Title: Process Orbitrap Isotopocule Data
Description: Read and process isotopocule data from an Orbitrap Isotope Solutions mass spectrometer. Citation: Kantnerova et al. (Nature Protocols, 2024).
Author: Caj Neubauer [aut, cre, cph] ,
Sebastian Kopf [aut] ,
Kristyna Kantnerova [aut]
Maintainer: Caj Neubauer <caj.neubauer@colorado.edu>
Diff between isoorbi versions 1.3.1 dated 2024-08-27 and 1.5.2 dated 2025-10-03
isoorbi-1.3.1/isoorbi/R/helpers.R |only isoorbi-1.3.1/isoorbi/R/isoorbi.R |only isoorbi-1.3.1/isoorbi/R/loading_functions.R |only isoorbi-1.3.1/isoorbi/R/plotting_functions.R |only isoorbi-1.3.1/isoorbi/R/settings.R |only isoorbi-1.3.1/isoorbi/R/utility_functions.R |only isoorbi-1.3.1/isoorbi/inst/doc/isoxl_demo.Rmd |only isoorbi-1.3.1/isoorbi/inst/doc/isoxl_demo.html |only isoorbi-1.3.1/isoorbi/inst/doc/quick_start.R |only isoorbi-1.3.1/isoorbi/inst/doc/quick_start.Rmd |only isoorbi-1.3.1/isoorbi/inst/doc/quick_start.html |only isoorbi-1.3.1/isoorbi/inst/doc/shot_noise.R |only isoorbi-1.3.1/isoorbi/inst/doc/shot_noise.Rmd |only isoorbi-1.3.1/isoorbi/inst/doc/shot_noise.html |only isoorbi-1.3.1/isoorbi/inst/extdata/description_testfiles.txt |only isoorbi-1.3.1/isoorbi/inst/extdata/testfile_dual_inlet_new.isox |only isoorbi-1.3.1/isoorbi/man/figures/figure_flowchart.png |only isoorbi-1.3.1/isoorbi/man/orbi_get_isotopocule_coverage.Rd |only isoorbi-1.3.1/isoorbi/man/orbi_plot_isotopocule_coverage.Rd |only isoorbi-1.3.1/isoorbi/tests/testthat/test_blocks_functions.R |only isoorbi-1.3.1/isoorbi/tests/testthat/test_export_functions.R |only isoorbi-1.3.1/isoorbi/tests/testthat/test_helper_functions.R |only isoorbi-1.3.1/isoorbi/tests/testthat/test_loading_functions.R |only isoorbi-1.3.1/isoorbi/tests/testthat/test_plotting_functions.R |only isoorbi-1.3.1/isoorbi/tests/testthat/test_ratio_functions.R |only isoorbi-1.3.1/isoorbi/tests/testthat/test_settings.R |only isoorbi-1.3.1/isoorbi/tests/testthat/test_shotnoise_functions.R |only isoorbi-1.3.1/isoorbi/tests/testthat/test_utility_functions.R |only isoorbi-1.3.1/isoorbi/vignettes/isoxl_demo.Rmd |only isoorbi-1.3.1/isoorbi/vignettes/isoxl_gui_screenshot.png |only isoorbi-1.3.1/isoorbi/vignettes/quick_start.Rmd |only isoorbi-1.3.1/isoorbi/vignettes/shot_noise.Rmd |only isoorbi-1.5.2/isoorbi/DESCRIPTION | 33 isoorbi-1.5.2/isoorbi/LICENSE | 2 isoorbi-1.5.2/isoorbi/MD5 | 211 - isoorbi-1.5.2/isoorbi/NAMESPACE | 30 isoorbi-1.5.2/isoorbi/NEWS.md | 64 isoorbi-1.5.2/isoorbi/R/aggregation.R |only isoorbi-1.5.2/isoorbi/R/blocks_functions.R | 1390 ++++++---- isoorbi-1.5.2/isoorbi/R/conditions-general.R |only isoorbi-1.5.2/isoorbi/R/export_functions.R | 215 + isoorbi-1.5.2/isoorbi/R/helpers-general.R |only isoorbi-1.5.2/isoorbi/R/isoorbi-package.R |only isoorbi-1.5.2/isoorbi/R/mapping.R |only isoorbi-1.5.2/isoorbi/R/options-general.R |only isoorbi-1.5.2/isoorbi/R/options-package.R |only isoorbi-1.5.2/isoorbi/R/plotting.R |only isoorbi-1.5.2/isoorbi/R/problems.R |only isoorbi-1.5.2/isoorbi/R/processing.R |only isoorbi-1.5.2/isoorbi/R/ratio_functions.R | 652 +++- isoorbi-1.5.2/isoorbi/R/read_isox.R |only isoorbi-1.5.2/isoorbi/R/read_raw.R |only isoorbi-1.5.2/isoorbi/R/shotnoise_functions.R | 259 + isoorbi-1.5.2/isoorbi/R/utilities.R |only isoorbi-1.5.2/isoorbi/R/zzz.R |only isoorbi-1.5.2/isoorbi/README.md | 137 isoorbi-1.5.2/isoorbi/build/vignette.rds |binary isoorbi-1.5.2/isoorbi/inst/doc/dual_inlet.R | 108 isoorbi-1.5.2/isoorbi/inst/doc/dual_inlet.Rmd | 123 isoorbi-1.5.2/isoorbi/inst/doc/dual_inlet.html | 583 ++-- isoorbi-1.5.2/isoorbi/inst/doc/flow_injection.R | 2 isoorbi-1.5.2/isoorbi/inst/doc/flow_injection.Rmd | 3 isoorbi-1.5.2/isoorbi/inst/doc/flow_injection.html | 91 isoorbi-1.5.2/isoorbi/inst/doc/functionality_guide.R |only isoorbi-1.5.2/isoorbi/inst/doc/functionality_guide.Rmd |only isoorbi-1.5.2/isoorbi/inst/doc/functionality_guide.html |only isoorbi-1.5.2/isoorbi/inst/extdata/README.md |only isoorbi-1.5.2/isoorbi/inst/extdata/nitrate_test_10scans.raw |only isoorbi-1.5.2/isoorbi/inst/extdata/nitrate_test_10scans.raw.cache.zip |only isoorbi-1.5.2/isoorbi/inst/extdata/nitrate_test_1scan.raw |only isoorbi-1.5.2/isoorbi/inst/extdata/nitrate_test_1scan.raw.cache.zip |only isoorbi-1.5.2/isoorbi/inst/licenses |only isoorbi-1.5.2/isoorbi/man/figures/README-example-1.png |only isoorbi-1.5.2/isoorbi/man/figures/README-map-isotopocules-1.png |only isoorbi-1.5.2/isoorbi/man/figures/README-process-data-1.png |only isoorbi-1.5.2/isoorbi/man/figures/README-read-raw-1.png |only isoorbi-1.5.2/isoorbi/man/figures/figure_flowchart.svg |only isoorbi-1.5.2/isoorbi/man/isoorbi-package.Rd | 10 isoorbi-1.5.2/isoorbi/man/orbi_add_blocks_to_plot.Rd | 2 isoorbi-1.5.2/isoorbi/man/orbi_adjust_block.Rd | 6 isoorbi-1.5.2/isoorbi/man/orbi_aggregate_raw.Rd |only isoorbi-1.5.2/isoorbi/man/orbi_aggregator.Rd |only isoorbi-1.5.2/isoorbi/man/orbi_analyze_shot_noise.Rd | 2 isoorbi-1.5.2/isoorbi/man/orbi_calculate_ions.Rd |only isoorbi-1.5.2/isoorbi/man/orbi_check_isoraw.Rd |only isoorbi-1.5.2/isoorbi/man/orbi_default_theme.Rd | 2 isoorbi-1.5.2/isoorbi/man/orbi_define_basepeak.Rd | 6 isoorbi-1.5.2/isoorbi/man/orbi_define_block_for_flow_injection.Rd | 4 isoorbi-1.5.2/isoorbi/man/orbi_define_blocks_for_dual_inlet.Rd | 8 isoorbi-1.5.2/isoorbi/man/orbi_export_data_to_excel.Rd | 16 isoorbi-1.5.2/isoorbi/man/orbi_filter_files.Rd |only isoorbi-1.5.2/isoorbi/man/orbi_filter_flagged_data.Rd | 2 isoorbi-1.5.2/isoorbi/man/orbi_filter_isotopocules.Rd |only isoorbi-1.5.2/isoorbi/man/orbi_filter_isox.Rd | 43 isoorbi-1.5.2/isoorbi/man/orbi_filter_satellite_peaks.Rd | 2 isoorbi-1.5.2/isoorbi/man/orbi_filter_scan_intensity.Rd | 2 isoorbi-1.5.2/isoorbi/man/orbi_filter_weak_isotopocules.Rd | 2 isoorbi-1.5.2/isoorbi/man/orbi_find_isox.Rd | 2 isoorbi-1.5.2/isoorbi/man/orbi_find_raw.Rd |only isoorbi-1.5.2/isoorbi/man/orbi_flag_outliers.Rd | 28 isoorbi-1.5.2/isoorbi/man/orbi_flag_satellite_peaks.Rd | 22 isoorbi-1.5.2/isoorbi/man/orbi_flag_weak_isotopocules.Rd | 21 isoorbi-1.5.2/isoorbi/man/orbi_get_blocks_info.Rd | 6 isoorbi-1.5.2/isoorbi/man/orbi_get_data.Rd |only isoorbi-1.5.2/isoorbi/man/orbi_get_example_files.Rd |only isoorbi-1.5.2/isoorbi/man/orbi_get_settings.Rd | 14 isoorbi-1.5.2/isoorbi/man/orbi_identify_isotopocules.Rd |only isoorbi-1.5.2/isoorbi/man/orbi_isotopocule_coverage.Rd |only isoorbi-1.5.2/isoorbi/man/orbi_options.Rd |only isoorbi-1.5.2/isoorbi/man/orbi_plot_raw_data.Rd | 20 isoorbi-1.5.2/isoorbi/man/orbi_plot_satellite_peaks.Rd | 11 isoorbi-1.5.2/isoorbi/man/orbi_plot_spectra.Rd |only isoorbi-1.5.2/isoorbi/man/orbi_read_isox.Rd | 4 isoorbi-1.5.2/isoorbi/man/orbi_read_raw.Rd |only isoorbi-1.5.2/isoorbi/man/orbi_segment_blocks.Rd | 4 isoorbi-1.5.2/isoorbi/man/orbi_set_settings.Rd | 37 isoorbi-1.5.2/isoorbi/man/orbi_simplify_isox.Rd | 2 isoorbi-1.5.2/isoorbi/man/orbi_summarize_results.Rd | 6 isoorbi-1.5.2/isoorbi/man/problems.Rd |only isoorbi-1.5.2/isoorbi/tests/testthat.R | 4 isoorbi-1.5.2/isoorbi/tests/testthat/_snaps |only isoorbi-1.5.2/isoorbi/tests/testthat/test-aggregation.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-blocks.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-conditions-general.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-export.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-helpers-general.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-mapping.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-options-general.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-options-package.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-plotting.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-problems.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-processing.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-ratios.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-read-isox.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-read-raw.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-shotnoise.R |only isoorbi-1.5.2/isoorbi/tests/testthat/test-utilities.R |only isoorbi-1.5.2/isoorbi/vignettes/dual_inlet.Rmd | 123 isoorbi-1.5.2/isoorbi/vignettes/flow_injection.Rmd | 3 isoorbi-1.5.2/isoorbi/vignettes/functionality_guide.Rmd |only 140 files changed, 2905 insertions(+), 1412 deletions(-)
Title: D-Score for Child Development
Description: The D-score summarizes a child's performance on developmental milestones
into a single number. Its key feature is its generic nature. The method
does not depend on a specific measurement instrument. The statistical
method underlying the D-score is described in van Buuren et al. (2025)
<doi:10.1177/01650254241294033>. This package implements model keys to
convert milestone scores to D-scores; maps instrument-specific item names
to a generic 9-position naming convention; computes D-scores and their
precision from a child's milestone scores; and converts D-scores to
Development-for-Age Z-scores (DAZ) using age-conditional reference
standards.
Author: Stef van Buuren [cre, aut],
Iris Eekhout [aut],
Arjan Huizing [aut],
Jonathan Seiden [aut]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between dscore versions 1.11.0 dated 2025-09-26 and 2.0.0 dated 2025-10-03
DESCRIPTION | 28 - MD5 | 76 +-- NEWS.md | 23 R/builtin_translate.R | 1 R/dscore.R | 12 R/get_age_equivalent.R | 4 R/get_itemnames.R | 10 R/get_reference.R | 2 R/rename_vector.R | 19 R/set_default.R | 6 README.md | 3 build/vignette.rds |binary data/builtin_itembank.rda |binary data/builtin_itemtable.rda |binary data/builtin_keys.rda |binary data/builtin_references.rda |binary data/builtin_translate.rda |binary inst/doc/custom_priors.R | 44 + inst/doc/custom_priors.Rmd | 46 + inst/doc/custom_priors.html | 56 +- inst/doc/getting_started.R | 6 inst/doc/getting_started.Rmd | 78 +-- inst/doc/getting_started.html | 1029 +++++------------------------------------- inst/doc/multiple_keys.R |only inst/doc/multiple_keys.Rmd |only inst/doc/multiple_keys.html |only inst/doc/scoring_GSED.R | 102 +--- inst/doc/scoring_GSED.Rmd | 234 ++------- inst/doc/scoring_GSED.html | 627 ++++++++----------------- inst/doc/using_DAZ.html | 24 man/builtin_translate.Rd | 1 man/dscore.Rd | 12 man/get_age_equivalent.Rd | 3 man/get_itemnames.Rd | 10 man/rename_vector.Rd | 17 tests/testthat/test-dscore.R | 15 vignettes/custom_priors.Rmd | 46 + vignettes/getting_started.Rmd | 78 +-- vignettes/multiple_keys.Rmd |only vignettes/references.bib | 15 vignettes/scoring_GSED.Rmd | 234 ++------- 41 files changed, 876 insertions(+), 1985 deletions(-)
Title: Distributed Multinomial Regression
Description: Fast distributed/parallel estimation for multinomial logistic regression via Poisson factorization and the 'gamlr' package. For details see: Taddy (2015, AoAS), Distributed Multinomial Regression, <doi:10.48550/arXiv.1311.6139>.
Author: Matt Taddy [aut],
Nelson Rayl [cre]
Maintainer: Nelson Rayl <nelsonrayl14@gmail.com>
Diff between distrom versions 1.0.1 dated 2022-03-28 and 1.0.2 dated 2025-10-03
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ inst/CITATION | 4 ++-- man/collapse.Rd | 6 +++--- man/dmr.Rd | 30 +++++++++++++++--------------- man/dmrcoef-class.Rd | 20 ++++++++++---------- 7 files changed, 44 insertions(+), 40 deletions(-)
Title: Systematic Comparison of Trip Distribution Laws and Models
Description: The main purpose of this package is to propose a rigorous framework to fairly compare trip distribution laws and models as described in Lenormand et al. (2016) <doi:10.1016/j.jtrangeo.2015.12.008>.
Author: Maxime Lenormand [aut, cre]
Maintainer: Maxime Lenormand <maxime.lenormand@inrae.fr>
Diff between TDLM versions 1.1.2 dated 2025-05-06 and 1.1.3 dated 2025-10-03
DESCRIPTION | 8 +- MD5 | 70 ++++++++++--------- NEWS.md | 24 ++++++ R/data.R | 119 +++++++++++++++++++++++--------- R/extract_opportunities.R | 2 R/gof.R | 2 R/run_law.R | 2 R/run_law_model.R | 2 R/run_model.R | 2 README.md | 20 ++++- build/vignette.rds |binary data/coords.rda |binary data/coords_xy.rda |binary data/county.rda |binary data/distance.rda |binary data/distance_mtp.rda |only data/mass.rda |binary data/mass_mtp.rda |only data/mtp.rda |only data/od.rda |binary data/od_mtp.rda |only inst/doc/TDLM.html | 168 +++++++++++++++++++++++----------------------- inst/java/Sij.jar |binary inst/java/TDLM.class |binary inst/java/TDLM.jar |binary inst/java/TDM.class |binary inst/java/TDM.jar |binary java/TDLM.java | 2 java/TDM.java | 2 man/coords.Rd | 10 +- man/coords_xy.Rd | 11 +-- man/county.Rd | 8 +- man/distance.Rd | 9 +- man/distance_mtp.Rd |only man/gof.Rd | 2 man/mass.Rd | 10 +- man/mass_mtp.Rd |only man/mtp.Rd |only man/od.Rd | 15 ++-- man/od_mtp.Rd |only 40 files changed, 288 insertions(+), 200 deletions(-)
Title: Visually Assessing the Specificity and Informativeness of Primer
Pairs
Description: Identifies potential target sequences for a given
set of primers and generates phylogenetic trees annotated with the
taxonomies of the predicted amplification products.
Author: Jim Hester [aut],
Matt Cannon [aut, cre]
Maintainer: Matt Cannon <matthewvc1@gmail.com>
Diff between primerTree versions 1.0.6 dated 2022-04-05 and 1.1.0 dated 2025-10-03
DESCRIPTION | 14 - MD5 | 36 +- R/filterResults.R | 67 ++-- R/plot.R | 277 +++++++++++++------- R/primerTree.R | 613 ++++++++++++++++++++++++++++----------------- R/search.R | 565 ++++++++++++++++++++++++----------------- R/sequence.R | 238 ++++++++++------- R/taxonomy.R | 134 +++++---- man/filter_seqs.Rd | 4 man/get_sequence.Rd | 2 man/get_sequences.Rd | 6 man/layout_tree_ape.Rd | 4 man/parse_primer_hits.Rd | 3 man/plot.primerTree.Rd | 2 man/primerTree.Rd | 1 man/primer_search.Rd | 9 man/search_primer_pair.Rd | 22 - man/seq_lengths.Rd | 6 man/tree_from_alignment.Rd | 4 19 files changed, 1215 insertions(+), 792 deletions(-)
Title: Fast Utilities for Year Month Day Objects
Description: A collection of utility functions for working with
Year Month Day objects. Includes functions for fast parsing of numeric
and character input based on algorithms described in Hinnant, H. (2021)
<https://howardhinnant.github.io/date_algorithms.html> as well as a branchless
calculation of leap years by Jerichaux (2025) <https://stackoverflow.com/a/79564914>.
Author: Tim Taylor [aut, cre] ,
Howard Hinnant [aut] ,
jerichaux [aut]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between fastymd versions 0.1.3 dated 2025-05-12 and 0.1.4 dated 2025-10-03
DESCRIPTION | 8 +-- MD5 | 28 ++++++------ NEWS.md | 4 + R/accessors.R | 32 +++++++------- R/fymd.R | 95 +++++++++++++++++++++---------------------- R/is_leap_year.R | 14 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/fastymd.R | 4 - inst/doc/fastymd.Rmd | 4 - inst/doc/fastymd.html | 52 +++++++++++------------ inst/tinytest/test_fastymd.R | 77 +++++++++++++++++----------------- man/fymd.Rd | 3 - tests/tinytest.R | 2 vignettes/fastymd.Rmd | 4 - 15 files changed, 164 insertions(+), 163 deletions(-)
Title: Simultaneous Clustering and (or) Dimensionality Reduction
Description: Methods for simultaneous clustering and dimensionality reduction such as: Double k-means, Reduced k-means, Factorial k-means, Clustering with Disjoint PCA but also methods for exclusively dimensionality reduction: Disjoint PCA, Disjoint FA. The statistical methods implemented refer to the following articles: de Soete G., Carroll J. (1994) "K-means clustering in a low-dimensional Euclidean space" <doi:10.1007/978-3-642-51175-2_24> ; Vichi M. (2001) "Double k-means Clustering for Simultaneous Classification of Objects and Variables" <doi:10.1007/978-3-642-59471-7_6> ; Vichi M., Kiers H.A.L. (2001) "Factorial k-means analysis for two-way data" <doi:10.1016/S0167-9473(00)00064-5> ; Vichi M., Saporta G. (2009) "Clustering and disjoint principal component analysis" <doi:10.1016/j.csda.2008.05.028> ; Vichi M. (2017) "Disjoint factor analysis with cross-loadings" <doi:10.1007/s11634-016-0263-9>.
Author: Ionel Prunila [aut, cre],
Maurizio Vichi [aut]
Maintainer: Ionel Prunila <ionel.prunila@uniroma1.it>
Diff between drclust versions 0.1 dated 2024-04-22 and 0.1.1 dated 2025-10-03
DESCRIPTION | 7 +++---- MD5 | 6 +++--- src/disfa.cpp | 3 ++- src/double_km.cpp | 8 ++++++-- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut],
Jim Hester [aut],
Winston Chang [aut],
Jennifer Bryan [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between devtools versions 2.4.5 dated 2022-10-11 and 2.4.6 dated 2025-10-03
devtools-2.4.5/devtools/man/figures/logo.svg |only devtools-2.4.6/devtools/DESCRIPTION | 38 devtools-2.4.6/devtools/LICENSE | 2 devtools-2.4.6/devtools/MD5 | 374 ++-- devtools-2.4.6/devtools/NAMESPACE | 257 +- devtools-2.4.6/devtools/NEWS.md | 20 devtools-2.4.6/devtools/R/R.R | 62 devtools-2.4.6/devtools/R/active.R | 98 - devtools-2.4.6/devtools/R/bash.R | 18 devtools-2.4.6/devtools/R/build-manual.R | 50 devtools-2.4.6/devtools/R/build-readme.R | 133 - devtools-2.4.6/devtools/R/build-site.R | 64 devtools-2.4.6/devtools/R/check-devtools.R | 288 +-- devtools-2.4.6/devtools/R/check-doc.R | 128 - devtools-2.4.6/devtools/R/check-git.R | 54 devtools-2.4.6/devtools/R/check-mac.R | 146 - devtools-2.4.6/devtools/R/check-win.R | 298 +-- devtools-2.4.6/devtools/R/check.R | 503 ++--- devtools-2.4.6/devtools/R/create.R | 22 devtools-2.4.6/devtools/R/dev-mode.R | 170 + devtools-2.4.6/devtools/R/devtools-package.R | 46 devtools-2.4.6/devtools/R/document.R | 70 devtools-2.4.6/devtools/R/git.R | 32 devtools-2.4.6/devtools/R/has-tests.R | 24 devtools-2.4.6/devtools/R/install.R | 381 ++-- devtools-2.4.6/devtools/R/lint.R | 46 devtools-2.4.6/devtools/R/missing-s3.R | 42 devtools-2.4.6/devtools/R/package-deps.R | 14 devtools-2.4.6/devtools/R/package.R | 190 +- devtools-2.4.6/devtools/R/pkgbuild.R | 80 devtools-2.4.6/devtools/R/pkgload.R | 44 devtools-2.4.6/devtools/R/r-hub.R | 90 devtools-2.4.6/devtools/R/release.R | 745 ++++---- devtools-2.4.6/devtools/R/reload.R | 74 devtools-2.4.6/devtools/R/remotes.R | 222 +- devtools-2.4.6/devtools/R/revdep.R | 188 +- devtools-2.4.6/devtools/R/run-examples.R | 200 +- devtools-2.4.6/devtools/R/run-source.R | 327 +-- devtools-2.4.6/devtools/R/save-all.R | 26 devtools-2.4.6/devtools/R/session-info.R | 74 devtools-2.4.6/devtools/R/show-news.R | 58 devtools-2.4.6/devtools/R/sitrep.R | 422 ++-- devtools-2.4.6/devtools/R/spell-check.R | 32 devtools-2.4.6/devtools/R/test.R | 369 ++-- devtools-2.4.6/devtools/R/uninstall.R | 54 devtools-2.4.6/devtools/R/usethis.R | 42 devtools-2.4.6/devtools/R/utils.R | 93 - devtools-2.4.6/devtools/R/vignette-r.R | 132 - devtools-2.4.6/devtools/R/vignettes.R | 264 +- devtools-2.4.6/devtools/R/wd.R | 34 devtools-2.4.6/devtools/R/zzz.R | 56 devtools-2.4.6/devtools/README.md | 350 +-- devtools-2.4.6/devtools/build/vignette.rds |binary devtools-2.4.6/devtools/inst/WORDLIST | 349 +-- devtools-2.4.6/devtools/inst/doc/dependencies.Rmd | 218 +- devtools-2.4.6/devtools/inst/doc/dependencies.html | 912 +++++----- devtools-2.4.6/devtools/inst/rstudio/addins.dcf | 48 devtools-2.4.6/devtools/man/as.package.Rd | 42 devtools-2.4.6/devtools/man/bash.Rd | 30 devtools-2.4.6/devtools/man/build.Rd | 183 +- devtools-2.4.6/devtools/man/build_manual.Rd | 42 devtools-2.4.6/devtools/man/build_rmd.Rd | 64 devtools-2.4.6/devtools/man/build_site.Rd | 38 devtools-2.4.6/devtools/man/build_vignettes.Rd | 154 - devtools-2.4.6/devtools/man/check.Rd | 303 +-- devtools-2.4.6/devtools/man/check_mac_release.Rd | 90 devtools-2.4.6/devtools/man/check_man.Rd | 54 devtools-2.4.6/devtools/man/check_rhub.Rd | 99 - devtools-2.4.6/devtools/man/check_win.Rd | 151 - devtools-2.4.6/devtools/man/clean_vignettes.Rd | 32 devtools-2.4.6/devtools/man/create.Rd | 56 devtools-2.4.6/devtools/man/dev_mode.Rd | 66 devtools-2.4.6/devtools/man/dev_packages.Rd | 24 devtools-2.4.6/devtools/man/dev_sitrep.Rd | 74 devtools-2.4.6/devtools/man/devtools-deprecated.Rd | 34 devtools-2.4.6/devtools/man/devtools-package.Rd | 102 - devtools-2.4.6/devtools/man/document.Rd | 54 devtools-2.4.6/devtools/man/figures/logo.png |only devtools-2.4.6/devtools/man/git_checks.Rd | 34 devtools-2.4.6/devtools/man/has_tests.Rd | 24 devtools-2.4.6/devtools/man/install.Rd | 225 +- devtools-2.4.6/devtools/man/install_deps.Rd | 177 + devtools-2.4.6/devtools/man/is.package.Rd | 24 devtools-2.4.6/devtools/man/lint.Rd | 52 devtools-2.4.6/devtools/man/load_all.Rd | 263 +- devtools-2.4.6/devtools/man/loaded_packages.Rd | 32 devtools-2.4.6/devtools/man/missing_s3.Rd | 30 devtools-2.4.6/devtools/man/package_file.Rd | 48 devtools-2.4.6/devtools/man/r_env_vars.Rd | 40 devtools-2.4.6/devtools/man/reexports.Rd | 69 devtools-2.4.6/devtools/man/release.Rd | 91 devtools-2.4.6/devtools/man/release_checks.Rd | 34 devtools-2.4.6/devtools/man/reload.Rd | 74 devtools-2.4.6/devtools/man/remote-reexports.Rd | 462 ++--- devtools-2.4.6/devtools/man/revdep.Rd | 110 - devtools-2.4.6/devtools/man/run_examples.Rd | 104 - devtools-2.4.6/devtools/man/save_all.Rd | 30 devtools-2.4.6/devtools/man/show_news.Rd | 40 devtools-2.4.6/devtools/man/source_gist.Rd | 112 - devtools-2.4.6/devtools/man/source_url.Rd | 86 devtools-2.4.6/devtools/man/spell_check.Rd | 42 devtools-2.4.6/devtools/man/submit_cran.Rd | 61 devtools-2.4.6/devtools/man/test.Rd | 112 - devtools-2.4.6/devtools/man/uninstall.Rd | 64 devtools-2.4.6/devtools/man/uses_testthat.Rd | 24 devtools-2.4.6/devtools/man/wd.Rd | 36 devtools-2.4.6/devtools/tests/spelling.R | 6 devtools-2.4.6/devtools/tests/testthat.R | 16 devtools-2.4.6/devtools/tests/testthat/_snaps/active.md | 42 devtools-2.4.6/devtools/tests/testthat/_snaps/build-readme.md | 32 devtools-2.4.6/devtools/tests/testthat/_snaps/check-win.md | 32 devtools-2.4.6/devtools/tests/testthat/_snaps/package.md | 54 devtools-2.4.6/devtools/tests/testthat/_snaps/run-source.md | 102 - devtools-2.4.6/devtools/tests/testthat/_snaps/sitrep.md | 78 devtools-2.4.6/devtools/tests/testthat/check-results-note.log | 150 - devtools-2.4.6/devtools/tests/testthat/helper.R | 34 devtools-2.4.6/devtools/tests/testthat/shallowRepo/HEAD | 2 devtools-2.4.6/devtools/tests/testthat/shallowRepo/config | 12 devtools-2.4.6/devtools/tests/testthat/shallowRepo/description | 2 devtools-2.4.6/devtools/tests/testthat/shallowRepo/info/exclude | 12 devtools-2.4.6/devtools/tests/testthat/shallowRepo/packed-refs | 4 devtools-2.4.6/devtools/tests/testthat/shallowRepo/refs/tags/v1.10.0 | 2 devtools-2.4.6/devtools/tests/testthat/shallowRepo/shallow | 2 devtools-2.4.6/devtools/tests/testthat/test-active.R | 51 devtools-2.4.6/devtools/tests/testthat/test-build-readme.R | 87 devtools-2.4.6/devtools/tests/testthat/test-build-site.R | 66 devtools-2.4.6/devtools/tests/testthat/test-check-doc.R | 46 devtools-2.4.6/devtools/tests/testthat/test-check-win.R | 28 devtools-2.4.6/devtools/tests/testthat/test-check.R | 32 devtools-2.4.6/devtools/tests/testthat/test-install.R | 146 - devtools-2.4.6/devtools/tests/testthat/test-package.R | 24 devtools-2.4.6/devtools/tests/testthat/test-reload.R | 60 devtools-2.4.6/devtools/tests/testthat/test-run-examples.R | 16 devtools-2.4.6/devtools/tests/testthat/test-run-source.R | 148 - devtools-2.4.6/devtools/tests/testthat/test-sitrep.R | 110 - devtools-2.4.6/devtools/tests/testthat/test-test.R | 118 - devtools-2.4.6/devtools/tests/testthat/test-uninstall.R | 26 devtools-2.4.6/devtools/tests/testthat/test-utils.R | 10 devtools-2.4.6/devtools/tests/testthat/test-vignettes.R | 118 - devtools-2.4.6/devtools/tests/testthat/testCheckExtrafile/DESCRIPTION | 18 devtools-2.4.6/devtools/tests/testthat/testCheckExtrafile/NAMESPACE | 2 devtools-2.4.6/devtools/tests/testthat/testCheckExtrafile/R/a.R | 6 devtools-2.4.6/devtools/tests/testthat/testCheckExtrafile/an_extra_file | 2 devtools-2.4.6/devtools/tests/testthat/testCheckExtrafile/man/a.Rd | 26 devtools-2.4.6/devtools/tests/testthat/testError/DESCRIPTION | 12 devtools-2.4.6/devtools/tests/testthat/testError/R/error.R | 14 devtools-2.4.6/devtools/tests/testthat/testHelp/DESCRIPTION | 16 devtools-2.4.6/devtools/tests/testthat/testHelp/NAMESPACE | 6 devtools-2.4.6/devtools/tests/testthat/testHelp/R/foofoo.R | 18 devtools-2.4.6/devtools/tests/testthat/testHelp/man/foofoo.Rd | 30 devtools-2.4.6/devtools/tests/testthat/testMarkdownVignettes/DESCRIPTION | 18 devtools-2.4.6/devtools/tests/testthat/testMarkdownVignettes/vignettes/test.Rmd | 26 devtools-2.4.6/devtools/tests/testthat/testMissingNsObject/DESCRIPTION | 12 devtools-2.4.6/devtools/tests/testthat/testMissingNsObject/NAMESPACE | 2 devtools-2.4.6/devtools/tests/testthat/testMissingNsObject/R/a.R | 2 devtools-2.4.6/devtools/tests/testthat/testPkgdown/DESCRIPTION | 24 devtools-2.4.6/devtools/tests/testthat/testPkgdown/NAMESPACE | 6 devtools-2.4.6/devtools/tests/testthat/testPkgdown/R/pkgdown-test-test.R | 22 devtools-2.4.6/devtools/tests/testthat/testPkgdown/_pkgdown.yml | 2 devtools-2.4.6/devtools/tests/testthat/testPkgdown/man/pkgdown_test_test.Rd | 34 devtools-2.4.6/devtools/tests/testthat/testPkgdown/vignettes/test.Rmd | 28 devtools-2.4.6/devtools/tests/testthat/testTest/DESCRIPTION | 28 devtools-2.4.6/devtools/tests/testthat/testTest/NAMESPACE | 4 devtools-2.4.6/devtools/tests/testthat/testTest/R/dummy.R | 2 devtools-2.4.6/devtools/tests/testthat/testTest/tests/testthat.R | 8 devtools-2.4.6/devtools/tests/testthat/testTest/tests/testthat/test-dummy.R | 6 devtools-2.4.6/devtools/tests/testthat/testTest/tests/testthat/test-envvar.R | 6 devtools-2.4.6/devtools/tests/testthat/testTestWithDepends/DESCRIPTION | 18 devtools-2.4.6/devtools/tests/testthat/testTestWithDepends/NAMESPACE | 2 devtools-2.4.6/devtools/tests/testthat/testTestWithDepends/tests/testthat.R | 8 devtools-2.4.6/devtools/tests/testthat/testTestWithDepends/tests/testthat/test-dummy.R | 6 devtools-2.4.6/devtools/tests/testthat/testTestWithFailure/DESCRIPTION | 20 devtools-2.4.6/devtools/tests/testthat/testTestWithFailure/NAMESPACE | 4 devtools-2.4.6/devtools/tests/testthat/testTestWithFailure/R/dummy.R | 2 devtools-2.4.6/devtools/tests/testthat/testTestWithFailure/tests/testthat.R | 8 devtools-2.4.6/devtools/tests/testthat/testTestWithFailure/tests/testthat/test-fail.R | 6 devtools-2.4.6/devtools/tests/testthat/testTestWithFailure/tests/testthat/test-warn.R | 6 devtools-2.4.6/devtools/tests/testthat/testUseData/DESCRIPTION | 14 devtools-2.4.6/devtools/tests/testthat/testUseData/NAMESPACE | 2 devtools-2.4.6/devtools/tests/testthat/testUseData/R/a.R | 2 devtools-2.4.6/devtools/tests/testthat/testVignetteExtras/DESCRIPTION | 14 devtools-2.4.6/devtools/tests/testthat/testVignetteExtras/vignettes/a.R | 2 devtools-2.4.6/devtools/tests/testthat/testVignetteExtras/vignettes/new.Rnw | 8 devtools-2.4.6/devtools/tests/testthat/testVignettes/DESCRIPTION | 14 devtools-2.4.6/devtools/tests/testthat/testVignettes/vignettes/new.Rnw | 10 devtools-2.4.6/devtools/tests/testthat/testVignettesBuilt/DESCRIPTION | 14 devtools-2.4.6/devtools/tests/testthat/testVignettesBuilt/R/code.R | 4 devtools-2.4.6/devtools/tests/testthat/testVignettesBuilt/vignettes/new.Rnw | 22 devtools-2.4.6/devtools/vignettes/dependencies.Rmd | 218 +- 189 files changed, 7854 insertions(+), 7863 deletions(-)
Title: General Purpose Optimization in R using C++
Description: Perform general purpose optimization in R using C++. A unified
wrapper interface is provided to call C functions of the five optimization
algorithms ('Nelder-Mead', 'BFGS', 'CG', 'L-BFGS-B' and 'SANN') underlying
optim().
Author: Yi Pan [aut, cre]
Maintainer: Yi Pan <ypan1988@gmail.com>
Diff between roptim versions 0.1.6 dated 2022-08-06 and 0.1.7 dated 2025-10-03
DESCRIPTION | 15 +++++++++------ MD5 | 2 +- 2 files changed, 10 insertions(+), 7 deletions(-)
Title: Read Human Mortality Database and Human Fertility Database Data
from the Web
Description: Utilities for reading data from the Human Mortality Database (<https://www.mortality.org>), Human Fertility Database (<https://www.humanfertility.org>), and similar databases from the web or locally into an R session as data.frame objects. These are the two most widely used sources of demographic data to study basic demographic change, trends, and develop new demographic methods. Other supported databases at this time include the Human Fertility Collection (<https://www.fertilitydata.org>), The Japanese Mortality Database (<https://www.ipss.go.jp/p-toukei/JMD/index-en.html>), and the Canadian Human Mortality Database (<http://www.bdlc.umontreal.ca/chmd/>). Arguments and data are standardized.
Author: Tim Riffe [aut, cre],
Carl Boe [aut],
Jason Hilton [aut],
Josh Goldstein [ctb],
Stephen Holzman [ctb],
Sam Hyun Yoo [ctb]
Maintainer: Tim Riffe <tim.riffe@gmail.com>
Diff between HMDHFDplus versions 2.0.6 dated 2025-01-21 and 2.0.8 dated 2025-10-03
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/HMDutils.R | 4 ++-- R/readHFD.R | 3 ++- 5 files changed, 20 insertions(+), 11 deletions(-)
Title: Multiple Class Area under ROC Curve
Description: An S4 implementation of Eq. (3) and Eq. (7) by
David J. Hand and Robert J. Till (2001) <DOI:10.1023/A:1010920819831>.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between HandTill2001 versions 1.0.2 dated 2025-05-24 and 1.0.3 dated 2025-10-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/consensus_auc.pdf |binary tests/testthat/test-throw.R | 2 +- 5 files changed, 12 insertions(+), 8 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014
<DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic
analysis of functional data through phase and amplitude separation.
Author: J. Derek Tucker [aut, cre] ,
Aymeric Stamm [ctb]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 2.4.1 dated 2025-09-23 and 2.4.2 dated 2025-10-03
DESCRIPTION | 8 ++--- MD5 | 12 +++++--- NAMESPACE | 1 NEWS.md | 3 ++ R/ppd.R |only R/utils.R | 82 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 2 - man/ppd.Rd |only 8 files changed, 98 insertions(+), 10 deletions(-)
Title: Joint Dimension Reduction and Spatial Clustering
Description: Joint dimension reduction and spatial clustering is conducted for
Single-cell RNA sequencing and spatial transcriptomics data, and more details can be referred to
Wei Liu, Xu Liao, Yi Yang, Huazhen Lin, Joe Yeong, Xiang Zhou, Xingjie Shi and Jin Liu. (2022) <doi:10.1093/nar/gkac219>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.
Author: Wei Liu [aut, cre],
Yi Yang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between DR.SC versions 3.5 dated 2025-03-29 and 3.6 dated 2025-10-03
DR.SC-3.5/DR.SC/build/partial.rdb |only DR.SC-3.5/DR.SC/data/datalist |only DR.SC-3.5/DR.SC/man/genspatialdata.Rd |only DR.SC-3.6/DR.SC/DESCRIPTION | 15 - DR.SC-3.6/DR.SC/MD5 | 69 ++--- DR.SC-3.6/DR.SC/NAMESPACE | 4 DR.SC-3.6/DR.SC/R/RcppExports.R | 8 DR.SC-3.6/DR.SC/R/main.R | 343 ++++++++++++++-------------- DR.SC-3.6/DR.SC/README.md | 3 DR.SC-3.6/DR.SC/build/vignette.rds |binary DR.SC-3.6/DR.SC/data/seu.rda |only DR.SC-3.6/DR.SC/inst/doc/DR-SC.R | 2 DR.SC-3.6/DR.SC/inst/doc/DR-SC.Rmd | 4 DR.SC-3.6/DR.SC/inst/doc/DR-SC.html | 185 ++++++++------- DR.SC-3.6/DR.SC/inst/doc/DR.SC.DLPFC.R | 8 DR.SC-3.6/DR.SC/inst/doc/DR.SC.DLPFC.Rmd | 10 DR.SC-3.6/DR.SC/inst/doc/DR.SC.DLPFC.html | 332 +++++++++++++++------------ DR.SC-3.6/DR.SC/inst/doc/DR.SC.Simu.R | 10 DR.SC-3.6/DR.SC/inst/doc/DR.SC.Simu.Rmd | 54 ++-- DR.SC-3.6/DR.SC/inst/doc/DR.SC.Simu.html | 294 +++++++++++++----------- DR.SC-3.6/DR.SC/man/DR.SC.Rd | 4 DR.SC-3.6/DR.SC/man/DR.SC.fit.Rd | 4 DR.SC-3.6/DR.SC/man/FindSVGs.Rd | 2 DR.SC-3.6/DR.SC/man/RunWPCA.Rd | 2 DR.SC-3.6/DR.SC/man/drscPlot.Rd | 2 DR.SC-3.6/DR.SC/man/getAdj.Rd | 4 DR.SC-3.6/DR.SC/man/mbicPlot.Rd | 2 DR.SC-3.6/DR.SC/man/selectModel.Rd | 4 DR.SC-3.6/DR.SC/man/seu_sim.Rd |only DR.SC-3.6/DR.SC/man/sp_means_Rcpp.Rd | 38 +-- DR.SC-3.6/DR.SC/man/sp_sums_Rcpp.Rd | 38 +-- DR.SC-3.6/DR.SC/man/spatialPlotClusters.Rd | 2 DR.SC-3.6/DR.SC/man/topSVGs.Rd | 2 DR.SC-3.6/DR.SC/src/RcppExports.cpp | 33 -- DR.SC-3.6/DR.SC/src/simulDRcluster_main.cpp | 54 ++++ DR.SC-3.6/DR.SC/vignettes/DR-SC.Rmd | 4 DR.SC-3.6/DR.SC/vignettes/DR.SC.DLPFC.Rmd | 10 DR.SC-3.6/DR.SC/vignettes/DR.SC.Simu.Rmd | 54 ++-- 38 files changed, 855 insertions(+), 745 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] ,
Christophe Dervieux [ctb] ,
JJ Allaire [ctb],
Albert Kim [ctb],
Alessandro Samuel-Rosa [ctb],
Andrzej Oles [ctb],
Atsushi Yasumoto [ctb] ,
Aust Frederik [ctb] ,
Bastiaan Quast [ctb],
Ben Marwick [ctb],
Chester Ismay [ctb],
Clif [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.44 dated 2025-08-21 and 0.45 dated 2025-10-03
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/html.R | 2 +- tests/testthat/test-gitbook.R | 24 ++++++++++++++++++++++++ 4 files changed, 31 insertions(+), 7 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-23 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-06 0.3.1
2020-10-03 0.2
2019-10-06 0.1