Title: Quantitative Text Kit
Description: Support package for the textbook "An Introduction to
Quantitative Text Analysis for Linguists: Reproducible Research Using
R" (Francom, 2024) <doi:10.4324/9781003393764>. Includes functions to
acquire, clean, and analyze text data as well as functions to document
and share the results of text analysis. The package is designed to be
used in conjunction with the book, but can also be used as a standalone
package for text analysis.
Author: Jerid Francom [aut, cre, cph]
Maintainer: Jerid Francom <francojc@wfu.edu>
Diff between qtkit versions 1.0.0 dated 2024-08-17 and 1.1.0 dated 2024-12-07
DESCRIPTION | 13 - MD5 | 119 +++++++++----- NAMESPACE | 15 - NEWS.md | 35 +++- R/add_pkg_to_bib.R | 33 ++-- R/calc_assoc_metrics.R | 106 ++++++++++--- R/calc_disp.R | 111 +++++++++++-- R/calc_normalized_entropy.R |only R/calc_type_metrics.R | 209 ++++++++++++++------------ R/confirm_permission.R | 20 +- R/create_data_dictionary.R | 23 +- R/create_data_origin.R | 111 +++++++------ R/curate_enntt_data.R |only R/curate_swda_data.R |only R/find_outliers.R | 176 ++++++++++++--------- R/get_archive_data.R | 110 ++++++++++--- R/get_gutenberg_data.R | 180 ++++++++++------------ R/write_gg.R | 120 +++++++------- R/write_kbl.R | 81 ++++++---- R/write_obj.R | 88 ++++++---- README.md | 14 - build/vignette.rds |binary inst/doc/document.R | 87 ++++++++++ inst/doc/document.Rmd | 162 +++++++++++++++++++- inst/doc/document.html | 163 +++++++++++++++++++- inst/doc/reports.R | 92 +++++++++++ inst/doc/reports.Rmd | 186 ++++++++++++++++++++++- inst/doc/reports.html | 174 ++++++++++++++++++++- inst/extdata/bigrams.R | 10 - inst/extdata/simul_enntt |only inst/extdata/simul_swda |only inst/extdata/tokenized.R | 19 +- inst/extdata/types_data.rds |binary man/add_pkg_to_bib.Rd | 27 ++- man/calc_df.Rd |only man/calc_dp.Rd |only man/calc_idf.Rd |only man/calc_normalized_entropy.Rd |only man/calc_orf.Rd |only man/calc_rf.Rd | 62 ++++++- man/calc_type_metrics.Rd | 80 +++++---- man/calculate_bigram_probabilities.Rd |only man/calculate_metrics.Rd |only man/clean_filenames.Rd |only man/confirm_if_needed.Rd |only man/create_data_origin.Rd | 33 ++-- man/curate_enntt_data.Rd |only man/curate_enntt_file.Rd |only man/curate_swda_data.Rd |only man/curate_swda_file.Rd |only man/download_and_decompress.Rd |only man/extract_dat_attrs.Rd |only man/extract_speaker_info.Rd |only man/extract_utterances.Rd |only man/find_enntt_files.Rd |only man/find_outliers.Rd | 53 +++++- man/get_archive_data.Rd | 55 ++++-- man/get_gutenberg_data.Rd | 13 - man/process_speaker_info.Rd |only man/validate_dir_path.Rd |only man/validate_file_extension.Rd |only man/validate_inputs_cam.Rd |only man/validate_inputs_ctm.Rd |only man/write_gg.Rd | 31 ++- man/write_kbl.Rd | 46 +++-- man/write_obj.Rd | 27 ++- tests/testthat/test-calc_normalized_entropy.R |only tests/testthat/test-calc_type_metrics.R | 17 +- tests/testthat/test-create_data_dictionary.R | 11 - tests/testthat/test-curate_enntt_data.R |only tests/testthat/test-curate_swda_data.R |only tests/testthat/test-get_gutenberg_data.R | 10 - vignettes/document.Rmd | 162 +++++++++++++++++++- vignettes/reports.Rmd | 186 ++++++++++++++++++++++- 74 files changed, 2460 insertions(+), 810 deletions(-)
Title: Document a Universe of Packages
Description: Creates a data frame containing the metadata associated with
the documentation of a collection of R packages. It allows for linking
topic names to their corresponding documentation online. If you
maintain a universe meta-package, it helps create a comprehensive
reference for its website.
Author: Mauro Lepore [aut, cre, cph]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between dverse versions 0.1.0 dated 2024-11-22 and 0.2.0 dated 2024-12-07
DESCRIPTION | 8 ++++---- MD5 | 19 +++++++++++-------- NAMESPACE | 1 + NEWS.md | 16 +++++++--------- R/document_universe.R | 30 +++++++++++++++++++++++------- R/is_online.R |only R/s3_strip_class.R | 12 ++++++------ README.md | 6 +++--- inst/WORDLIST | 1 + man/is_online.Rd |only tests/testthat/test-document_universe.R | 21 ++++++++++++--------- tests/testthat/test-is_online.R |only 12 files changed, 68 insertions(+), 46 deletions(-)
Title: Friendly R Startup Configuration
Description: Adds support for R startup configuration via '.Renviron.d' and '.Rprofile.d' directories in addition to '.Renviron' and '.Rprofile' files. This makes it possible to keep private / secret environment variables separate from other environment variables. It also makes it easier to share specific startup settings by simply copying a file to a directory.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between startup versions 0.22.0 dated 2024-07-29 and 0.23.0 dated 2024-12-07
DESCRIPTION | 6 +- MD5 | 42 ++++++++------ NEWS.md | 34 +++++++++++ R/debug.R | 39 +++++++++++++ R/is_ark.R |only R/is_positron.R |only R/is_webr.R | 2 R/is_wine.R | 4 - R/options.R | 17 +++++ R/renviron_d.R | 14 +++- R/rprofile_d.R | 34 +++++++++-- R/startup.R | 126 +++++++++++++++++++++++++++----------------- R/sysinfo.R | 14 ++-- README.md | 33 ++++++++--- build/vignette.rds |binary inst/WORDLIST | 6 ++ inst/doc/startup-intro.html | 65 ++++++++++++++++++---- inst/doc/startup-intro.md | 33 ++++++++--- man/is_ark.Rd |only man/is_positron.Rd |only man/is_webr.Rd | 2 man/is_wine.Rd | 4 - man/startup.options.Rd | 17 +++++ vignettes/startup-intro.md | 33 ++++++++--- 24 files changed, 388 insertions(+), 137 deletions(-)
Title: Spatial Modeling of Infectious Disease with Reinfection
Description: Geographically Dependent Individual Level Models (GDILMs) within the Susceptible-Exposed-Infectious-Recovered-Susceptible (SEIRS) framework are applied to model infectious disease transmission, incorporating reinfection dynamics. This package employs a likelihood based Monte Carlo Expectation Conditional Maximization (MCECM) algorithm for estimating model parameters. It also provides tools for GDILM fitting, parameter estimation, AIC calculation on real pandemic data, and simulation studies customized to user-defined model settings.
Author: Amin Abed [aut, cre, cph] ,
Mahmoud Torabi [ths],
Zeinab Mashreghi [ths]
Maintainer: Amin Abed <abeda@myumanitoba.ca>
Diff between GDILM.SEIRS versions 0.0.1 dated 2024-12-05 and 0.0.2 dated 2024-12-07
DESCRIPTION | 10 +- MD5 | 14 ++-- R/GDILM_SEIRS_Par_Est.R | 84 ++++++++++++++++-------- R/GDILM_SEIRS_Sim_Par_Est.R | 89 +++++++++++++++++--------- man/GDILM_SEIRS_Par_Est.Rd | 7 +- man/GDILM_SEIRS_Sim_Par_Est.Rd | 7 +- tests/testthat/test-GDILM_SEIRS_Par_Est.R | 2 tests/testthat/test-GDILM_SEIRS_Sim_Par_Est.R | 2 8 files changed, 140 insertions(+), 75 deletions(-)
Title: An API Wrapper for 'DAWA' - 'The Danish Address Web API'
Description: Functions for interacting with all sections of
the official 'Danish Address Web API' (also known as 'DAWA')
<https://api.dataforsyningen.dk>. The development of this package is
completely independent from the government agency, Klimadatastyrelsen,
who maintains the API.
Author: Aleksander Bang-Larsen [aut, cre, cph]
,
Agency of Climate Data [ctb]
Maintainer: Aleksander Bang-Larsen <contact@aleksanderbl.dk>
Diff between dawaR versions 0.2.6 dated 2024-11-24 and 0.2.7 dated 2024-12-07
DESCRIPTION | 26 ++-- MD5 | 124 +++++++++++++-------- NEWS.md | 4 R/base_api.R | 31 ++++- R/get_data.R | 14 ++ R/get_map_data.R | 12 ++ R/status_check.R | 12 +- README.md | 2 inst/CITATION | 15 ++ inst/WORDLIST | 22 +++ inst/doc/dawaR.R | 6 - inst/doc/dawaR.Rmd | 6 - inst/doc/dawaR.html | 2 inst/doc/status.html | 8 - man/autocomplete.Rd | 4 man/dawa.Rd | 6 - man/get_data.Rd | 11 + man/get_map_data.Rd | 5 man/reverse.Rd | 4 man/status_check.Rd | 13 +- tests/fixtures |only tests/testthat/_snaps/afstemningsomraader.md | 14 +- tests/testthat/_snaps/autocomplete.md | 32 ++--- tests/testthat/_snaps/base_api.md | 4 tests/testthat/_snaps/get_data.md | 68 +++++------ tests/testthat/_snaps/get_map_data-kommuner.md | 2 tests/testthat/_snaps/get_map_data-politikredse.md | 58 ++++----- tests/testthat/_snaps/get_map_data-regioner.md | 18 +-- tests/testthat/_snaps/get_map_data-vote.md | 2 tests/testthat/_snaps/reverse.md | 19 ++- tests/testthat/_snaps/status_check.md | 8 - tests/testthat/helper-vcr.R |only tests/testthat/test-1-dawa-sections.R | 1 tests/testthat/test-3-get_map_data-sections.R | 1 tests/testthat/test-afstemningsomraader.R | 66 +++++++---- tests/testthat/test-autocomplete.R | 115 +++++++++++++++---- tests/testthat/test-base_api.R | 40 ++++-- tests/testthat/test-get_data.R | 39 +++++- tests/testthat/test-get_map_data-kommuner.R | 2 tests/testthat/test-get_map_data-politikredse.R | 4 tests/testthat/test-get_map_data-postnumre.R | 6 - tests/testthat/test-get_map_data-regioner.R | 4 tests/testthat/test-get_map_data-vote.R | 2 tests/testthat/test-get_map_data.R | 1 tests/testthat/test-reverse.R | 50 +++++--- tests/testthat/test-status_check.R | 2 vignettes/dawaR.Rmd | 6 - 47 files changed, 600 insertions(+), 291 deletions(-)
Title: Self-Validated Ensemble Models with Elastic Net Regression
Description: Implements Self-Validated Ensemble Models (SVEM, Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) using Elastic Net regression via 'glmnet' (Friedman et al. <doi:10.18637/jss.v033.i01>). SVEM averages predictions from multiple models fitted to fractionally weighted bootstraps of the data, tuned with anti-correlated validation weights. Also implements the randomized permutation whole model test for SVEM (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). \\Code for the whole model test was taken from the supplementary material of Karl (2024). Development of this package was assisted by 'GPT o1-preview' for code structure and documentation.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 1.1.1 dated 2024-11-29 and 1.2.1 dated 2024-12-07
DESCRIPTION | 11 - MD5 | 30 ++-- NAMESPACE | 8 + NEWS | 5 R/SVEMnet-package.R | 1 R/globals.R | 2 R/predict.svem_lasso.R | 3 R/svem_significance_test.R | 23 ++- R/svem_significance_test_parallel.R |only inst/doc/SVEMnet_vignette.R | 2 inst/doc/SVEMnet_vignette.Rmd | 50 +++----- inst/doc/SVEMnet_vignette.html | 204 ++++++++++++++++----------------- man/SVEMnet-package.Rd | 1 man/svem_significance_test.Rd | 14 +- man/svem_significance_test_parallel.Rd |only vignettes/SVEMnet_vignette.Rmd | 50 +++----- vignettes/figures/whole_model_2.png |binary 17 files changed, 213 insertions(+), 191 deletions(-)
Title: The Cauchy-Cacoullos (Discrete Cauchy) Distribution
Description: Maximum likelihood estimation of the Cauchy-Cacoullos (discrete Cauchy) distribution. Probability mass, distribution and quantile function are also included. The reference paper is: Papadatos N. (2022). "The Characteristic Function of the Discrete Cauchy Distribution in Memory of T. Cacoullos". Journal of Statistical Theory Practice, 16(3): 47. <doi:10.1007/s42519-022-00268-6>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between CCd versions 1.0 dated 2024-09-26 and 1.1 dated 2024-12-07
DESCRIPTION | 11 ++++++----- MD5 | 18 ++++++++++-------- NAMESPACE | 4 ++-- R/cc.mle.R | 4 ++-- R/cc.reg.R |only R/loc0.test.R | 2 +- man/CCd-package.Rd | 7 +++---- man/cc.mle.Rd | 20 ++++++++++++++------ man/cc.reg.Rd |only man/dcc.Rd | 5 ++--- man/loc0.test.Rd | 3 +-- 11 files changed, 41 insertions(+), 33 deletions(-)
Title: Miscellaneous, Analytic R Kernels
Description: Miscellaneous functions and wrappers for development in other
packages created, maintained by Jordan Mark Barbone.
Author: Jordan Mark Barbone [aut, cph, cre]
Maintainer: Jordan Mark Barbone <jmbarbone@gmail.com>
Diff between mark versions 0.8.1 dated 2024-09-29 and 0.8.2 dated 2024-12-07
DESCRIPTION | 9 +- MD5 | 19 ++--- NAMESPACE | 1 NEWS.md | 8 ++ R/clipboard.R | 136 ++++++++++++++++++++++++++-------------- README.md | 2 man/clipboard.Rd | 7 +- tests/testthat/Rplots.pdf |only tests/testthat/test-clipboard.R | 68 +++++++++++++++----- tests/testthat/test-diff-time.R | 2 tests/testthat/test-strings.R | 1 11 files changed, 173 insertions(+), 80 deletions(-)
Title: Rewrite of gWidgets API for Simplified GUI Construction
Description: Re-implementation of the 'gWidgets' API. The API is defined in this
package. A second, toolkit-specific package is required to use it. At this point only 'gWidgets2tcltk' is viable.
Author: John Verzani [aut, cre]
Maintainer: John Verzani <jverzani@gmail.com>
Diff between gWidgets2 versions 1.0-9 dated 2022-01-10 and 1.0-10 dated 2024-12-07
DESCRIPTION | 11 +-- MD5 | 24 +++--- NAMESPACE | 8 ++ R/gWidgets2-package.R | 166 +++++++++++++++++++++++------------------------ R/icons.R | 13 +-- man/add.Rd | 2 man/gWidgets2-package.Rd | 6 - man/gedit.Rd | 2 man/gfile.Rd | 7 + man/gmenu.Rd | 2 man/gnotebook.Rd | 2 man/gtoolbar.Rd | 2 man/gwindow.Rd | 4 - 13 files changed, 128 insertions(+), 121 deletions(-)
Title: Categorical Landscape Simulation Facility
Description: Simulates categorical maps on actual geographical realms, starting from either empty landscapes or landscapes provided by the user (e.g. land use maps). Allows to tweak or create landscapes while retaining a high degree of control on its features, without the hassle of specifying each location attribute. In this it differs from other tools which generate null or neutral landscapes in a theoretical space. The basic algorithm currently implemented uses a simple agent style/cellular automata growth model, with no rules (apart from areas of exclusion) and von Neumann neighbourhood (four cells, aka Rook case). Outputs are raster dataset exportable to any common GIS format.
Author: Dario Masante [aut, cre],
Lora Murphy [ctb]
Maintainer: Dario Masante <dario.masante@gmail.com>
Diff between landscapeR versions 1.3 dated 2024-11-01 and 1.3.1 dated 2024-12-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ inst/doc/landscapeR.Rmd | 9 +++------ inst/doc/landscapeR.html | 34 ++++++++++++++++------------------ vignettes/landscapeR.Rmd | 9 +++------ 6 files changed, 36 insertions(+), 39 deletions(-)
Title: Helper Functions for Creating Tutorials
Description: Helper functions for creating, editing, and testing tutorials
created with the 'learnr' package. Provides a simple method for allowing
students to download their answers to tutorial questions. For examples
of its use, see the 'r4ds.tutorials' package.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Diff between tutorial.helpers versions 0.3.0 dated 2024-06-26 and 0.3.1 dated 2024-12-07
DESCRIPTION | 8 MD5 | 44 ++-- NEWS.md | 6 README.md | 11 - build/vignette.rds |binary inst/doc/addins.R | 45 ++++ inst/doc/addins.Rmd | 17 - inst/doc/addins.html | 15 - inst/doc/books.Rmd | 12 - inst/doc/books.html | 12 - inst/doc/cloud.Rmd | 4 inst/doc/cloud.html | 4 inst/doc/downloads.Rmd | 6 inst/doc/downloads.html | 5 inst/doc/instructions.Rmd | 167 +++++++++-------- inst/doc/instructions.html | 156 ++++++++-------- inst/tutorials/getting-started/tutorial.Rmd | 72 ++++++- inst/tutorials/getting-started/tutorial.html | 254 +++++++++++++++------------ vignettes/addins.Rmd | 17 - vignettes/books.Rmd | 12 - vignettes/cloud.Rmd | 4 vignettes/downloads.Rmd | 6 vignettes/instructions.Rmd | 167 +++++++++-------- 23 files changed, 598 insertions(+), 446 deletions(-)
More information about tutorial.helpers at CRAN
Permanent link
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating
random and regular graphs, graph visualization, centrality methods and
much more.
Author: Gabor Csardi [aut] ,
Tamas Nepusz [aut] ,
Vincent Traag [aut] ,
Szabolcs Horvat [aut] ,
Fabio Zanini [aut] ,
Daniel Noom [aut],
Kirill Mueller [aut, cre] ,
Maelle Salmon [ctb],
Michael Antonov [ctb],
Chan Zuckerberg Initiative [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between igraph versions 2.1.1 dated 2024-10-19 and 2.1.2 dated 2024-12-07
DESCRIPTION | 11 ++- MD5 | 104 ++++++++++++++++++------------------ NEWS.md | 25 ++++++++ R/centrality.R | 2 R/community.R | 21 +++---- R/foreign.R | 27 +++++++-- R/interface.R | 4 - R/motifs.R | 21 ++++++- R/palette.R | 4 - R/paths.R | 10 +-- build/partial.rdb |binary build/vignette.rds |binary configure | 2 inst/doc/igraph.R | 26 ++++----- inst/doc/igraph.html | 70 ++++++++++++------------ inst/doc/igraph_ES.R | 28 +++++---- inst/doc/igraph_ES.html | 70 ++++++++++++------------ man/all_simple_paths.Rd | 10 +-- man/as_directed.Rd | 2 man/as_graphnel.Rd | 2 man/cluster_fast_greedy.Rd | 3 - man/cluster_label_prop.Rd | 2 man/cluster_leiden.Rd | 2 man/cluster_louvain.Rd | 2 man/cluster_optimal.Rd | 7 +- man/cluster_spinglass.Rd | 3 - man/cluster_walktrap.Rd | 2 man/diverging_pal.Rd | 2 man/fastgreedy.community.Rd | 3 - man/fit_hrg.Rd | 2 man/graph.motifs.est.Rd | 3 - man/graph_from_graphnel.Rd | 2 man/label.propagation.community.Rd | 2 man/layout_in_circle.Rd | 2 man/multilevel.community.Rd | 2 man/optimal.community.Rd | 7 +- man/predict_edges.Rd | 2 man/read_graph.Rd | 2 man/sample_degseq.Rd | 4 - man/sample_motifs.Rd | 5 + man/sample_pref.Rd | 4 - man/sequential_pal.Rd | 2 man/spinglass.community.Rd | 3 - man/walktrap.community.Rd | 2 man/write.graph.Rd | 2 man/write_graph.Rd | 29 ++++++++-- src/rinterface_extra.c | 17 ++--- tests/testthat/_snaps/centrality.md | 71 ------------------------ tests/testthat/test-centrality.R | 9 ++- tests/testthat/test-get.adjlist.R | 42 ++++++++++++++ tests/testthat/test-interface.R | 61 +++++++++++++++++++++ tests/testthat/test-motifs.R | 16 +++++ tests/testthat/test-plot.R | 2 53 files changed, 450 insertions(+), 308 deletions(-)
Title: Precipitation R Recipes
Description: An open-access tool/framework to download, validate, visualize, and
analyze multi-source precipitation data. More information and an example of
implementation can be found in Vargas Godoy and Markonis (2023,
<doi:10.1016/j.envsoft.2023.105711>).
Author: Mijael Rodrigo Vargas Godoy [aut, cre]
,
Yannis Markonis [aut, ths]
Maintainer: Mijael Rodrigo Vargas Godoy <mirovago@gmail.com>
Diff between pRecipe versions 3.0.1-3 dated 2024-01-31 and 3.0.2 dated 2024-12-07
pRecipe-3.0.1-3/pRecipe/R/crop_data.R |only pRecipe-3.0.1-3/pRecipe/R/csi.R |only pRecipe-3.0.1-3/pRecipe/R/download_e_obs.R |only pRecipe-3.0.1-3/pRecipe/R/download_trmm_3b43.R |only pRecipe-3.0.1-3/pRecipe/R/download_udel.R |only pRecipe-3.0.1-3/pRecipe/R/far.R |only pRecipe-3.0.1-3/pRecipe/R/fldmean.R |only pRecipe-3.0.1-3/pRecipe/R/infoNC.R |only pRecipe-3.0.1-3/pRecipe/R/label.R |only pRecipe-3.0.1-3/pRecipe/R/muldpm.R |only pRecipe-3.0.1-3/pRecipe/R/nse.R |only pRecipe-3.0.1-3/pRecipe/R/pRecipe_masks.R |only pRecipe-3.0.1-3/pRecipe/R/pod.R |only pRecipe-3.0.1-3/pRecipe/R/remap.R |only pRecipe-3.0.1-3/pRecipe/R/saveNC.R |only pRecipe-3.0.1-3/pRecipe/R/subset_data.R |only pRecipe-3.0.1-3/pRecipe/R/tabular.R |only pRecipe-3.0.1-3/pRecipe/R/trend.R |only pRecipe-3.0.1-3/pRecipe/R/yearstat.R |only pRecipe-3.0.1-3/pRecipe/man/crop_data.Rd |only pRecipe-3.0.1-3/pRecipe/man/csi.Rd |only pRecipe-3.0.1-3/pRecipe/man/download_e_obs.Rd |only pRecipe-3.0.1-3/pRecipe/man/download_trmm_3b43.Rd |only pRecipe-3.0.1-3/pRecipe/man/download_udel.Rd |only pRecipe-3.0.1-3/pRecipe/man/far.Rd |only pRecipe-3.0.1-3/pRecipe/man/fldmean.Rd |only pRecipe-3.0.1-3/pRecipe/man/infoNC.Rd |only pRecipe-3.0.1-3/pRecipe/man/label.Rd |only pRecipe-3.0.1-3/pRecipe/man/muldpm.Rd |only pRecipe-3.0.1-3/pRecipe/man/nse.Rd |only pRecipe-3.0.1-3/pRecipe/man/pRecipe_masks.Rd |only pRecipe-3.0.1-3/pRecipe/man/pod.Rd |only pRecipe-3.0.1-3/pRecipe/man/remap.Rd |only pRecipe-3.0.1-3/pRecipe/man/saveNC.Rd |only pRecipe-3.0.1-3/pRecipe/man/subset_data.Rd |only pRecipe-3.0.1-3/pRecipe/man/tabular.Rd |only pRecipe-3.0.1-3/pRecipe/man/trend.Rd |only pRecipe-3.0.1-3/pRecipe/man/yearstat.Rd |only pRecipe-3.0.2/pRecipe/DESCRIPTION | 23 pRecipe-3.0.2/pRecipe/MD5 | 201 +--- pRecipe-3.0.2/pRecipe/NAMESPACE | 42 pRecipe-3.0.2/pRecipe/NEWS.md | 6 pRecipe-3.0.2/pRecipe/R/core_functions.R |only pRecipe-3.0.2/pRecipe/R/dataset_check.R | 16 pRecipe-3.0.2/pRecipe/R/download_20cr.R | 7 pRecipe-3.0.2/pRecipe/R/download_all.R | 4 pRecipe-3.0.2/pRecipe/R/download_chirps.R | 6 pRecipe-3.0.2/pRecipe/R/download_cmap.R | 5 pRecipe-3.0.2/pRecipe/R/download_cmorph.R | 7 pRecipe-3.0.2/pRecipe/R/download_cpc.R | 6 pRecipe-3.0.2/pRecipe/R/download_cru_ts.R | 4 pRecipe-3.0.2/pRecipe/R/download_data.R | 6 pRecipe-3.0.2/pRecipe/R/download_em_earth.R | 4 pRecipe-3.0.2/pRecipe/R/download_era20c.R | 5 pRecipe-3.0.2/pRecipe/R/download_era5.R | 3 pRecipe-3.0.2/pRecipe/R/download_era5_land.R |only pRecipe-3.0.2/pRecipe/R/download_fldas.R | 4 pRecipe-3.0.2/pRecipe/R/download_ghcn.R | 4 pRecipe-3.0.2/pRecipe/R/download_gldas_clsm.R | 6 pRecipe-3.0.2/pRecipe/R/download_gldas_noah.R | 5 pRecipe-3.0.2/pRecipe/R/download_gldas_vic.R | 5 pRecipe-3.0.2/pRecipe/R/download_gpcc.R | 5 pRecipe-3.0.2/pRecipe/R/download_gpcp.R | 7 pRecipe-3.0.2/pRecipe/R/download_gpm_imerg.R | 7 pRecipe-3.0.2/pRecipe/R/download_gsmap.R |only pRecipe-3.0.2/pRecipe/R/download_jra55.R | 7 pRecipe-3.0.2/pRecipe/R/download_merra2.R | 7 pRecipe-3.0.2/pRecipe/R/download_mswep.R | 7 pRecipe-3.0.2/pRecipe/R/download_ncep_doe.R | 7 pRecipe-3.0.2/pRecipe/R/download_ncep_ncar.R | 7 pRecipe-3.0.2/pRecipe/R/download_persiann.R | 7 pRecipe-3.0.2/pRecipe/R/download_precl.R | 4 pRecipe-3.0.2/pRecipe/R/download_terraclimate.R | 4 pRecipe-3.0.2/pRecipe/R/globals.R | 6 pRecipe-3.0.2/pRecipe/R/plot_map.R | 85 - 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Title: Testing DBI Backends
Description: A helper that tests DBI back ends for conformity to the
interface.
Author: Kirill Mueller [aut, cre] ,
RStudio [cph],
R Consortium [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between DBItest versions 1.8.1 dated 2024-03-31 and 1.8.2 dated 2024-12-07
DESCRIPTION | 12 +-- MD5 | 112 +++++++++++++++---------------- NEWS.md | 19 +++++ R/spec-meta-bind-.R | 20 ++--- R/spec-meta-bind-arrow-stream.R | 50 ++++++------- R/spec-meta-bind-arrow.R | 18 ++-- R/spec-meta-bind-expr.R | 8 +- R/spec-meta-bind-runner.R | 34 +++++---- R/spec-meta-bind-stream.R | 50 ++++++------- R/spec-meta-bind.R | 22 +++--- R/spec-result-roundtrip.R | 10 +- R/spec-sql-write-table.R | 16 ++-- build/vignette.rds |binary inst/doc/DBItest.html | 2 man/context.Rd | 4 - man/spec_arrow_append_table_arrow.Rd | 6 - man/spec_arrow_create_table_arrow.Rd | 4 - man/spec_arrow_get_query_arrow.Rd | 4 - man/spec_arrow_read_table_arrow.Rd | 6 - man/spec_arrow_send_query_arrow.Rd | 12 +-- man/spec_arrow_write_table_arrow.Rd | 6 - man/spec_compliance_methods.Rd | 6 - man/spec_driver_connect.Rd | 2 man/spec_driver_constructor.Rd | 2 man/spec_driver_data_type.Rd | 2 man/spec_get_info.Rd | 16 ++-- man/spec_meta_bind.Rd | 42 +++++------ man/spec_meta_column_info.Rd | 2 man/spec_meta_get_row_count.Rd | 8 +- man/spec_meta_get_rows_affected.Rd | 8 +- man/spec_meta_get_statement.Rd | 6 - man/spec_meta_has_completed.Rd | 8 +- man/spec_meta_is_valid.Rd | 12 +-- man/spec_result_clear_result.Rd | 2 man/spec_result_execute.Rd | 4 - man/spec_result_fetch.Rd | 2 man/spec_result_get_query.Rd | 4 - man/spec_result_roundtrip.Rd | 4 - man/spec_result_send_query.Rd | 12 +-- man/spec_result_send_statement.Rd | 12 +-- man/spec_sql_append_table.Rd | 6 - man/spec_sql_create_table.Rd | 4 - man/spec_sql_exists_table.Rd | 6 - man/spec_sql_list_fields.Rd | 4 - man/spec_sql_list_objects.Rd | 14 +-- man/spec_sql_list_tables.Rd | 2 man/spec_sql_quote_identifier.Rd | 6 - man/spec_sql_quote_literal.Rd | 4 - man/spec_sql_quote_string.Rd | 4 - man/spec_sql_read_table.Rd | 8 +- man/spec_sql_remove_table.Rd | 8 +- man/spec_sql_unquote_identifier.Rd | 10 +- man/spec_sql_write_table.Rd | 10 +- man/spec_transaction_with_transaction.Rd | 6 - man/test_data_type.Rd | 2 man/tweaks.Rd | 4 - tests/testthat/test-DBItest.R | 2 57 files changed, 349 insertions(+), 320 deletions(-)
Title: Seamless Integration Between R and 'Julia'
Description: Provides an R interface to 'Julia',
which is a high-level, high-performance dynamic programming language
for numerical computing, see <https://julialang.org/> for more information.
It provides a high-level interface as well as a low-level interface.
Using the high level interface, you could call any 'Julia' function just like
any R function with automatic type conversion. Using the low level interface,
you could deal with C-level SEXP directly while enjoying the convenience of
using a high-level programming language like 'Julia'.
Author: Changcheng Li [aut, cre],
Christopher Rackauckas [ctb],
Randy Lai [ctb],
Dmitri Grominski [ctb],
Nagi Teramo [ctb]
Maintainer: Changcheng Li <cxl508@psu.edu>
Diff between JuliaCall versions 0.17.5 dated 2022-09-08 and 0.17.6 dated 2024-12-07
DESCRIPTION | 16 LICENSE | 4 MD5 | 202 ++-- NAMESPACE | 166 +-- NEWS.md | 674 ++++++------- R/JuliaCall.R | 116 +- R/JuliaObject.R | 298 +++--- R/JuliaObjectExt.R | 106 +- R/JuliaPlain.R | 52 - R/Jupyter.R | 10 R/RMarkdown.R | 403 ++++---- R/RcppExports.R | 38 R/aaa.R | 204 ++-- R/argument.R | 18 R/console.R | 132 +- R/dispatch.R | 364 +++---- R/installJulia.R | 295 ++---- R/interface.R | 456 ++++----- R/internal_generic.R | 34 R/package.R | 128 +- R/package_wrap.R | 154 +-- R/piper.R | 52 - R/plotsViewer.R | 42 R/util.R | 30 R/zzz.R | 520 +++++----- README.md | 730 +++++++------- build/vignette.rds |binary inst/CITATION | 30 inst/doc/JuliaCall_in_Jupyter_R_Notebook.R | 12 inst/doc/JuliaCall_in_Jupyter_R_Notebook.Rmd | 48 inst/doc/JuliaCall_in_Jupyter_R_Notebook.html | 1129 +++++++++++------------ inst/doc/Julia_in_RMarkdown.R | 6 inst/doc/Julia_in_RMarkdown.Rmd | 28 inst/doc/Julia_in_RMarkdown.html | 809 ++++++++-------- inst/js/plotly-latest.min.js | 154 +-- inst/julia/JuliaObject.jl | 198 ++-- inst/julia/REPLhook.jl | 26 inst/julia/RmdStd.jl | 58 - inst/julia/asR.jl | 28 inst/julia/convert.jl | 34 inst/julia/dispatch.jl | 200 ++-- inst/julia/display/IRjulia.jl | 132 +- inst/julia/display/RmdJulia.jl | 78 - inst/julia/display/basic.jl | 96 - inst/julia/display/plotsViewer.jl | 90 - inst/julia/incomplete_console.jl | 16 inst/julia/install_dependency.jl | 84 - inst/julia/interface1.jl | 70 - inst/julia/libjulia.jl | 34 inst/julia/rebuildRCall.jl | 116 +- inst/julia/setup.jl | 498 +++++----- man/JuliaCall.Rd | 118 +- man/JuliaObject.Rd | 56 - man/JuliaObjectFields.Rd | 68 - man/autowrap.Rd | 38 man/call.Rd | 116 +- man/eng_juliacall.Rd | 38 man/grapes-greater-than-J-grapes.Rd | 50 - man/install_julia.Rd | 40 man/julia_assign.Rd | 54 - man/julia_command.Rd | 64 - man/julia_console.Rd | 34 man/julia_eval.Rd | 74 - man/julia_exists.Rd | 46 man/julia_help.Rd | 46 man/julia_markdown_setup.Rd | 36 man/julia_notebook_setup.Rd | 30 man/julia_package.Rd | 94 - man/julia_pkg_wrap.Rd | 90 - man/julia_setup.Rd | 129 +- man/julia_source.Rd | 28 man/plotsViewer.Rd | 22 src/libjulia.cpp | 2 src/libjulia.h | 2 tests/testthat.R | 8 tests/testthat/Rmd_error_test.Rmd | 38 tests/testthat/Rmd_error_test1.Rmd | 40 tests/testthat/Rmd_test.Rmd | 78 - tests/testthat/Rmd_test.md | 96 - tests/testthat/simplesource.jl | 2 tests/testthat/test_AD.R | 168 +-- tests/testthat/test_JuliaObject.R | 150 +-- tests/testthat/test_JuliaTuple.R | 30 tests/testthat/test_RCall.R | 28 tests/testthat/test_arguments.R | 28 tests/testthat/test_array_related_dispatching.R | 82 - tests/testthat/test_asR.R | 18 tests/testthat/test_autowrap_JuliaObject.R | 56 - tests/testthat/test_basic.R | 56 - tests/testthat/test_dispatch.R | 238 ++-- tests/testthat/test_error.R | 24 tests/testthat/test_ifelse_related_dispatching.R | 132 +- tests/testthat/test_julia_package.R | 32 tests/testthat/test_julia_source.R | 22 tests/testthat/test_pkgwrap.R | 30 tests/testthat/test_rebuild.R | 22 tests/testthat/test_rmd.R | 26 tests/testthat/test_rmd_error.R | 24 vignettes/JuliaCall_in_Jupyter_R_Notebook.Rmd | 48 vignettes/JuliaCall_in_Jupyter_R_Notebook1.md | 530 +++++----- vignettes/JuliaCall_in_RMarkdown.md | 124 +- vignettes/Julia_in_RMarkdown.Rmd | 28 102 files changed, 6321 insertions(+), 6330 deletions(-)
Title: Toolkit for Reduced Form and Structural Smooth Transition Vector
Autoregressive Models
Description: Maximum likelihood estimation of smooth transition vector
autoregressive models with various types of transition weight functions,
conditional distributions, and identification methods. Constrained
estimation with various types of constraints is available. Residual based
model diagnostics, forecasting, simulations, and calculation of impulse
response functions, generalized impulse response functions, and generalized
forecast error variance decompositions. See
Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>,
Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>,
Markku Lanne, Savi Virolainen (2024) <doi:10.48550/arXiv.2403.14216>,
Savi Virolainen (2024) <doi:10.48550/arXiv.2404.19707>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between sstvars versions 1.1.0 dated 2024-11-29 and 1.1.1 dated 2024-12-07
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Title: Data and Software for "Lessons in Statistical Thinking"
Description: "Lessons in Statistical Thinking" D.T. Kaplan (2014)
<https://dtkaplan.github.io/Lessons-in-statistical-thinking/>
is a textbook for a first or second course in statistics that embraces
data wrangling, causal reasoning, modeling, statistical adjustment,
and simulation. 'LSTbook' supports the student-centered, tidy,
pipeline-oriented computing style featured in the book.
Author: Daniel Kaplan [aut, cre],
Randall Pruim [aut]
Maintainer: Daniel Kaplan <dtkaplan@gmail.com>
Diff between LSTbook versions 0.5.0 dated 2024-02-23 and 0.6 dated 2024-12-07
LSTbook-0.5.0/LSTbook/R/pointplot.R |only LSTbook-0.5.0/LSTbook/R/sample.R |only LSTbook-0.5.0/LSTbook/data/FEV.rda |only LSTbook-0.5.0/LSTbook/man/FEV.Rd |only LSTbook-0.5.0/LSTbook/man/sample.Rd |only LSTbook-0.6/LSTbook/DESCRIPTION | 15 - LSTbook-0.6/LSTbook/MD5 | 121 ++++---- LSTbook-0.6/LSTbook/NAMESPACE | 13 LSTbook-0.6/LSTbook/NEWS.md | 33 ++ LSTbook-0.6/LSTbook/R/AAUP.R | 2 LSTbook-0.6/LSTbook/R/FARS.R | 2 LSTbook-0.6/LSTbook/R/FEV.R | 4 LSTbook-0.6/LSTbook/R/data_from_tilde.R | 21 + LSTbook-0.6/LSTbook/R/datasim_helpers.R | 4 LSTbook-0.6/LSTbook/R/model_eval.R | 24 - LSTbook-0.6/LSTbook/R/model_plot.R | 7 LSTbook-0.6/LSTbook/R/model_skeleton.R | 2 LSTbook-0.6/LSTbook/R/model_type.R | 8 LSTbook-0.6/LSTbook/R/mosaic-do.R | 2 LSTbook-0.6/LSTbook/R/ntiles.R | 4 LSTbook-0.6/LSTbook/R/point_plot.R |only LSTbook-0.6/LSTbook/R/print.R | 1 LSTbook-0.6/LSTbook/R/print_model_object.R | 1 LSTbook-0.6/LSTbook/R/random_terms.R |only LSTbook-0.6/LSTbook/R/regression_summary.R | 2 LSTbook-0.6/LSTbook/R/sims.R | 2 LSTbook-0.6/LSTbook/R/take_sample.R |only LSTbook-0.6/LSTbook/R/trials.R | 2 LSTbook-0.6/LSTbook/R/zzz.R | 6 LSTbook-0.6/LSTbook/README.md | 52 +-- LSTbook-0.6/LSTbook/build/vignette.rds |binary LSTbook-0.6/LSTbook/data/CRDS.rda |only LSTbook-0.6/LSTbook/inst/Natality_2014.R |only LSTbook-0.6/LSTbook/inst/doc/DAGs.R | 26 - LSTbook-0.6/LSTbook/inst/doc/DAGs.Rmd | 26 - LSTbook-0.6/LSTbook/inst/doc/DAGs.html | 206 +++----------- LSTbook-0.6/LSTbook/inst/doc/LSTbook.R | 2 LSTbook-0.6/LSTbook/inst/doc/LSTbook.Rmd | 30 +- LSTbook-0.6/LSTbook/inst/doc/LSTbook.html | 135 +++------ LSTbook-0.6/LSTbook/inst/doc/modeling.Rmd | 4 LSTbook-0.6/LSTbook/inst/doc/modeling.html | 23 - LSTbook-0.6/LSTbook/man/AAUP.Rd | 2 LSTbook-0.6/LSTbook/man/CRDS.Rd |only LSTbook-0.6/LSTbook/man/FARS.Rd | 2 LSTbook-0.6/LSTbook/man/add_plot_labels.Rd | 2 LSTbook-0.6/LSTbook/man/datasim_make.Rd | 2 LSTbook-0.6/LSTbook/man/figures/README-README1euiBE-1.png |binary LSTbook-0.6/LSTbook/man/figures/README-README2lz92Z-1.png |binary LSTbook-0.6/LSTbook/man/figures/README-READMEDfxgmm-1.png |binary LSTbook-0.6/LSTbook/man/model_eval.Rd | 4 LSTbook-0.6/LSTbook/man/model_skeleton.Rd | 2 LSTbook-0.6/LSTbook/man/mosaic_cull_for_do.Rd | 2 LSTbook-0.6/LSTbook/man/ntiles.Rd | 4 LSTbook-0.6/LSTbook/man/point_plot.Rd | 2 LSTbook-0.6/LSTbook/man/random_terms.Rd |only LSTbook-0.6/LSTbook/man/regression_summaries.Rd | 2 LSTbook-0.6/LSTbook/man/take_sample.Rd |only LSTbook-0.6/LSTbook/man/trials.Rd | 2 LSTbook-0.6/LSTbook/tests/testthat/test-dags.R | 10 LSTbook-0.6/LSTbook/tests/testthat/test-dagsim.R | 40 +- LSTbook-0.6/LSTbook/tests/testthat/test-mix_with.R | 6 LSTbook-0.6/LSTbook/tests/testthat/test-model_eval.R | 6 LSTbook-0.6/LSTbook/tests/testthat/test-model_train.R | 6 LSTbook-0.6/LSTbook/tests/testthat/test-pointplot.R | 8 LSTbook-0.6/LSTbook/tests/testthat/test-sample.R | 20 - LSTbook-0.6/LSTbook/vignettes/DAGs.Rmd | 26 - LSTbook-0.6/LSTbook/vignettes/LSTbook.Rmd | 30 +- LSTbook-0.6/LSTbook/vignettes/modeling.Rmd | 4 68 files changed, 435 insertions(+), 527 deletions(-)
Title: A Wrapper for the Phonetic Software 'Praat'
Description: It allows running 'Praat' scripts from R and it provides some
wrappers for basic plotting. It also adds support for literate markdown
tangling. The package is designed to bring reproducible phonetic research
into R.
Author: Stefano Coretta [aut, cre]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>
Diff between speakr versions 3.2.2 dated 2024-01-29 and 3.2.4 dated 2024-12-07
speakr-3.2.2/speakr/man/figures/logo.png |only speakr-3.2.2/speakr/man/figures/vowels.png |only speakr-3.2.4/speakr/DESCRIPTION | 19 ++--- speakr-3.2.4/speakr/MD5 | 32 ++++----- speakr-3.2.4/speakr/NEWS.md | 8 ++ speakr-3.2.4/speakr/build/vignette.rds |binary speakr-3.2.4/speakr/inst/doc/praat-lmt.html | 2 speakr-3.2.4/speakr/inst/doc/praat-plot.R | 14 ++-- speakr-3.2.4/speakr/inst/doc/praat-plot.html | 2 speakr-3.2.4/speakr/inst/doc/run-praat.R | 54 ++++++++-------- speakr-3.2.4/speakr/inst/doc/run-praat.html | 8 +- speakr-3.2.4/speakr/man/figures/README-vowel-plot-1.png |binary speakr-3.2.4/speakr/man/get_praat_path.Rd | 2 speakr-3.2.4/speakr/man/praat_path.Rd | 2 speakr-3.2.4/speakr/man/praat_plot.Rd | 14 ++-- speakr-3.2.4/speakr/man/praat_run.Rd | 4 - speakr-3.2.4/speakr/man/set_praat_path.Rd | 2 speakr-3.2.4/speakr/man/speakr-package.Rd | 4 - 18 files changed, 85 insertions(+), 82 deletions(-)
Title: Tidy Prediction and Plotting of Generalised Additive Models
Description: Provides functions that compute predictions from Generalised
Additive Models (GAMs) fitted with 'mgcv' and return them as a tibble.
These can be plotted with a generic plot()-method that uses 'ggplot2' or
plotted as any other data frame. The main function is predict_gam().
Author: Stefano Coretta [aut, cre]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>
Diff between tidygam versions 0.2.0 dated 2023-05-09 and 0.2.2 dated 2024-12-07
DESCRIPTION | 12 ++-- MD5 | 14 ++--- NEWS.md | 10 +++ README.md | 4 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/get-started.R | 2 inst/doc/get-started.html | 119 +++++++++++++++++++++++++--------------------- 8 files changed, 92 insertions(+), 69 deletions(-)
Title: Fast Imputation of Missing Values
Description: Alternative implementation of the beautiful 'MissForest'
algorithm used to impute mixed-type data sets by chaining random
forests, introduced by Stekhoven, D.J. and Buehlmann, P. (2012)
<doi:10.1093/bioinformatics/btr597>. Under the hood, it uses the
lightning fast random forest package 'ranger'. Between the iterative
model fitting, we offer the option of using predictive mean matching.
This firstly avoids imputation with values not already present in the
original data (like a value 0.3334 in 0-1 coded variable). Secondly,
predictive mean matching tries to raise the variance in the resulting
conditional distributions to a realistic level. This would allow,
e.g., to do multiple imputation when repeating the call to
missRanger(). Out-of-sample application is supported as well.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between missRanger versions 2.6.0 dated 2024-08-17 and 2.6.1 dated 2024-12-07
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 7 +++++++ R/missRanger.R | 17 +++++++++++++---- inst/doc/missRanger.html | 4 ++-- inst/doc/multiple_imputation.html | 4 ++-- inst/doc/working_with_censoring.html | 4 ++-- tests/testthat/test-helper.R | 8 ++++++++ 8 files changed, 44 insertions(+), 20 deletions(-)
Title: Codon Usage Bias Analysis
Description: A suite of functions for rapid and flexible analysis of codon
usage bias. It provides in-depth analysis at the codon level, including
relative synonymous codon usage (RSCU), tRNA weight calculations, machine
learning predictions for optimal or preferred codons, and visualization of
codon-anticodon pairing. Additionally, it can calculate various gene-
specific codon indices such as codon adaptation index (CAI), effective
number of codons (ENC), fraction of optimal codons (Fop), tRNA adaptation
index (tAI), mean codon stabilization coefficients (CSCg), and GC contents
(GC/GC3s/GC4d). It also supports both standard and non-standard genetic
code tables found in NCBI, as well as custom genetic code tables.
Author: Hong Zhang [aut, cre] ,
Mengyue Liu [aut],
Bu Zi [aut]
Maintainer: Hong Zhang <mt1022.dev@gmail.com>
Diff between cubar versions 1.0.0 dated 2024-08-01 and 1.1.0 dated 2024-12-07
cubar-1.0.0/cubar/tests/testthat/test-codon_weight.R |only cubar-1.1.0/cubar/DESCRIPTION | 12 + cubar-1.1.0/cubar/MD5 | 65 ++++----- cubar-1.1.0/cubar/NEWS.md | 6 cubar-1.1.0/cubar/R/codon_info.R | 8 - cubar-1.1.0/cubar/R/codon_weight.R | 40 +++-- cubar-1.1.0/cubar/R/gene_index.R | 100 +++++++++----- cubar-1.1.0/cubar/R/sequences.R | 2 cubar-1.1.0/cubar/R/utils.R | 6 cubar-1.1.0/cubar/R/window.R | 6 cubar-1.1.0/cubar/README.md | 7 cubar-1.1.0/cubar/inst/doc/cubar.html | 31 ++-- cubar-1.1.0/cubar/inst/doc/non_standard_genetic_code.html | 2 cubar-1.1.0/cubar/man/codon_diff.Rd | 3 cubar-1.1.0/cubar/man/codon_optimize.Rd | 3 cubar-1.1.0/cubar/man/count_codons.Rd | 2 cubar-1.1.0/cubar/man/create_codon_table.Rd | 2 cubar-1.1.0/cubar/man/est_csc.Rd | 2 cubar-1.1.0/cubar/man/est_optimal_codons.Rd | 10 - cubar-1.1.0/cubar/man/est_rscu.Rd | 18 +- cubar-1.1.0/cubar/man/est_trna_weight.Rd | 2 cubar-1.1.0/cubar/man/get_cai.Rd | 8 - cubar-1.1.0/cubar/man/get_codon_table.Rd | 4 cubar-1.1.0/cubar/man/get_cscg.Rd | 4 cubar-1.1.0/cubar/man/get_dp.Rd | 21 ++ cubar-1.1.0/cubar/man/get_enc.Rd | 9 - cubar-1.1.0/cubar/man/get_fop.Rd | 9 - cubar-1.1.0/cubar/man/get_gc3s.Rd | 9 - cubar-1.1.0/cubar/man/get_gc4d.Rd | 10 - cubar-1.1.0/cubar/man/get_tai.Rd | 4 cubar-1.1.0/cubar/man/plot_ca_pairing.Rd | 3 cubar-1.1.0/cubar/man/show_codon_tables.Rd | 2 cubar-1.1.0/cubar/man/slide_apply.Rd | 4 cubar-1.1.0/cubar/man/slide_plot.Rd | 2 34 files changed, 253 insertions(+), 163 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.3.6 dated 2024-11-07 and 0.4.0 dated 2024-12-07
DESCRIPTION | 13 +- MD5 | 186 +++++++++++++++++++++--------------------- NAMESPACE | 4 R/areaplot.R | 5 - R/barplot.R | 38 +++++++- R/boxviolinplot.R | 20 ++++ R/chordplot.R | 7 + R/clustreeplot.R | 7 + R/common_args.R | 3 R/corplot.R | 17 +++ R/densityplot.R | 21 ++++ R/dimplot.R | 12 ++ R/dotplot.R | 13 ++ R/enrich.R | 10 +- R/heatmap.R | 117 ++++++++++++++++---------- R/lineplot.R | 6 + R/piechart.R | 6 + R/radarplot.R | 10 +- R/rarefractionplot.R | 6 + R/ringplot.R | 7 + R/roccurve.R |only R/scatterplot.R | 8 + R/theming.R | 19 +++- R/trendplot.R | 6 + R/upsetplot.R | 4 R/utils.R | 50 +++++++++++ R/venndiagram.R | 4 R/volcanoplot.R | 12 +- R/wordcloudplot.R | 4 README.md | 11 +- man/AreaPlot.Rd | 8 + man/AreaPlotAtomic.Rd | 7 + man/BarPlotAtomic.Rd | 11 ++ man/BarPlotGrouped.Rd | 11 ++ man/BarPlotSingle.Rd | 7 + man/BoxViolinPlot-internal.Rd | 10 +- man/BoxViolinPlotAtomic.Rd | 10 +- man/ChordPlotAtomic.Rd | 7 + man/ClustreePlot.Rd | 9 +- man/ClustreePlotAtomic.Rd | 7 + man/CorPairsPlot.Rd | 10 +- man/CorPlot.Rd | 9 +- man/CorPlotAtomic.Rd | 7 + man/DensityHistoPlotAtomic.Rd | 7 + man/DimPlotAtomic.Rd | 7 + man/DotPlotAtomic.Rd | 7 + man/EnrichMapAtomic.Rd | 7 + man/EnrichNetworkAtomic.Rd | 7 + man/Heatmap.Rd | 25 +++++ man/HeatmapAtomic.Rd | 16 +++ man/LinePlot.Rd | 9 +- man/LinePlotAtomic.Rd | 7 + man/LinePlotGrouped.Rd | 7 + man/LinePlotSingle.Rd | 7 + man/Network.Rd | 7 + man/PieChart.Rd | 9 +- man/PieChartAtomic.Rd | 7 + man/ROCCurve.Rd |only man/ROCCurveAtomic.Rd |only man/RadarPlotAtomic.Rd | 7 + man/RarefactionPlot.Rd | 9 +- man/RarefactionPlotAtomic.Rd | 7 + man/RidgePlot.Rd | 9 +- man/RidgePlotAtomic.Rd | 7 + man/RingPlot.Rd | 10 +- man/RingPlotAtomic.Rd | 7 + man/ScatterPlot.Rd | 11 ++ man/ScatterPlotAtomic.Rd | 7 + man/SplitBarPlotAtomic.Rd | 7 + man/TrendPlot.Rd | 9 +- man/TrendPlotAtomic.Rd | 7 + man/UpsetPlotAtomic.Rd | 7 + man/VennDiagramAtomic.Rd | 7 + man/VolcanoPlot.Rd | 10 +- man/VolcanoPlotAtomic.Rd | 7 + man/WordCloudPlot.Rd | 7 + man/WordCloudPlotAtomic.Rd | 7 + man/barplot.Rd | 14 ++- man/boxviolinplot.Rd | 20 +++- man/check_palcolor.Rd |only man/check_palette.Rd |only man/chordplot.Rd | 9 +- man/common_args.Rd | 7 + man/densityhistoplot.Rd | 11 ++ man/dimplot.Rd | 11 ++ man/dotplot.Rd | 12 ++ man/enrichmap1.Rd | 9 +- man/figures/area-trend.png |binary man/get_cutoffs_data.Rd |only man/gsea.Rd | 7 + man/palette_this.Rd | 8 + man/radarplot.Rd | 9 +- man/sankeyplot.Rd | 7 + man/upsetplot1.Rd | 7 + man/validate_common_args.Rd | 7 + man/venndiagram1.Rd | 7 + tests |only 97 files changed, 845 insertions(+), 310 deletions(-)