb_shared_params.Rd | 43 - man/gpboost.Rd | 43 - man/set_optim_params.GPModel.Rd | 2 man/set_optim_params.Rd | 2 src/boosting/gbdt.cpp | 16 src/boosting/gbdt.h | 2 src/include/GPBoost/CG_utils.h | 3 src/include/GPBoost/optim_utils.h | 4 src/include/GPBoost/re_model.h | 12 src/include/GPBoost/re_model_template.h | 349 ++++++++---- src/include/LightGBM/config.h | 8 src/include/LightGBM/objective_function.h | 23 src/io/config_auto.cpp | 4 src/objective/binary_objective.hpp | 13 src/objective/multiclass_objective.hpp | 19 src/objective/objective_function.cpp | 3 src/objective/rank_objective.hpp | 14 src/objective/regression_objective.hpp | 21 src/objective/xentropy_objective.hpp | 19 src/re_model.cpp | 58 + tests/testthat/test_z_GPBoost_algorithm.R | 138 ++++ tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data.R | 92 +++ 35 files changed, 811 insertions(+), 328 deletions(-)
Title: Generative Neural Networks
Description: Tools to set up, train, store, load, investigate and analyze
generative neural networks. In particular, functionality for
generative moment matching networks is provided.
Author: Marius Hofert [aut, cre] ,
Avinash Prasad [aut]
Maintainer: Marius Hofert <mhofert@hku.hk>
Diff between gnn versions 0.0-3 dated 2021-09-20 and 0.0-4 dated 2024-02-28
gnn-0.0-3/gnn/man/Tensorflow_available.Rd |only gnn-0.0-4/gnn/DESCRIPTION | 15 ++++------ gnn-0.0-4/gnn/MD5 | 36 ++++++++++++------------ gnn-0.0-4/gnn/NAMESPACE | 45 ++++++++++++++++-------------- gnn-0.0-4/gnn/R/GNN_class.R | 2 - gnn-0.0-4/gnn/R/auxiliaries.R | 9 ++++-- gnn-0.0-4/gnn/R/ffGNN.R | 2 - gnn-0.0-4/gnn/R/find_box.R |only gnn-0.0-4/gnn/R/fitGNN.R | 11 ++----- gnn-0.0-4/gnn/R/loss.R | 8 +++-- gnn-0.0-4/gnn/R/plot.R | 23 ++++++++------- gnn-0.0-4/gnn/R/save_load.R | 6 ++-- gnn-0.0-4/gnn/TODO | 6 +++- gnn-0.0-4/gnn/build/partial.rdb |binary gnn-0.0-4/gnn/man/FNN.Rd | 14 ++++----- gnn-0.0-4/gnn/man/TensorFlow_available.Rd |only gnn-0.0-4/gnn/man/find_box.Rd |only gnn-0.0-4/gnn/man/fitGNN.Rd | 6 ++-- gnn-0.0-4/gnn/man/plot.Rd | 4 +- gnn-0.0-4/gnn/man/save_load.Rd | 20 ++++++------- gnn-0.0-4/gnn/man/time.Rd | 1 21 files changed, 106 insertions(+), 102 deletions(-)
Title: REDCap Castellated Data Handling
Description: Originally forked from the R part of 'REDCapRITS' by Paul Egeler.
See <https://github.com/pegeler/REDCapRITS>.
'REDCap' database casting and handling of castellated data when using
repeated instruments and longitudinal projects. Keeps a focused data export
approach, by allowing to only export required data from the database.
'REDCap' (Research Electronic Data Capture) is a secure, web-based software
platform designed to support data capture for research studies, providing
1) an intuitive interface for validated data capture; 2) audit trails for
tracking data manipulation and export procedures; 3) automated export
procedures for seamless data downloads to common statistical packages; and
4) procedures for data integration and interoperability with external
sources (Harris et al (2009) <doi:10.1016/j.jbi.2008.08.010>;
Harris et al (2019) <doi:10.1016/j.jbi.2019.103208>).
Author: Andreas Gammelgaard Damsbo [aut, cre]
,
Paul Egeler [aut]
Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>
Diff between REDCapCAST versions 24.1.1 dated 2024-01-09 and 24.2.1 dated 2024-02-28
REDCapCAST-24.1.1/REDCapCAST/tests/spelling.Rout.save |only REDCapCAST-24.2.1/REDCapCAST/DESCRIPTION | 32 REDCapCAST-24.2.1/REDCapCAST/MD5 | 96 + REDCapCAST-24.2.1/REDCapCAST/NAMESPACE | 12 REDCapCAST-24.2.1/REDCapCAST/NEWS.md | 24 REDCapCAST-24.2.1/REDCapCAST/R/REDCap_split.r | 98 + REDCapCAST-24.2.1/REDCapCAST/R/ds2dd.R | 21 REDCapCAST-24.2.1/REDCapCAST/R/ds2dd_detailed.R |only REDCapCAST-24.2.1/REDCapCAST/R/easy_redcap.R | 29 REDCapCAST-24.2.1/REDCapCAST/R/mtcars_redcap.R |only REDCapCAST-24.2.1/REDCapCAST/R/process_user_input.r | 4 REDCapCAST-24.2.1/REDCapCAST/R/read_redcap_instrument.R |only REDCapCAST-24.2.1/REDCapCAST/R/read_redcap_tables.R | 66 - REDCapCAST-24.2.1/REDCapCAST/R/redcap_wider.R | 199 ++-- REDCapCAST-24.2.1/REDCapCAST/R/redcapcast_data.R | 14 REDCapCAST-24.2.1/REDCapCAST/R/redcapcast_meta.R | 2 REDCapCAST-24.2.1/REDCapCAST/R/shiny_cast.R |only REDCapCAST-24.2.1/REDCapCAST/R/sysdata.rda |binary REDCapCAST-24.2.1/REDCapCAST/R/utils.r | 387 +++++-- REDCapCAST-24.2.1/REDCapCAST/README.md | 18 REDCapCAST-24.2.1/REDCapCAST/build/vignette.rds |binary REDCapCAST-24.2.1/REDCapCAST/data/mtcars_redcap.csv |only REDCapCAST-24.2.1/REDCapCAST/data/mtcars_redcap.rda |only REDCapCAST-24.2.1/REDCapCAST/data/redcapcast_data.rda |binary REDCapCAST-24.2.1/REDCapCAST/inst/WORDLIST | 32 REDCapCAST-24.2.1/REDCapCAST/inst/doc/Database-creation.R |only REDCapCAST-24.2.1/REDCapCAST/inst/doc/Database-creation.Rmd |only REDCapCAST-24.2.1/REDCapCAST/inst/doc/Database-creation.html |only REDCapCAST-24.2.1/REDCapCAST/inst/doc/Introduction.R | 20 REDCapCAST-24.2.1/REDCapCAST/inst/doc/Introduction.Rmd | 22 REDCapCAST-24.2.1/REDCapCAST/inst/doc/Introduction.html | 491 ++++++---- REDCapCAST-24.2.1/REDCapCAST/man/REDCap_split.Rd | 17 REDCapCAST-24.2.1/REDCapCAST/man/d2w.Rd | 6 REDCapCAST-24.2.1/REDCapCAST/man/deploy_shiny.Rd |only REDCapCAST-24.2.1/REDCapCAST/man/ds2dd.Rd | 12 REDCapCAST-24.2.1/REDCapCAST/man/ds2dd_detailed.Rd |only REDCapCAST-24.2.1/REDCapCAST/man/easy_redcap.Rd | 6 REDCapCAST-24.2.1/REDCapCAST/man/file_extension.Rd |only REDCapCAST-24.2.1/REDCapCAST/man/get_id_name.Rd |only REDCapCAST-24.2.1/REDCapCAST/man/guess_time_only_filter.Rd |only REDCapCAST-24.2.1/REDCapCAST/man/hms2character.Rd |only REDCapCAST-24.2.1/REDCapCAST/man/is_repeated_longitudinal.Rd |only REDCapCAST-24.2.1/REDCapCAST/man/mark_complete.Rd |only REDCapCAST-24.2.1/REDCapCAST/man/mtcars_redcap.Rd |only REDCapCAST-24.2.1/REDCapCAST/man/read_input.Rd |only REDCapCAST-24.2.1/REDCapCAST/man/read_redcap_instrument.Rd |only REDCapCAST-24.2.1/REDCapCAST/man/read_redcap_tables.Rd | 9 REDCapCAST-24.2.1/REDCapCAST/man/redcap_wider.Rd | 67 + REDCapCAST-24.2.1/REDCapCAST/man/redcapcast_data.Rd | 12 REDCapCAST-24.2.1/REDCapCAST/man/sanitize_split.Rd | 2 REDCapCAST-24.2.1/REDCapCAST/man/server_factory.Rd |only REDCapCAST-24.2.1/REDCapCAST/man/shiny_cast.Rd |only REDCapCAST-24.2.1/REDCapCAST/man/split_non_repeating_forms.Rd | 6 REDCapCAST-24.2.1/REDCapCAST/man/strsplitx.Rd | 5 REDCapCAST-24.2.1/REDCapCAST/man/time_only_correction.Rd |only REDCapCAST-24.2.1/REDCapCAST/man/ui_factory.Rd |only REDCapCAST-24.2.1/REDCapCAST/tests/testthat/data/create-ref-data.R | 31 REDCapCAST-24.2.1/REDCapCAST/tests/testthat/helper-ExampleProject_R_2018-06-07_1129.r | 28 REDCapCAST-24.2.1/REDCapCAST/tests/testthat/test-csv-exports.R | 63 - REDCapCAST-24.2.1/REDCapCAST/tests/testthat/test-utils.R | 22 REDCapCAST-24.2.1/REDCapCAST/vignettes/Database-creation.Rmd |only REDCapCAST-24.2.1/REDCapCAST/vignettes/Introduction.Rmd | 22 62 files changed, 1154 insertions(+), 721 deletions(-)
Title: Working with the Neotoma Paleoecology Database
Description: Access and manipulation of data using the Neotoma Paleoecology Database.
<https://api.neotomadb.org/api-docs/>.
Author: Dominguez Vidana Socorro [aut, cre]
,
Simon Goring [aut]
Maintainer: Dominguez Vidana Socorro <s.dominguez@ht-data.com>
Diff between neotoma2 versions 1.0.2 dated 2023-06-29 and 1.0.3 dated 2024-02-28
neotoma2-1.0.2/neotoma2/man/clean.Rd |only neotoma2-1.0.2/neotoma2/man/clean.collunits.Rd |only neotoma2-1.0.2/neotoma2/man/clean.datasets.Rd |only neotoma2-1.0.2/neotoma2/man/clean.sites.Rd |only neotoma2-1.0.2/neotoma2/man/cleanNULL.Rd |only neotoma2-1.0.2/neotoma2/man/fix_null.Rd |only neotoma2-1.0.2/neotoma2/man/parse_location.Rd |only neotoma2-1.0.2/neotoma2/man/plot-sites-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/sub-collunits-numeric-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/sub-datasets-numeric-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/sub-site-character-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/sub-site-numeric-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/sub-sites-numeric-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/sub-specimens-numeric-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/sub-sub-chronologies-numeric-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/sub-sub-collunits-numeric-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/sub-sub-contacts-numeric-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/sub-sub-datasets-numeric-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/sub-sub-publications-numeric-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/sub-sub-samples-numeric-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/sub-sub-sites-numeric-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/sub-sub-specimens-numeric-ANY-method.Rd |only neotoma2-1.0.2/neotoma2/man/testNull.Rd |only neotoma2-1.0.2/neotoma2/man/use_na.Rd |only neotoma2-1.0.3/neotoma2/DESCRIPTION | 26 neotoma2-1.0.3/neotoma2/LICENSE | 2 neotoma2-1.0.3/neotoma2/MD5 | 164 neotoma2-1.0.3/neotoma2/NAMESPACE | 12 neotoma2-1.0.3/neotoma2/NEWS.md | 22 neotoma2-1.0.3/neotoma2/R/02_genericDefinitions.R | 2 neotoma2-1.0.3/neotoma2/R/build_sample.R | 2 neotoma2-1.0.3/neotoma2/R/check_contacts.R | 8 neotoma2-1.0.3/neotoma2/R/clean.R | 12 neotoma2-1.0.3/neotoma2/R/cleanNULL.R | 3 neotoma2-1.0.3/neotoma2/R/collunits-methods.R | 1 neotoma2-1.0.3/neotoma2/R/filter.R | 182 neotoma2-1.0.3/neotoma2/R/fix_nulls.r | 3 neotoma2-1.0.3/neotoma2/R/get_datasets.R | 55 neotoma2-1.0.3/neotoma2/R/get_downloads.R | 2 neotoma2-1.0.3/neotoma2/R/get_sites.R | 48 neotoma2-1.0.3/neotoma2/R/get_specimens.R | 2 neotoma2-1.0.3/neotoma2/R/get_stats.R |only neotoma2-1.0.3/neotoma2/R/parseURL.R | 5 neotoma2-1.0.3/neotoma2/R/parse_body.R | 1 neotoma2-1.0.3/neotoma2/R/parse_location.R | 4 neotoma2-1.0.3/neotoma2/R/plotLeaflet.R | 7 neotoma2-1.0.3/neotoma2/R/set_chronology.R | 2 neotoma2-1.0.3/neotoma2/R/set_collunit.R | 2 neotoma2-1.0.3/neotoma2/R/set_contacts.R | 3 neotoma2-1.0.3/neotoma2/R/set_dataset.R | 2 neotoma2-1.0.3/neotoma2/R/set_sample.R | 2 neotoma2-1.0.3/neotoma2/R/set_site.R | 2 neotoma2-1.0.3/neotoma2/R/site-methods.R | 35 neotoma2-1.0.3/neotoma2/R/specimens.R | 27 neotoma2-1.0.3/neotoma2/R/testNull.R | 3 neotoma2-1.0.3/neotoma2/R/toJSON.R | 2 neotoma2-1.0.3/neotoma2/R/use_na.R | 3 neotoma2-1.0.3/neotoma2/README.md | 26 neotoma2-1.0.3/neotoma2/build/vignette.rds |binary neotoma2-1.0.3/neotoma2/inst/CITATION |only neotoma2-1.0.3/neotoma2/inst/doc/neotoma2-package.Rmd | 4 neotoma2-1.0.3/neotoma2/inst/doc/neotoma2-package.html | 4228 +++++++--- neotoma2-1.0.3/neotoma2/man/build_sample.Rd | 2 neotoma2-1.0.3/neotoma2/man/cite_data-site-method.Rd | 2 neotoma2-1.0.3/neotoma2/man/filter.Rd | 66 neotoma2-1.0.3/neotoma2/man/filter.sites.Rd | 66 neotoma2-1.0.3/neotoma2/man/get_datasets.Rd | 2 neotoma2-1.0.3/neotoma2/man/get_datasets.site.Rd |only neotoma2-1.0.3/neotoma2/man/get_downloads.Rd | 2 neotoma2-1.0.3/neotoma2/man/get_sites.Rd | 16 neotoma2-1.0.3/neotoma2/man/get_sites.default.Rd | 7 neotoma2-1.0.3/neotoma2/man/get_sites.numeric.Rd | 5 neotoma2-1.0.3/neotoma2/man/get_sites.sites.Rd | 7 neotoma2-1.0.3/neotoma2/man/get_specimens.Rd | 2 neotoma2-1.0.3/neotoma2/man/get_stats.Rd |only neotoma2-1.0.3/neotoma2/man/parseURL.Rd | 2 neotoma2-1.0.3/neotoma2/man/parsebody.Rd | 1 neotoma2-1.0.3/neotoma2/man/plot-sites-method.Rd |only neotoma2-1.0.3/neotoma2/man/plotLeaflet.Rd | 2 neotoma2-1.0.3/neotoma2/man/set_chronology.Rd | 3 neotoma2-1.0.3/neotoma2/man/set_collunit.Rd | 3 neotoma2-1.0.3/neotoma2/man/set_contact.Rd | 3 neotoma2-1.0.3/neotoma2/man/set_dataset.Rd | 3 neotoma2-1.0.3/neotoma2/man/set_sample.Rd | 3 neotoma2-1.0.3/neotoma2/man/set_site.Rd | 2 neotoma2-1.0.3/neotoma2/man/sub-collunits-numeric-method.Rd |only neotoma2-1.0.3/neotoma2/man/sub-datasets-numeric-method.Rd |only neotoma2-1.0.3/neotoma2/man/sub-site-character-method.Rd |only neotoma2-1.0.3/neotoma2/man/sub-site-numeric-method.Rd |only neotoma2-1.0.3/neotoma2/man/sub-sites-numeric-method.Rd |only neotoma2-1.0.3/neotoma2/man/sub-specimens-numeric-method.Rd |only neotoma2-1.0.3/neotoma2/man/sub-sub-chronologies-numeric-method.Rd |only neotoma2-1.0.3/neotoma2/man/sub-sub-collunits-numeric-method.Rd |only neotoma2-1.0.3/neotoma2/man/sub-sub-contacts-numeric-method.Rd |only neotoma2-1.0.3/neotoma2/man/sub-sub-datasets-numeric-method.Rd |only neotoma2-1.0.3/neotoma2/man/sub-sub-publications-numeric-method.Rd |only neotoma2-1.0.3/neotoma2/man/sub-sub-samples-numeric-method.Rd |only neotoma2-1.0.3/neotoma2/man/sub-sub-sites-numeric-method.Rd |only neotoma2-1.0.3/neotoma2/man/sub-sub-specimens-numeric-method.Rd |only neotoma2-1.0.3/neotoma2/man/toJSON-sites-method.Rd | 2 neotoma2-1.0.3/neotoma2/tests/testthat/test_check_contacts.R |only neotoma2-1.0.3/neotoma2/tests/testthat/test_datasets.R | 6 neotoma2-1.0.3/neotoma2/tests/testthat/test_generaltests.R | 18 neotoma2-1.0.3/neotoma2/tests/testthat/test_specimens.R | 13 neotoma2-1.0.3/neotoma2/vignettes/neotoma2-package.Rmd | 4 105 files changed, 3794 insertions(+), 1352 deletions(-)
Title: Mediation Analysis Using Joint Significance
Description: A set of helper functions to conduct joint-significance tests
for mediation analysis, as recommended by Yzerbyt, Muller, Batailler,
& Judd. (2018) <doi:10.1037/pspa0000132>.
Author: Cedric Batailler [aut, cre] ,
Dominique Muller [aut] ,
Vincent Yzerbyt [aut],
Charles Judd [aut],
Yoann Julliard [ctb] ,
Arnold Ho [dtc],
Nour Kteily [dtc],
Jacqueline Chen [dtc],
Simone Dohle [dtc],
Michael Siegrist [dtc]
Maintainer: Cedric Batailler <cedric.batailler@gmail.com>
Diff between JSmediation versions 0.2.1 dated 2023-02-05 and 0.2.2 dated 2024-02-28
DESCRIPTION | 10 MD5 | 54 NEWS.md | 9 R/check_assumptions.R | 9 R/check_variables.R | 26 R/compute_indirect_effect_for.R | 12 R/mdt_simple.R | 2 R/plot_assumptions.R | 18 R/utils-tidy-eval.R | 2 README.md | 2 inst/doc/jsmediation.R | 20 inst/doc/jsmediation.Rmd | 6 inst/doc/jsmediation.html | 210 inst/doc/moderated-mediation.R | 2 inst/doc/moderated-mediation.html | 285 man/JSmediation-package.Rd | 1 man/check_assumptions.Rd | 6 man/compute_indirect_effect_for.Rd | 10 man/extract_tidy_models.Rd | 4 man/mdt_simple.Rd | 2 man/mdt_within.Rd | 2 man/mdt_within_wide.Rd | 2 man/plot_assumptions.Rd | 6 man/tidyeval.Rd | 1 tests/testthat/_snaps/plot_assumptions/last-plot-plot-assumptions-produces.svg | 5296 +++++----- tests/testthat/test-check_assumptions.R | 2 tests/testthat/test-plot_assumptions.R | 2 vignettes/jsmediation.Rmd | 6 28 files changed, 3024 insertions(+), 2983 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-13 2.0.0
2023-12-10 1.0.0
Title: High Performance Remote File System, Database and 'Geospatial'
Access Using 'duckdb'
Description: Provides friendly wrappers for creating 'duckdb'-backed connections
to tabular datasets ('csv', parquet, etc) on local or remote file systems.
This mimics the behaviour of "open_dataset" in the 'arrow' package,
but in addition to 'S3' file system also generalizes to any list of 'http' URLs.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between duckdbfs versions 0.0.3 dated 2023-10-19 and 0.0.4 dated 2024-02-28
DESCRIPTION | 13 +- MD5 | 37 ++++-- NAMESPACE | 3 NEWS.md | 13 ++ R/duckdb_config.R | 5 R/open_dataset.R | 94 +++++++++++++--- R/spatial_join.R |only R/st_read_meta.R |only R/to_sf.R | 27 +++- R/utils.R |only R/write_dataset.R | 2 README.md | 228 +++++++++++++++++++++++++++++++---------- inst/WORDLIST | 8 + inst/examples/more-spatial.R |only inst/examples/spatial_module.R |only inst/extdata/metro.fgb |only inst/extdata/world.fgb |only inst/extdata/world.gpkg |only man/as_view.Rd |only man/figures |only man/open_dataset.Rd | 6 - man/spatial_join.Rd |only man/st_read_meta.Rd |only man/to_sf.Rd | 10 + tests/testthat/test-spatial.R | 69 ++++++++++++ 25 files changed, 405 insertions(+), 110 deletions(-)