Title: Create TLGs using the 'tidyverse'
Description: Generate tables, listings, and graphs (TLG) using 'tidyverse.'
Tables can be created functionally, using a standard TLG process, or by
specifying table and column metadata to create generic analysis summaries.
The 'envsetup' package can also be leveraged to create environments for table
creation.
Author: Nicholas Masel [aut],
Steven Haesendonckx [aut],
Pelagia Alexandra Papadopoulou [aut],
Sheng-Wei Wang [aut],
Eli Miller [aut] ,
Nathan Kosiba [aut] ,
Aidan Ceney [aut] ,
Janssen R&D [cph, fnd],
David Hugh-Jones [cph] ,
Konrad Pagacz [aut, cre]
Maintainer: Konrad Pagacz <kpagacz@its.jnj.com>
Diff between tidytlg versions 0.1.4 dated 2023-10-18 and 0.1.5 dated 2024-06-14
tidytlg-0.1.4/tidytlg/R/zzz.R |only tidytlg-0.1.4/tidytlg/tests/testthat/_snaps/png/png1.rtf |only tidytlg-0.1.4/tidytlg/tests/testthat/_snaps/png/png2.rtf |only tidytlg-0.1.4/tidytlg/tests/testthat/_snaps/titles/tsidem01.rtf |only tidytlg-0.1.4/tidytlg/tests/testthat/_snaps/tlgsetup/test-tlgsetup.rtf |only tidytlg-0.1.4/tidytlg/tests/testthat/test_outputs/test-tlgsetup.rtf |only tidytlg-0.1.5/tidytlg/DESCRIPTION | 44 tidytlg-0.1.5/tidytlg/MD5 | 177 - tidytlg-0.1.5/tidytlg/NAMESPACE | 21 tidytlg-0.1.5/tidytlg/NEWS.md | 10 tidytlg-0.1.5/tidytlg/R/add_bottom_borders.R |only tidytlg-0.1.5/tidytlg/R/freq.R | 4 tidytlg-0.1.5/tidytlg/R/gentlg.R | 1096 +--------- tidytlg-0.1.5/tidytlg/R/gentlg_single.R |only tidytlg-0.1.5/tidytlg/R/insert_empty_rows.R |only tidytlg-0.1.5/tidytlg/R/is_output_type.R |only tidytlg-0.1.5/tidytlg/R/quick_rtf_jnj.R | 279 +- tidytlg-0.1.5/tidytlg/R/remove_zero_padding.R |only tidytlg-0.1.5/tidytlg/R/rmdpstitle.R | 80 tidytlg-0.1.5/tidytlg/R/spanning_headers.R | 8 tidytlg-0.1.5/tidytlg/R/tidytlg-package.R | 47 tidytlg-0.1.5/tidytlg/R/tlgsetup.R | 13 tidytlg-0.1.5/tidytlg/build/vignette.rds |binary tidytlg-0.1.5/tidytlg/data/cdisc_adae.rda |binary tidytlg-0.1.5/tidytlg/data/cdisc_adsl.rda |binary tidytlg-0.1.5/tidytlg/inst/doc/freq.R | 54 tidytlg-0.1.5/tidytlg/inst/doc/freq.Rmd | 57 tidytlg-0.1.5/tidytlg/inst/doc/freq.html | 262 +- tidytlg-0.1.5/tidytlg/inst/doc/symbols.R | 26 tidytlg-0.1.5/tidytlg/inst/doc/symbols.Rmd | 31 tidytlg-0.1.5/tidytlg/inst/doc/symbols.html | 106 tidytlg-0.1.5/tidytlg/inst/doc/tbl_manipulation.R | 29 tidytlg-0.1.5/tidytlg/inst/doc/tbl_manipulation.Rmd | 30 tidytlg-0.1.5/tidytlg/inst/doc/tbl_manipulation.html | 417 ++- tidytlg-0.1.5/tidytlg/inst/doc/tidytlg.R | 48 tidytlg-0.1.5/tidytlg/inst/doc/tidytlg.Rmd | 46 tidytlg-0.1.5/tidytlg/inst/doc/tidytlg.html | 911 ++++---- tidytlg-0.1.5/tidytlg/inst/doc/tlgsetup.R | 6 tidytlg-0.1.5/tidytlg/inst/doc/tlgsetup.Rmd | 7 tidytlg-0.1.5/tidytlg/inst/doc/tlgsetup.html | 110 - tidytlg-0.1.5/tidytlg/inst/doc/univar.R | 44 tidytlg-0.1.5/tidytlg/inst/doc/univar.Rmd | 47 tidytlg-0.1.5/tidytlg/inst/doc/univar.html | 100 tidytlg-0.1.5/tidytlg/man/add_bottom_borders.Rd |only tidytlg-0.1.5/tidytlg/man/col_borders.Rd |only tidytlg-0.1.5/tidytlg/man/freq.Rd | 4 tidytlg-0.1.5/tidytlg/man/gentlg.Rd | 53 tidytlg-0.1.5/tidytlg/man/insert_empty_rows.Rd |only tidytlg-0.1.5/tidytlg/man/no_borders.Rd |only tidytlg-0.1.5/tidytlg/man/old_format.Rd |only tidytlg-0.1.5/tidytlg/man/remove_zero_padding.Rd |only tidytlg-0.1.5/tidytlg/man/rmdpstitle.Rd | 8 tidytlg-0.1.5/tidytlg/man/row_border.Rd |only tidytlg-0.1.5/tidytlg/man/single_border.Rd |only tidytlg-0.1.5/tidytlg/man/spanning_borders.Rd |only tidytlg-0.1.5/tidytlg/man/tidytlg.Rd | 6 tidytlg-0.1.5/tidytlg/tests/testthat/_snaps/borders |only tidytlg-0.1.5/tidytlg/tests/testthat/_snaps/colheader/colheader1.rtf | 16 tidytlg-0.1.5/tidytlg/tests/testthat/_snaps/colheader/colheader2.rtf | 16 tidytlg-0.1.5/tidytlg/tests/testthat/_snaps/colspan/colspan1.rtf | 32 tidytlg-0.1.5/tidytlg/tests/testthat/_snaps/colspan/colspan2.rtf | 48 tidytlg-0.1.5/tidytlg/tests/testthat/_snaps/colspan/colspan3.rtf | 32 tidytlg-0.1.5/tidytlg/tests/testthat/_snaps/insert_empty_rows |only tidytlg-0.1.5/tidytlg/tests/testthat/_snaps/multiple-tables-in-rtf |only tidytlg-0.1.5/tidytlg/tests/testthat/_snaps/page_numbers |only tidytlg-0.1.5/tidytlg/tests/testthat/_snaps/png/test2plots.rtf | 6 tidytlg-0.1.5/tidytlg/tests/testthat/_snaps/titles/gsvit01a.rtf | 14 tidytlg-0.1.5/tidytlg/tests/testthat/_snaps/tlgsetup/testtlgsetup.rtf |only tidytlg-0.1.5/tidytlg/tests/testthat/test-borders.R |only tidytlg-0.1.5/tidytlg/tests/testthat/test-colheader.R | 3 tidytlg-0.1.5/tidytlg/tests/testthat/test-colspan.R | 17 tidytlg-0.1.5/tidytlg/tests/testthat/test-insert_empty_rows.R |only tidytlg-0.1.5/tidytlg/tests/testthat/test-multiple-tables-in-rtf.R |only tidytlg-0.1.5/tidytlg/tests/testthat/test-page_numbers.R |only tidytlg-0.1.5/tidytlg/tests/testthat/test-png.R | 56 tidytlg-0.1.5/tidytlg/tests/testthat/test-quick_rtf_jnj.R |only tidytlg-0.1.5/tidytlg/tests/testthat/test-remove_zero_padding.R |only tidytlg-0.1.5/tidytlg/tests/testthat/test-tlgsetup.R | 20 tidytlg-0.1.5/tidytlg/tests/testthat/test_data/zero_padding |only tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/borders |only tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/colheader1.rtf | 16 tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/colheader2.rtf | 16 tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/colspan1.rtf | 32 tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/colspan2.rtf | 48 tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/colspan3.rtf | 32 tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/emptyrowsinsertions |only tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/gsvit01a.rtf | 14 tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/multiple_tables_in_one_file |only tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/pagenumbers.rtf |only tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/pagenumberstable.rtf |only tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/png1.png |binary tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/png1.rtf | 8 tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/png2.png |binary tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/png2.rtf | 8 tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/test2plots.rtf | 6 tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/testtlgsetup.rtf | 64 tidytlg-0.1.5/tidytlg/tests/testthat/test_outputs/tsidem01.rtf | 14 tidytlg-0.1.5/tidytlg/vignettes/freq.Rmd | 57 tidytlg-0.1.5/tidytlg/vignettes/symbols.Rmd | 31 tidytlg-0.1.5/tidytlg/vignettes/tbl_manipulation.Rmd | 30 tidytlg-0.1.5/tidytlg/vignettes/tidytlg.Rmd | 46 tidytlg-0.1.5/tidytlg/vignettes/tlgsetup.Rmd | 7 tidytlg-0.1.5/tidytlg/vignettes/univar.Rmd | 47 103 files changed, 2214 insertions(+), 2703 deletions(-)
Title: A Collection of Process Capability Index Functions
Description: A collection of process capability index functions, such as
C_p(), C_pk(), C_pm(), and others, along with metadata about each, like
'LaTeX' equations and 'R' expressions. Its primary purpose is to form a
foundation for other quality control packages to build on top of, by providing
basic resources and functions. The indices belong to the field of statistical
quality control, and quantify the degree to which a manufacturing process is
able to create items that adhere to a certain standard of quality. For details
see Montgomery, D. C. (2019, ISBN:978-1-119-39930-8).
Author: Sam Semegne [aut, cre]
Maintainer: Sam Semegne <sam.ahoi@hotmail.com>
Diff between pci versions 1.0.0 dated 2024-06-13 and 1.0.1 dated 2024-06-14
DESCRIPTION | 6 - MD5 | 29 +++--- NAMESPACE | 14 +-- NEWS.md |only R/C_p.R | 131 +++++++++++++++--------------- R/C_pk.R | 139 ++++++++++++++++---------------- R/C_pl.R | 121 ++++++++++++++-------------- R/C_pm.R | 152 +++++++++++++++++------------------ R/C_pu.R | 123 ++++++++++++++-------------- R/helpers.R | 15 +++ inst/tinytest/test_C_p.R | 163 +++++++++++++++++++------------------- inst/tinytest/test_C_pk.R | 183 ++++++++++++++++++++++--------------------- inst/tinytest/test_C_pl.R | 119 ++++++++++++++------------- inst/tinytest/test_C_pm.R | 179 ++++++++++++++++++++++-------------------- inst/tinytest/test_C_pu.R | 119 ++++++++++++++------------- inst/tinytest/test_helpers.R | 78 +++++++++++++----- 16 files changed, 832 insertions(+), 739 deletions(-)
Title: Handwriting Analysis in R
Description: Perform statistical writership analysis of scanned handwritten documents.
Webpage provided at: <https://github.com/CSAFE-ISU/handwriter>.
Author: Iowa State University of Science and Technology on behalf of its Center
for Statistics and Applications in Forensic Evidence [aut, cph,
fnd],
Nick Berry [aut],
Stephanie Reinders [aut, cre],
James Taylor [aut],
Felix Baez-Santiago [ctb],
Jon Gonzalez [...truncated...]
Maintainer: Stephanie Reinders <srein@iastate.edu>
Diff between handwriter versions 3.1.0 dated 2024-06-10 and 3.1.1 dated 2024-06-14
handwriter-3.1.0/handwriter/inst/extdata/example_images |only handwriter-3.1.1/handwriter/DESCRIPTION | 6 - handwriter-3.1.1/handwriter/MD5 | 58 ++++------ handwriter-3.1.1/handwriter/NEWS.md | 7 + handwriter-3.1.1/handwriter/R/RcppExports.R | 6 - handwriter-3.1.1/handwriter/R/cluster_assignment.R | 6 - handwriter-3.1.1/handwriter/R/cluster_format.R | 6 - handwriter-3.1.1/handwriter/R/cluster_model.R | 8 - handwriter-3.1.1/handwriter/R/cluster_templates.R | 4 handwriter-3.1.1/handwriter/R/data.R | 20 +-- handwriter-3.1.1/handwriter/README.md | 12 +- handwriter-3.1.1/handwriter/data/example_analysis.rda |binary handwriter-3.1.1/handwriter/data/example_model.rda |binary handwriter-3.1.1/handwriter/inst/doc/handwriter.html | 31 +---- handwriter-3.1.1/handwriter/man/example_cluster_template.Rd | 17 +- handwriter-3.1.1/handwriter/man/figures/README-unnamed-chunk-10-1.png |binary handwriter-3.1.1/handwriter/man/figures/README-unnamed-chunk-15-1.png |binary handwriter-3.1.1/handwriter/man/figures/README-unnamed-chunk-7-1.png |binary handwriter-3.1.1/handwriter/man/fit_model.Rd | 8 - handwriter-3.1.1/handwriter/man/make_clustering_template.Rd | 4 handwriter-3.1.1/handwriter/src/ClusterFuncs.cpp | 4 handwriter-3.1.1/handwriter/tests/testthat/fixtures/template/data/model_clusters.rds |binary handwriter-3.1.1/handwriter/tests/testthat/fixtures/template/data/questioned_clusters.rds |binary handwriter-3.1.1/handwriter/tests/testthat/test-ClusterModeling_datafunctions.R | 12 -- handwriter-3.1.1/handwriter/tests/testthat/test-ClusterModeling_modelfunctions.R | 54 +-------- handwriter-3.1.1/handwriter/tests/testthat/test-slow-functions.R | 47 ++++---- 26 files changed, 124 insertions(+), 186 deletions(-)
Title: Create Layout Plots of Biological Culture Plates and Microplates
Description: Enables users to create simple plots of biological culture plates as well as microplates. Both continuous and discrete values can be plotted onto the plate layout.
Author: Jan-Philipp Quast [aut, cre]
Maintainer: Jan-Philipp Quast <quast@imsb.biol.ethz.ch>
Diff between ggplate versions 0.1.2 dated 2024-06-14 and 0.1.3 dated 2024-06-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/plate_plot.R | 3 +++ 4 files changed, 13 insertions(+), 6 deletions(-)
Title: 'caret' Applications for Spatial-Temporal Models
Description: Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. CAST includes functions to improve spatial or spatial-temporal modelling tasks using 'caret'. It includes the newly suggested 'Nearest neighbor distance matching' cross-validation to estimate the performance of spatial prediction models and allows for spatial variable selection to selects suitable predictor variables in view to their contribution to the spatial model performance. CAST further includes functionality to estimate the (spatial) area of applicability of prediction models. Methods are described in Meyer et al. (2018) <doi:10.1016/j.envsoft.2017.12.001>; Meyer et al. (2019) <doi:10.1016/j.ecolmodel.2019.108815>; Meyer and Pebesma (2021) <doi:10.1111/2041-210X.13650>; Milà et al. (2022) <doi:10.1111/2041-210X.13851>; Meyer and Pebesma (2022) <doi:10.1038/s41467-022-29838-9>; L [...truncated...]
Author: Hanna Meyer [cre, aut],
Carles Mila [aut],
Marvin Ludwig [aut],
Jan Linnenbrink [aut],
Fabian Schumacher [aut],
Philipp Otto [ctb],
Chris Reudenbach [ctb],
Thomas Nauss [ctb],
Edzer Pebesma [ctb]
Maintainer: Hanna Meyer <hanna.meyer@uni-muenster.de>
Diff between CAST versions 1.0.1 dated 2024-04-25 and 1.0.2 dated 2024-06-14
DESCRIPTION | 16 +++++---- MD5 | 53 ++++++++++++++++--------------- NEWS.md | 3 + R/aoa.R | 8 ++-- R/geodist.R | 16 ++++++--- R/global_validation.R | 2 + README.md | 21 +++++++++++- inst/doc/cast01-CAST-intro.R | 7 ---- inst/doc/cast01-CAST-intro.Rmd | 11 +----- inst/doc/cast01-CAST-intro.html | 33 ++++++++----------- inst/doc/cast02-plotgeodist.html | 6 +-- inst/doc/cast03-CV.html | 4 +- inst/doc/cast04-AOA-tutorial.Rmd | 2 - inst/doc/cast04-AOA-tutorial.html | 16 ++++----- inst/doc/cast05-parallel.html | 10 ++--- man/CAST.Rd | 1 man/figures |only man/global_validation.Rd | 2 + tests/testthat/test-aoa.R | 9 ++++- tests/testthat/test-errorProfiles.R | 8 ++++ tests/testthat/test-fss.R | 8 ++++ tests/testthat/test-geodist.R | 54 +++++++++++++------------------- tests/testthat/test-global_validation.R | 6 ++- tests/testthat/test-knndm.R | 21 +----------- tests/testthat/test-nndm.R | 6 --- tests/testthat/test_trainDI.R | 48 ++++++++++++++-------------- vignettes/cast01-CAST-intro.Rmd | 11 +----- vignettes/cast04-AOA-tutorial.Rmd | 2 - 28 files changed, 197 insertions(+), 187 deletions(-)
Title: Useful Functions for Programming and Generating Documents
Description: Tools to help developers and producers manipulate R objects and outputs. It includes tools for displaying results and objects, and for formatting them in the correct format.
Author: Tanguy Barthelemy [aut, cre]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between TBox versions 0.1.0 dated 2024-06-07 and 0.1.2 dated 2024-06-14
DESCRIPTION | 13 ++- MD5 | 18 +++-- NAMESPACE | 3 NEWS.md |only R/TBox-package.R | 3 R/format_code.R | 176 ++++++++++++++++++++++++++++++++++++---------------- README.md | 19 ++++- man/TBox-package.Rd | 9 ++ man/render_code.Rd | 23 ++++-- tests |only 10 files changed, 188 insertions(+), 76 deletions(-)
Title: Cross-Fitting for Doubly Robust Evaluation of High-Dimensional
Surrogate Markers
Description: Doubly robust methods for evaluating surrogate markers as outlined in: Agniel D, Hejblum BP, Thiebaut R & Parast L (2022).
"Doubly robust evaluation of high-dimensional surrogate markers", Biostatistics <doi:10.1093/biostatistics/kxac020>. You can use these methods to determine how much of the overall treatment effect is explained by a (possibly high-dimensional) set of surrogate markers.
Author: Denis Agniel [aut, cre],
Boris P. Hejblum [aut]
Maintainer: Denis Agniel <dagniel@rand.org>
Diff between crossurr versions 1.0.6 dated 2022-10-21 and 1.1.1 dated 2024-06-14
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/xfit_dr.R | 24 +++++++++++++++++------- README.md | 3 ++- inst/CITATION | 18 ++++++++++-------- 6 files changed, 42 insertions(+), 24 deletions(-)
Title: Basic Data Wrangling for NEON Observational Data
Description: NEON observational data are provided via the NEON Data Portal <https://www.neonscience.org>
and NEON API, and can be downloaded and reformatted by the 'neonUtilities' package. NEON observational data
(human-observed measurements, and analyses derived from human-collected samples, such as tree diameters and
algal chemistry) are published in a format consisting of one or more tabular data files. This package provides
tools for performing common operations on NEON observational data, including checking for duplicates and
joining tables.
Author: Claire Lunch [aut, cre, ctb] ,
Eric Sokol [aut, ctb] ,
Natalie Robinson [aut, ctb] ,
NEON [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonOS versions 1.0.0 dated 2022-09-29 and 1.1.0 dated 2024-06-14
DESCRIPTION | 12 +-- MD5 | 15 ++-- NEWS.md |only R/dupProcess.R |only R/getAPI.R | 12 ++- R/joinTableNEON.R | 25 +++++-- R/removeDups.R | 182 +++++++++++++++++++++++---------------------------- man/dupProcess.Rd |only man/joinTableNEON.Rd | 7 + man/removeDups.Rd | 6 + 10 files changed, 140 insertions(+), 119 deletions(-)
Title: Tools for Analyzing Cross-National Military Deployment and
Basing Data
Description: These functions generate data frames on troop deployments and military basing using U.S. Department of Defense data on overseas military deployments. This package provides functions for pulling country-year troop deployment and basing data. Subsequent versions will hopefully include cross-national data on deploying countries.
Author: Michael Flynn [aut, cre]
Maintainer: Michael Flynn <meflynn@ksu.edu>
Diff between troopdata versions 0.1.5 dated 2022-01-31 and 1.0.0 dated 2024-06-14
troopdata-0.1.5/troopdata/data/troopdata.rda |only troopdata-0.1.5/troopdata/man/troopdata.Rd |only troopdata-1.0.0/troopdata/DESCRIPTION | 18 troopdata-1.0.0/troopdata/MD5 | 33 - troopdata-1.0.0/troopdata/NAMESPACE | 2 troopdata-1.0.0/troopdata/NEWS.md | 18 troopdata-1.0.0/troopdata/R/data.R | 118 ++++- troopdata-1.0.0/troopdata/R/get_basedata.R | 12 troopdata-1.0.0/troopdata/R/get_builddata.R | 12 troopdata-1.0.0/troopdata/R/get_troopdata.R | 191 +++++++- troopdata-1.0.0/troopdata/R/troopdata-package.R | 2 troopdata-1.0.0/troopdata/README.md | 246 +++++------ troopdata-1.0.0/troopdata/build |only troopdata-1.0.0/troopdata/data/troopdata_rebuild_long.rda |only troopdata-1.0.0/troopdata/data/troopdata_rebuild_reports.rda |only troopdata-1.0.0/troopdata/inst/WORDLIST | 15 troopdata-1.0.0/troopdata/man/basedata.Rd | 2 troopdata-1.0.0/troopdata/man/get_troopdata.Rd | 32 + troopdata-1.0.0/troopdata/man/troopdata-package.Rd | 12 troopdata-1.0.0/troopdata/man/troopdata_rebuild_long.Rd |only troopdata-1.0.0/troopdata/man/troopdata_rebuild_reports.Rd |only 21 files changed, 496 insertions(+), 217 deletions(-)
Title: Models, Datasets and Transformations for Images
Description: Provides access to datasets, models and preprocessing
facilities for deep learning with images. Integrates seamlessly
with the 'torch' package and it's 'API' borrows heavily from
'PyTorch' vision package.
Author: Daniel Falbel [aut, cre],
Christophe Regouby [ctb],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torchvision versions 0.5.1 dated 2023-04-14 and 0.6.0 dated 2024-06-14
DESCRIPTION | 11 +-- MD5 | 108 ++++++++++++++++---------------- NEWS.md | 6 + R/dataset-mnist.R | 8 +- R/models-alexnet.R | 2 R/models-inception.R | 2 R/models-mobilenetv2.R | 2 R/models-resnet.R | 28 ++++---- R/models-vgg.R | 18 ++--- R/tiny-imagenet-dataset.R | 6 - R/transforms-defaults.R | 2 R/transforms-generics.R | 7 +- R/transforms-tensor.R | 2 R/utils.R | 2 R/vision_utils.R | 4 + README.md | 3 man/draw_bounding_boxes.Rd | 2 man/draw_keypoints.Rd | 2 man/model_resnet.Rd | 10 +- man/model_vgg.Rd | 2 man/transform_adjust_brightness.Rd | 2 man/transform_adjust_contrast.Rd | 2 man/transform_adjust_gamma.Rd | 2 man/transform_adjust_hue.Rd | 2 man/transform_adjust_saturation.Rd | 2 man/transform_affine.Rd | 5 - man/transform_center_crop.Rd | 2 man/transform_color_jitter.Rd | 2 man/transform_convert_image_dtype.Rd | 2 man/transform_crop.Rd | 2 man/transform_five_crop.Rd | 2 man/transform_grayscale.Rd | 2 man/transform_hflip.Rd | 2 man/transform_linear_transformation.Rd | 2 man/transform_normalize.Rd | 2 man/transform_pad.Rd | 2 man/transform_perspective.Rd | 2 man/transform_random_affine.Rd | 5 - man/transform_random_apply.Rd | 2 man/transform_random_choice.Rd | 2 man/transform_random_crop.Rd | 2 man/transform_random_erasing.Rd | 4 - man/transform_random_grayscale.Rd | 2 man/transform_random_horizontal_flip.Rd | 2 man/transform_random_order.Rd | 2 man/transform_random_perspective.Rd | 2 man/transform_random_resized_crop.Rd | 2 man/transform_random_rotation.Rd | 7 +- man/transform_random_vertical_flip.Rd | 2 man/transform_rgb_to_grayscale.Rd | 2 man/transform_rotate.Rd | 5 - man/transform_ten_crop.Rd | 2 man/transform_to_tensor.Rd | 2 man/transform_vflip.Rd | 2 tests/testthat/test-transforms.R | 44 +++++++++++++ 55 files changed, 208 insertions(+), 147 deletions(-)
Title: Projection Based Clustering
Description: A clustering approach applicable to every projection method is proposed here. The two-dimensional scatter plot of any projection method can construct a topographic map which displays unapparent data structures by using distance and density information of the data. The generalized U*-matrix renders this visualization in the form of a topographic map, which can be used to automatically define the clusters of high-dimensional data. The whole system is based on Thrun and Ultsch, "Using Projection based Clustering to Find Distance and Density based Clusters in High-Dimensional Data" <DOI:10.1007/s00357-020-09373-2>. Selecting the correct projection method will result in a visualization in which mountains surround each cluster. The number of clusters can be determined by counting valleys on the topographic map. Most projection methods are wrappers for already available methods in R. By contrast, the neighbor retrieval visualizer (NeRV) is based on C++ source code of the 'dredviz' softw [...truncated...]
Author: Michael Thrun [aut, cre, cph],
Quirin Stier [ctb, rev] ,
Brinkmann Luca [ctb],
Florian Lerch [aut],
Felix Pape [aut],
Tim Schreier [aut],
Luis Winckelmann [aut],
Kristian Nybo [cph],
Jarkko Venna [cph],
van der Maaten Laurens [cph]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between ProjectionBasedClustering versions 1.2.1 dated 2023-10-11 and 1.2.2 dated 2024-06-14
DESCRIPTION | 13 ++++++------- MD5 | 22 +++++++++++----------- R/PolarSwarm.R | 2 +- R/helperTopographicIsland.R | 10 ++++++---- R/interactiveGeneralizedUmatrixIsland.R | 19 +++++++++++-------- R/interactiveGeneralizedUmatrixIsland_ggplot.R | 16 ++++++++-------- R/interactiveGeneralizedUmatrixIsland_plotly.R | 9 +++++---- build/partial.rdb |binary man/ContTrustMeasure.Rd | 13 ++++++++----- man/KLMeasure.Rd | 16 ++++++++++++---- man/PolarSwarm.Rd | 3 ++- man/interactiveGeneralizedUmatrixIsland.Rd | 22 ++++++++++++++++------ 12 files changed, 86 insertions(+), 59 deletions(-)
More information about ProjectionBasedClustering at CRAN
Permanent link
Title: Triangle Meshes and Related Geometry Tools
Description: Generate planar and spherical triangle meshes,
compute finite element calculations for 1- and 2-dimensional flat and curved
manifolds with associated basis function spaces, methods for lines and
polygons, and transparent handling of coordinate reference systems and
coordinate transformation, including 'sf' and 'sp' geometries. The core
'fmesher' library code was originally part of the 'INLA' package, and
implements parts of "Triangulations and Applications" by
Hjelle and Daehlen (2006) <doi:10.1007/3-540-33261-8>.
Author: Finn Lindgren [aut, cre, cph] ,
Seaton Andy [ctb] ,
Suen Man Ho [ctb] ,
Fabian E. Bachl [ctb]
Maintainer: Finn Lindgren <finn.lindgren@gmail.com>
Diff between fmesher versions 0.1.5 dated 2023-12-20 and 0.1.6 dated 2024-06-14
DESCRIPTION | 12 - MD5 | 93 +++++------ NAMESPACE | 13 + NEWS.md | 12 + R/RcppExports.R | 26 +++ R/bary.R | 56 ++++-- R/bbox.R | 72 +++++++- R/crs.R | 14 + R/evaluator.R | 44 ++++- R/fem.R | 51 ++++++ R/fm.R | 6 R/integration.R | 32 +++ R/lattice_2d.R | 12 + R/local.R | 29 ++- R/manifold.R | 57 ++++-- R/matern.R | 2 R/mesh_2d.R | 63 ++++++- R/plot.R | 24 ++ R/print.R | 33 ++++ R/sp_mesh.R | 2 R/tensor.R | 27 ++- README.md | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/basic_use.html | 180 +++++++++++----------- inst/doc/fmesher_library.html | 3 man/figures/README-example1-plot-1.png |binary man/fm_CRS_sp.Rd | 6 man/fm_as_fm.Rd | 3 man/fm_bary.Rd | 15 + man/fm_basis.Rd | 14 + man/fm_bbox.Rd | 22 ++ man/fm_fem.Rd | 7 man/fm_int_mesh_2d_core.Rd | 2 man/fm_lattice_2d.Rd | 12 + man/fm_manifold.Rd | 5 man/fm_tensor.Rd | 11 + man/fm_unify_coords.Rd | 2 man/fmesher-print.Rd | 3 man/fmesher_subdivide.Rd |only man/plot.fm_segm.Rd | 4 src/RcppExports.cpp | 17 ++ src/Rcpp_interface.cc | 112 +++++++++++++ src/fmesher_helpers.cc | 2 src/mesh.cc | 270 ++++++++++++++++++++++++++------- src/mesh.h | 67 ++++++-- src/meshc.cc | 40 ++-- tests/testthat/test-sf.R | 13 + 48 files changed, 1147 insertions(+), 351 deletions(-)
Title: Validation of Seasonal Weather Forecasts
Description: Provides tools for processing and evaluating seasonal weather forecasts,
with an emphasis on tercile forecasts. We follow the World Meteorological Organization's
"Guidance on Verification of Operational Seasonal Climate Forecasts",
S.J.Mason (2018, ISBN: 978-92-63-11220-0, URL: <https://library.wmo.int/idurl/4/56227>).
The development was supported by the European Union’s Horizon 2020 research and innovation
programme under grant agreement no. 869730 (CONFER).
A comprehensive online tutorial is available at <https://seasonalforecastingengine.github.io/SeaValDoc/>.
Author: Claudio Heinrich-Mertsching [aut, cre, cph]
,
Celine Cunen [ctb],
Michael Scheuerer [ctb]
Maintainer: Claudio Heinrich-Mertsching <claudio.heinrich@hotmail.de>
Diff between SeaVal versions 1.1.1 dated 2023-11-25 and 1.2.0 dated 2024-06-14
DESCRIPTION | 22 - MD5 | 41 +- NAMESPACE | 4 NEWS.md | 16 R/auxiliary_functions.R | 13 R/chirps.R | 5 R/diagrams.R | 236 -------------- R/ncdf_to_dt.R | 75 +++- R/plotting.R | 612 ++++++++++++++++++++++++++++++++----- R/seasonal.R |only README.md | 4 data/chirps_monthly.rda |binary data/ecmwf_monthly.rda |binary man/SeaVal-package.Rd | 6 man/convert_monthly_to_seasonal.Rd |only man/dt_to_netcdf.Rd | 3 man/ggplot_dt.Rd | 8 man/lt_cols.Rd |only man/modify_dt_map_plotting.Rd |only man/season_strings_to_int.Rd |only man/tercile_plot.Rd | 13 man/tfc_gha_plot.Rd |only man/tfc_plot.Rd |only man/ver_map.Rd | 7 man/ver_map_chirps.Rd | 5 25 files changed, 698 insertions(+), 372 deletions(-)
Title: Sequential Monte Carlo Methods for 'nimble'
Description: Includes five particle filtering algorithms for use with state space
models in the 'nimble' system: 'Auxiliary', 'Bootstrap', 'Ensemble Kalman filter',
'Iterated Filtering 2', and 'Liu-West', as described in Michaud et al. (2021),
<doi:10.18637/jss.v100.i03>. A full User Manual is available at
<https://r-nimble.org>.
Author: Nick Michaud [aut],
Perry de Valpine [aut],
Christopher Paciorek [aut, cre],
Daniel Turek [aut],
Benjamin R. Goldstein [ctb] ,
Dao Nguyen [ctb] ,
The Regents of the University of California [cph]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimbleSMC versions 0.11.0 dated 2023-09-10 and 0.11.1 dated 2024-06-14
nimbleSMC-0.11.0/nimbleSMC/inst/NEWS |only nimbleSMC-0.11.1/nimbleSMC/DESCRIPTION | 9 ++--- nimbleSMC-0.11.1/nimbleSMC/LICENSE | 2 - nimbleSMC-0.11.1/nimbleSMC/MD5 | 14 +++---- nimbleSMC-0.11.1/nimbleSMC/R/IF2Filter.R | 2 - nimbleSMC-0.11.1/nimbleSMC/R/MCMCSamplers.R | 18 +++++++--- nimbleSMC-0.11.1/nimbleSMC/inst/NEWS.md |only nimbleSMC-0.11.1/nimbleSMC/inst/test-utils/filteringTestLog_Correct.Rout | 18 +++++----- nimbleSMC-0.11.1/nimbleSMC/man/buildIteratedFilter2.Rd | 2 - 9 files changed, 38 insertions(+), 27 deletions(-)
Title: Stable Distribution Functions...For You
Description: Tools for fast and accurate evaluation of skew stable distributions
(CDF, PDF and quantile functions), random number generation, and parameter
estimation. This is 'libstableR' as per Royuela del Val, Simmross-Wattenberg,
and Alberola López (2017) <doi:10.18637/jss.v078.i01> under a new maintainer.
Author: Javier Royuela del Val [aut],
Federico Simmross-Wattenberg [aut],
Carlos Alberola Lopez [aut],
Bob Rudis [ctb] ,
Bruce Swihart [ctb, cre]
Maintainer: Bruce Swihart <bruce.swihart@gmail.com>
Diff between libstable4u versions 1.0.3 dated 2023-09-01 and 1.0.4 dated 2024-06-14
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ R/libstable4u-pkg.r | 2 +- inst/CITATION | 20 ++++++++------------ man/libstable4u-package.Rd | 2 +- 6 files changed, 26 insertions(+), 22 deletions(-)
Title: Ensemble Platform for Species Distribution Modeling
Description: Functions for species distribution modeling, calibration and evaluation,
ensemble of models, ensemble forecasting and visualization. The package permits to run
consistently up to 10 single models on a presence/absences (resp presences/pseudo-absences)
dataset and to combine them in ensemble models and ensemble projections. Some bench of other
evaluation and visualisation tools are also available within the package.
Author: Wilfried Thuiller [aut],
Damien Georges [aut],
Maya Gueguen [aut, cre],
Robin Engler [aut],
Frank Breiner [aut],
Bruno Lafourcade [aut],
Remi Patin [aut],
Helene Blancheteau [aut]
Maintainer: Maya Gueguen <maya.gueguen@univ-grenoble-alpes.fr>
Diff between biomod2 versions 4.2-5 dated 2024-05-02 and 4.2-5-2 dated 2024-06-14
biomod2-4.2-5-2/biomod2/DESCRIPTION | 8 biomod2-4.2-5-2/biomod2/MD5 | 65 +++---- biomod2-4.2-5-2/biomod2/R/BIOMOD_EnsembleForecasting.R | 18 + biomod2-4.2-5-2/biomod2/R/BIOMOD_EnsembleModeling.R | 39 ++-- biomod2-4.2-5-2/biomod2/R/BIOMOD_LoadModels.R | 6 biomod2-4.2-5-2/biomod2/R/BIOMOD_Modeling.R | 28 +-- biomod2-4.2-5-2/biomod2/R/BIOMOD_Projection.R | 17 - biomod2-4.2-5-2/biomod2/R/biomod2_classes_0.R | 4 biomod2-4.2-5-2/biomod2/R/biomod2_classes_1.R | 4 biomod2-4.2-5-2/biomod2/R/biomod2_classes_3.R | 24 +- biomod2-4.2-5-2/biomod2/R/biomod2_internal.R | 5 biomod2-4.2-5-2/biomod2/R/bm_PlotEvalMean.R | 6 biomod2-4.2-5-2/biomod2/R/bm_RunModelsLoop.R | 12 - biomod2-4.2-5-2/biomod2/README.md | 16 + biomod2-4.2-5-2/biomod2/build/vignette.rds |binary biomod2-4.2-5-2/biomod2/inst/doc/news.Rmd | 45 ++++ biomod2-4.2-5-2/biomod2/inst/doc/news.html | 92 +++++++--- biomod2-4.2-5-2/biomod2/inst/doc/vignette_modelingOptions.Rmd | 2 biomod2-4.2-5-2/biomod2/inst/doc/vignette_modelingOptions.html | 2 biomod2-4.2-5-2/biomod2/inst/doc/vignette_presentation.Rmd |only biomod2-4.2-5-2/biomod2/inst/doc/vignette_presentation.html |only biomod2-4.2-5-2/biomod2/man/BIOMOD_EnsembleForecasting.Rd | 12 - biomod2-4.2-5-2/biomod2/man/BIOMOD_EnsembleModeling.Rd | 30 +-- biomod2-4.2-5-2/biomod2/man/BIOMOD_LoadModels.Rd | 6 biomod2-4.2-5-2/biomod2/man/BIOMOD_Modeling.Rd | 6 biomod2-4.2-5-2/biomod2/man/BIOMOD_Projection.Rd | 12 - biomod2-4.2-5-2/biomod2/man/bm_PlotEvalMean.Rd | 6 biomod2-4.2-5-2/biomod2/man/bm_RunModelsLoop.Rd | 6 biomod2-4.2-5-2/biomod2/man/getters.out.Rd | 24 +- biomod2-4.2-5-2/biomod2/vignettes/news.Rmd | 45 ++++ biomod2-4.2-5-2/biomod2/vignettes/pictures/LogoBiomod.png |only biomod2-4.2-5-2/biomod2/vignettes/pictures/SCHEMA_BIOMOD2_WORKFLOW_functions.pdf |only biomod2-4.2-5-2/biomod2/vignettes/pictures/SCHEMA_BIOMOD2_WORKFLOW_functions.png |binary biomod2-4.2-5-2/biomod2/vignettes/pictures/biomod2_presentation.workflow_05_2024.pdf |only biomod2-4.2-5-2/biomod2/vignettes/vignette_modelingOptions.Rmd | 2 biomod2-4.2-5-2/biomod2/vignettes/vignette_presentation.Rmd |only biomod2-4.2-5/biomod2/tests |only 37 files changed, 350 insertions(+), 192 deletions(-)
Title: Wrapper for MUMPS Library
Description: Some basic features of 'MUMPS' (Multifrontal Massively Parallel
sparse direct Solver) are wrapped in a class whose methods can be used
for sequentially solving a sparse linear system (symmetric or not)
with one or many right hand sides (dense or sparse).
There is a possibility to do separately symbolic analysis,
LU (or LDL^t) factorization and system solving.
Third part ordering libraries are included and can be used: 'PORD', 'METIS', 'SCOTCH'.
'MUMPS' method was first described in Amestoy et al. (2001) <doi:10.1137/S0895479899358194>
and Amestoy et al. (2006) <doi:10.1016/j.parco.2005.07.004>.
Author: Serguei Sokol [aut, cre],
Emmanuel Agullo [ctb],
Patrick Amestoy [ctb, cph],
Maurice Bremond [ctb],
Alfredo Buttari [ctb],
Philippe Combes [ctb],
Marie Durand [ctb],
Aurelia Fevre [ctb],
Abdou Guermouche [ctb],
Guillaume Joslin [ctb],
Jacko Koster [c [...truncated...]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.2.1-29 dated 2024-03-29 and 5.2.1-30 dated 2024-06-14
DESCRIPTION | 8 MD5 | 12 NEWS | 6 R/RcppExports.R | 202 ++++++++-------- src/lib/MUMPS_5.2.1/Makefile.inc | 1 src/lib/Makefile | 3 src/lib/scotch_6.0.9/src/libscotch/vgraph_separate_gg.c | 3 7 files changed, 123 insertions(+), 112 deletions(-)
Title: Summary Tables and Plots for Statistical Models and Data:
Beautiful, Customizable, and Publication-Ready
Description: Create beautiful and customizable tables to summarize several
statistical models side-by-side. Draw coefficient plots, multi-level
cross-tabs, dataset summaries, balance tables (a.k.a. "Table 1s"), and
correlation matrices. This package supports dozens of statistical models, and
it can produce tables in HTML, LaTeX, Word, Markdown, PDF, PowerPoint, Excel,
RTF, JPG, or PNG. Tables can easily be embedded in 'Rmarkdown' or 'knitr'
dynamic documents. Details can be found in Arel-Bundock (2022)
<doi:10.18637/jss.v103.i01>.
Author: Vincent Arel-Bundock [aut, cre]
,
Joachim Gassen [ctb] ,
Nathan Eastwood [ctb],
Nick Huntington-Klein [ctb] ,
Moritz Schwarz [ctb] ,
Benjamin Elbers [ctb] ,
Grant McDermott [ctb] ,
Lukas Wallrich [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between modelsummary versions 2.1.0 dated 2024-05-19 and 2.1.1 dated 2024-06-14
DESCRIPTION | 6 - MD5 | 36 +++++----- NEWS.md | 13 +++ R/datasummary_correlation.R | 5 + R/factory.R | 2 R/get_estimates.R | 4 + R/modelsummary.R | 12 ++- R/sanity_checks.R | 9 ++ inst/tinytest/_tinysnapshot/escape-correlation_latex_FALSE.txt | 26 +++---- inst/tinytest/test-datasummary_correlation.R | 15 +++- man/datasummary.Rd | 18 ++--- man/datasummary_balance.Rd | 18 ++--- man/datasummary_correlation.Rd | 18 ++--- man/datasummary_crosstab.Rd | 18 ++--- man/datasummary_df.Rd | 2 man/datasummary_skim.Rd | 18 ++--- man/dsummary.Rd | 18 ++--- man/modelsummary.Rd | 27 +++++-- man/msummary.Rd | 27 +++++-- 19 files changed, 186 insertions(+), 106 deletions(-)
Title: Interpreting Glucose Data from Continuous Glucose Monitors
Description: Implements a wide range of metrics for measuring glucose control and glucose variability based on continuous glucose monitoring data. The list of implemented metrics is summarized in Rodbard (2009) <doi:10.1089/dia.2009.0015>. Additional visualization tools include time-series plots, lasagna plots and ambulatory glucose profile report.
Author: Elizabeth Chun [aut],
Steve Broll [aut],
David Buchanan [aut],
John Muschelli [aut] ,
Nathaniel Fernandes [aut] ,
Jung Hoon Seo [ctb],
Johnathan Shih [ctb],
Jacek Urbanek [ctb],
John Schwenck [ctb],
Marielle Hicban [ctb],
Mary Martin [ctb],
Pratik Pa [...truncated...]
Maintainer: Irina Gaynanova <irinagn@umich.edu>
Diff between iglu versions 4.0.0 dated 2024-02-23 and 4.1.6 dated 2024-06-14
DESCRIPTION | 14 MD5 | 230 +-- NAMESPACE | 1 NEWS.md | 21 R/above_percent.R | 13 R/active_percent.R | 10 R/adrr.R | 4 R/agp.R | 2 R/agp_metrics.R | 41 R/cv_glu.R | 4 R/ea1c.R | 4 R/epicalc_profile.R | 2 R/gmi.R | 4 R/grade.R | 4 R/gri.R | 2 R/gvp.r | 2 R/hbgi.R | 6 R/heatmap.R | 6 R/hyper_index.R | 4 R/hypo_index.R | 4 R/j_index.R | 4 R/lasagna_plots.R | 60 R/lbgi.R | 4 R/mad_glu.r | 2 R/mag.R | 6 R/mage.R | 22 R/mage_ma_single.R | 76 - R/meal_metrics.R | 130 + R/pgs.R | 31 R/plot_daily.R | 5 R/plot_glu.R | 68 R/plot_meals.R |only R/plot_roc.R | 4 R/process_data.R | 21 R/quantile_glu.R | 10 R/range_glu.R | 8 R/read_raw_data.r | 21 R/roc.R | 14 R/sd_glu.R | 8 R/sd_measures.R | 2 R/sd_roc.R | 2 R/summary_glu.R | 10 R/utils.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 inst/doc/AGP_and_Episodes.html | 6 inst/doc/MAGE.R | 15 inst/doc/MAGE.Rmd | 528 ++++++- inst/doc/MAGE.html | 699 ++++++++-- inst/doc/iglu.Rmd | 2 inst/doc/iglu.html | 17 inst/doc/lasagna_plots.html | 72 - man/above_percent.Rd | 15 man/active_percent.Rd | 10 man/adrr.Rd | 4 man/agp.Rd | 5 man/agp_metrics.Rd | 41 man/cv_glu.Rd | 4 man/ea1c.Rd | 4 man/gmi.Rd | 4 man/grade.Rd | 4 man/gvp.Rd | 2 man/hbgi.Rd | 6 man/hyper_index.Rd | 4 man/hypo_index.Rd | 4 man/j_index.Rd | 4 man/lbgi.Rd | 4 man/mad_glu.Rd | 2 man/mag.Rd | 6 man/mage.Rd | 34 man/mage_ma_single.Rd | 36 man/meal_metrics.Rd | 15 man/metrics_heatmap.Rd | 5 man/pgs.Rd | 31 man/plot_agp.Rd | 4 man/plot_daily.Rd | 12 man/plot_glu.Rd | 31 man/plot_lasagna.Rd | 5 man/plot_lasagna_1subject.Rd | 8 man/plot_meals.Rd |only man/process_data.Rd | 21 man/quantile_glu.Rd | 10 man/range_glu.Rd | 8 man/read_raw_data.Rd | 19 man/roc.Rd | 14 man/sd_glu.Rd | 8 man/sd_measures.Rd | 2 man/sd_roc.Rd | 2 man/summary_glu.Rd | 10 tests/testthat/test-mage.R | 2 vignettes/MAGE.Rmd | 528 ++++++- vignettes/iglu.Rmd | 2 vignettes/iglu_files/figure-html/unnamed-chunk-23-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-23-2.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-24-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-25-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-26-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-27-1.png |binary vignettes/lasagna_plots_files/figure-html/unnamed-chunk-10-1.png |binary vignettes/lasagna_plots_files/figure-html/unnamed-chunk-11-1.png |binary vignettes/lasagna_plots_files/figure-html/unnamed-chunk-12-1.png |binary vignettes/lasagna_plots_files/figure-html/unnamed-chunk-16-1.png |binary vignettes/lasagna_plots_files/figure-html/unnamed-chunk-17-1.png |binary vignettes/lasagna_plots_files/figure-html/unnamed-chunk-18-1.png |binary vignettes/lasagna_plots_files/figure-html/unnamed-chunk-19-1.png |binary vignettes/lasagna_plots_files/figure-html/unnamed-chunk-2-1.png |binary vignettes/lasagna_plots_files/figure-html/unnamed-chunk-2-2.png |binary vignettes/lasagna_plots_files/figure-html/unnamed-chunk-3-1.png |binary vignettes/lasagna_plots_files/figure-html/unnamed-chunk-4-1.png |binary vignettes/mage_figures/Figure4_boxplots.png |binary vignettes/mage_figures/boxplot-of-errors.png |binary vignettes/mage_figures/boxplot-of-errors2.png |only vignettes/mage_figures/corr_matrix_basic.rda |only vignettes/mage_figures/correlation_matrix.png |only vignettes/mage_figures/correlation_matrix.rda |only vignettes/mage_figures/hyper-param-tuning.png |binary vignettes/mage_figures/whiplash1.png |binary vignettes/mage_figures/whiplash2.png |binary 119 files changed, 2347 insertions(+), 814 deletions(-)
Title: Bayesian Structure and Causal Learning of Gaussian Directed
Graphs
Description: A collection of functions for structure learning of causal networks and estimation of joint causal effects from observational Gaussian data. Main algorithm consists of a Markov chain Monte Carlo scheme for posterior inference of causal structures, parameters and causal effects between variables.
References:
F. Castelletti and A. Mascaro (2021) <doi:10.1007/s10260-021-00579-1>,
F. Castelletti and A. Mascaro (2022) <doi:10.48550/arXiv.2201.12003>.
Author: Federico Castelletti [aut],
Alessandro Mascaro [aut, cre, cph]
Maintainer: Alessandro Mascaro <alessandro.mascaro@upf.edu>
Diff between BCDAG versions 1.1.0 dated 2024-02-09 and 1.1.1 dated 2024-06-14
DESCRIPTION | 10 MD5 | 26 NAMESPACE | 1 NEWS.md | 5 R/causaleffect.R | 146 +-- R/confint.bcdagCE.R |only README.md | 180 ++-- build/vignette.rds |binary inst/doc/bcdag_generatedata.R | 88 +- inst/doc/bcdag_generatedata.html | 1020 +++++++++++++------------- inst/doc/bcdag_getfamily.R | 256 +++--- inst/doc/bcdag_getfamily.html | 1518 +++++++++++++++++++-------------------- inst/doc/bcdag_learnDAG.R | 250 +++--- inst/doc/bcdag_learnDAG.html | 1488 +++++++++++++++++++------------------- man/confint.bcdagCE.Rd |only 15 files changed, 2498 insertions(+), 2490 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-28 1.0.3
2023-06-29 1.0.2
2023-05-23 1.0.1
2023-04-20 1.0.0
Title: Create Layout Plots of Biological Culture Plates and Microplates
Description: Enables users to create simple plots of biological culture plates as well as microplates. Both continuous and discrete values can be plotted onto the plate layout.
Author: Jan-Philipp Quast [aut, cre]
Maintainer: Jan-Philipp Quast <quast@imsb.biol.ethz.ch>
Diff between ggplate versions 0.1.1 dated 2023-12-02 and 0.1.2 dated 2024-06-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/plate_plot.R | 4 ++-- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Access to the 'Geospatial Data Abstraction Library' ('GDAL')
Description: Provides low-level access to 'GDAL' functionality.
'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats
that presents a single raster abstract data model and single vector abstract data model to the calling application
for all supported formats <https://gdal.org/>. This package is focussed on providing exactly and only what GDAL does, to enable
developing further tools.
Author: Michael Sumner [aut, cre] ,
Simon Wotherspoon [ctb] ,
Mark Padgham [ctb] ),
Edzer Pebesma [ctb] ,
Roger Bivand [ctb] ,
Jim Hester [ctb, cph] ,
Timothy Keitt [ctb] ,
Jeroen Ooms [ctb] ,
Dale Maschette [ctb] ,
Joseph Stachelek [ctb],
Even Rouault [ctb] [...truncated...]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between vapour versions 0.9.5 dated 2023-04-11 and 0.10.0 dated 2024-06-14
vapour-0.10.0/vapour/DESCRIPTION | 19 vapour-0.10.0/vapour/MD5 | 128 vapour-0.10.0/vapour/NAMESPACE | 6 vapour-0.10.0/vapour/NEWS.md | 41 vapour-0.10.0/vapour/R/00_read_block.R | 66 vapour-0.10.0/vapour/R/00_utils.R | 27 vapour-0.10.0/vapour/R/00_warpgeneral.R | 76 vapour-0.10.0/vapour/R/RcppExports.R | 40 vapour-0.10.0/vapour/R/raster-info.R | 35 vapour-0.10.0/vapour/R/raster-input.R | 76 vapour-0.10.0/vapour/R/read_stream_internal.R | 99 vapour-0.10.0/vapour/R/vapour-gdal-library.R | 21 vapour-0.10.0/vapour/R/vapour-package.R | 11 vapour-0.10.0/vapour/R/vapour_vrt.R | 125 vapour-0.10.0/vapour/README.md | 14 vapour-0.10.0/vapour/build/vignette.rds |binary vapour-0.10.0/vapour/configure | 2692 +++++----- vapour-0.10.0/vapour/configure.ac | 4 vapour-0.10.0/vapour/inst/WORDLIST | 46 vapour-0.10.0/vapour/inst/doc/feature-access.R | 2 vapour-0.10.0/vapour/inst/doc/feature-access.html | 78 vapour-0.10.0/vapour/inst/doc/vapour.R | 2 vapour-0.10.0/vapour/inst/doc/vapour.Rmd | 2 vapour-0.10.0/vapour/inst/doc/vapour.html | 632 +- vapour-0.10.0/vapour/inst/extdata/sst_c.fgb |only vapour-0.10.0/vapour/inst/include/common |only vapour-0.10.0/vapour/inst/include/gdalapplib/gdalapplib.h | 212 vapour-0.10.0/vapour/inst/include/gdalarrowstream/gdalvectorstream.h | 666 +- vapour-0.10.0/vapour/inst/include/gdallibrary/gdallibrary.h | 250 vapour-0.10.0/vapour/inst/include/gdalraster/gdalraster.h | 177 vapour-0.10.0/vapour/inst/include/gdalreadwrite/gdalreadwrite.h | 202 vapour-0.10.0/vapour/inst/include/gdalwarpgeneral/gdalwarpgeneral.h | 137 vapour-0.10.0/vapour/inst/include/gdalwarpmem/gdalwarpmem.h | 408 - vapour-0.10.0/vapour/man/GDAL-library.Rd | 5 vapour-0.10.0/vapour/man/buildvrt.Rd |only vapour-0.10.0/vapour/man/gdal_raster_data.Rd | 41 vapour-0.10.0/vapour/man/sst_c.Rd | 8 vapour-0.10.0/vapour/man/vapour-package.Rd | 30 vapour-0.10.0/vapour/man/vapour_create.Rd | 27 vapour-0.10.0/vapour/man/vapour_crs_is_lonlat.Rd | 9 vapour-0.10.0/vapour/man/vapour_geolocation.Rd |only vapour-0.10.0/vapour/man/vapour_read_raster.Rd | 5 vapour-0.10.0/vapour/man/vapour_read_raster_block.Rd | 5 vapour-0.10.0/vapour/man/vapour_read_raster_raw.Rd | 5 vapour-0.10.0/vapour/man/vapour_set_config.Rd | 2 vapour-0.10.0/vapour/man/vapour_vrt.Rd | 8 vapour-0.10.0/vapour/man/vapour_warp_raster.Rd | 5 vapour-0.10.0/vapour/man/vector_vrt.Rd |only vapour-0.10.0/vapour/src/000-stream.cpp | 35 vapour-0.10.0/vapour/src/000-warpgeneral.cpp | 8 vapour-0.10.0/vapour/src/00_gdal.cpp | 5 vapour-0.10.0/vapour/src/00_raster.cpp | 63 vapour-0.10.0/vapour/src/00_raster_block_io.cpp | 22 vapour-0.10.0/vapour/src/00_vrt.cpp | 12 vapour-0.10.0/vapour/src/Makevars.ucrt | 8 vapour-0.10.0/vapour/src/RcppExports.cpp | 131 vapour-0.10.0/vapour/src/warpscratch.cpp |only vapour-0.10.0/vapour/tests/testthat/test-create.R |only vapour-0.10.0/vapour/tests/testthat/test-crs-less-warp.R | 23 vapour-0.10.0/vapour/tests/testthat/test-features.R | 29 vapour-0.10.0/vapour/tests/testthat/test-gdal.R | 4 vapour-0.10.0/vapour/tests/testthat/test-helpers.R | 6 vapour-0.10.0/vapour/tests/testthat/test-layers.R | 2 vapour-0.10.0/vapour/tests/testthat/test-proj.R |only vapour-0.10.0/vapour/tests/testthat/test-vrt.R | 2 vapour-0.10.0/vapour/tests/testthat/test-warper.R | 13 vapour-0.10.0/vapour/tools/winlibs.R | 2 vapour-0.10.0/vapour/vignettes/vapour.Rmd | 2 vapour-0.9.5/vapour/inst/extdata/cutline_sst.gpkg |only vapour-0.9.5/vapour/tests/testthat/test-test-on-rhub.R |only 70 files changed, 3755 insertions(+), 3056 deletions(-)
Title: Calibration Plots for the Transition Probabilities from
Multistate Models
Description: Assess the calibration of an existing (i.e. previously developed) multistate
model through calibration plots.
Calibration is assessed using one of three methods. 1) Calibration methods for
binary logistic regression models applied at a fixed time point in conjunction
with inverse probability of censoring weights. 2) Calibration methods for
multinomial logistic regression models applied at a fixed time point in conjunction
with inverse probability of censoring weights. 3) Pseudo-values estimated using
the Aalen-Johansen estimator of observed risk. All methods are applied in conjunction
with landmarking when required. These calibration plots evaluate the calibration
(in a validation cohort of interest) of the transition probabilities estimated from an
existing multistate model. While package development has focused on multistate
models, calibration plots can be produced for any model which utilises information
post baseline to update predictions (e.g. dynamic models); competing risks mod [...truncated...]
Author: Alexander Pate [aut, cre, cph]
,
Glen P Martin [fnd, rev]
Maintainer: Alexander Pate <alexander.pate@manchester.ac.uk>
Diff between calibmsm versions 1.1.0 dated 2024-05-13 and 1.1.1 dated 2024-06-14
DESCRIPTION | 6 - MD5 | 55 ++++++++-------- NAMESPACE | 3 NEWS.md | 10 +-- R/calibmsm.R | 102 ++++++++++++++++++++----------- R/internal_calib_aj.R | 54 ++++++++-------- R/internal_calib_blr_ipcw.R | 44 ++++++------- R/internal_calib_mlr_ipcw.R | 16 ++-- R/internal_calib_pv.R | 78 +++++++++++------------ R/internal_extract_ids_states.R | 54 ++++++++-------- R/plot_calib.R | 4 - R/weights.R | 20 +++--- README.md | 6 + build/partial.rdb |only build/vignette.rds |binary inst/CITATION |only man/calc_weights.Rd | 12 +-- man/calib_msm.Rd | 23 ++++-- man/calibmsm-package.Rd | 2 man/figures/README-example-1.png |binary man/metadata.Rd |only man/plot.calib_mlr.Rd | 2 man/plot.calib_msm.Rd | 2 tests/testthat/test-calib_aj.R | 16 ++-- tests/testthat/test-calib_blr.R | 90 +++++++++++++-------------- tests/testthat/test-calib_mlr.R | 40 ++++++------ tests/testthat/test-calib_pv.R | 54 ++++++++-------- tests/testthat/test-extract_ids_states.R | 2 tests/testthat/test-plot_calib.R | 16 ++-- tests/testthat/test-weights.R | 26 +++---- 30 files changed, 394 insertions(+), 343 deletions(-)
Title: Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis
Tests
Description: Compute and plot predictions, slopes, marginal means, and comparisons (contrasts, risk ratios, odds, etc.) for over 100 classes of statistical and machine learning models in R. Conduct linear and non-linear hypothesis tests, or equivalence tests. Calculate uncertainty estimates using the delta method, bootstrapping, or simulation-based inference.
Author: Vincent Arel-Bundock [aut, cre, cph]
,
Noah Greifer [ctb] ,
Etienne Bacher [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between marginaleffects versions 0.20.1 dated 2024-05-08 and 0.21.0 dated 2024-06-14
DESCRIPTION | 54 +++++---- MD5 | 53 +++++---- NEWS.md | 18 +++ R/comparisons.R | 3 R/datagrid.R | 2 R/get_contrast_data_factor.R | 2 R/get_hypothesis.R | 3 R/hypothesis_helper.R | 54 ++++++--- R/methods_mlogit.R | 3 R/methods_survey.R | 3 R/predictions.R | 11 + R/sanitize_hypothesis.R | 4 R/sanitize_hypothesis_formula.R |only R/sanitize_newdata.R | 74 ++++++------- R/sanitize_variables.R | 5 R/slopes.R | 69 +++++++----- README.md | 39 ++++++- inst/CITATION |only inst/WORDLIST | 221 ++++++++++++++++++++-------------------- man/comparisons.Rd | 30 ++++- man/figures/zoo_header.png |only man/get_model_matrix.Rd | 10 - man/get_predict.Rd | 10 - man/hypotheses.Rd | 17 ++- man/predictions.Rd | 38 +++++- man/sanitize_model_specific.Rd | 10 - man/slopes.Rd | 50 ++++++--- man/specify_hypothesis.Rd | 14 +- tests/tinytest.R | 3 29 files changed, 498 insertions(+), 302 deletions(-)
More information about marginaleffects at CRAN
Permanent link
Title: 'Rstudio' Addin to Sync Settings and Keymaps
Description: Provides a 'Rstudio' addin to download, merge and upload 'Rstudio'
settings and keymaps, essentially 'syncing them' at will. It uses 'Google Drive'
as a cloud storage to keep the settings and keymaps files.
Author: Andre Plancha [aut, cre]
Maintainer: Andre Plancha <andre.plancha@hotmail.com>
Diff between settingsSync versions 3.0.1 dated 2024-06-13 and 3.0.2 dated 2024-06-14
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 7 ++++++- R/mimic.R | 11 ++++++++--- R/sync.R | 4 +--- R/utils.R | 4 ++-- README.md | 9 ++++++--- 7 files changed, 32 insertions(+), 21 deletions(-)
Title: Diagnostic Index Expectation Maximisation in R
Description: Likelihood-based genome polarisation finds which alleles of genomic markers
belong to which side of the barrier.
Co-estimates which individuals belong to either side of the barrier and barrier strength.
Uses expectation maximisation in likelihood framework. The method is described in
Baird et al. (2023) <doi:10.1111/2041-210X.14010>.
Author: Natalia Martinkova [aut, cre] ,
Stuart Baird [aut]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Diff between diemr versions 1.2.3 dated 2024-04-28 and 1.3 dated 2024-06-14
diemr-1.2.3/diemr/inst/extdata/data6x3.txt |only diemr-1.3/diemr/DESCRIPTION | 10 diemr-1.3/diemr/MD5 | 66 - diemr-1.3/diemr/NAMESPACE | 1 diemr-1.3/diemr/NEWS.md | 15 diemr-1.3/diemr/R/CheckDiemFormat.r | 21 diemr-1.3/diemr/R/ModelOfDiagnostic.r | 32 diemr-1.3/diemr/R/diem.r | 152 ++- diemr-1.3/diemr/R/extdata.r | 28 diemr-1.3/diemr/R/importPolarized.r | 2 diemr-1.3/diemr/R/vcf2diem.r | 150 ++- diemr-1.3/diemr/build/vignette.rds |binary diemr-1.3/diemr/inst/doc/Importing-data-for-genome-polarisation.R | 14 diemr-1.3/diemr/inst/doc/Importing-data-for-genome-polarisation.Rmd | 349 ++++---- diemr-1.3/diemr/inst/doc/Importing-data-for-genome-polarisation.html | 232 +++-- diemr-1.3/diemr/inst/doc/diem_output.R |only diemr-1.3/diemr/inst/doc/diem_output.Rmd |only diemr-1.3/diemr/inst/doc/diem_output.html |only diemr-1.3/diemr/inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.R | 81 +- diemr-1.3/diemr/inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.Rmd | 151 ++- diemr-1.3/diemr/inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.html | 392 +++++----- diemr-1.3/diemr/inst/extdata/brenthis.vcf |only diemr-1.3/diemr/inst/extdata/data7x3.txt |only diemr-1.3/diemr/inst/extdata/testdata.vcf |only diemr-1.3/diemr/man/CheckDiemFormat.Rd | 10 diemr-1.3/diemr/man/ModelOfDiagnostic.Rd | 27 diemr-1.3/diemr/man/brenthis.Rd |only diemr-1.3/diemr/man/diem.Rd | 22 diemr-1.3/diemr/man/importPolarized.Rd | 2 diemr-1.3/diemr/man/testdata.Rd |only diemr-1.3/diemr/man/vcf2diem.Rd | 74 + diemr-1.3/diemr/tests/testthat/_snaps/vcf2diem.md | 8 diemr-1.3/diemr/tests/testthat/test_CheckDiemFormat.r | 32 diemr-1.3/diemr/tests/testthat/test_importPolarized.r | 10 diemr-1.3/diemr/tests/testthat/test_vcf2diem.r | 17 diemr-1.3/diemr/vignettes/Importing-data-for-genome-polarisation.Rmd | 349 ++++---- diemr-1.3/diemr/vignettes/diemOutput.png |only diemr-1.3/diemr/vignettes/diem_output.Rmd |only diemr-1.3/diemr/vignettes/diemr-diagnostic-index-expecation-maximisation-in-r.Rmd | 151 ++- diemr-1.3/diemr/vignettes/refs.bib |only 40 files changed, 1390 insertions(+), 1008 deletions(-)
Title: Build and Manipulate Study Cohorts Using a Common Data Model
Description: Create and manipulate study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Nuria Mercade-Besora [aut] ,
Marta Alcalde-Herraiz [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Xihang Chen [aut] ,
Kim Lopez [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CohortConstructor versions 0.2.0 dated 2024-06-12 and 0.2.1 dated 2024-06-14
DESCRIPTION | 6 MD5 | 18 R/requireCohortIntersectFlag.R | 296 ++++++------ R/requireConceptIntersectFlag.R | 270 +++++------ R/requireTableIntersectFlag.R | 258 +++++------ inst/doc/a01_building_base_cohorts.html | 4 tests/testthat/setup.R | 105 ++-- tests/testthat/test-requireCohortIntersect.R | 592 ++++++++++++------------- tests/testthat/test-requireConceptIntersect.R | 605 +++++++++++++------------- tests/testthat/test-requireTableIntersect.R | 591 ++++++++++++------------- 10 files changed, 1375 insertions(+), 1370 deletions(-)
More information about CohortConstructor at CRAN
Permanent link
Title: Prioritize and Delete Erroneous Taxa in a Large Phylogenetic
Tree
Description: Finds, prioritizes and deletes erroneous taxa in a phylogenetic tree. This package calculates scores for taxa in a tree. Higher score means the taxon is more erroneous. If the score is zero for a taxon, the taxon is not erroneous. This package also can remove all erroneous taxa automatically by iterating score calculation and pruning taxa with the highest score.
Author: Satoshi Aoki [aut, cph, cre]
Maintainer: Satoshi Aoki <aokis1ll1@gmail.com>
Diff between Apoderoides versions 1.0.1 dated 2024-01-14 and 2.0.0 dated 2024-06-14
Apoderoides-1.0.1/Apoderoides/inst/doc/vingnette.R |only Apoderoides-1.0.1/Apoderoides/inst/doc/vingnette.Rmd |only Apoderoides-1.0.1/Apoderoides/inst/doc/vingnette.html |only Apoderoides-1.0.1/Apoderoides/vignettes/vingnette.Rmd |only Apoderoides-2.0.0/Apoderoides/DESCRIPTION | 8 Apoderoides-2.0.0/Apoderoides/MD5 | 31 - Apoderoides-2.0.0/Apoderoides/NAMESPACE | 2 Apoderoides-2.0.0/Apoderoides/NEWS | 9 Apoderoides-2.0.0/Apoderoides/R/Apoderoides.R | 298 +++++++++----- Apoderoides-2.0.0/Apoderoides/build/vignette.rds |binary Apoderoides-2.0.0/Apoderoides/inst/doc/vignette.R |only Apoderoides-2.0.0/Apoderoides/inst/doc/vignette.Rmd |only Apoderoides-2.0.0/Apoderoides/inst/doc/vignette.html |only Apoderoides-2.0.0/Apoderoides/man/Apoderoides-internal.Rd | 2 Apoderoides-2.0.0/Apoderoides/man/autoDeletion.Rd | 11 Apoderoides-2.0.0/Apoderoides/man/calc.Score.Rd | 8 Apoderoides-2.0.0/Apoderoides/man/deleteAnomaly.Rd | 5 Apoderoides-2.0.0/Apoderoides/man/getAllCentroids.Rd | 5 Apoderoides-2.0.0/Apoderoides/man/getAllMRCAs.Rd |only Apoderoides-2.0.0/Apoderoides/src/source.cpp | 81 ++- Apoderoides-2.0.0/Apoderoides/vignettes/vignette.Rmd |only 21 files changed, 294 insertions(+), 166 deletions(-)
Title: Simplify 'ggplot2' Visualisation
Description: Simplify 'ggplot2' visualisation with 'ggblanket' wrapper
functions.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggblanket versions 9.1.0 dated 2024-05-25 and 9.1.1 dated 2024-06-14
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-23 2.0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-21 0.0.60
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-25 2.0.1
2020-07-16 1.1.2
2019-01-03 1.0
2018-06-14 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-27 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-14 1.4
2018-05-29 1.3
2017-04-13 1.2
2017-03-06 1.1
2016-11-01 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-17 2.0.2
2023-12-12 2.0.0
2022-05-10 1.0.0
2022-02-01 0.1.1
2021-07-26 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-09-25 0.1.0
Title: Tidy Verbs for Fast Data Manipulation
Description: A toolkit of tidy data manipulation verbs with 'data.table' as the backend.
Combining the merits of syntax elegance from 'dplyr' and computing performance from 'data.table',
'tidyfst' intends to provide users with state-of-the-art data manipulation tools with least pain.
This package is an extension of 'data.table'. While enjoying a tidy syntax,
it also wraps combinations of efficient functions to facilitate frequently-used data operations.
Author: Tian-Yuan Huang [aut, cre]
Maintainer: Tian-Yuan Huang <huang.tian-yuan@qq.com>
Diff between tidyfst versions 1.7.8 dated 2024-04-15 and 1.7.9 dated 2024-06-14
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