Title: Nonlinear Mixed Effects Models in Population PK/PD
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'rxode2' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Anne Keunecke [ctb],
Rik Schoemaker [ctb] ,
Justin Wilkins [ctb] ,
Wenping Wang [ctb],
Mirjam Trame [ctb],
John Harrold [ctb],
Bill Denney [ctb] ,
Theodoros Papathanasiou [ctb],
Richard Hooijmaijers [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2 versions 3.0.1 dated 2024-10-28 and 3.0.2 dated 2025-02-19
DESCRIPTION | 14 +++++--------- MD5 | 16 ++++++++-------- NAMESPACE | 2 ++ NEWS.md | 12 +++++++++++- R/hardReexports.R | 2 +- R/reexports.R | 4 ++++ R/utils.R | 1 + man/reexports.Rd | 3 ++- man/saemControl.Rd | 2 +- 9 files changed, 35 insertions(+), 21 deletions(-)
Title: Quickly Find, Extract, and Marginalize U.S. Census Tables
Description: Extracting desired data using the proper Census variable names can
be time-consuming. This package takes the pain out of that process by
providing functions to quickly locate variables and download labeled tables
from the Census APIs (<https://www.census.gov/data/developers/data-sets.html>).
Author: Cory McCartan [aut, cre]
Maintainer: Cory McCartan <mccartan@psu.edu>
Diff between easycensus versions 1.1.1 dated 2023-03-20 and 1.1.3 dated 2025-02-19
DESCRIPTION | 12 ++++----- MD5 | 12 ++++----- NEWS.md | 5 +++ R/utils.R | 3 +- README.md | 58 ++++++++++++++++++++++------------------------ man/cens_margin_to.Rd | 3 +- man/easycensus-package.Rd | 2 - 7 files changed, 50 insertions(+), 45 deletions(-)
Title: Detecting Influence Paths with Information Theory
Description: Traces information spread through interactions between features, utilising information theory measures and a higher-order generalisation of the concept of widest paths in graphs.
In particular, 'vistla' can be used to better understand the results of high-throughput biomedical experiments, by organising the effects of the investigated intervention in a tree-like hierarchy from direct to indirect ones, following the plausible information relay circuits.
Due to its higher-order nature, 'vistla' can handle multi-modality and assign multiple roles to a single feature.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>
Diff between vistla versions 2.1.0 dated 2025-02-06 and 2.1.1 dated 2025-02-19
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- inst/NEWS | 7 +++++++ inst/doc/walkthrough.R | 24 ++++++++++++------------ inst/doc/walkthrough.Rnw | 9 ++++----- inst/doc/walkthrough.pdf |binary vignettes/vig.bib | 27 +-------------------------- vignettes/walkthrough.Rnw | 9 ++++----- 8 files changed, 38 insertions(+), 58 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data sets,
regression models, and more. The code to create the tables is concise
and highly customizable. Data frames can be summarized with any
function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] ,
Joseph Larmarange [aut] ,
Michael Curry [aut] ,
Jessica Lavery [aut] ,
Karissa Whiting [aut] ,
Emily C. Zabor [aut] ,
Xing Bai [ctb],
Esther Drill [ctb] ,
Jessica Flynn [ctb] ,
Margie Hannum [ctb] ,
Stephanie Lobaugh [c [...truncated...]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 2.0.4 dated 2024-11-30 and 2.1.0 dated 2025-02-19
gtsummary-2.0.4/gtsummary/build/stage23.rdb |only gtsummary-2.0.4/gtsummary/tests/testthat/test-add_global_p.R |only gtsummary-2.1.0/gtsummary/DESCRIPTION | 13 gtsummary-2.1.0/gtsummary/MD5 | 320 - gtsummary-2.1.0/gtsummary/NAMESPACE | 18 gtsummary-2.1.0/gtsummary/NEWS.md | 54 gtsummary-2.1.0/gtsummary/R/add_ci.R | 47 gtsummary-2.1.0/gtsummary/R/add_glance.R | 4 gtsummary-2.1.0/gtsummary/R/add_n_regression.R | 2 gtsummary-2.1.0/gtsummary/R/add_nevent.R | 2 gtsummary-2.1.0/gtsummary/R/add_overall.R | 12 gtsummary-2.1.0/gtsummary/R/add_p.tbl_cross.R | 2 gtsummary-2.1.0/gtsummary/R/add_q.R | 2 gtsummary-2.1.0/gtsummary/R/add_significance_stars.R | 6 gtsummary-2.1.0/gtsummary/R/add_stat.R | 2 gtsummary-2.1.0/gtsummary/R/add_variable_group_header.R |only gtsummary-2.1.0/gtsummary/R/as_flex_table.R | 201 gtsummary-2.1.0/gtsummary/R/as_gt.R | 197 gtsummary-2.1.0/gtsummary/R/as_gtsummary.R |only gtsummary-2.1.0/gtsummary/R/as_hux_table.R | 75 gtsummary-2.1.0/gtsummary/R/as_kable_extra.R | 161 gtsummary-2.1.0/gtsummary/R/bold_italicize_labels_levels.R | 88 gtsummary-2.1.0/gtsummary/R/bold_p.R | 4 gtsummary-2.1.0/gtsummary/R/custom_tidiers.R | 3 gtsummary-2.1.0/gtsummary/R/deprecated.R | 2 gtsummary-2.1.0/gtsummary/R/deprecated_ci_column.R | 2 gtsummary-2.1.0/gtsummary/R/deprecated_modify_footnote.R |only gtsummary-2.1.0/gtsummary/R/inline_text.tbl_cross.R | 1 gtsummary-2.1.0/gtsummary/R/inline_text.tbl_survfit.R | 1 gtsummary-2.1.0/gtsummary/R/modify.R | 160 gtsummary-2.1.0/gtsummary/R/modify_abbreviation.R |only gtsummary-2.1.0/gtsummary/R/modify_bold_italic.R |only gtsummary-2.1.0/gtsummary/R/modify_caption.R | 10 gtsummary-2.1.0/gtsummary/R/modify_column_alignment.R | 10 gtsummary-2.1.0/gtsummary/R/modify_column_hide.R | 10 gtsummary-2.1.0/gtsummary/R/modify_column_indent.R | 16 gtsummary-2.1.0/gtsummary/R/modify_column_merge.R | 67 gtsummary-2.1.0/gtsummary/R/modify_footnote.R |only gtsummary-2.1.0/gtsummary/R/modify_missing_symbol.R |only gtsummary-2.1.0/gtsummary/R/modify_source_note.R | 5 gtsummary-2.1.0/gtsummary/R/modify_table_styling.R | 205 gtsummary-2.1.0/gtsummary/R/plot.R | 2 gtsummary-2.1.0/gtsummary/R/rows_argument.R |only gtsummary-2.1.0/gtsummary/R/separate_p_footnotes.R | 4 gtsummary-2.1.0/gtsummary/R/sysdata.rda |binary gtsummary-2.1.0/gtsummary/R/tbl_ard_continuous.R | 4 gtsummary-2.1.0/gtsummary/R/tbl_ard_summary.R | 29 gtsummary-2.1.0/gtsummary/R/tbl_continuous.R | 6 gtsummary-2.1.0/gtsummary/R/tbl_cross.R | 4 gtsummary-2.1.0/gtsummary/R/tbl_custom_summary.R | 16 gtsummary-2.1.0/gtsummary/R/tbl_hierarchical.R | 2 gtsummary-2.1.0/gtsummary/R/tbl_merge.R | 178 gtsummary-2.1.0/gtsummary/R/tbl_nesting.R |only gtsummary-2.1.0/gtsummary/R/tbl_regression.R | 2 gtsummary-2.1.0/gtsummary/R/tbl_split.R | 2 gtsummary-2.1.0/gtsummary/R/tbl_stack.R | 18 gtsummary-2.1.0/gtsummary/R/tbl_strata.R | 8 gtsummary-2.1.0/gtsummary/R/tbl_strata_nested_stack.R |only gtsummary-2.1.0/gtsummary/R/tbl_summary.R | 9 gtsummary-2.1.0/gtsummary/R/tbl_survfit.R | 48 gtsummary-2.1.0/gtsummary/R/tbl_uvregression.R | 2 gtsummary-2.1.0/gtsummary/R/tbl_wide_summary.R | 2 gtsummary-2.1.0/gtsummary/R/theme_gtsummary.R | 44 gtsummary-2.1.0/gtsummary/R/utils-as.R | 203 gtsummary-2.1.0/gtsummary/R/utils-gtsummary_core.R | 171 gtsummary-2.1.0/gtsummary/R/utils-misc.R | 17 gtsummary-2.1.0/gtsummary/R/utils-tbl_custom_summary.R | 10 gtsummary-2.1.0/gtsummary/R/utils-tbl_regression.R | 16 gtsummary-2.1.0/gtsummary/build/vignette.rds |binary gtsummary-2.1.0/gtsummary/inst/WORDLIST | 8 gtsummary-2.1.0/gtsummary/inst/doc/gtsummary_definition.R | 98 gtsummary-2.1.0/gtsummary/inst/doc/gtsummary_definition.Rmd | 159 gtsummary-2.1.0/gtsummary/inst/doc/gtsummary_definition.html | 2350 +++++++--- gtsummary-2.1.0/gtsummary/man/add_ci.Rd | 2 gtsummary-2.1.0/gtsummary/man/add_glance.Rd | 4 gtsummary-2.1.0/gtsummary/man/add_n_regression.Rd | 2 gtsummary-2.1.0/gtsummary/man/add_nevent_regression.Rd | 2 gtsummary-2.1.0/gtsummary/man/add_q.Rd | 2 gtsummary-2.1.0/gtsummary/man/add_significance_stars.Rd | 4 gtsummary-2.1.0/gtsummary/man/add_stat.Rd | 2 gtsummary-2.1.0/gtsummary/man/add_variable_group_header.Rd |only gtsummary-2.1.0/gtsummary/man/as_flex_table.Rd | 2 gtsummary-2.1.0/gtsummary/man/as_gt.Rd | 2 gtsummary-2.1.0/gtsummary/man/as_gtsummary.Rd |only gtsummary-2.1.0/gtsummary/man/as_hux_table.Rd | 2 gtsummary-2.1.0/gtsummary/man/as_tibble.gtsummary.Rd | 2 gtsummary-2.1.0/gtsummary/man/continuous_summary.Rd | 2 gtsummary-2.1.0/gtsummary/man/custom_tidiers.Rd | 3 gtsummary-2.1.0/gtsummary/man/deprecated.Rd | 2 gtsummary-2.1.0/gtsummary/man/deprecated_ci_column.Rd | 2 gtsummary-2.1.0/gtsummary/man/deprecated_modify_footnote.Rd |only gtsummary-2.1.0/gtsummary/man/dot-create_gtsummary_object.Rd | 10 gtsummary-2.1.0/gtsummary/man/figures/README-tbl_merge_ex1-1.png |binary gtsummary-2.1.0/gtsummary/man/figures/README-tbl_regression_printa-1.png |binary gtsummary-2.1.0/gtsummary/man/figures/README-tbl_summary_print_extra-1.png |binary gtsummary-2.1.0/gtsummary/man/figures/README-tbl_summary_print_simple-1.png |binary gtsummary-2.1.0/gtsummary/man/inline_text.tbl_cross.Rd | 1 gtsummary-2.1.0/gtsummary/man/inline_text.tbl_survfit.Rd | 1 gtsummary-2.1.0/gtsummary/man/modify.Rd | 52 gtsummary-2.1.0/gtsummary/man/modify_abbreviation.Rd |only gtsummary-2.1.0/gtsummary/man/modify_bold_italic.Rd |only gtsummary-2.1.0/gtsummary/man/modify_caption.Rd | 9 gtsummary-2.1.0/gtsummary/man/modify_column_alignment.Rd | 2 gtsummary-2.1.0/gtsummary/man/modify_column_merge.Rd | 6 gtsummary-2.1.0/gtsummary/man/modify_footnote2.Rd |only gtsummary-2.1.0/gtsummary/man/modify_missing_symbol.Rd |only gtsummary-2.1.0/gtsummary/man/modify_source_note.Rd | 9 gtsummary-2.1.0/gtsummary/man/modify_table_styling.Rd | 30 gtsummary-2.1.0/gtsummary/man/plot.Rd | 2 gtsummary-2.1.0/gtsummary/man/proportion_summary.Rd | 4 gtsummary-2.1.0/gtsummary/man/ratio_summary.Rd | 4 gtsummary-2.1.0/gtsummary/man/rows_argument.Rd |only gtsummary-2.1.0/gtsummary/man/separate_p_footnotes.Rd | 2 gtsummary-2.1.0/gtsummary/man/tbl_continuous.Rd | 2 gtsummary-2.1.0/gtsummary/man/tbl_custom_summary.Rd | 16 gtsummary-2.1.0/gtsummary/man/tbl_hierarchical.Rd | 2 gtsummary-2.1.0/gtsummary/man/tbl_merge.Rd | 9 gtsummary-2.1.0/gtsummary/man/tbl_regression.Rd | 2 gtsummary-2.1.0/gtsummary/man/tbl_split.Rd | 2 gtsummary-2.1.0/gtsummary/man/tbl_strata.Rd | 8 gtsummary-2.1.0/gtsummary/man/tbl_strata_nested_stack.Rd |only gtsummary-2.1.0/gtsummary/man/tbl_summary.Rd | 4 gtsummary-2.1.0/gtsummary/man/tbl_survfit.Rd | 28 gtsummary-2.1.0/gtsummary/man/tbl_uvregression.Rd | 2 gtsummary-2.1.0/gtsummary/man/tbl_wide_summary.Rd | 2 gtsummary-2.1.0/gtsummary/man/tests.Rd | 30 gtsummary-2.1.0/gtsummary/tests/testthat.R | 2 gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/as_hux_table.md | 40 gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/as_kable_extra.md | 6 gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/modify_abbreviation.md |only gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/modify_column_merge.md | 10 gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/modify_footnote_body.md |only gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/modify_footnote_spanning_header.md |only gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/modify_spanning_header.md | 28 gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/modify_table_styling.md | 20 gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/separate_p_footnotes.md | 41 gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/show_header_names.md | 20 gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/tbl_ard_summary.md | 1 gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/tbl_merge.md | 4 gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/tbl_strata_nested_stack.md |only gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/tbl_summary.md | 2 gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/tbl_survfit.md |only gtsummary-2.1.0/gtsummary/tests/testthat/_snaps/tbl_svysummary.md | 2 gtsummary-2.1.0/gtsummary/tests/testthat/test-add_ci.tbl_summary.R | 139 gtsummary-2.1.0/gtsummary/tests/testthat/test-add_variable_group_header.R |only gtsummary-2.1.0/gtsummary/tests/testthat/test-as_flex_table.R | 97 gtsummary-2.1.0/gtsummary/tests/testthat/test-as_gt.R | 109 gtsummary-2.1.0/gtsummary/tests/testthat/test-as_hux_table.R | 64 gtsummary-2.1.0/gtsummary/tests/testthat/test-as_kable.R | 5 gtsummary-2.1.0/gtsummary/tests/testthat/test-as_kable_extra.R | 40 gtsummary-2.1.0/gtsummary/tests/testthat/test-as_tibble.R | 2 gtsummary-2.1.0/gtsummary/tests/testthat/test-bold_italicize_labels_levels.R | 4 gtsummary-2.1.0/gtsummary/tests/testthat/test-combine_terms.R | 5 gtsummary-2.1.0/gtsummary/tests/testthat/test-modify_abbreviation.R |only gtsummary-2.1.0/gtsummary/tests/testthat/test-modify_bold_italic.R |only gtsummary-2.1.0/gtsummary/tests/testthat/test-modify_caption.R | 16 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Title: Estimate Real-Time Case Counts and Time-Varying Epidemiological
Parameters
Description: Estimates the time-varying reproduction number,
rate of spread, and doubling time using a range of open-source tools
(Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and
current best practices (Gostic et al. (2020)
<doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some
of the limitations of naive implementations in a framework that is
informed by community feedback and is actively supported.
Author: Sam Abbott [aut] ,
Joel Hellewell [aut] ,
Katharine Sherratt [aut],
Katelyn Gostic [aut],
Joe Hickson [aut],
Hamada S. Badr [aut] ,
Michael DeWitt [aut] ,
James M. Azam [aut] ,
Robin Thompson [ctb],
Sophie Meakin [ctb],
James Munday [ctb],
Nikos Boss [...truncated...]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between EpiNow2 versions 1.7.0 dated 2025-02-05 and 1.7.1 dated 2025-02-19
EpiNow2-1.7.0/EpiNow2/data/generation_times.rda |only EpiNow2-1.7.0/EpiNow2/data/incubation_periods.rda |only EpiNow2-1.7.0/EpiNow2/man/adjust_infection_to_report.Rd |only EpiNow2-1.7.0/EpiNow2/man/check_na_setting_against_data.Rd |only EpiNow2-1.7.0/EpiNow2/man/create_clean_reported_cases.Rd |only EpiNow2-1.7.0/EpiNow2/man/dist_spec.Rd |only EpiNow2-1.7.0/EpiNow2/man/gamma_dist_def.Rd |only EpiNow2-1.7.0/EpiNow2/man/generation_times.Rd |only EpiNow2-1.7.0/EpiNow2/man/get_dist.Rd |only EpiNow2-1.7.0/EpiNow2/man/get_generation_time.Rd |only EpiNow2-1.7.0/EpiNow2/man/get_incubation_period.Rd |only EpiNow2-1.7.0/EpiNow2/man/incubation_periods.Rd |only EpiNow2-1.7.0/EpiNow2/man/init_cumulative_fit.Rd |only EpiNow2-1.7.0/EpiNow2/man/lognorm_dist_def.Rd |only EpiNow2-1.7.0/EpiNow2/man/report_cases.Rd |only EpiNow2-1.7.0/EpiNow2/man/rstan_opts.Rd |only EpiNow2-1.7.0/EpiNow2/man/rstan_sampling_opts.Rd |only EpiNow2-1.7.0/EpiNow2/man/rstan_vb_opts.Rd |only EpiNow2-1.7.0/EpiNow2/man/sample_approx_dist.Rd |only EpiNow2-1.7.0/EpiNow2/man/setup_forecast.Rd |only EpiNow2-1.7.0/EpiNow2/man/test_data_complete.Rd |only EpiNow2-1.7.0/EpiNow2/tests/testthat/test-create_clean_reported_cases.R |only EpiNow2-1.7.0/EpiNow2/tests/testthat/test-utilities.R |only EpiNow2-1.7.1/EpiNow2/DESCRIPTION | 6 EpiNow2-1.7.1/EpiNow2/MD5 | 129 EpiNow2-1.7.1/EpiNow2/NAMESPACE | 13 EpiNow2-1.7.1/EpiNow2/NEWS.md | 12 EpiNow2-1.7.1/EpiNow2/R/checks.R | 91 EpiNow2-1.7.1/EpiNow2/R/create.R | 45 EpiNow2-1.7.1/EpiNow2/R/data.R | 17 EpiNow2-1.7.1/EpiNow2/R/deprecated.R | 458 -- EpiNow2-1.7.1/EpiNow2/R/epinow.R | 41 EpiNow2-1.7.1/EpiNow2/R/estimate_infections.R | 88 EpiNow2-1.7.1/EpiNow2/R/estimate_secondary.R | 49 EpiNow2-1.7.1/EpiNow2/R/estimate_truncation.R | 6 EpiNow2-1.7.1/EpiNow2/R/fit.R | 1 EpiNow2-1.7.1/EpiNow2/R/opts.R | 143 EpiNow2-1.7.1/EpiNow2/R/preprocessing.R | 7 EpiNow2-1.7.1/EpiNow2/R/regional_epinow.R | 20 EpiNow2-1.7.1/EpiNow2/R/simulate_infections.R | 16 EpiNow2-1.7.1/EpiNow2/R/simulate_secondary.R | 3 EpiNow2-1.7.1/EpiNow2/R/utilities.R | 17 EpiNow2-1.7.1/EpiNow2/inst/doc/estimate_infections.Rmd | 6 EpiNow2-1.7.1/EpiNow2/inst/doc/estimate_infections.html | 7 EpiNow2-1.7.1/EpiNow2/inst/stan/functions/gaussian_process.stan | 2 EpiNow2-1.7.1/EpiNow2/man/create_shifted_cases.Rd | 3 EpiNow2-1.7.1/EpiNow2/man/delay_opts.Rd | 12 EpiNow2-1.7.1/EpiNow2/man/dist_skel.Rd | 3 EpiNow2-1.7.1/EpiNow2/man/epinow.Rd | 29 EpiNow2-1.7.1/EpiNow2/man/estimate_infections.Rd | 29 EpiNow2-1.7.1/EpiNow2/man/estimate_secondary.Rd | 21 EpiNow2-1.7.1/EpiNow2/man/forecast_infections.Rd | 2 EpiNow2-1.7.1/EpiNow2/man/generation_time_opts.Rd | 26 EpiNow2-1.7.1/EpiNow2/man/regional_epinow.Rd | 5 EpiNow2-1.7.1/EpiNow2/man/simulate_infections.Rd | 8 EpiNow2-1.7.1/EpiNow2/man/simulate_secondary.Rd | 5 EpiNow2-1.7.1/EpiNow2/man/stan_opts.Rd | 7 EpiNow2-1.7.1/EpiNow2/man/stan_pathfinder_opts.Rd | 3 EpiNow2-1.7.1/EpiNow2/src/stanExports_dist_fit.cc | 34 EpiNow2-1.7.1/EpiNow2/src/stanExports_estimate_infections.cc | 34 EpiNow2-1.7.1/EpiNow2/src/stanExports_estimate_infections.h | 1544 +++++----- EpiNow2-1.7.1/EpiNow2/src/stanExports_estimate_secondary.cc | 34 EpiNow2-1.7.1/EpiNow2/src/stanExports_estimate_truncation.cc | 34 EpiNow2-1.7.1/EpiNow2/src/stanExports_simulate_infections.cc | 34 EpiNow2-1.7.1/EpiNow2/src/stanExports_simulate_infections.h | 1318 ++++---- EpiNow2-1.7.1/EpiNow2/src/stanExports_simulate_secondary.cc | 34 EpiNow2-1.7.1/EpiNow2/tests/testthat/test-checks.R | 81 EpiNow2-1.7.1/EpiNow2/tests/testthat/test-create_shifted_cases.R | 4 EpiNow2-1.7.1/EpiNow2/tests/testthat/test-delays.R | 10 EpiNow2-1.7.1/EpiNow2/tests/testthat/test-dist_spec.R | 4 EpiNow2-1.7.1/EpiNow2/tests/testthat/test-epinow.R | 21 EpiNow2-1.7.1/EpiNow2/tests/testthat/test-estimate_infections.R | 62 EpiNow2-1.7.1/EpiNow2/tests/testthat/test-estimate_secondary.R | 11 EpiNow2-1.7.1/EpiNow2/tests/testthat/test-gp_opts.R | 13 EpiNow2-1.7.1/EpiNow2/tests/testthat/test-obs_opts.R | 20 EpiNow2-1.7.1/EpiNow2/tests/testthat/test-rt_opts.R | 12 EpiNow2-1.7.1/EpiNow2/vignettes/estimate_infections.Rmd | 6 77 files changed, 1735 insertions(+), 2905 deletions(-)
Title: Calculates the Density-Based Clustering Validation (DBCV) Index
Description: A metric called 'Density-Based Clustering Validation index' (DBCV) index to evaluate clustering results, following the <https://github.com/pajaskowiak/clusterConfusion/blob/main/R/dbcv.R> 'R' implementation by Pablo Andretta Jaskowiak. Original 'DBCV' index article: Moulavi, D., Jaskowiak, P. A., Campello, R. J., Zimek, A., and Sander, J. (April 2014), "Density-based clustering validation", Proceedings of SDM 2014 -- the 2014 SIAM International Conference on Data Mining (pp. 839-847), <doi:10.1137/1.9781611973440.96>.
Author: Davide Chicco [cre] ,
Pablo Andretta Jaskowiak [aut]
Maintainer: Davide Chicco <davidechicco@davidechicco.it>
Diff between DBCVindex versions 1.3 dated 2025-02-13 and 1.4 dated 2025-02-19
DESCRIPTION | 18 ++++++++++++------ MD5 | 2 +- 2 files changed, 13 insertions(+), 7 deletions(-)
Title: A Functional Data Analysis Package for Spatial Single Cell Data
Description: Methods and tools for deriving spatial summary functions from single-cell imaging
data and performing functional data analyses. Functions can be applied to other single-cell
technologies such as spatial transcriptomics. Functional regression and functional principal component analysis methods
are in the 'refund' package <https://cran.r-project.org/package=refund> while calculation of the
spatial summary functions are from the 'spatstat' package <https://spatstat.org/>.
Author: Julia Wrobel [aut] ,
Alex Soupir [aut, cre]
Maintainer: Alex Soupir <alex.soupir@moffitt.org>
Diff between mxfda versions 0.2.2 dated 2024-10-07 and 0.2.2-1 dated 2025-02-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/run_sofr.R | 27 +++++++++++++++++++++------ README.md | 2 +- inst/doc/mx_fda.html | 7 +++---- inst/doc/mx_fpca.html | 2 +- inst/doc/mx_funreg.html | 2 +- 7 files changed, 37 insertions(+), 23 deletions(-)
Title: Hot-Spot Analysis with Simple Features
Description: Identify and understand clusters of points (typically representing
the locations of places or events) stored in simple-features (SF) objects.
This is useful for analysing, for example, hot-spots of crime events. The
package emphasises producing results from point SF data in a single step
using reasonable default values for all other arguments, to aid rapid data
analysis by users who are starting out. Functions available include kernel
density estimation (for details, see Yip (2020)
<doi:10.22224/gistbok/2020.1.12>), analysis of spatial association (Getis
and Ord (1992) <doi:10.1111/j.1538-4632.1992.tb00261.x>) and hot-spot
classification (Chainey (2020) ISBN:158948584X).
Author: Matt Ashby [aut, cre]
Maintainer: Matt Ashby <matthew.ashby@ucl.ac.uk>
Diff between sfhotspot versions 0.9.0 dated 2025-02-10 and 0.9.1 dated 2025-02-19
DESCRIPTION | 8 MD5 | 56 ++-- NEWS.md | 15 + R/autoplot.R | 30 +- R/count_points_in_polygons.R | 66 ++--- R/create_grid.R | 43 +-- R/get_cell_size.R |only R/gistar.R | 40 +-- R/hotspot_change.R | 114 ++++---- R/hotspot_classify.R | 136 +++++----- R/hotspot_classify_params.R | 24 - R/hotspot_count.R | 9 R/hotspot_dual_kde.R | 170 ++++++++----- R/hotspot_gistar.R | 52 ++-- R/hotspot_kde.R | 31 ++ R/kernel_density.R | 51 ++- R/set_bandwidth.R | 29 +- R/set_cell_size.R | 24 - R/validate_inputs.R | 321 ++++++++++++++++--------- README.md | 3 inst/doc/introduction.html | 20 - tests/testthat/test-count_points_in_polygons.R | 76 ++++- tests/testthat/test-create_grid.R | 13 - tests/testthat/test-get_cell_size.R |only tests/testthat/test-hotspot_change.R | 40 +++ tests/testthat/test-hotspot_dual_kde.R | 87 ++++++ tests/testthat/test-hotspot_kde.R | 14 + tests/testthat/test-kernel_density.R | 57 +++- tests/testthat/test-set_bandwidth.R | 13 - tests/testthat/test-validate_inputs.R | 46 +++ 30 files changed, 1033 insertions(+), 555 deletions(-)
Title: Calculation of the Water Deficit Index (WDI) and the Evaporative
Fraction (EF) on Rasters
Description: Calculates the Water Deficit Index (WDI) and the Evaporative Fraction (EF) using geospatial data,
such as fractional vegetation cover (FVC) and surface-air temperature difference (TS-TA).
Terms like "raster", "CRS" are part of standard geospatial terminology.
Author: Gaelle Hamelin [aut, cre]
Maintainer: Gaelle Hamelin <gaelle.hamelin@institut-agro.fr>
Diff between wdiEF versions 1.0.2 dated 2024-12-02 and 1.0.3 dated 2025-02-19
DESCRIPTION | 7 +++--- MD5 | 9 ++++--- NEWS.md |only R/calculate_EF.R | 63 +++++++++++++++++++++++++++--------------------------- R/calculate_WDI.R | 26 ++++++++++------------ R/zzz.R | 1 6 files changed, 54 insertions(+), 52 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
Posit Software, PBC [cph, fnd],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.54 dated 2024-11-01 and 0.55 dated 2025-02-19
DESCRIPTION | 6 +++--- MD5 | 11 +++++++---- R/latex.R | 22 ++++++++++++---------- R/platforms.R |only R/tlmgr.R | 9 --------- man/latexmk.Rd | 5 +++-- tests/test-ci/test-dvi.tex |only tests/test-ci/test-latex.R |only 8 files changed, 25 insertions(+), 28 deletions(-)
Title: Primal or Dual Cone Projections with Routines for Constrained
Regression
Description: Routines doing cone projection and quadratic programming, as well as doing estimation and inference for constrained parametric regression and shape-restricted regression problems. See Mary C. Meyer (2013)<doi:10.1080/03610918.2012.659820> for more details.
Author: Mary C. Meyer [aut],
Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>
Diff between coneproj versions 1.19 dated 2024-06-11 and 1.20 dated 2025-02-19
ChangeLog | 4 + DESCRIPTION | 14 +++-- MD5 | 10 +-- R/coneproj.R | 8 +-- man/coneA.Rd | 144 +++++++++++++++++++++++++++---------------------------- src/coneproj.cpp | 30 ++++++++--- 6 files changed, 117 insertions(+), 93 deletions(-)
Title: Clustering and Simulation of Spherical Cauchy and PKBD Models
Description: Provides tools for estimation and clustering of spherical data, seamlessly integrated with the 'flexmix' package. Includes the necessary M-step implementations for both Poisson Kernel-Based Distribution (PKBD) and spherical Cauchy distribution. Additionally, the package provides random number generators for PKBD and spherical Cauchy distribution. Methods are based on Golzy M., Markatou M. (2020) <doi:10.1080/10618600.2020.1740713>, Kato S., McCullagh P. (2020) <doi:10.3150/20-bej1222> and Sablica L., Hornik K., Leydold J. (2023) <doi:10.1214/23-ejs2149>.
Author: Lukas Sablica [aut, cre] ,
Kurt Hornik [aut] ,
Bettina Gruen [aut] ,
Josef Leydold [aut]
Maintainer: Lukas Sablica <lsablica@wu.ac.at>
Diff between circlus versions 0.0.1 dated 2024-10-17 and 0.0.2 dated 2025-02-19
circlus-0.0.1/circlus/man/FLXMCpkbd.Rd |only circlus-0.0.1/circlus/man/FLXMRpkbd.Rd |only circlus-0.0.1/circlus/man/dpkbd.Rd |only circlus-0.0.1/circlus/man/rpkbd.Rd |only circlus-0.0.2/circlus/DESCRIPTION | 8 ++-- circlus-0.0.2/circlus/MD5 | 28 ++++++++-------- circlus-0.0.2/circlus/NAMESPACE | 8 ++-- circlus-0.0.2/circlus/R/Estimation.R | 50 ++++++++++++++--------------- circlus-0.0.2/circlus/R/PKBD_sample.R | 14 ++++---- circlus-0.0.2/circlus/man/FLXMCpkb.Rd |only circlus-0.0.2/circlus/man/FLXMCspcauchy.Rd | 2 - circlus-0.0.2/circlus/man/FLXMRpkb.Rd |only circlus-0.0.2/circlus/man/FLXMRspcauchy.Rd | 2 - circlus-0.0.2/circlus/man/dpkb.Rd |only circlus-0.0.2/circlus/man/rPKBD_Saw.Rd | 4 +- circlus-0.0.2/circlus/man/rpkb.Rd |only circlus-0.0.2/circlus/src/pkbd.cpp | 1 circlus-0.0.2/circlus/src/rpkbd.cpp | 2 - circlus-0.0.2/circlus/src/sCauchy.cpp | 2 - 19 files changed, 61 insertions(+), 60 deletions(-)
Title: Create Spreadsheet Publications Following Best Practice
Description: Generate spreadsheet publications that follow best practice
guidance from the UK government's Analysis Function, available at
<https://analysisfunction.civilservice.gov.uk/policy-store/releasing-statistics-in-spreadsheets/>,
with a focus on accessibility. See also the 'Python' package 'gptables'.
Author: Matt Dray [aut],
Tim Taylor [ctb],
Matt Kerlogue [ctb],
Crown Copyright [cph],
Olivia Box Power [cre, ctb]
Maintainer: Olivia Box Power <Olivia.BoxPower@dhsc.gov.uk>
Diff between aftables versions 1.0.1 dated 2025-02-19 and 1.0.2 dated 2025-02-19
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NEWS.md | 2 +- inst/doc/aftables.html | 40 ++++++++++++++++++++-------------------- man/aftables-package.Rd | 2 +- 5 files changed, 32 insertions(+), 32 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.50 dated 2025-01-07 and 0.51 dated 2025-02-19
DESCRIPTION | 11 ++--- LICENSE | 2 MD5 | 34 ++++++++-------- NAMESPACE | 1 NEWS.md | 10 ++++ R/data-structure.R | 12 ++++- R/image.R | 23 ++++++----- R/io.R | 55 +++++++++++--------------- R/json.R | 90 ++++++++++++++++++++++++++++++++------------ R/record.R | 12 +++-- R/string.R | 16 +++++-- R/yaml.R | 2 inst/doc/xfun.html | 22 +++++----- man/download_file.Rd | 28 ++++++------- man/raw_string.Rd | 2 man/tojson.Rd | 32 ++++++++++++--- man/upload_imgur.Rd | 13 +++--- tests/test-cran/test-json.R | 29 ++++++-------- 18 files changed, 241 insertions(+), 153 deletions(-)
Title: Mine Metrics from Common Places on the Web
Description: Mine metrics on common places on the web through the power of their APIs (application programming interfaces).
It also helps make the data in a format that is easily used for a dashboard or other purposes.
There is an associated dashboard template and tutorials that are underdevelopment that help you
fully utilize 'metricminer'.
Author: Candace Savonen [aut, cre],
Howard Baek [aut]
Maintainer: Candace Savonen <cansav09@gmail.com>
Diff between metricminer versions 0.5.1 dated 2024-02-02 and 1.0.0 dated 2025-02-19
metricminer-0.5.1/metricminer/man/get_all_ga_metrics.Rd |only metricminer-1.0.0/metricminer/DESCRIPTION | 14 metricminer-1.0.0/metricminer/MD5 | 113 +- metricminer-1.0.0/metricminer/NAMESPACE | 8 metricminer-1.0.0/metricminer/NEWS.md | 5 metricminer-1.0.0/metricminer/R/auth.R | 132 ++- metricminer-1.0.0/metricminer/R/citations.R |only metricminer-1.0.0/metricminer/R/github.R | 401 +++++++--- metricminer-1.0.0/metricminer/R/google-analytics.R | 214 +++-- metricminer-1.0.0/metricminer/R/google-forms.R | 38 metricminer-1.0.0/metricminer/R/scopes.R | 12 metricminer-1.0.0/metricminer/R/slido.R | 16 metricminer-1.0.0/metricminer/R/token-handlers.R | 4 metricminer-1.0.0/metricminer/R/utils-pipe.R |only metricminer-1.0.0/metricminer/R/utils.R | 15 metricminer-1.0.0/metricminer/R/write-data.R | 189 ++++ metricminer-1.0.0/metricminer/R/youtube.R | 17 metricminer-1.0.0/metricminer/README.md | 22 metricminer-1.0.0/metricminer/build/vignette.rds |binary metricminer-1.0.0/metricminer/inst/doc/example-data.html | 45 - metricminer-1.0.0/metricminer/inst/doc/getting-started.Rmd | 21 metricminer-1.0.0/metricminer/inst/doc/getting-started.html | 99 +- metricminer-1.0.0/metricminer/inst/extdata/_config_automation.yml |only metricminer-1.0.0/metricminer/man/app_set_up.Rd | 6 metricminer-1.0.0/metricminer/man/auth_from_secret.Rd | 28 metricminer-1.0.0/metricminer/man/authorize.Rd | 15 metricminer-1.0.0/metricminer/man/clean_ga_metrics.Rd | 6 metricminer-1.0.0/metricminer/man/clean_repo_metrics.Rd | 6 metricminer-1.0.0/metricminer/man/delete_creds.Rd | 6 metricminer-1.0.0/metricminer/man/get_citation_count.Rd |only metricminer-1.0.0/metricminer/man/get_config_file.Rd |only metricminer-1.0.0/metricminer/man/get_ga_metadata.Rd | 3 metricminer-1.0.0/metricminer/man/get_ga_properties.Rd | 2 metricminer-1.0.0/metricminer/man/get_ga_property_info.Rd |only metricminer-1.0.0/metricminer/man/get_ga_stats.Rd | 8 metricminer-1.0.0/metricminer/man/get_ga_user.Rd | 3 metricminer-1.0.0/metricminer/man/get_github.Rd | 4 metricminer-1.0.0/metricminer/man/get_github_metrics.Rd | 42 - metricminer-1.0.0/metricminer/man/get_github_repo_summary.Rd | 32 metricminer-1.0.0/metricminer/man/get_github_repo_timecourse.Rd | 32 metricminer-1.0.0/metricminer/man/get_github_user.Rd | 4 metricminer-1.0.0/metricminer/man/get_google_form.Rd | 4 metricminer-1.0.0/metricminer/man/get_multiple_forms.Rd | 9 metricminer-1.0.0/metricminer/man/get_multiple_ga_metrics.Rd |only metricminer-1.0.0/metricminer/man/get_multiple_repos_metrics.Rd | 45 - metricminer-1.0.0/metricminer/man/get_org_repo_list.Rd | 16 metricminer-1.0.0/metricminer/man/get_question_metadata.Rd | 2 metricminer-1.0.0/metricminer/man/get_slido_files.Rd | 5 metricminer-1.0.0/metricminer/man/get_timestamp_repo_metrics.Rd | 6 metricminer-1.0.0/metricminer/man/get_user_repo_list.Rd | 16 metricminer-1.0.0/metricminer/man/gh_repo_wrapper.Rd | 14 metricminer-1.0.0/metricminer/man/list_example_data.Rd | 1 metricminer-1.0.0/metricminer/man/pipe.Rd |only metricminer-1.0.0/metricminer/man/request_ga.Rd | 3 metricminer-1.0.0/metricminer/man/request_google_forms.Rd | 4 metricminer-1.0.0/metricminer/man/setup_folders.Rd |only metricminer-1.0.0/metricminer/man/write_playlist_details.Rd | 17 metricminer-1.0.0/metricminer/man/write_to_gsheet.Rd | 16 metricminer-1.0.0/metricminer/tests/testthat/test-calendly.R | 6 metricminer-1.0.0/metricminer/tests/testthat/test-citation.R |only metricminer-1.0.0/metricminer/tests/testthat/test-github.R | 13 metricminer-1.0.0/metricminer/tests/testthat/test-google-analytics.R | 11 metricminer-1.0.0/metricminer/vignettes/getting-started.Rmd | 21 63 files changed, 1251 insertions(+), 520 deletions(-)
Title: Analytics & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or
data scientist to get quick and robust results, without the need of repetitive coding or
advanced R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.2.12 dated 2025-02-19 and 5.2.13 dated 2025-02-19
DESCRIPTION | 6 MD5 | 522 +++---- NAMESPACE | 1100 ++++++++-------- R/apis.R | 68 - R/audio.R | 368 ++--- R/cache.R | 334 ++-- R/chatgpt.R | 936 ++++++------- R/checks.R | 334 ++-- R/clusters.R | 694 +++++----- R/colour_palettes.R | 394 ++--- R/confidence.R | 172 +- R/correlations.R | 1116 ++++++++-------- R/cran.R | 176 +- R/credentials.R | 196 +- R/crossbrand.R | 682 +++++----- R/crossbrand2.R | 936 ++++++------- R/crosstab.R | 202 +-- R/currency.R | 146 +- R/dalex_explainers.R | 436 +++--- R/dataframe_str.R | 462 +++--- R/datasets.R | 160 +- R/dim_reduction.R | 336 ++--- R/distribution.R | 950 +++++++------- R/dropbox.R | 246 +-- R/encoding.R | 44 R/facebook.R | 1528 +++++++++++----------- R/family.R | 104 - R/forecasting.R | 710 +++++----- R/frequencies.R | 1724 ++++++++++++------------- R/gemini.R | 166 +- R/geodata.R | 524 +++---- R/google_analytics.R | 128 - R/google_sheets.R | 258 +-- R/google_trends.R | 380 ++--- R/hubspot.R | 398 ++--- R/hubspot_f1.R | 502 +++---- R/lares.R | 306 ++-- R/lasso.R | 264 +-- R/linkedin.R | 114 - R/logo.R | 98 - R/mails.R | 190 +- R/maze.R | 668 ++++----- R/missings.R | 260 +-- R/model_functions.R | 1956 ++++++++++++++--------------- R/model_metrics.R | 1232 +++++++++--------- R/model_plots.R | 2928 +++++++++++++++++++++---------------------- R/model_predict.R | 328 ++-- R/model_preprocessing.R | 490 +++---- R/numble.R | 54 R/object_detection.R | 120 - R/onehotencoding.R | 1052 +++++++-------- R/other_functions.R | 2262 ++++++++++++++++----------------- R/other_plots.R | 548 ++++---- R/outliers.R | 364 ++--- R/plot_scales.R | 224 +-- R/querieSQL.R | 64 R/robyn.R | 1583 ++++++++++++----------- R/rtistry.R | 96 - R/scrabble.R | 996 +++++++------- R/shapley.R | 538 ++++---- R/shiny.R | 2 R/slack.R | 92 - R/statusbar.R | 158 +- R/stocks.R | 3014 ++++++++++++++++++++++----------------------- R/sudoku.R | 178 +- R/surveys.R | 84 - R/text_mining.R | 1124 ++++++++-------- R/theme_lares.R | 820 ++++++------ R/tictoc.R | 188 +- R/trees.R | 298 ++-- R/twitter.R | 56 R/typeform.R | 98 - R/update.R | 74 - R/wordle.R | 596 ++++---- R/wrangling.R | 1750 +++++++++++++------------- R/x2y.R | 736 +++++----- R/zzz.R | 198 +- README.md | 146 +- inst/_pkgdown.yml | 20 inst/docs/config.yml | 28 inst/docs/stocksReport.Rmd | 160 +- man/ROC.Rd | 132 - man/autoline.Rd | 154 +- man/balance_data.Rd | 126 - man/bind_files.Rd | 114 - man/bring_api.Rd | 154 +- man/cache_write.Rd | 170 +- man/categ_reducer.Rd | 172 +- man/checks.Rd | 256 +-- man/chr2num.Rd | 142 +- man/ci_lower.Rd | 74 - man/ci_var.Rd | 72 - man/clean_text.Rd | 214 +-- man/clusterKmeans.Rd | 236 +-- man/clusterOptimalK.Rd | 116 - man/clusterVisualK.Rd | 86 - man/conf_mat.Rd | 144 +- man/corr.Rd | 208 +-- man/corr_cross.Rd | 218 +-- man/corr_var.Rd | 230 +-- man/cran_logs.Rd | 74 - man/crosstab.Rd | 146 +- man/dalex_local.Rd | 64 man/dalex_residuals.Rd | 48 man/dalex_variable.Rd | 88 - man/date_cuts.Rd | 102 - man/date_feats.Rd | 206 +-- man/db_download.Rd | 212 +-- man/db_upload.Rd | 174 +- man/df_str.Rd | 122 - man/dfr.Rd | 70 - man/dft.Rd | 98 - man/dist2d.Rd | 70 - man/distr.Rd | 268 ++-- man/errors.Rd | 132 - man/etf_sector.Rd | 68 - man/export_plot.Rd | 180 +- man/export_results.Rd | 196 +- man/fb_accounts.Rd | 144 +- man/fb_ads.Rd | 174 +- man/fb_creatives.Rd | 134 +- man/fb_insights.Rd | 294 ++-- man/fb_process.Rd | 114 - man/fb_report_check.Rd | 150 +- man/fb_rf.Rd | 306 ++-- man/fb_token.Rd | 116 - man/file_name.Rd | 156 +- man/filesGD.Rd | 86 - man/files_functions.Rd | 148 +- man/filterdata.Rd | 246 +-- man/font_exists.Rd | 138 +- man/forecast_arima.Rd | 162 +- man/formatColoured.Rd | 144 +- man/format_string.Rd | 324 ++-- man/freqs.Rd | 272 ++-- man/freqs_df.Rd | 178 +- man/freqs_list.Rd | 258 +-- man/freqs_plot.Rd | 180 +- man/gain_lift.Rd | 142 +- man/gemini_ask.Rd | 198 +- man/get_credentials.Rd | 268 ++-- man/get_currency.Rd | 88 - man/get_mp3.Rd | 174 +- man/get_tweets.Rd | 68 - man/gg_fill_customs.Rd | 162 +- man/glued.Rd | 192 +- man/google_sheets.Rd | 174 +- man/google_trends.Rd | 106 - man/gpt_ask.Rd | 352 ++--- man/gpt_prompter.Rd | 276 ++-- man/grepl_letters.Rd | 68 - man/grepm.Rd | 158 +- man/h2o_automl.Rd | 426 +++--- man/h2o_explainer.Rd | 140 +- man/h2o_results.Rd | 142 +- man/h2o_selectmodel.Rd | 154 +- man/h2o_shap.Rd | 154 +- man/haveInternet.Rd | 118 - man/holidays.Rd | 176 +- man/image_metadata.Rd | 112 - man/importxlsx.Rd | 114 - man/impute.Rd | 140 +- man/install_recommended.Rd | 38 man/ip_data.Rd | 156 +- man/iter_seeds.Rd | 84 - man/json2vector.Rd | 122 - man/lares-exports.Rd | 18 man/lares.Rd | 44 man/lares_logo.Rd | 36 man/lares_pal.Rd | 114 - man/lasso_vars.Rd | 188 +- man/left_right.Rd | 106 - man/li_auth.Rd | 88 - man/li_profile.Rd | 78 - man/list_cats.Rd | 134 +- man/listfiles.Rd | 152 +- man/loglossBinary.Rd | 58 man/mail_send.Rd | 218 +-- man/markdown2df.Rd | 120 - man/maze_solve.Rd | 182 +- man/missingness.Rd | 140 +- man/model_metrics.Rd | 248 +-- man/model_preprocess.Rd | 230 +-- man/move_files.Rd | 120 - man/mplot_conf.Rd | 180 +- man/mplot_cuts.Rd | 134 +- man/mplot_cuts_error.Rd | 128 - man/mplot_density.Rd | 138 +- man/mplot_full.Rd | 188 +- man/mplot_gain.Rd | 192 +- man/mplot_importance.Rd | 164 +- man/mplot_lineal.Rd | 118 - man/mplot_metrics.Rd | 104 - man/mplot_response.Rd | 186 +- man/mplot_roc.Rd | 174 +- man/mplot_splits.Rd | 158 +- man/mplot_topcats.Rd | 98 - man/msplit.Rd | 172 +- man/myip.Rd | 116 - man/ngrams.Rd | 98 - man/noPlot.Rd | 82 - man/normalize.Rd | 108 - man/num_abbr.Rd | 114 - man/ohe_commas.Rd | 140 +- man/ohse.Rd | 248 +-- man/outlier_tukey.Rd | 66 man/outlier_zscore.Rd | 68 - man/outlier_zscore_plot.Rd | 86 - man/plot_cats.Rd | 72 - man/plot_chord.Rd | 110 - man/plot_df.Rd | 72 - man/plot_nums.Rd | 80 - man/plot_palette.Rd | 82 - man/plot_survey.Rd | 74 - man/plot_timeline.Rd | 182 +- man/prophesize.Rd | 104 - man/quants.Rd | 132 - man/queryDB.Rd | 72 - man/queryGA.Rd | 158 +- man/quiet.Rd | 118 - man/read.file.Rd | 128 - man/reduce_pca.Rd | 128 - man/reduce_tsne.Rd | 102 - man/remove_stopwords.Rd | 82 - man/replaceall.Rd | 182 +- man/replacefactor.Rd | 114 - man/robyn_crossmmm.Rd | 250 +-- man/robyn_hypsbuilder.Rd | 126 - man/robyn_modelselector.Rd | 174 +- man/robyn_performance.Rd | 146 +- man/rtistry_sphere.Rd | 36 man/scale_x_comma.Rd | 208 +-- man/scrabble.Rd | 318 ++-- man/sentimentBreakdown.Rd | 110 - man/seq_surnames.Rd | 60 man/shap_var.Rd | 118 - man/slackSend.Rd | 124 - man/spread_list.Rd | 82 - man/statusbar.Rd | 182 +- man/stocks_hist.Rd | 170 +- man/stocks_report.Rd | 336 ++--- man/sudoku_solver.Rd | 96 - man/target_set.Rd | 56 man/textCloud.Rd | 112 - man/textFeats.Rd | 134 +- man/textTokenizer.Rd | 204 +-- man/theme_lares.Rd | 210 +-- man/tic.Rd | 200 +- man/topics_rake.Rd | 72 - man/tree_var.Rd | 254 +-- man/trim_mp3.Rd | 72 - man/try_require.Rd | 148 +- man/updateLares.Rd | 130 - man/vector2text.Rd | 132 - man/warnifnot.Rd | 118 - man/weighted_value.Rd | 102 - man/what_size.Rd | 146 +- man/winsorize.Rd | 64 man/wordle.Rd | 156 +- man/x2y.Rd | 256 +-- man/year_month.Rd | 110 - man/zerovar.Rd | 98 - 262 files changed, 35209 insertions(+), 35182 deletions(-)
Title: Kernel Functions and Tools for Machine Learning Applications
Description: Kernel functions for diverse types of data (including, but not
restricted to: nonnegative and real vectors, real matrices, categorical
and ordinal variables, sets, strings), plus other utilities like kernel
similarity, kernel Principal Components Analysis (PCA) and features'
importance for Support Vector Machines (SVMs), which expand other 'R'
packages like 'kernlab'.
Author: Elies Ramon [aut, cre, cph]
Maintainer: Elies Ramon <eramon@everlyrusher.com>
Diff between kerntools versions 1.1.0 dated 2024-10-25 and 1.2.0 dated 2025-02-19
DESCRIPTION | 6 MD5 | 49 +-- NAMESPACE | 4 NEWS.md | 15 R/importancies.R | 74 ++++ R/kernel_functions.R | 170 +++++++++- R/kernel_study.R | 22 - README.md | 7 inst/WORDLIST | 18 + inst/doc/Kernel-PCA-and-CIA.html | 12 inst/doc/Kernel-functions.R | 33 ++ inst/doc/Kernel-functions.Rmd | 131 +++++++- inst/doc/Kernel-functions.html | 534 +++++++++++++++++++++------------ inst/doc/kerntools.R | 14 inst/doc/kerntools.Rmd | 26 + inst/doc/kerntools.html | 198 +++++++----- man/Chi2.Rd |only man/KTA.Rd | 2 man/Laplace.Rd | 2 man/RBF.Rd | 2 man/aggregate_imp.Rd |only man/cLinear.Rd |only man/heatK.Rd | 3 tests/testthat/test-importancies.R | 23 + tests/testthat/test-kernel_functions.R | 77 ++++ vignettes/Kernel-functions.Rmd | 131 +++++++- vignettes/kerntools.Rmd | 26 + 27 files changed, 1240 insertions(+), 339 deletions(-)
Title: A Simple and Robust JSON Parser and Generator for R
Description: A reasonably fast JSON parser and generator, optimized for statistical
data and the web. Offers simple, flexible tools for working with JSON in R, and
is particularly powerful for building pipelines and interacting with a web API.
The implementation is based on the mapping described in the vignette (Ooms, 2014).
In addition to converting JSON data from/to R objects, 'jsonlite' contains
functions to stream, validate, and prettify JSON data. The unit tests included
with the package verify that all edge cases are encoded and decoded consistently
for use with dynamic data in systems and applications.
Author: Jeroen Ooms [aut, cre] ,
Duncan Temple Lang [ctb],
Lloyd Hilaiel [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between jsonlite versions 1.8.9 dated 2024-09-20 and 1.9.0 dated 2025-02-19
jsonlite-1.8.9/jsonlite/src/modp_stdint.h |only jsonlite-1.9.0/jsonlite/DESCRIPTION | 6 ++--- jsonlite-1.9.0/jsonlite/MD5 | 17 +++++++--------- jsonlite-1.9.0/jsonlite/NEWS | 3 ++ jsonlite-1.9.0/jsonlite/build/vignette.rds |binary jsonlite-1.9.0/jsonlite/inst/doc/json-aaquickstart.html | 10 ++++----- jsonlite-1.9.0/jsonlite/inst/doc/json-mapping.pdf |binary jsonlite-1.9.0/jsonlite/man/stream_in.Rd | 2 - jsonlite-1.9.0/jsonlite/src/modp_numtoa.c | 5 ++-- jsonlite-1.9.0/jsonlite/src/modp_numtoa.h | 4 ++- 10 files changed, 26 insertions(+), 21 deletions(-)
Title: Viral Load and CD4 Lymphocytes Regression Models
Description: Provides a comprehensive framework for building, evaluating, and visualizing regression models for analyzing viral load and CD4 (Cluster of Differentiation 4) lymphocytes data. It leverages the principles of the tidymodels ecosystem of Max Kuhn and Hadley Wickham (2020) <https://www.tidymodels.org> to offer a user-friendly experience in model development. This package includes functions for data preprocessing, feature engineering, model training, tuning, and evaluation, along with visualization tools to enhance the interpretation of model results. It is specifically designed for researchers in biostatistics, computational biology, and HIV research who aim to perform reproducible and rigorous analyses to gain insights into disease dynamics. The main focus is on improving the understanding of the relationships between viral load, CD4 lymphocytes, and other relevant covariates to contribute to HIV research and the visibility of vulnerable seropositive populations.
Author: Juan Pablo Acuna Gonzalez [aut, cre]
Maintainer: Juan Pablo Acuna Gonzalez <acua6307@gmail.com>
Diff between viralmodels versions 1.3.1 dated 2024-10-18 and 1.3.3 dated 2025-02-19
DESCRIPTION | 6 +- MD5 | 32 ++++++------- NAMESPACE | 1 NEWS.md | 12 ++++- R/viralmodel.R | 64 +++++++++++++-------------- R/viralpreds.R | 88 +++++++++++++++++++++++++++++-------- R/viraltab.R | 89 ++++++++++++++++++++++---------------- R/viralvis.R | 60 ++++++++++++------------- man/viralmodel.Rd | 2 man/viralpreds.Rd | 24 +++++++--- man/viraltab.Rd | 11 +++- man/viralvis.Rd | 2 tests/testthat/_snaps/viraltab.md | 2 tests/testthat/test-viralmodel.R | 2 tests/testthat/test-viralpreds.R | 2 tests/testthat/test-viraltab.R | 4 - tests/testthat/test-viralvis.R | 3 - 17 files changed, 247 insertions(+), 157 deletions(-)
Title: Fitting and Simulating Mixtures of Watson Distributions
Description: Tools for fitting and simulating mixtures of Watson distributions.
The random sampling scheme of the package offers two sampling
algorithms that are based of the results of Sablica, Hornik and Leydold (2022)
<doi:10.1080/10618600.2024.2416521>.
What is more, the package offers a smart tool to combine these two methods,
and based on the selected parameters, it approximates the relative sampling
speed for both methods and picks the faster one. In addition, the package
offers a fitting function for the mixtures of Watson distribution, that
uses the expectation-maximization (EM) algorithm. Special features are
the possibility to use multiple variants of the E-step and M-step,
sparse matrices for the data representation and state of the art methods
for numerical evaluation of needed special functions using the results of
Sablica and Hornik (2022) <doi:10.1090/mcom/3690> and
Sablica and Hornik (2024) <doi:10.1016/j.jmaa.2024.128262>.
Author: Lukas Sablica [aut, cre] ,
Kurt Hornik [aut] ,
Josef Leydold [aut] ,
Gerard Jungman [ctb, cph] ,
Brian Gough [ctb, cph]
Maintainer: Lukas Sablica <lsablica@wu.ac.at>
Diff between watson versions 0.5 dated 2024-11-19 and 0.6 dated 2025-02-19
DESCRIPTION | 13 ++++++++----- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/RcppExports.R | 4 ++-- man/rmwat.Rd | 4 ++-- src/rwat.cpp | 8 ++++---- 6 files changed, 27 insertions(+), 18 deletions(-)
Title: An Analyzer of International Large Scale Assessments in
Education
Description: An easy way to analyze international large-scale assessments and surveys in education or any other dataset that includes replicated weights (Balanced Repeated Replication (BRR) weights, Jackknife replicate weights,...) while also allowing for analysis with multiply imputed variables (plausible values). It supports the estimation of univariate statistics (e.g. mean, variance, standard deviation, quantiles), frequencies, correlation, linear regression and any other model already implemented in R that takes a data frame and weights as parameters. It also includes options to prepare the results for publication, following the table formatting standards of the Organization for Economic Cooperation and Development (OECD).
Author: Rodolfo Ilizaliturri [aut, cre],
Francesco Avvisati [aut],
Francois Keslair [aut]
Maintainer: Rodolfo Ilizaliturri <rodolfo.ilizaliturri@oecd.org>
Diff between Rrepest versions 1.5.3 dated 2025-02-17 and 1.5.4 dated 2025-02-19
DESCRIPTION | 6 +++--- MD5 | 14 ++++++++------ R/coverage_daggers.R | 4 +--- R/data.R | 21 ++++++++++++++++++++- R/pv_rrepest_frequencies.R | 2 ++ R/repest_auxiliaries.R | 19 +++++++++++++++++++ data/talis18_tt3g23o_freq.rda |only man/coverage_daggers.Rd | 4 +--- man/talis18_tt3g23o_freq.Rd |only 9 files changed, 54 insertions(+), 16 deletions(-)
Title: Bayesian Dynamic Borrowing with Propensity Score
Description: A tool which aims to help evaluate the effect of external borrowing using an integrated approach described in Lewis et al., (2019) <doi:10.1080/19466315.2018.1497533> that combines propensity score and Bayesian dynamic borrowing methods.
Author: Isaac Gravestock [cre, ctb],
Craig Gower-Page [aut],
Matt Secrest [ctb],
Yichen Lu [aut],
Aijing Lin [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between psborrow versions 0.2.1 dated 2023-03-03 and 0.2.2 dated 2025-02-19
DESCRIPTION | 6 +-- MD5 | 10 +++--- NEWS.md | 4 ++ R/apply_mcmc.R | 2 - build/vignette.rds |binary tests/testthat/test-apply_mcmc.R | 63 +++++++++++++++++++++++++++++++++++++++ 6 files changed, 76 insertions(+), 9 deletions(-)
Title: Miscellaneous Functions for Metabarcoding Analysis
Description: Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
Author: Adrien Taudiere [aut, cre, cph]
Maintainer: Adrien Taudiere <adrien.taudiere@zaclys.net>
Diff between MiscMetabar versions 0.12.1 dated 2025-01-29 and 0.14.1 dated 2025-02-19
DESCRIPTION | 6 MD5 | 124 +-- NAMESPACE | 6 NEWS.md | 15 R/MiscMetabar-package.R | 2 R/alpha_div_test.R | 4 R/beta_div_test.R | 20 R/blast.R | 392 ++++++++-- R/dada_phyloseq.R | 245 +++++- R/miscellanous.R | 5 R/plot_functions.R | 24 R/targets_misc.R | 2 R/taxonomy.R |only R/vsearch.R | 41 - inst/doc/MiscMetabar.html | 34 inst/extdata/100_sp_UNITE_sh_general_release_dynamic_dadaSpecies.fasta |only man/LCBD_pq.Rd | 2 man/SRS_curve_pq.Rd | 2 man/add_blast_info.Rd | 2 man/add_new_taxonomy_pq.Rd | 29 man/adonis_pq.Rd | 2 man/ancombc_pq.Rd | 4 man/assign_blastn.Rd |only man/assign_dada2.Rd |only man/assign_idtaxa.Rd | 10 man/assign_sintax.Rd | 17 man/assign_vsearch_lca.Rd | 17 man/blast_pq.Rd | 8 man/blast_to_derep.Rd | 4 man/blast_to_phyloseq.Rd | 5 man/chimera_removal_vs.Rd | 2 man/diff_fct_diff_class.Rd | 2 man/dist_bycol.Rd | 2 man/filter_asv_blast.Rd | 4 man/format2dada2.Rd |only man/format2dada2_species.Rd |only man/format2sintax.Rd |only man/get_file_extension.Rd | 3 man/ggaluv_pq.Rd | 2 man/ggbetween_pq.Rd | 2 man/ggscatt_pq.Rd | 2 man/glmutli_pq.Rd | 2 man/hill_curves_pq.Rd | 2 man/hill_test_rarperm_pq.Rd | 2 man/lulu_pq.Rd | 2 man/multipatt_pq.Rd | 2 man/plot_LCBD_pq.Rd | 2 man/plot_SCBD_pq.Rd | 2 man/plot_tsne_pq.Rd | 2 man/postcluster_pq.Rd | 2 man/read_pq.Rd | 2 man/resolve_vector_ranks.Rd |only man/sample_data_with_new_names.Rd | 2 man/save_pq.Rd | 2 man/tbl_sum_samdata.Rd | 2 man/tbl_sum_taxtable.Rd | 2 man/track_wkflow.Rd | 2 man/treemap_pq.Rd | 2 man/tsne_pq.Rd | 2 man/umap_pq.Rd | 2 man/upset_pq.Rd | 2 man/upset_test_pq.Rd | 2 man/vs_search_global.Rd | 6 man/write_pq.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test_vsearch.R | 4 vignettes/bibliography.bib | 18 67 files changed, 842 insertions(+), 269 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.5.0 dated 2025-01-07 and 0.5.1 dated 2025-02-19
DESCRIPTION | 6 +- MD5 | 28 +++++----- NEWS.md | 6 ++ R/build_schedule_entry.R | 1 R/roxy_maestro.R | 4 - R/run_schedule.R | 2 R/utils.R | 9 +-- inst/doc/maestro-1-quick-start.html | 8 +-- inst/doc/maestro-2-motivation-concepts.html | 3 - inst/doc/maestro-3-use-cases.html | 3 - inst/doc/maestro-4-advanced-scheduling.html | 11 +--- inst/doc/maestro-5-directed-acyclic-graphs.html | 22 ++++---- inst/doc/maestro-6-logging.html | 63 +++++++++++------------- man/convert_to_seconds.Rd | 2 man/parse_rounding_unit.Rd | 2 15 files changed, 86 insertions(+), 84 deletions(-)
Title: A Fast and Light Package to Compute Polygenic Risk Scores
Description: Quickly computes polygenic scores from GWAS summary statistics of either case-control or quantitative traits without parameter tuning. Reales,G., Vigorito, E., Kelemen,M., Wallace,C. (2021) <doi:10.1101/2020.07.24.220392> "RápidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset".
Author: Guillermo Reales [aut, cre] ,
Chris Wallace [aut] ,
Olly Burren [ctb]
Maintainer: Guillermo Reales <gr440@cam.ac.uk>
Diff between RapidoPGS versions 2.3.0 dated 2023-10-13 and 2.3.1 dated 2025-02-19
DESCRIPTION | 8 MD5 | 39 +- NEWS.md | 14 R/data.R | 8 R/rapfunc.R | 12 README.md | 10 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 2 inst/doc/Computing_RapidoPGSmulti.R | 26 - inst/doc/Computing_RapidoPGSmulti.html | 503 +++++++++++++++++++++----- inst/doc/Computing_RapidoPGSsingle.R | 36 - inst/doc/Computing_RapidoPGSsingle.Rmd | 2 inst/doc/Computing_RapidoPGSsingle.html | 599 +++++++++++++++++++++++--------- man/EUR_ld.blocks19.Rd | 2 man/EUR_ld.blocks38.Rd | 2 man/michailidou19.Rd | 2 man/michailidou38.Rd | 2 man/rapidopgs_multi.Rd | 2 man/rapidopgs_single.Rd | 2 vignettes/Computing_RapidoPGSsingle.Rmd | 2 21 files changed, 933 insertions(+), 340 deletions(-)
Title: Analytics & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or
data scientist to get quick and robust results, without the need of repetitive coding or
advanced R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.2.11 dated 2025-01-09 and 5.2.12 dated 2025-02-19
lares-5.2.11/lares/man/outlier_turkey.Rd |only lares-5.2.12/lares/DESCRIPTION | 6 - lares-5.2.12/lares/MD5 | 37 ++++---- lares-5.2.12/lares/NAMESPACE | 3 lares-5.2.12/lares/R/cache.R | 12 +- lares-5.2.12/lares/R/google_analytics.R | 3 lares-5.2.12/lares/R/lares.R | 2 lares-5.2.12/lares/R/outliers.R | 5 - lares-5.2.12/lares/R/robyn.R | 108 ++++++++++++++++++++++---- lares-5.2.12/lares/R/stocks.R | 21 ++--- lares-5.2.12/lares/man/cache_write.Rd | 5 + lares-5.2.12/lares/man/outlier_tukey.Rd |only lares-5.2.12/lares/man/outlier_zscore.Rd | 2 lares-5.2.12/lares/man/outlier_zscore_plot.Rd | 2 lares-5.2.12/lares/man/queryGA.Rd | 3 lares-5.2.12/lares/man/robyn_hypsbuilder.Rd | 1 lares-5.2.12/lares/man/robyn_marginal.Rd |only lares-5.2.12/lares/man/robyn_modelselector.Rd | 1 lares-5.2.12/lares/man/robyn_performance.Rd | 5 + lares-5.2.12/lares/man/stocks_report.Rd | 7 - lares-5.2.12/lares/man/winsorize.Rd | 2 21 files changed, 164 insertions(+), 61 deletions(-)
Title: Robust Trimmed Clustering
Description: Provides functions for robust trimmed clustering. The methods are
described in Garcia-Escudero (2008) <doi:10.1214/07-AOS515>,
Fritz et al. (2012) <doi:10.18637/jss.v047.i12>,
Garcia-Escudero et al. (2011) <doi:10.1007/s11222-010-9194-z> and others.
Author: Valentin Todorov [aut, cre] ,
Luis Angel Garcia Escudero [aut],
Agustin Mayo Iscar [aut],
Javier Crespo Guerrero [aut],
Heinrich Fritz [aut]
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between tclust versions 2.0-5 dated 2024-10-15 and 2.1-0 dated 2025-02-19
ChangeLog | 15 + DESCRIPTION | 10 MD5 | 29 +- NAMESPACE | 5 R/RcppExports.R | 85 +++++++ R/print.tclust.R | 3 R/randIndex.R |only R/tclust.R | 40 +-- R/tclustIC.R | 4 man/estepRR.Rd |only man/randIndex.Rd |only src/RcppExports.cpp | 36 ++- src/rlg.cpp | 2 src/tclust.cpp | 560 +++++++++++++++++++++++++++++------------------- src/tkmeans.cpp | 2 tests/ttclust.R | 18 + tests/ttclust.Rout.save | 328 ++++++++++++++++++---------- 17 files changed, 752 insertions(+), 385 deletions(-)
Title: Identify Relevant Clinical Codes and Evaluate Their Use
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre] ,
Marti Catala [ctb] ,
Xihang Chen [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [ctb] ,
Danielle Newby [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CodelistGenerator versions 3.3.2 dated 2025-01-28 and 3.4.0 dated 2025-02-19
DESCRIPTION | 14 - MD5 | 36 +-- R/drugCodes.R | 62 +++--- R/getRoutes.R | 121 ++++++------ R/mockVocabRef.R | 98 +++++----- R/runSearch.R | 4 R/stratifyByRoute.R | 267 +++++++++++++--------------- R/subsetOnRouteCategory.R | 190 +++++++++---------- R/summariseCodeUse.R | 56 +++++ inst/doc/a04_Vocab_based_codelists.html | 57 ----- man/getDrugIngredientCodes.Rd | 3 man/summariseCodeUse.Rd | 5 tests/testthat/test-codesFrom.R | 5 tests/testthat/test-dbms.R | 5 tests/testthat/test-drugCodes.R | 5 tests/testthat/test-findUnmappedCodes.R | 5 tests/testthat/test-getCandidateCodes.R | 4 tests/testthat/test-subsetOnRouteCategory.R | 58 +++--- tests/testthat/test-summariseCodeUse.R | 85 ++++++++ 19 files changed, 583 insertions(+), 497 deletions(-)
More information about CodelistGenerator at CRAN
Permanent link
Title: Extending the Newman Studentized Range Statistic to
Transcriptomics
Description: Extends the classical Newman studentized range statistic
in various ways that can be applied to genome-scale transcriptomic
or other expression data.
Author: Zachary B. Abrams [aut],
Greg Gershkowitz [aut],
Anoushka Joglekar [aut],
Chao Liu [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between NewmanOmics versions 1.0.11 dated 2024-04-28 and 1.0.13 dated 2025-02-19
NewmanOmics-1.0.11/NewmanOmics/tests/01-bankedTest.R |only NewmanOmics-1.0.11/NewmanOmics/tests/01-bankedTest.Rout.save |only NewmanOmics-1.0.11/NewmanOmics/tests/03-betamix.R |only NewmanOmics-1.0.11/NewmanOmics/tests/03-betamix.Rout.save |only NewmanOmics-1.0.13/NewmanOmics/DESCRIPTION | 23 NewmanOmics-1.0.13/NewmanOmics/MD5 | 18 NewmanOmics-1.0.13/NewmanOmics/R/02-betamix3.R | 13 NewmanOmics-1.0.13/NewmanOmics/build/vignette.rds |binary NewmanOmics-1.0.13/NewmanOmics/data/GSE6631.rda |binary NewmanOmics-1.0.13/NewmanOmics/data/LungPair.rda |binary NewmanOmics-1.0.13/NewmanOmics/inst/doc/newmanomics.html | 287 +++++------ NewmanOmics-1.0.13/NewmanOmics/man/02-pairedStat.Rd | 4 12 files changed, 181 insertions(+), 164 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut] ,
Yoonkyoung Jeon [aut],
Jaewoong Heo [aut],
Youngsun Park [aut] ,
Hyungwoo Jo [aut],
Jeongmin Seo [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.6.1 dated 2025-01-08 and 1.6.3 dated 2025-02-19
DESCRIPTION | 8 MD5 | 32 - NAMESPACE | 1 NEWS.md | 9 R/coxph.R | 248 ++++++++---- R/forestcox.R | 108 ++++- R/forestglm.R | 46 ++ R/jsBasicGadget.R | 16 R/jsPropensityGadget.R | 48 +- R/jsRepeatedGadget.R | 48 +- R/jsSurveyGadget.R | 654 ++++++++++++++++----------------- R/kaplan.R | 134 ++++-- inst/doc/jsmodule.html | 4 inst/doc/jsmodule_subgroup_cmprsk.html | 4 man/coxModule.Rd | 8 man/forestcoxServer.Rd | 8 man/kaplanModule.Rd | 8 17 files changed, 835 insertions(+), 549 deletions(-)
Title: Frequently Used Functions for Easy R Programming
Description: Some utility functions for validation and data manipulation. These functions can be helpful to reduce internal codes everywhere in package development.
Author: Yuchen Li [aut, cre]
Maintainer: Yuchen Li <ycli1995@outlook.com>
Diff between easy.utils versions 0.0.5 dated 2024-09-24 and 0.1.0 dated 2025-02-19
easy.utils-0.0.5/easy.utils/R/All_S3_Generics.R |only easy.utils-0.0.5/easy.utils/R/color_palettes.R |only easy.utils-0.0.5/easy.utils/man/checkColorMap.Rd |only easy.utils-0.0.5/easy.utils/man/pal_discrete.Rd |only easy.utils-0.0.5/easy.utils/man/setColor.Rd |only easy.utils-0.1.0/easy.utils/DESCRIPTION | 11 +++++------ easy.utils-0.1.0/easy.utils/MD5 | 13 ++++--------- easy.utils-0.1.0/easy.utils/NAMESPACE | 8 -------- easy.utils-0.1.0/easy.utils/NEWS.md | 5 +++++ easy.utils-0.1.0/easy.utils/man/easy.utils-package.Rd | 2 +- 10 files changed, 15 insertions(+), 24 deletions(-)
Title: Biologically Explainable Machine Learning Framework
Description: Biologically Explainable Machine Learning Framework for Phenotype Prediction using omics data described in Chen and Schwarz (2017) <doi:10.48550/arXiv.1712.00336>.Identifying reproducible and interpretable biological patterns from high-dimensional omics data is a critical factor in understanding the risk mechanism of complex disease. As such, explainable machine learning can offer biological insight in addition to personalized risk scoring.In this process, a feature space of biological pathways will be generated, and the feature space can also be subsequently analyzed using WGCNA (Described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559> ) methods.
Author: Shunjie Zhang [aut, cre],
Junfang Chen [aut]
Maintainer: Shunjie Zhang <zhang.shunjie@qq.com>
Diff between BioM2 versions 1.1.0 dated 2024-09-20 and 1.1.1 dated 2025-02-19
DESCRIPTION | 6 ++-- MD5 | 8 ++--- R/BioM2.R | 78 +++++++++++++++++++++++++++++++++++-------------------- man/BioM2.Rd | 3 ++ man/baseModel.Rd | 2 - 5 files changed, 62 insertions(+), 35 deletions(-)
Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut] ,
Kurt Hornik [aut, cre] ,
Artifex Software, Inc. [ctb, cph]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tm versions 0.7-15 dated 2024-11-18 and 0.7-16 dated 2025-02-19
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/NEWS.Rd | 7 +++++++ inst/doc/extensions.pdf |binary inst/doc/tm.pdf |binary man/Source.Rd | 1 - 6 files changed, 16 insertions(+), 10 deletions(-)
Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with
arbitrary domains, featuring relational algebra, predicate functions,
and fitters for consensus relations.
Author: David Meyer [aut] ,
Kurt Hornik [aut, cre] ,
Christian Buchta [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between relations versions 0.6-14 dated 2024-11-13 and 0.6-15 dated 2025-02-19
DESCRIPTION | 12 +++++---- MD5 | 16 ++++++------- build/vignette.rds |binary inst/NEWS.Rd | 6 ++++ inst/doc/relations.Rnw | 2 - inst/doc/relations.pdf |binary man/choice.Rd | 4 ++- man/consensus.Rd | 58 ++++++++++++++++++++++++++---------------------- vignettes/relations.Rnw | 2 - 9 files changed, 58 insertions(+), 42 deletions(-)
Title: Construct and Visualize TDA Mapper Graphs
Description: Topological data analysis (TDA) is a method of data analysis that
uses techniques from topology to analyze high-dimensional data. Here we
implement Mapper, an algorithm from this area developed by Singh, Mémoli and
Carlsson (2007) which generalizes the concept of a
Reeb graph <https://en.wikipedia.org/wiki/Reeb_graph>.
Author: George Clare Kennedy [aut, cre]
Maintainer: George Clare Kennedy <george-clarekennedy@uiowa.edu>
Diff between mappeR versions 2.0.0 dated 2025-02-16 and 2.0.1 dated 2025-02-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/clusterer_farm.R | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with [...truncated...]
Author: Mary Meyer [aut],
Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>
Diff between cgam versions 1.22 dated 2025-02-17 and 1.23 dated 2025-02-19
ChangeLog | 5 +- DESCRIPTION | 8 +-- MD5 | 8 +-- R/cgam.R | 124 +++++++++++++++++++++++++++---------------------------- man/plotpersp.Rd | 6 +- 5 files changed, 77 insertions(+), 74 deletions(-)
Title: An R Package for Extended Behavior Genetics Analysis
Description: Provides functions for behavior genetics analysis,
including variance component model identification [Hunter et al. (2021) <doi:10.1007/s10519-021-10055-x>],
calculation of relatedness coefficients using path-tracing methods
[Wright (1922) <doi:10.1086/279872>; McArdle & McDonald (1984) <doi:10.1111/j.2044-8317.1984.tb00802.x>],
inference of relatedness, pedigree conversion, and simulation of multi-generational family data
[Lyu et al. (2024) <doi:10.1101/2024.12.19.629449>]. For a full overview,
see Garrison et al. (2025) <doi:10.21105/joss.06203>.
Author: S. Mason Garrison [aut, cre] ,
Michael D. Hunter [aut] ,
Xuanyu Lyu [aut] ,
Rachel N. Good [ctb],
Jonathan D. Trattner [aut] ,
S. Alexandra Burt [aut]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>
Diff between BGmisc versions 1.3.2 dated 2024-06-18 and 1.3.3 dated 2025-02-19
BGmisc-1.3.2/BGmisc/tests/testthat/test-clean.X |only BGmisc-1.3.3/BGmisc/DESCRIPTION | 19 BGmisc-1.3.3/BGmisc/MD5 | 94 - BGmisc-1.3.3/BGmisc/NEWS.md | 11 BGmisc-1.3.3/BGmisc/R/buildPedigree.R | 18 BGmisc-1.3.3/BGmisc/R/checkIDs.R | 12 BGmisc-1.3.3/BGmisc/R/checkSex.R | 24 BGmisc-1.3.3/BGmisc/R/computeRelatedness.R | 2 BGmisc-1.3.3/BGmisc/R/convertPedigree.R | 448 ++++-- BGmisc-1.3.3/BGmisc/R/readPedigree.R | 431 +++--- BGmisc-1.3.3/BGmisc/R/simulatePedigree.R | 4 BGmisc-1.3.3/BGmisc/R/summarizePedigree.R | 210 +- BGmisc-1.3.3/BGmisc/R/tweakPedigree.R | 4 BGmisc-1.3.3/BGmisc/README.md | 2 BGmisc-1.3.3/BGmisc/build/partial.rdb |only BGmisc-1.3.3/BGmisc/build/vignette.rds |binary BGmisc-1.3.3/BGmisc/inst/doc/analyticrelatedness.html | 18 BGmisc-1.3.3/BGmisc/inst/doc/modelingrelatedness.html | 188 +- BGmisc-1.3.3/BGmisc/inst/doc/network.html | 80 - BGmisc-1.3.3/BGmisc/inst/doc/pedigree.html | 14 BGmisc-1.3.3/BGmisc/inst/doc/validation.R | 201 +- BGmisc-1.3.3/BGmisc/inst/doc/validation.Rmd | 197 +- BGmisc-1.3.3/BGmisc/inst/doc/validation.html | 779 +++++------ BGmisc-1.3.3/BGmisc/man/BGmisc-package.Rd | 2 BGmisc-1.3.3/BGmisc/man/calculateSummaryDT.Rd | 5 BGmisc-1.3.3/BGmisc/man/checkSex.Rd | 24 BGmisc-1.3.3/BGmisc/man/compute_transpose.Rd |only BGmisc-1.3.3/BGmisc/man/ped2add.Rd | 26 BGmisc-1.3.3/BGmisc/man/ped2ce.Rd | 4 BGmisc-1.3.3/BGmisc/man/ped2cn.Rd | 26 BGmisc-1.3.3/BGmisc/man/ped2com.Rd | 26 BGmisc-1.3.3/BGmisc/man/ped2fam.Rd | 5 BGmisc-1.3.3/BGmisc/man/ped2graph.Rd | 5 BGmisc-1.3.3/BGmisc/man/ped2maternal.Rd | 5 BGmisc-1.3.3/BGmisc/man/ped2mit.Rd | 26 BGmisc-1.3.3/BGmisc/man/ped2paternal.Rd | 5 BGmisc-1.3.3/BGmisc/man/recodeSex.Rd | 17 BGmisc-1.3.3/BGmisc/man/repairSex.Rd | 17 BGmisc-1.3.3/BGmisc/man/summarizeFamilies.Rd | 16 BGmisc-1.3.3/BGmisc/man/summarizeMatrilines.Rd | 16 BGmisc-1.3.3/BGmisc/man/summarizePatrilines.Rd | 16 BGmisc-1.3.3/BGmisc/man/summarizePedigrees.Rd | 36 BGmisc-1.3.3/BGmisc/tests/testthat.R | 1 BGmisc-1.3.3/BGmisc/tests/testthat/Rplots.pdf |binary BGmisc-1.3.3/BGmisc/tests/testthat/test-convertPedigree.R |only BGmisc-1.3.3/BGmisc/tests/testthat/test-identifyModel.R | 3 BGmisc-1.3.3/BGmisc/tests/testthat/test-networks.R | 212 -- BGmisc-1.3.3/BGmisc/tests/testthat/test-readPedigrees.R | 18 BGmisc-1.3.3/BGmisc/tests/testthat/test-summarizePedigrees.R | 75 - BGmisc-1.3.3/BGmisc/vignettes/validation.Rmd | 197 +- 50 files changed, 1989 insertions(+), 1550 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.5.5.1 dated 2025-01-20 and 1.5.6 dated 2025-02-19
gpboost-1.5.5.1/gpboost/tests/testthat/_snaps |only gpboost-1.5.6/gpboost/DESCRIPTION | 8 gpboost-1.5.6/gpboost/MD5 | 36 gpboost-1.5.6/gpboost/R/GPModel.R | 33 gpboost-1.5.6/gpboost/R/gpb.cv.R | 56 - gpboost-1.5.6/gpboost/configure.ac | 2 gpboost-1.5.6/gpboost/demo/GPBoost_algorithm.R | 22 gpboost-1.5.6/gpboost/demo/compare_usage_lme4_gpboost.R | 3 gpboost-1.5.6/gpboost/demo/generalized_linear_Gaussian_process_mixed_effects_models.R | 5 gpboost-1.5.6/gpboost/src/CG_utils.cpp | 39 gpboost-1.5.6/gpboost/src/Vecchia_utils.cpp | 4 gpboost-1.5.6/gpboost/src/include/GPBoost/CG_utils.h | 28 gpboost-1.5.6/gpboost/src/include/GPBoost/cov_fcts.h | 294 +++-- gpboost-1.5.6/gpboost/src/include/GPBoost/likelihoods.h | 494 ++++++---- gpboost-1.5.6/gpboost/src/include/GPBoost/re_comp.h | 22 gpboost-1.5.6/gpboost/src/include/GPBoost/re_model_template.h | 97 + gpboost-1.5.6/gpboost/src/include/GPBoost/utils.h | 8 gpboost-1.5.6/gpboost/src/objective/regression_objective.hpp | 2 gpboost-1.5.6/gpboost/tests/testthat/test_GPModel_gaussian_process.R | 268 ++--- gpboost-1.5.6/gpboost/tests/testthat/test_GPModel_non_Gaussian_data.R | 50 - 20 files changed, 884 insertions(+), 587 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: Bindings to 'libcurl' <https://curl.se/libcurl/> for performing fully
configurable HTTP/FTP requests where responses can be processed in memory, on
disk, or streaming via the callback or connection interfaces. Some knowledge
of 'libcurl' is recommended; for a more-user-friendly web client see the
'httr2' package which builds on this package with http specific tools and logic.
Author: Jeroen Ooms [aut, cre] ,
Hadley Wickham [ctb],
Posit Software, PBC [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between curl versions 6.2.0 dated 2025-01-23 and 6.2.1 dated 2025-02-19
DESCRIPTION | 6 +- MD5 | 30 +++++----- NAMESPACE | 1 NEWS | 7 ++ R/echo.R | 23 +++++--- R/multi_download.R | 2 R/options.R | 3 - R/utilities.R | 22 +++++-- inst/doc/intro.html | 98 +++++++++++++++++------------------ man/multi_download.Rd | 2 src/curl-common.h | 1 src/dryrun.c |only src/init.c | 2 src/multi.c | 9 --- src/utils.c | 10 ++- tests/testthat/test-errors.R |only tests/testthat/test-multi-download.R | 4 + 17 files changed, 125 insertions(+), 95 deletions(-)
Title: An API Generator for R
Description: Gives the ability to automatically generate and serve an HTTP API
from R functions using the annotations in the R documentation around your
functions.
Author: Barret Schloerke [cre, aut] ,
Jeff Allen [aut, ccp],
Bruno Tremblay [ctb],
Frans van Dunne [ctb],
Sebastiaan Vandewoude [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between plumber versions 1.2.2 dated 2024-03-25 and 1.3.0 dated 2025-02-19
plumber-1.2.2/plumber/build |only plumber-1.2.2/plumber/inst/validate_api_spec |only plumber-1.3.0/plumber/DESCRIPTION | 13 - plumber-1.3.0/plumber/MD5 | 66 +++--- plumber-1.3.0/plumber/NAMESPACE | 8 plumber-1.3.0/plumber/NEWS.md | 26 ++ plumber-1.3.0/plumber/R/find-port.R | 100 ++++++---- plumber-1.3.0/plumber/R/openapi-spec.R | 1 plumber-1.3.0/plumber/R/options_plumber.R | 2 plumber-1.3.0/plumber/R/parse-body.R | 72 +++++-- plumber-1.3.0/plumber/R/plumber-step.R | 15 + plumber-1.3.0/plumber/R/plumber.R | 41 ++-- plumber-1.3.0/plumber/R/pr.R | 2 plumber-1.3.0/plumber/R/pr_set.R | 14 + plumber-1.3.0/plumber/R/serializer.R | 86 +++++++- plumber-1.3.0/plumber/R/utils.R | 3 plumber-1.3.0/plumber/R/validate_api_spec.R | 97 +++------ plumber-1.3.0/plumber/README.md | 12 - plumber-1.3.0/plumber/inst/WORDLIST | 15 - plumber-1.3.0/plumber/man/Plumber.Rd | 6 plumber-1.3.0/plumber/man/endpoint_serializer.Rd | 4 plumber-1.3.0/plumber/man/forward.Rd | 14 + plumber-1.3.0/plumber/man/parsers.Rd | 9 plumber-1.3.0/plumber/man/pr_set_debug.Rd | 14 + plumber-1.3.0/plumber/man/serializers.Rd | 28 ++ plumber-1.3.0/plumber/man/validate_api_spec.Rd | 18 + plumber-1.3.0/plumber/tests/spelling.R | 3 plumber-1.3.0/plumber/tests/testthat/files/include/test.html | 14 - plumber-1.3.0/plumber/tests/testthat/test-find-port.R | 52 +++-- plumber-1.3.0/plumber/tests/testthat/test-parse-body.R | 38 +++ plumber-1.3.0/plumber/tests/testthat/test-plumber-run.R | 41 ---- plumber-1.3.0/plumber/tests/testthat/test-plumber.R | 7 plumber-1.3.0/plumber/tests/testthat/test-serializer-device.R | 13 + plumber-1.3.0/plumber/tests/testthat/test-serializer-excel.R |only plumber-1.3.0/plumber/tests/testthat/test-shared-secret.R | 2 35 files changed, 531 insertions(+), 305 deletions(-)
Title: Tabulate P.L. 94-171 Redistricting Data Summary Files
Description: Tools to process legacy format summary redistricting data files
produced by the United States Census Bureau pursuant to P.L. 94-171. These
files are generally available earlier but are difficult to work with as-is.
Author: Cory McCartan [aut, cre],
Christopher T. Kenny [aut]
Maintainer: Cory McCartan <mccartan@psu.edu>
Diff between PL94171 versions 1.1.2 dated 2022-09-11 and 1.1.3 dated 2025-02-19
DESCRIPTION | 12 +-- MD5 | 24 +++---- NEWS.md | 3 R/pl_get_baf.R | 2 R/pl_select_standard.R | 4 - R/pl_subset.R | 2 build/vignette.rds |binary inst/doc/PL94171.R | 18 ++--- inst/doc/PL94171.html | 152 +++++++++++++++++++++++----------------------- man/PL94171-package.Rd | 2 man/pl_get_baf.Rd | 2 man/pl_select_standard.Rd | 2 man/pl_subset.Rd | 2 13 files changed, 117 insertions(+), 108 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-28 1.1
2022-04-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-26 24.2.0
2023-12-19 23.12.0