Title: Frequency Distribution Tables, Histograms and Polygons
Description: Perform frequency distribution tables, associated histograms
and polygons from vector, data.frame and matrix objects for
numerical and categorical variables.
Author: Jose C. Faria [aut, cre],
Ivan B. Allaman [aut],
Enio G. Jelihovschi [aut]
Maintainer: Jose C. Faria <joseclaudio.faria@gmail.com>
Diff between fdth versions 1.3-0 dated 2023-11-17 and 1.3-4 dated 2026-05-11
fdth-1.3-0/fdth/NEWS |only fdth-1.3-4/fdth/DESCRIPTION | 25 +- fdth-1.3-4/fdth/INDEX | 4 fdth-1.3-4/fdth/MD5 | 62 +++-- fdth-1.3-4/fdth/NEWS.md |only fdth-1.3-4/fdth/R/fdt.R | 3 fdth-1.3-4/fdth/R/mfv.default.R | 8 fdth-1.3-4/fdth/R/mfv.fdt.R | 4 fdth-1.3-4/fdth/R/quantile.fdt.R | 67 ++++-- fdth-1.3-4/fdth/R/sd.R | 2 fdth-1.3-4/fdth/R/var.R | 2 fdth-1.3-4/fdth/README.md |only fdth-1.3-4/fdth/build/vignette.rds |binary fdth-1.3-4/fdth/inst/CITATION | 10 fdth-1.3-4/fdth/inst/doc/latex_fdt.R | 170 ++++++++------- fdth-1.3-4/fdth/inst/doc/latex_fdt.Rnw | 350 ++++++++++++++++++++++---------- fdth-1.3-4/fdth/inst/doc/latex_fdt.pdf |binary fdth-1.3-4/fdth/man/fdt.Rd | 38 +-- fdth-1.3-4/fdth/man/fdt_cat.Rd | 21 + fdth-1.3-4/fdth/man/fdth-package.Rd | 81 +++---- fdth-1.3-4/fdth/man/make.fdt.Rd | 18 - fdth-1.3-4/fdth/man/mean.fdt.Rd | 8 fdth-1.3-4/fdth/man/median.fdt.Rd | 14 - fdth-1.3-4/fdth/man/mfv.Rd | 99 +++++---- fdth-1.3-4/fdth/man/plot.Rd | 44 ++-- fdth-1.3-4/fdth/man/print.Rd | 38 +-- fdth-1.3-4/fdth/man/quantile.fdt.Rd | 113 +++++++--- fdth-1.3-4/fdth/man/sd.Rd | 26 +- fdth-1.3-4/fdth/man/summary.Rd | 34 +-- fdth-1.3-4/fdth/man/var.Rd | 24 +- fdth-1.3-4/fdth/man/xtable.fdt.Rd | 14 - fdth-1.3-4/fdth/tests |only fdth-1.3-4/fdth/vignettes/latex_fdt.Rnw | 350 ++++++++++++++++++++++---------- 33 files changed, 1026 insertions(+), 603 deletions(-)
Title: Bayesian Dynamic Borrowing Analysis and Simulation
Description: Bayesian dynamic borrowing is an approach to incorporating external
data to supplement a randomized, controlled trial analysis in which
external data are incorporated in a dynamic way (e.g., based on similarity
of outcomes); see Viele 2013 <doi:10.1002/pst.1589> for an overview.
This package implements the hierarchical commensurate prior approach to dynamic borrowing
as described in Hobbes 2011 <doi:10.1111/j.1541-0420.2011.01564.x>.
There are three main functionalities. First, 'psborrow2' provides a user-friendly
interface for applying dynamic borrowing on the study results handles the Markov Chain
Monte Carlo sampling on behalf of the user. Second, 'psborrow2' provides a
simulation framework to compare different borrowing parameters (e.g. full borrowing, no
borrowing, dynamic borrowing) and other trial and borrowing characteristics
(e.g. sample size, covariates) in a unified way. Third, 'psborrow2' provides
a set of functions to generate data for simulation studies, and a [...truncated...]
Author: Matt Secrest [aut, cre] ,
Isaac Gravestock [aut],
Craig Gower-Page [ctb],
Manoj Khanal [ctb],
Mingyang Shan [ctb],
Kexin Jin [ctb],
Zhi Yang [ctb],
Genentech, Inc. [cph, fnd]
Maintainer: Matt Secrest <secrestm@gene.com>
Diff between psborrow2 versions 0.0.4.0 dated 2025-02-12 and 0.0.5.0 dated 2026-05-11
psborrow2-0.0.4.0/psborrow2/vignettes/figure-match_weight_01_methods-unnamed-chunk-28-1.png |only psborrow2-0.0.4.0/psborrow2/vignettes/figure-match_weight_01_methods-unnamed-chunk-61-1.png |only psborrow2-0.0.4.0/psborrow2/vignettes/figure-match_weight_01_methods-unnamed-chunk-62-1.png |only psborrow2-0.0.4.0/psborrow2/vignettes/figure-match_weight_01_methods-unnamed-chunk-67-1.png |only psborrow2-0.0.4.0/psborrow2/vignettes/figure-match_weight_02_application-unnamed-chunk-31-1.png |only psborrow2-0.0.4.0/psborrow2/vignettes/figure-match_weight_02_application-unnamed-chunk-32-1.png |only psborrow2-0.0.4.0/psborrow2/vignettes/figure-match_weight_02_application-unnamed-chunk-32-2.png |only psborrow2-0.0.4.0/psborrow2/vignettes/figure-match_weight_02_application-unnamed-chunk-42-1.png |only psborrow2-0.0.4.0/psborrow2/vignettes/figure-match_weight_02_application-unnamed-chunk-43-1.png |only psborrow2-0.0.4.0/psborrow2/vignettes/figure-match_weight_02_application-unnamed-chunk-44-1.png 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psborrow2-0.0.5.0/psborrow2/R/prior_cauchy.R | 9 psborrow2-0.0.5.0/psborrow2/R/prior_exponential.R | 8 psborrow2-0.0.5.0/psborrow2/R/prior_gamma.R | 8 psborrow2-0.0.5.0/psborrow2/R/prior_half_cauchy.R | 8 psborrow2-0.0.5.0/psborrow2/R/prior_normal.R | 21 psborrow2-0.0.5.0/psborrow2/R/prior_poisson.R | 11 psborrow2-0.0.5.0/psborrow2/R/sim_borrowing_list.R | 5 psborrow2-0.0.5.0/psborrow2/R/sim_covariate_list.R | 3 psborrow2-0.0.5.0/psborrow2/R/sim_data_list.R | 6 psborrow2-0.0.5.0/psborrow2/R/sim_outcome_list.R | 5 psborrow2-0.0.5.0/psborrow2/R/sim_treatment_list.R | 3 psborrow2-0.0.5.0/psborrow2/R/simulate_data.R | 72 psborrow2-0.0.5.0/psborrow2/R/simulate_data_baseline.R | 2 psborrow2-0.0.5.0/psborrow2/R/simulation_class.R | 10 psborrow2-0.0.5.0/psborrow2/build/partial.rdb |binary psborrow2-0.0.5.0/psborrow2/build/vignette.rds |binary psborrow2-0.0.5.0/psborrow2/inst/WORDLIST | 14 psborrow2-0.0.5.0/psborrow2/inst/doc/data_simulation.Rmd | 47 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Title: Build Reproducible Network Studies for OMOP Common Data Model
Description: Streamlines the setup and execution of network studies using
the Observational Medical Outcomes Partnership (OMOP) Common Data
Model (CDM). Creates standardised project structures with template
code, manages dependencies with 'renv', provides code review
utilities, and supports containerised execution with 'Docker' for
reproducible multi-site studies. Includes 'GitHub' integration for
collaboration and version control.
Author: Folu Akintola [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Folu Akintola <folu.akintola@ndorms.ox.ac.uk>
Diff between OmopStudyBuilder versions 0.1.0 dated 2026-04-28 and 0.1.1 dated 2026-05-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/linkGitHub.R | 5 +++++ tests/testthat/test-linkGitHub.R | 35 ++++++++--------------------------- 4 files changed, 20 insertions(+), 34 deletions(-)
More information about OmopStudyBuilder at CRAN
Permanent link
Title: Cooperative Learning for Multi-View Analysis
Description: Cooperative learning combines the usual squared error loss of predictions with an agreement penalty to encourage the predictions from different data views to agree. By varying the weight of the agreement penalty, we get a continuum of solutions that include the well-known early and late fusion approaches. Cooperative learning chooses the degree of agreement (or fusion) in an adaptive manner, using a validation set or cross-validation to estimate test set prediction error. In the setting of cooperative regularized linear regression, the method combines the lasso penalty with the agreement penalty (Ding, D., Li, S., Narasimhan, B., Tibshirani, R. (2021) <doi:10.1073/pnas.2202113119>).
Author: Daisy Yi Ding [aut],
Robert J. Tibshirani [aut],
Balasubramanian Narasimhan [aut, cre],
Trevor Hastie [aut],
Kenneth Tay [aut],
James Yang [aut],
Jonathan Taylor [aut]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between multiview versions 0.8 dated 2023-03-31 and 1.0 dated 2026-05-11
multiview-0.8/multiview/src/glmnetpp/CMakeLists.txt |only multiview-0.8/multiview/src/glmnetpp/benchmark |only multiview-0.8/multiview/src/glmnetpp/clean-build.sh |only multiview-0.8/multiview/src/glmnetpp/cmake |only multiview-0.8/multiview/src/glmnetpp/docs |only multiview-0.8/multiview/src/glmnetpp/src |only multiview-0.8/multiview/src/glmnetpp/test |only multiview-1.0/multiview/DESCRIPTION | 20 - multiview-1.0/multiview/MD5 | 158 ++-------- multiview-1.0/multiview/NEWS.md | 13 multiview-1.0/multiview/R/buildPredmat.coxnetlist.R | 15 multiview-1.0/multiview/R/coxpath.R | 68 +--- multiview-1.0/multiview/R/multiview.R | 18 - multiview-1.0/multiview/R/multiview.control.R | 12 multiview-1.0/multiview/R/response.coxnet.R | 2 multiview-1.0/multiview/R/view.contribution.R | 6 multiview-1.0/multiview/build/vignette.rds |binary multiview-1.0/multiview/inst/doc/multiview.R | 20 - multiview-1.0/multiview/inst/doc/multiview.pdf |binary multiview-1.0/multiview/inst/hexlogo |only multiview-1.0/multiview/man/figures/logo.png |binary multiview-1.0/multiview/man/get_cox_lambda_max.Rd | 2 multiview-1.0/multiview/man/multiview.control.Rd | 22 + multiview-1.0/multiview/man/multiview.cox.path.Rd | 10 multiview-1.0/multiview/src/glmnetpp/coxdev |only multiview-1.0/multiview/src/glmnetpp/include/glmnetpp_bits/elnet_driver/cox.hpp |only multiview-1.0/multiview/src/glmnetpp/include/glmnetpp_bits/elnet_path/cox_base.hpp |only multiview-1.0/multiview/src/glmnetpp/include/glmnetpp_bits/elnet_path/cox_naive.hpp |only multiview-1.0/multiview/src/glmnetpp/include/glmnetpp_bits/elnet_path/sp_cox_naive.hpp |only multiview-1.0/multiview/src/glmnetpp/include/glmnetpp_bits/elnet_point/cox_base.hpp |only multiview-1.0/multiview/src/glmnetpp/include/glmnetpp_bits/elnet_point/cox_naive.hpp |only multiview-1.0/multiview/src/glmnetpp/include/glmnetpp_bits/elnet_point/internal/binomial_base.hpp | 2 multiview-1.0/multiview/src/glmnetpp/include/glmnetpp_bits/elnet_point/internal/cox_base.hpp |only multiview-1.0/multiview/src/glmnetpp/include/glmnetpp_bits/elnet_point/internal/cox_naive.hpp |only multiview-1.0/multiview/src/glmnetpp/include/glmnetpp_bits/elnet_point/internal/sp_cox_naive.hpp |only multiview-1.0/multiview/src/glmnetpp/include/glmnetpp_bits/elnet_point/sp_cox_naive.hpp |only multiview-1.0/multiview/src/glmnetpp/include/glmnetpp_bits/util/cox_adapter.hpp |only multiview-1.0/multiview/src/glmnetpp/include/glmnetpp_bits/util/macros.hpp | 10 multiview-1.0/multiview/src/glmnetpp/include/glmnetpp_bits/util/types.hpp | 12 39 files changed, 175 insertions(+), 215 deletions(-)
Title: F1 Pit Stop Datasets
Description: Formula 1 pit stop data. The package provides information on teams and drivers across seasons (2019 or higher). It also includes a function to visualize pit stop performance.
Author: Jose Jordan-Soria [aut, cre]
Maintainer: Jose Jordan-Soria <jjose.jjordan@gmail.com>
Diff between f1pits versions 1.2.0 dated 2026-04-02 and 1.3.0 dated 2026-05-11
DESCRIPTION | 6 MD5 | 29 ++-- NAMESPACE | 11 + NEWS.md | 8 + R/globals.R | 3 R/pitchamp.R | 4 R/pitelo.R |only R/pits.R | 2 inst/doc/f1pits-intro.R | 35 +++++ inst/doc/f1pits-intro.Rmd | 53 ++++++++ inst/doc/f1pits-intro.html | 242 ++++++++++++++++++++++++++++++++------- man/pitchamp.Rd | 4 man/pitelo.Rd |only man/pits.Rd | 2 tests/testthat/test-pitelo.R |only tests/testthat/testdata/1aus.csv | 70 +++++------ vignettes/f1pits-intro.Rmd | 53 ++++++++ 17 files changed, 416 insertions(+), 106 deletions(-)
Title: Biplot Analysis for Multivariate Data Using Principal Components
Description: Provides tools for creating 2D and 3D biplots of multivariate data
based on principal components analysis, together with diagnostics for
reduction quality and enhanced visualization of variables and objects.
Author: Jose C. Faria [aut, cre],
Ivan B. Allaman [aut],
Clarice G. B. Demetrio [aut]
Maintainer: Jose C. Faria <joseclaudio.faria@gmail.com>
Diff between bpca versions 1.3-9 dated 2026-04-21 and 1.4-3 dated 2026-05-11
bpca-1.3-9/bpca/INDEX |only bpca-1.3-9/bpca/NEWS |only bpca-1.3-9/bpca/inst/doc/latex-bpca.R |only bpca-1.4-3/bpca/DESCRIPTION | 42 +- bpca-1.4-3/bpca/MD5 | 102 +++--- bpca-1.4-3/bpca/NAMESPACE | 29 - bpca-1.4-3/bpca/NEWS.md |only bpca-1.4-3/bpca/R/bpca.default.R | 29 + bpca-1.4-3/bpca/R/bpca.prcomp.R | 5 bpca-1.4-3/bpca/R/dt.tools.R | 12 bpca-1.4-3/bpca/R/plot.bpca.2d.R | 328 ++++++++++---------- bpca-1.4-3/bpca/R/plot.bpca.3d.R | 301 +++++++++++------- bpca-1.4-3/bpca/R/plot.qbpca.R | 184 ++++++++++- bpca-1.4-3/bpca/R/print.xtable.bpca.R | 158 +++++++-- bpca-1.4-3/bpca/R/qbpca.R | 12 bpca-1.4-3/bpca/R/summary.bpca.R | 31 - bpca-1.4-3/bpca/R/var.rbf.R | 11 bpca-1.4-3/bpca/R/var.rdf.R | 2 bpca-1.4-3/bpca/R/xtable.bpca.R | 2 bpca-1.4-3/bpca/README.md | 97 ++++-- bpca-1.4-3/bpca/build/vignette.rds |binary bpca-1.4-3/bpca/demo/00Index | 22 - bpca-1.4-3/bpca/demo/bpca-dinamic-3d.R | 39 +- bpca-1.4-3/bpca/demo/bpca-static-2d.R | 22 - bpca-1.4-3/bpca/demo/bpca-static-3d.R | 32 - bpca-1.4-3/bpca/demo/bpca.R | 451 ++++++++++------------------ bpca-1.4-3/bpca/demo/dt-tools.R | 13 bpca-1.4-3/bpca/demo/gge-check.R | 21 - bpca-1.4-3/bpca/demo/iris-var-rd.R | 16 bpca-1.4-3/bpca/demo/iris.R | 12 bpca-1.4-3/bpca/demo/rock-var-rd.R | 19 - bpca-1.4-3/bpca/demo/var-rb-2d.R | 18 - bpca-1.4-3/bpca/demo/var-rb-3d.R | 18 - bpca-1.4-3/bpca/demo/var-rd-2d.R | 68 ++-- bpca-1.4-3/bpca/inst/doc/bpca-overview.Rmd |only bpca-1.4-3/bpca/inst/doc/bpca-overview.html |only bpca-1.4-3/bpca/inst/doc/latex-bpca.Rnw | 385 ++++++++++++++--------- bpca-1.4-3/bpca/inst/doc/latex-bpca.pdf |binary bpca-1.4-3/bpca/man/bpca-package.Rd | 42 +- bpca-1.4-3/bpca/man/bpca.Rd | 85 ++--- bpca-1.4-3/bpca/man/dt.tools.Rd | 16 bpca-1.4-3/bpca/man/gabriel1971.Rd | 8 bpca-1.4-3/bpca/man/gge2003.Rd | 18 - bpca-1.4-3/bpca/man/marina.Rd | 4 bpca-1.4-3/bpca/man/ontario.Rd | 9 bpca-1.4-3/bpca/man/plot.Rd | 183 ++++++++--- bpca-1.4-3/bpca/man/print.xtable.Rd | 34 +- bpca-1.4-3/bpca/man/qbpca.Rd | 32 + bpca-1.4-3/bpca/man/summary.bpca.Rd | 14 bpca-1.4-3/bpca/man/var.rbf.Rd | 10 bpca-1.4-3/bpca/man/var.rdf.Rd | 37 +- bpca-1.4-3/bpca/man/xtable.bpca.Rd | 21 - bpca-1.4-3/bpca/tests |only bpca-1.4-3/bpca/vignettes/bpca-overview.Rmd |only bpca-1.4-3/bpca/vignettes/latex-bpca.Rnw | 385 ++++++++++++++--------- 55 files changed, 1986 insertions(+), 1393 deletions(-)
More information about spatialRegroup at CRAN
Permanent link
Title: Soft Windowing for Linear and Non-Linear Models
Description: Fits symmetric soft windowing to linear and non-linear models by assigning exponential weights over time around specified modes; bandwidth and sharpness of the windows are chosen by a grid search and comparison diagnostics (Hamed Haselimashhadi et al (2019) <doi:10.1093/bioinformatics/btz744>).
Author: Hamed Haselimashhadi [aut, cre]
Maintainer: Hamed Haselimashhadi <hamedhaseli@gmail.com>
This is a re-admission after prior archival of version 3.0.0 dated 2019-07-27
Diff between SmoothWin versions 3.0.0 dated 2019-07-27 and 3.0.1 dated 2026-05-11
DESCRIPTION | 31 - MD5 | 15 NAMESPACE | 45 +- R/auxFuncs.R | 1052 +++++++++++++++++++++++++------------------------- R/main.R | 6 man/SmoothWin.Rd | 731 +++++++++++++++++----------------- man/expWeight.Rd | 283 ++++++------- man/lseq.Rd |only man/plot.SmoothWin.Rd | 115 ++--- 9 files changed, 1153 insertions(+), 1125 deletions(-)
Title: Create 'RStudio' Themes from Visual Studio Code, Positron and
'TextMate' Themes
Description: Create and install 'RStudio' themes derived from Visual
Studio Code, Positron and 'TextMate' themes. Provides functions to
convert between 'TextMate' and Visual Studio Code or Positron themes,
as well as ports of several Visual Studio Code themes.
Author: Diego Hernangomez [aut, cre, cph] ,
Garrick Aden-Buie [cph] function)
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between rstudiothemes versions 1.1.0 dated 2026-04-07 and 1.1.1 dated 2026-05-11
DESCRIPTION | 11 - MD5 | 72 ++++---- NEWS.md | 68 ++++---- R/convert-tm-to-vs.R | 83 +++------ R/convert-to-rs.R | 44 +---- R/convert-vs-to-tm.R | 40 ++-- R/on-rstudio.R | 84 +++++----- R/read-tm-theme.R | 26 +-- R/read-vs-theme.R | 29 --- R/rstudiothemes-actions.R | 74 +++----- R/rstudiothemes-package.R | 20 +- R/utils.R | 5 README.md | 16 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/rstudiothemes.html | 10 - inst/doc/rstudiothemes.qmd | 10 - inst/schemaorg.json | 4 man/convert_tm_to_vs_theme.Rd | 6 man/convert_to_rstudio_theme.Rd | 6 man/convert_vs_to_tm_theme.Rd | 6 man/generate_uuid.Rd | 6 man/on_rstudio.Rd | 48 ++--- man/read_tm_theme.Rd | 6 man/read_vs_theme.Rd | 6 man/rstudiothemes-package.Rd | 5 tests/testthat.R | 24 +- tests/testthat/_snaps/convert-tm-to-vs.md | 3 tests/testthat/_snaps/convert-tm-to-vs/skeletor-syntax-color-theme.json | 1 tests/testthat/test-convert-tm-to-vs.R | 18 -- tests/testthat/test-convert-vs-to-tm.R | 8 tests/testthat/test-generate_uuid.R | 48 ++--- tests/testthat/test-read-tm-theme.R | 14 - tests/testthat/test-read-vs-theme.R | 8 tests/testthat/test-rstudiothemes-actions.R | 5 tests/testthat/test-utils.R | 34 ---- vignettes/rstudiothemes.qmd | 10 - 37 files changed, 374 insertions(+), 484 deletions(-)
Title: Solvers for Maximum Weight Connected Subgraph Problem and Its
Variants
Description: Algorithms for solving various Maximum
Weight Connected Subgraph Problems, including variants with
budget constraints, cardinality constraints, weighted edges and signals.
The package represents an R interface to high-efficient solvers based on
relax-and-cut approach (Álvarez-Miranda E., Sinnl M. (2017) <doi:10.1016/j.cor.2017.05.015>)
mixed-integer programming (Loboda A., Artyomov M., and Sergushichev A. (2016) <doi:10.1007/978-3-319-43681-4_17>)
and simulated annealing.
Author: Alexander Loboda [aut, cre],
Nikolay Poperechnyi [aut],
Eduardo Alvarez-Miranda [aut],
Markus Sinnl [aut],
Alexey Sergushichev [aut],
Paul Hosler Jr. [cph] ,
www.hamcrest.org [cph] ,
Barak Naveh and Contributors [cph] ,
The Apache Software Foundation [...truncated...]
Maintainer: Alexander Loboda <aleks.loboda@gmail.com>
Diff between mwcsr versions 0.1.10 dated 2025-11-05 and 0.1.11 dated 2026-05-11
DESCRIPTION | 11 MD5 | 40 +-- NAMESPACE | 7 R/parameters.R | 7 R/scipjack.R | 6 R/virgo.R | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/tutorial.R | 2 inst/doc/tutorial.Rmd | 11 inst/doc/tutorial.html | 453 +++++++++++++++++++--------------------- man/scipjack_solver.Rd | 6 man/virgo_solver.Rd | 4 src/annealing/subgraph.cpp | 37 +++ src/r_helper.cpp | 2 src/rmwcs/SolverBudget.cpp | 2 src/rmwcs/SolverCardinality.cpp | 2 src/rmwcs/SolverClassic.cpp | 4 tests/testthat/test_rnc.R | 10 tests/testthat/test_sa.R | 24 +- vignettes/tutorial.Rmd | 11 21 files changed, 355 insertions(+), 290 deletions(-)
Title: Data Quality in Epidemiological Research
Description: Data quality assessments guided by a
'data quality framework introduced by Schmidt and colleagues, 2021'
<doi:10.1186/s12874-021-01252-7> target the
data quality dimensions integrity, completeness, consistency, and
accuracy. The scope of applicable functions rests on the
availability of extensive metadata which can be provided in
spreadsheet tables. Either standardized (e.g. as 'html5' reports) or
individually tailored reports can be generated. For an introduction
into the specification of corresponding metadata, please refer to the
'package website'
<https://dataquality.qihs.uni-greifswald.de/VIN_Annotation_of_Metadata.html>.
Author: University Medicine Greifswald [cph],
Elisa Kasbohm [aut] ,
Elena Salogni [aut] ,
Joany Marino [aut] ,
Adrian Richter [aut] ,
Carsten Oliver Schmidt [aut] ,
Stephan Struckmann [aut, cre] ,
German Research Foundation [fnd],
National Research Data Inf [...truncated...]
Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>
Diff between dataquieR versions 2.8.7 dated 2026-01-08 and 2.8.9 dated 2026-05-11
dataquieR-2.8.7/dataquieR/R/util_standardise_ordinal_codes.R |only dataquieR-2.8.7/dataquieR/tests/testthat/test-util_standardise_ordinal_codes.R |only dataquieR-2.8.9/dataquieR/DESCRIPTION | 16 dataquieR-2.8.9/dataquieR/MD5 | 929 +- dataquieR-2.8.9/dataquieR/NAMESPACE | 10 dataquieR-2.8.9/dataquieR/NEWS.md | 39 dataquieR-2.8.9/dataquieR/R/000_globs.R | 37 dataquieR-2.8.9/dataquieR/R/000_options.R | 37 dataquieR-2.8.9/dataquieR/R/acc_cat_distributions.R | 3 dataquieR-2.8.9/dataquieR/R/acc_distributions.R | 17 dataquieR-2.8.9/dataquieR/R/acc_distributions_ecdf.R | 4 dataquieR-2.8.9/dataquieR/R/acc_loess.R | 64 dataquieR-2.8.9/dataquieR/R/acc_mahalanobis.R | 536 - dataquieR-2.8.9/dataquieR/R/acc_mahalanobis_ratio.R |only dataquieR-2.8.9/dataquieR/R/acc_margins.R | 40 dataquieR-2.8.9/dataquieR/R/acc_multivariate_outlier.R | 3 dataquieR-2.8.9/dataquieR/R/acc_shape_or_scale.R | 32 dataquieR-2.8.9/dataquieR/R/acc_univariate_outlier.R | 4 dataquieR-2.8.9/dataquieR/R/acc_varcomp.R | 16 dataquieR-2.8.9/dataquieR/R/com_item_missingness.R | 3 dataquieR-2.8.9/dataquieR/R/com_qualified_item_missingness.R | 49 dataquieR-2.8.9/dataquieR/R/com_segment_missingness.R | 10 dataquieR-2.8.9/dataquieR/R/con_contradictions.R | 4 dataquieR-2.8.9/dataquieR/R/con_contradictions_redcap.R | 4 dataquieR-2.8.9/dataquieR/R/con_inadmissible_categorical.R | 11 dataquieR-2.8.9/dataquieR/R/con_limit_deviations.R | 6 dataquieR-2.8.9/dataquieR/R/des_scatterplot_matrix.R | 28 dataquieR-2.8.9/dataquieR/R/dq_report2.R | 136 dataquieR-2.8.9/dataquieR/R/dq_report_by.R | 318 dataquieR-2.8.9/dataquieR/R/html_dependency_dataquieR.R | 6 dataquieR-2.8.9/dataquieR/R/int_all_datastructure_segment.R | 29 dataquieR-2.8.9/dataquieR/R/int_datatype_matrix.R | 6 dataquieR-2.8.9/dataquieR/R/int_encoding_errors.R | 3 dataquieR-2.8.9/dataquieR/R/menu_env.R | 25 dataquieR-2.8.9/dataquieR/R/meta_data_env.R | 4 dataquieR-2.8.9/dataquieR/R/plot.dataquieR_summary.R | 48 dataquieR-2.8.9/dataquieR/R/prep_add_computed_variables.R | 9 dataquieR-2.8.9/dataquieR/R/prep_add_data_frames.R | 16 dataquieR-2.8.9/dataquieR/R/prep_add_missing_codes.R | 190 dataquieR-2.8.9/dataquieR/R/prep_get_data_frame.R | 17 dataquieR-2.8.9/dataquieR/R/prep_load_folder_with_metadata.R | 8 dataquieR-2.8.9/dataquieR/R/prep_load_workbook_like_file.R | 44 dataquieR-2.8.9/dataquieR/R/prep_map_labels.R | 4 dataquieR-2.8.9/dataquieR/R/prep_meta_data_v1_to_item_level_meta_data.R | 4 dataquieR-2.8.9/dataquieR/R/prep_pmap.R | 2 dataquieR-2.8.9/dataquieR/R/prep_prepare_dataframes.R | 51 dataquieR-2.8.9/dataquieR/R/prep_purge_data_frame_cache.R | 2 dataquieR-2.8.9/dataquieR/R/prep_render_pie_chart_from_summaryclasses_ggplot2.R | 10 dataquieR-2.8.9/dataquieR/R/prep_render_pie_chart_from_summaryclasses_plotly.R | 12 dataquieR-2.8.9/dataquieR/R/print.ReportSummaryTable.R | 28 dataquieR-2.8.9/dataquieR/R/print.dataquieR_result.R | 5 dataquieR-2.8.9/dataquieR/R/print.dataquieR_resultset2.R | 1429 +++ dataquieR-2.8.9/dataquieR/R/print.dataquieR_summary.R | 6 dataquieR-2.8.9/dataquieR/R/pro_applicability_matrix.R | 4 dataquieR-2.8.9/dataquieR/R/reflection.R | 26 dataquieR-2.8.9/dataquieR/R/summary.dataquieR_resultset2.R | 2 dataquieR-2.8.9/dataquieR/R/util_acc_loess_bin.R | 74 dataquieR-2.8.9/dataquieR/R/util_acc_loess_continuous.R | 76 dataquieR-2.8.9/dataquieR/R/util_acc_varcomp.R | 10 dataquieR-2.8.9/dataquieR/R/util_add_computed_internals.R | 24 dataquieR-2.8.9/dataquieR/R/util_bar_plot.R | 2 dataquieR-2.8.9/dataquieR/R/util_call_with_only_existing_formals.R |only dataquieR-2.8.9/dataquieR/R/util_combine_list_report_summaries.R | 26 dataquieR-2.8.9/dataquieR/R/util_combine_res.R | 13 dataquieR-2.8.9/dataquieR/R/util_condition_constructor_factory.R | 30 dataquieR-2.8.9/dataquieR/R/util_correct_variable_use.R | 1588 ++- dataquieR-2.8.9/dataquieR/R/util_create_mahalanobis_ggplot.R |only dataquieR-2.8.9/dataquieR/R/util_create_page_file.R | 17 dataquieR-2.8.9/dataquieR/R/util_create_report_by_overview.R | 1083 +- dataquieR-2.8.9/dataquieR/R/util_dashboard_table.R | 70 dataquieR-2.8.9/dataquieR/R/util_df_escape.R | 3 dataquieR-2.8.9/dataquieR/R/util_duplicated_inclding_first.R | 2 dataquieR-2.8.9/dataquieR/R/util_ensure_label.R | 32 dataquieR-2.8.9/dataquieR/R/util_ensure_suggested.R | 20 dataquieR-2.8.9/dataquieR/R/util_error.R | 2 dataquieR-2.8.9/dataquieR/R/util_eval_rule.R | 2 dataquieR-2.8.9/dataquieR/R/util_evaluate_calls.R | 11 dataquieR-2.8.9/dataquieR/R/util_expand_pattern_rules.R |only dataquieR-2.8.9/dataquieR/R/util_expect_data_frame.R | 17 dataquieR-2.8.9/dataquieR/R/util_expect_scalar.R | 22 dataquieR-2.8.9/dataquieR/R/util_extract_all_ids.R | 2 dataquieR-2.8.9/dataquieR/R/util_filter_names_by_regexps.R | 55 dataquieR-2.8.9/dataquieR/R/util_finalize_sizing_hints.R | 231 dataquieR-2.8.9/dataquieR/R/util_fix_columns_in_dashboard_for_overview.R |only dataquieR-2.8.9/dataquieR/R/util_fix_encoding.R |only dataquieR-2.8.9/dataquieR/R/util_fix_merge_dups.R | 9 dataquieR-2.8.9/dataquieR/R/util_float_index_menu.R | 3 dataquieR-2.8.9/dataquieR/R/util_generate_calls.R | 18 dataquieR-2.8.9/dataquieR/R/util_generate_calls_for_function.R | 10 dataquieR-2.8.9/dataquieR/R/util_generate_mahalanobis_dist.R |only dataquieR-2.8.9/dataquieR/R/util_generate_pages_from_report.R | 500 - dataquieR-2.8.9/dataquieR/R/util_geom_pointrange_robust.R |only dataquieR-2.8.9/dataquieR/R/util_get_concept_links.R |only dataquieR-2.8.9/dataquieR/R/util_get_redcap_rule_env.R | 39 dataquieR-2.8.9/dataquieR/R/util_get_thresholds.R | 2 dataquieR-2.8.9/dataquieR/R/util_heatmap_1th.R | 4 dataquieR-2.8.9/dataquieR/R/util_histogram.R | 6 dataquieR-2.8.9/dataquieR/R/util_html_for_dims.R | 46 dataquieR-2.8.9/dataquieR/R/util_html_for_var.R | 117 dataquieR-2.8.9/dataquieR/R/util_html_table.R | 1205 +- dataquieR-2.8.9/dataquieR/R/util_iframe_it_if_needed.R | 22 dataquieR-2.8.9/dataquieR/R/util_is_numeric_in.R | 23 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dataquieR-2.8.9/dataquieR/man/util_int_duplicate_content_dataframe.Rd | 12 dataquieR-2.8.9/dataquieR/man/util_int_duplicate_content_segment.Rd | 12 dataquieR-2.8.9/dataquieR/man/util_int_duplicate_ids_dataframe.Rd | 12 dataquieR-2.8.9/dataquieR/man/util_int_duplicate_ids_segment.Rd | 12 dataquieR-2.8.9/dataquieR/man/util_int_unexp_records_set_dataframe.Rd | 12 dataquieR-2.8.9/dataquieR/man/util_int_unexp_records_set_segment.Rd | 12 dataquieR-2.8.9/dataquieR/tests/testthat.R | 15 dataquieR-2.8.9/dataquieR/tests/testthat/_snaps/R4.4/acc_loess/loess-combined-plot-for-crp-0-both-ok.svg | 93 dataquieR-2.8.9/dataquieR/tests/testthat/_snaps/R4.4/acc_loess/loess-combined-plot-for-crp-0-combined-ok.svg | 93 dataquieR-2.8.9/dataquieR/tests/testthat/_snaps/R4.4/acc_loess/loess-combined-plot-for-crp-0-ok.svg | 93 dataquieR-2.8.9/dataquieR/tests/testthat/_snaps/R4.4/acc_loess/loess-combined-plot-for-crp-0-with-covars-ok.svg | 94 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More information about warmthcompetence at CRAN
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More information about randomForestSGT at CRAN
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Title: Spatiotemporal Nutrient Balance Analysis Across Agricultural and
Municipal Systems
Description: A comprehensive framework for analyzing agricultural nutrient
balances across multiple spatial scales (county, 'HUC8', 'HUC2') with
integration of wastewater treatment plant ('WWTP') effluent loads for both
nitrogen and phosphorus. Supports classification of spatial units as
nutrient sources, sinks, or balanced areas based on agricultural surplus
and deficit calculations. Includes visualization tools, spatial transition
probability analysis, and nutrient flow network mapping. Built-in datasets
include agricultural nutrient balance data from the Nutrient Use Geographic
Information System ('NuGIS'; The Fertilizer Institute and Plant Nutrition
Canada, 1987-2016) <https://nugis.tfi.org/tabular_data/> and U.S. Environmental
Protection Agency ('EPA') wastewater discharge data from the 'ECHO' Discharge
Monitoring Report ('DMR') Loading Tool (2007-2016)
<https://echo.epa.gov/trends/loading-tool/water-pollution-search>. Data
are downloaded on demand from the Open Science Framework ( [...truncated...]
Author: Olatunde D. Akanbi [aut, cre, cph] ,
Vibha Mandayam [aut] ,
Atharva Gupta [aut] ,
K. Colton Flynn [aut] ,
Jeffrey Yarus [aut] ,
Erika I. Barcelos [aut, cph] ,
Roger H. French [aut, cph]
Maintainer: Olatunde D. Akanbi <olatunde.akanbi@case.edu>
Diff between manureshed versions 0.1.4 dated 2026-03-09 and 0.1.5 dated 2026-05-11
DESCRIPTION | 15 MD5 | 33 - NAMESPACE | 39 + NEWS.md | 13 R/hub_functions.R |only R/utils.R | 16 build/vignette.rds |binary inst/CITATION | 2 inst/doc/advanced-features.html | 9 inst/doc/custom-efficiency-analyis.html | 4 inst/doc/data-integration.html | 4 inst/doc/getting-started.html | 4 inst/doc/hub-site-selection.R |only inst/doc/hub-site-selection.Rmd |only inst/doc/hub-site-selection.html |only inst/doc/visualization-guide.html | 4 inst/shiny/dashboard/app.R | 896 ++++++++++++++++++-------------- man/download_cafo_data.Rd |only man/export_hub_results.Rd |only man/map_hub_sites.Rd |only man/score_hub_sites.Rd |only vignettes/hub-site-selection.Rmd |only 22 files changed, 618 insertions(+), 421 deletions(-)
Title: Download and Visualize Essential Climate Change Data
Description: Provides easy access to essential climate change datasets to non-climate experts. Users can download the latest raw data from authoritative sources and view it via pre-defined 'ggplot2' charts. Datasets include atmospheric CO2, methane, emissions, instrumental and proxy temperature records, sea levels, Arctic/Antarctic sea-ice, Hurricanes, and Paleoclimate data. Sources include: NOAA Mauna Loa Laboratory <https://gml.noaa.gov/ccgg/trends/data.html>, Global Carbon Project <https://www.globalcarbonproject.org/carbonbudget/>, NASA GISTEMP <https://data.giss.nasa.gov/gistemp/>, National Snow and Sea Ice Data Center <https://nsidc.org/home>, CSIRO <https://research.csiro.au/slrwavescoast/sea-level/measurements-and-data/sea-level-data/>, NOAA Laboratory for Satellite Altimetry <https://www.star.nesdis.noaa.gov/socd/lsa/SeaLevelRise/> and HURDAT Atlantic Hurricane Database <https://www.aoml.noaa.gov/hrd/hurdat/Data_Storm.html>, Vostok Paleo carbon dio [...truncated...]
Author: Hernando Cortina [aut, cre]
Maintainer: Hernando Cortina <hch@alum.mit.edu>
Diff between hockeystick versions 0.8.6 dated 2025-08-19 and 0.8.7 dated 2026-05-11
DESCRIPTION | 12 + MD5 | 66 +++++---- NEWS.md | 3 R/emissions.R | 6 R/hurricanes.R | 9 - R/instrumental_temp.R | 14 +- R/seaice.R | 4 README.md | 127 +++++++++++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 236 +++++++++++++++++----------------- inst/doc/usinghockeystick.R | 24 +-- inst/doc/usinghockeystick.html | 70 +++------- inst/doc/usinghockeystick.qmd | 2 man/figures/README-carbon-1.png |binary man/figures/README-dailytemp-1.png |binary man/figures/README-emissions-1.png |binary man/figures/README-emissions-2.png |binary man/figures/README-emissionsmap-1.png |binary man/figures/README-grid-1.png |binary man/figures/README-hurricanes-1.png |binary man/figures/README-hurricanes-2.png |binary man/figures/README-icecurves-1.png |binary man/figures/README-methane-1.png |binary man/figures/README-si-1.png |binary man/figures/README-stripes-1.png |binary man/figures/README-stripes2-1.png |binary man/figures/README-temp-1.png |binary man/figures/README-tempcarbon-1.png |binary man/hockeystick-package.Rd | 5 man/hockeystick_cache.Rd | 2 tests/testthat |only tests/testthat.R |only vignettes/usinghockeystick.qmd | 2 34 files changed, 333 insertions(+), 249 deletions(-)
Title: Dyad Ratios Algorithm for Latent Variable Estimation
Description: Implements the Dyad Ratios algorithm for estimating latent
variables from time-series survey data. The algorithm estimates a
latent mood dimension (or two dimensions) from a set of issue opinion
series. Supports annual, quarterly, monthly, and daily aggregation
intervals, optional exponential smoothing, and up to two latent
dimensions. Input data can be provided as a data frame or read from
delimited text files. Based on Stimson's 'MCalc' C++ program.
See Stimson (2018) <doi:10.1177/0759106318761614> for more details.
Author: James Stimson [aut] ,
Dave Armstrong [cre, aut]
Maintainer: Dave Armstrong <davearmstrong.ps@gmail.com>
Diff between DyadRatios versions 2.0 dated 2026-05-08 and 2.1 dated 2026-05-11
DESCRIPTION | 8 +-- MD5 | 21 +++++---- R/RcppExports.R | 4 - R/dyad_ratios.R | 38 ++++++++++++++--- R/methods.R | 21 ++++++++- inst/doc/extract-vignette.html | 82 ++++++++++++++++++------------------- inst/scripts |only man/boot_dr.Rd | 12 ++++- man/extract.Rd | 19 +++++++- src/RcppExports.cpp | 9 ++-- src/dyadratios_core.cpp | 89 +++++++++++++++++++++++++++++++++++------ tests/testthat/Rplots.pdf |binary 12 files changed, 214 insertions(+), 89 deletions(-)
More information about contentValidity at CRAN
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Title: Automated REtrieval from TExt
Description: A Python based pipeline for extraction of species occurrence data through the usage of large language models. Includes validation tools designed to handle model hallucinations for a scientific, rigorous use of LLM. Currently supports usage of GPT with more planned, including local and non-proprietary models. For more details on the methodology used please consult the references listed under each function, such as Kent, A. et al. (1995) <doi:10.1002/asi.5090060209>, van Rijsbergen, C.J. (1979, ISBN:978-0408709293, Levenshtein, V.I. (1966) <https://nymity.ch/sybilhunting/pdf/Levenshtein1966a.pdf> and Klaus Krippendorff (2011) <https://repository.upenn.edu/handle/20.500.14332/2089>.
Author: Vasco V. Branco [cre, aut] ,
Vaughn Shirey [ctb] ,
Thomas Merrien [ctb] ,
Pedro Cardoso [aut]
Maintainer: Vasco V. Branco <vasco.branco@helsinki.fi>
Diff between arete versions 0.1 dated 2025-10-20 and 0.2 dated 2026-05-11
DESCRIPTION | 8 - MD5 | 46 ++++---- R/00_auxiliary_functions.R | 211 +++++++++++++++++++++++++++++++++++++++-- R/00_data.R | 19 ++- R/01_arete_setup.R | 23 ++-- R/01_install_python_packages.R | 17 ++- R/02_create_training_data.R | 32 ++---- R/02_file_comparison.R | 17 ++- R/02_webanno_creator.R | 2 R/02_webanno_open.R | 18 ++- R/04_string_to_coords.R | 28 ++++- R/05_gazetteer.R | 21 ++-- R/05_get_geodata.R | 7 + R/06_performance_report.R | 10 + inst/doc/request_example.html | 35 +++--- inst/extdata/requirements.txt |only inst/path.txt |only man/arete_data.Rd | 19 ++- man/arete_setup.Rd | 4 man/aux_string_to_coords.Rd | 4 man/figures/logo.png |binary man/file_comparison.Rd | 2 man/get_geodata.Rd | 7 + man/install_python_packages.Rd | 4 man/string_to_coords.Rd | 11 +- 25 files changed, 417 insertions(+), 128 deletions(-)
Title: Estimate a Sparse Mixed Frequency Gaussian Factor Model Using a
Two-Step Procedure
Description: Estimate a sparse Gaussian state-space model with mixed frequency
data via sparse principal components analysis and the Kalman filter
and smoother. For more details see Franjic and Schweikert (2024) <doi:10.2139/ssrn.4733872>.
Author: Domenic Franjic [aut, cre]
Maintainer: Domenic Franjic <franjic@uni-hohenheim.de>
Diff between TwoStepSDFM versions 0.2.0 dated 2026-04-21 and 0.2.1 dated 2026-05-11
DESCRIPTION | 6 MD5 | 51 ++-- NEWS.md | 2 R/EstimateFactors.R | 90 +++++--- R/PlotterHelper.R | 17 + R/RcppExports.R | 8 README.md | 14 - build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 13 + inst/doc/IntroTwoStepSDFM.R | 10 inst/doc/IntroTwoStepSDFM.Rmd | 14 - inst/doc/IntroTwoStepSDFM.html | 93 +++++--- man/crossVal.Rd | 420 +++++++++++++++++++------------------- man/factor_model.Rd | 82 +++---- man/kalmanFilterSmoother.Rd | 286 +++++++++++++------------- man/mixed_freq_factor_model.Rd | 84 +++---- man/noOfFactors.Rd | 174 ++++++++------- man/nowcast.Rd | 396 ++++++++++++++++++------------------ man/plotInformationCrit.Rd |only man/simFM.Rd | 448 ++++++++++++++++++++--------------------- man/sparsePCA.Rd | 322 ++++++++++++++--------------- man/twoStepDenseDFM.Rd | 268 ++++++++++++------------ src/Orders.cpp | 63 ++++- src/RWrapperSparsePCA.cpp | 8 src/RcppExports.cpp | 23 +- vignettes/IntroTwoStepSDFM.Rmd | 14 - 27 files changed, 1530 insertions(+), 1376 deletions(-)
Title: Datasets and Functions for the Class "Modelling and Data
Analysis for Pharmaceutical Sciences"
Description: Provides datasets and functions for the class "Modelling and Data Analysis for Pharmaceutical Sciences".
The datasets can be used to present various methods of data analysis and statistical modeling.
Functions for data visualization are also implemented.
Author: Lionel Voirol [aut, cre],
Stephane Guerrier [aut],
Yuming Zhang [aut],
Luca Insolia [aut]
Maintainer: Lionel Voirol <lionelvoirol@hotmail.com>
Diff between idarps versions 0.0.5 dated 2025-05-02 and 0.0.6 dated 2026-05-11
idarps-0.0.5/idarps/data/centenarian.rda |only idarps-0.0.6/idarps/DESCRIPTION | 10 idarps-0.0.6/idarps/MD5 | 58 - idarps-0.0.6/idarps/NAMESPACE | 36 idarps-0.0.6/idarps/NEWS.md | 39 idarps-0.0.6/idarps/R/boxplot_w_points.R | 170 +-- idarps-0.0.6/idarps/R/compare_to_normal.R | 198 +-- idarps-0.0.6/idarps/R/compute_transparent_color.R | 26 idarps-0.0.6/idarps/R/document_data.R | 751 +++++++------- idarps-0.0.6/idarps/README.md | 138 +- idarps-0.0.6/idarps/data/centenarian.RData |only idarps-0.0.6/idarps/data/pm_exposure.rda |only idarps-0.0.6/idarps/man/BreastCancer.Rd | 58 - idarps-0.0.6/idarps/man/HP13Cbicarbonate.Rd | 50 idarps-0.0.6/idarps/man/PeruvianBP.Rd | 52 idarps-0.0.6/idarps/man/boxplot_w_points.Rd | 116 +- idarps-0.0.6/idarps/man/bronchitis.Rd | 42 idarps-0.0.6/idarps/man/centenarian.Rd | 50 idarps-0.0.6/idarps/man/codex.Rd | 72 - idarps-0.0.6/idarps/man/cortisol.Rd | 54 - idarps-0.0.6/idarps/man/covid.Rd | 62 - idarps-0.0.6/idarps/man/data_covid_switzerland_spatial.Rd | 62 - idarps-0.0.6/idarps/man/diabetes.Rd | 80 - idarps-0.0.6/idarps/man/diet.Rd | 48 idarps-0.0.6/idarps/man/fev.Rd | 44 idarps-0.0.6/idarps/man/hist_compare_to_normal.Rd | 118 +- idarps-0.0.6/idarps/man/kuwait_bp.Rd | 54 - idarps-0.0.6/idarps/man/pharmacy.Rd | 44 idarps-0.0.6/idarps/man/pm_exposure.Rd |only idarps-0.0.6/idarps/man/reading.Rd | 42 idarps-0.0.6/idarps/man/snoring.Rd | 48 idarps-0.0.6/idarps/man/students.Rd | 38 32 files changed, 1292 insertions(+), 1268 deletions(-)
Title: Alternating Optimization
Description: Implementation of an iterative process that optimizes a function by
alternately performing restricted optimization over parameter subsets.
Instead of solving one joint optimization problem, alternating optimization
breaks it into smaller sub-problems. This approach can make optimization
feasible when joint optimization is too difficult.
Author: Lennart Oelschlaeger [aut, cre] ,
Siddhartha Chib [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between ao versions 1.2.2 dated 2025-12-15 and 1.2.3 dated 2026-05-11
DESCRIPTION | 29 MD5 | 37 NAMESPACE | 1 NEWS.md | 14 R/ao-package.R | 86 - R/ao.R | 1139 +++++++++++---------- R/helpers.R |only R/process.R | 2033 +++++++++++++++++++-------------------- README.md | 146 +- build/vignette.rds |binary inst/doc/ao.R | 13 inst/doc/ao.Rmd | 779 +++++++------- inst/doc/ao.html | 226 ++-- man/Process.Rd | 85 - man/ao-package.Rd | 73 + man/ao.Rd | 107 +- man/generate_random_partition.Rd |only man/merge_results.Rd |only man/split_by_target.Rd |only tests/testthat/test-ao.R | 308 +++-- tests/testthat/test-helpers.R |only vignettes/ao.Rmd | 779 +++++++------- 22 files changed, 3055 insertions(+), 2800 deletions(-)
Title: Analysis of Sex Differences in Omics Data for Complex Diseases
Description: Tools to analyze sex differences in omics data for complex diseases. It includes functions for differential expression analysis using the 'limma' method <doi:10.1093/nar/gkv007>, interaction testing between sex and disease, pathway enrichment with 'clusterProfiler' <doi:10.1089/omi.2011.0118>, and gene regulatory network (GRN) construction and analysis using 'igraph'. The package enables a reproducible workflow from raw data processing to biological interpretation.
Author: Enrico Glaab [aut, cre],
Sophie Le Bars [aut],
Mohamed Soudy [aut],
Murodzhon Akhmedov [cph]
Maintainer: Enrico Glaab <enrico.glaab@uni.lu>
Diff between XYomics versions 0.1.3 dated 2026-01-08 and 0.1.4 dated 2026-05-11
XYomics-0.1.3/XYomics/R/generate_report_sc.R |only XYomics-0.1.3/XYomics/R/pathway_enrichment_sc.R |only XYomics-0.1.3/XYomics/R/ppi_analysis_sc.R |only XYomics-0.1.3/XYomics/README.md |only XYomics-0.1.3/XYomics/inst/extdata/STRING_9606_700.rds |only XYomics-0.1.3/XYomics/inst/extdata/Template_report_hormonal_network.Rmd |only XYomics-0.1.3/XYomics/man/categorize_sex_sc.Rd |only XYomics-0.1.3/XYomics/man/categorized_enrich_sc.Rd |only XYomics-0.1.3/XYomics/man/convertdf2enr.Rd |only XYomics-0.1.3/XYomics/man/generate_boxplot.Rd |only XYomics-0.1.3/XYomics/man/generate_report.Rd |only XYomics-0.1.3/XYomics/man/identify_sex_specific_genes.Rd |only XYomics-0.1.3/XYomics/man/improved_pathway_enrichment.Rd |only XYomics-0.1.3/XYomics/man/visualize_network.Rd |only XYomics-0.1.4/XYomics/DESCRIPTION | 15 XYomics-0.1.4/XYomics/MD5 | 107 XYomics-0.1.4/XYomics/NAMESPACE | 61 XYomics-0.1.4/XYomics/R/PCSF.R | 2 XYomics-0.1.4/XYomics/R/categorise_sex.R |only XYomics-0.1.4/XYomics/R/generate_report.R |only XYomics-0.1.4/XYomics/R/pathway_enrichment.R | 320 + XYomics-0.1.4/XYomics/R/plotting_and_reporting_functions.R | 547 ++- XYomics-0.1.4/XYomics/R/ppi_analysis.R |only XYomics-0.1.4/XYomics/R/sex_interaction_analysis_bulk.R | 152 XYomics-0.1.4/XYomics/R/sex_interaction_analysis_sc.R | 273 + XYomics-0.1.4/XYomics/R/sex_stratified_analysis_bulk.R | 508 ++ XYomics-0.1.4/XYomics/R/sex_stratified_analysis_sc.R | 538 +-- XYomics-0.1.4/XYomics/build/vignette.rds |binary XYomics-0.1.4/XYomics/inst/doc/XYomics_bulk_example.R | 374 -- XYomics-0.1.4/XYomics/inst/doc/XYomics_bulk_example.Rmd | 591 +-- XYomics-0.1.4/XYomics/inst/doc/XYomics_bulk_example.html | 1591 ++++----- XYomics-0.1.4/XYomics/inst/doc/XYomics_sc_example.R | 384 +- XYomics-0.1.4/XYomics/inst/doc/XYomics_sc_example.Rmd | 589 +-- XYomics-0.1.4/XYomics/inst/doc/XYomics_sc_example.html | 1735 ++++------ XYomics-0.1.4/XYomics/inst/extdata/Template_report.Rmd | 514 +- XYomics-0.1.4/XYomics/inst/extdata/Template_report_bulk.Rmd | 378 -- XYomics-0.1.4/XYomics/inst/extdata/bulk_expression.rds |only XYomics-0.1.4/XYomics/inst/extdata/bulk_interaction_results.rds |only XYomics-0.1.4/XYomics/inst/extdata/bulk_network_results.rds |only XYomics-0.1.4/XYomics/inst/extdata/bulk_neutral_network.rds |only XYomics-0.1.4/XYomics/inst/extdata/bulk_pathway_results.rds |only XYomics-0.1.4/XYomics/inst/extdata/bulk_phenotype.rds |only XYomics-0.1.4/XYomics/inst/extdata/bulk_results_cat.rds |only XYomics-0.1.4/XYomics/inst/extdata/bulk_results_degs.rds |only XYomics-0.1.4/XYomics/inst/extdata/bulk_sex.rds |only XYomics-0.1.4/XYomics/inst/extdata/sc_interaction_results_small.rds |only XYomics-0.1.4/XYomics/inst/extdata/sc_network_results_small.rds |only XYomics-0.1.4/XYomics/inst/extdata/sc_pathway_single_small.rds |only XYomics-0.1.4/XYomics/inst/extdata/sc_pathway_single_small_df.rds |only XYomics-0.1.4/XYomics/inst/extdata/sc_results_degs_small.rds |only XYomics-0.1.4/XYomics/inst/extdata/sc_results_small.rds |only XYomics-0.1.4/XYomics/inst/extdata/sc_toy_seurat.rds |only XYomics-0.1.4/XYomics/man/PCSF.Rd | 160 XYomics-0.1.4/XYomics/man/call_sr.Rd | 52 XYomics-0.1.4/XYomics/man/categorize_sex.Rd |only XYomics-0.1.4/XYomics/man/categorized_enrich.Rd |only XYomics-0.1.4/XYomics/man/construct_ppi_pcsf.Rd | 2 XYomics-0.1.4/XYomics/man/convert_gene_ids.Rd |only XYomics-0.1.4/XYomics/man/generate_cat_report.Rd | 10 XYomics-0.1.4/XYomics/man/generate_dotplot_sc.Rd |only XYomics-0.1.4/XYomics/man/generate_violinplot_bulk.Rd |only XYomics-0.1.4/XYomics/man/get_string_network.Rd | 7 XYomics-0.1.4/XYomics/man/get_top_hubs.Rd |only XYomics-0.1.4/XYomics/man/plot_enrichment_dotplots.Rd |only XYomics-0.1.4/XYomics/man/plot_network.Rd | 63 XYomics-0.1.4/XYomics/man/plot_network_pipeline.Rd |only XYomics-0.1.4/XYomics/man/plot_volcano_deg.Rd |only XYomics-0.1.4/XYomics/man/ppi_pipeline.Rd |only XYomics-0.1.4/XYomics/man/sex_interaction_analysis_bulk.Rd | 46 XYomics-0.1.4/XYomics/man/sex_interaction_analysis_sc.Rd | 27 XYomics-0.1.4/XYomics/man/sex_interaction_pipeline_sc.Rd |only XYomics-0.1.4/XYomics/man/sex_stratified_analysis_bulk.Rd | 74 XYomics-0.1.4/XYomics/man/sex_stratified_analysis_sc.Rd | 34 XYomics-0.1.4/XYomics/man/sex_stratified_pipeline_sc.Rd |only XYomics-0.1.4/XYomics/man/validate_input_bulk.Rd |only XYomics-0.1.4/XYomics/man/validate_input_sc.Rd |only XYomics-0.1.4/XYomics/vignettes/XYomics_bulk_example.Rmd | 591 +-- XYomics-0.1.4/XYomics/vignettes/XYomics_sc_example.Rmd | 589 +-- 78 files changed, 5433 insertions(+), 4901 deletions(-)
Title: Access 'Wharton Research Data Services' ('WRDS')
Description: Provides simple functions for accessing data from 'Wharton Research
Data Services' ('WRDS'), a widely used financial database in academic
research. Includes credential management via the system keyring,
database tools, and functions for downloading generic tables, 'Compustat'
fundamentals, and linking tables.
Author: Ulrich Atz [aut, cre, cph]
Maintainer: Ulrich Atz <ulrich.atz@unibocconi.it>
Diff between wrds versions 0.0.1 dated 2026-01-19 and 0.1.1 dated 2026-05-11
wrds-0.0.1/wrds/man/list_libraries.Rd |only wrds-0.1.1/wrds/DESCRIPTION | 11 - wrds-0.1.1/wrds/MD5 | 35 ++--- wrds-0.1.1/wrds/NAMESPACE | 3 wrds-0.1.1/wrds/NEWS.md | 16 ++ wrds-0.1.1/wrds/R/list.R | 53 ++++++-- wrds-0.1.1/wrds/R/wrds-connect.R | 78 +++++++++-- wrds-0.1.1/wrds/README.md | 14 +- wrds-0.1.1/wrds/man/list_subscriptions.Rd |only wrds-0.1.1/wrds/man/wrds-package.Rd | 5 wrds-0.1.1/wrds/man/wrds_connect.Rd | 7 - wrds-0.1.1/wrds/man/wrds_update_password.Rd |only wrds-0.1.1/wrds/tests/testthat/_problems |only wrds-0.1.1/wrds/tests/testthat/test-get-company.R | 7 - wrds-0.1.1/wrds/tests/testthat/test-get-compustat.R | 22 ++- wrds-0.1.1/wrds/tests/testthat/test-get-table.R | 36 ++++- wrds-0.1.1/wrds/tests/testthat/test-link.R | 24 +-- wrds-0.1.1/wrds/tests/testthat/test-list.R | 35 ----- wrds-0.1.1/wrds/tests/testthat/test-smart-collect-abort.R | 1 wrds-0.1.1/wrds/tests/testthat/test-wrds-connect.R | 92 +++++++++++++- wrds-0.1.1/wrds/tests/testthat/testthat-problems.rds |only 21 files changed, 317 insertions(+), 122 deletions(-)
Title: Interface to the 'Pharmpy' 'Pharmacometrics' Library
Description: Interface to the 'Pharmpy' 'pharmacometrics' library. The 'Reticulate' package is used to interface Python from R.
Author: Rikard Nordgren [aut, cre, cph],
Stella Belin [aut, cph],
Mats O. Karlsson [sad],
Andrew C. Hooker [sad],
Xiaomei Chen [sad],
Sebastian Ueckert [sad] ,
Simon Buatois [rev],
Joao A. Abrantes [rev],
Emilie Schindler [rev],
F. Hoffmann-La Roche Ltd. [fn [...truncated...]
Maintainer: Rikard Nordgren <rikard.nordgren@uu.se>
Diff between pharmr versions 1.7.2 dated 2025-05-22 and 2.1.0 dated 2026-05-11
DESCRIPTION | 12 MD5 | 384 +-- NAMESPACE | 28 R/functions_wrapper.R | 2390 ++++++++++++----------- R/install.R | 2 R/internals.R | 12 R/printing.R | 14 R/zzz.R | 12 README.md | 8 man/add_admid.Rd | 2 man/add_allometry.Rd | 2 man/add_bioavailability.Rd | 2 man/add_cmt.Rd | 2 man/add_covariate_effect.Rd | 4 man/add_derivative.Rd | 4 man/add_effect_compartment.Rd | 2 man/add_estimation_step.Rd | 2 man/add_iiv.Rd | 4 man/add_indirect_effect.Rd | 6 man/add_individual_parameter.Rd | 2 man/add_iov.Rd | 4 man/add_lag_time.Rd | 2 man/add_metabolite.Rd | 2 man/add_output_variables.Rd |only man/add_parameter_uncertainty_step.Rd | 2 man/add_pd_iiv.Rd | 4 man/add_peripheral_compartment.Rd | 2 man/add_pk_iiv.Rd | 4 man/add_population_parameter.Rd | 2 man/add_predictions.Rd | 2 man/add_residuals.Rd | 2 man/add_time_after_dose.Rd | 6 man/add_time_of_last_dose.Rd |only man/append_estimation_step_options.Rd | 6 man/binarize_dataset.Rd |only man/bump_model_number.Rd | 4 man/calculate_aic.Rd | 2 man/calculate_bic.Rd | 2 man/calculate_epsilon_gradient_expression.Rd | 2 man/calculate_eta_gradient_expression.Rd | 2 man/calculate_individual_parameter_statistics.Rd | 2 man/calculate_pk_parameters_statistics.Rd | 2 man/calculate_summary_statistic.Rd |only man/calculate_ucp_scale.Rd | 2 man/check_dataset.Rd | 2 man/check_high_correlations.Rd | 2 man/check_parameters_near_bounds.Rd | 2 man/cholesky_decompose.Rd |only man/cleanup_model.Rd | 4 man/convert_model.Rd | 4 man/convert_unit.Rd |only man/create_basic_kpd_model.Rd |only man/create_basic_pd_model.Rd |only man/create_basic_pk_model.Rd | 2 man/create_joint_distribution.Rd | 4 man/create_symbol.Rd | 2 man/drop_columns.Rd | 4 man/drop_dropped_columns.Rd | 4 man/expand_additional_doses.Rd | 4 man/export_model_files.Rd |only man/filter_dataset.Rd | 4 man/fix_or_unfix_parameters.Rd | 2 man/fix_parameters.Rd | 2 man/fix_parameters_to.Rd | 2 man/get_column_name.Rd |only man/get_concentration_parameters_from_data.Rd | 2 man/get_covariate_effects.Rd | 2 man/get_individual_parameters.Rd | 2 man/get_individual_prediction_expression.Rd | 2 man/get_mu_connected_to_parameter.Rd | 2 man/get_nested_model.Rd | 6 man/get_observation_expression.Rd | 2 man/get_observations.Rd | 2 man/get_omegas.Rd | 2 man/get_parameter_rv.Rd | 2 man/get_pd_parameters.Rd | 2 man/get_pk_parameters.Rd | 2 man/get_population_prediction_expression.Rd | 2 man/get_rv_parameters.Rd | 2 man/get_sigmas.Rd | 2 man/get_thetas.Rd | 2 man/get_unit_of.Rd | 12 man/greekify_model.Rd | 2 man/has_additive_error_model.Rd | 2 man/has_combined_error_model.Rd | 2 man/has_covariate_effect.Rd | 2 man/has_first_order_absorption.Rd | 2 man/has_instantaneous_absorption.Rd | 2 man/has_mu_reference.Rd | 2 man/has_proportional_error_model.Rd | 2 man/has_random_effect.Rd | 2 man/has_seq_zo_fo_absorption.Rd | 5 man/has_weibull_absorption.Rd | 3 man/has_weighted_error_model.Rd | 2 man/infer_datatypes.Rd |only man/insert_ebes_into_dataset.Rd |only man/is_binary.Rd |only man/load_dataset.Rd | 2 man/load_example_model.Rd | 2 man/make_declarative.Rd | 2 man/map_eta_parameters.Rd |only man/mu_reference_model.Rd | 4 man/plot_eta_distributions.Rd | 2 man/plot_individual_predictions.Rd | 8 man/plot_transformed_eta_distributions.Rd | 10 man/plot_vpc.Rd | 2 man/print_fit_summary.Rd | 2 man/print_model_symbols.Rd | 2 man/read_model.Rd | 2 man/read_model_from_string.Rd | 2 man/remove_bioavailability.Rd | 2 man/remove_covariate_effect.Rd | 10 man/remove_derivative.Rd | 4 man/remove_error_model.Rd | 4 man/remove_estimation_step.Rd | 2 man/remove_iiv.Rd | 4 man/remove_iov.Rd | 4 man/remove_lag_time.Rd | 2 man/remove_loq_data.Rd | 4 man/remove_peripheral_compartment.Rd | 2 man/remove_predictions.Rd | 4 man/remove_residuals.Rd | 4 man/remove_unused_columns.Rd |only man/remove_unused_parameters_and_rvs.Rd | 4 man/rename_symbols.Rd | 4 man/replace_fixed_thetas.Rd | 2 man/replace_non_random_rvs.Rd | 2 man/resample_data.Rd | 2 man/retrieve_model.Rd | 2 man/retrieve_models.Rd | 2 man/run_bootstrap.Rd | 18 man/run_covsearch.Rd | 4 man/run_iivsearch.Rd | 18 man/run_iovsearch.Rd | 6 man/run_linearize.Rd | 2 man/run_modelrank.Rd |only man/run_modelsearch.Rd | 6 man/run_pdsearch.Rd |only man/run_qa.Rd |only man/run_retries.Rd | 6 man/run_ruvsearch.Rd | 6 man/run_structsearch.Rd | 17 man/run_vpc.Rd |only man/sample_parameters_from_covariance_matrix.Rd | 4 man/sample_parameters_uniformly.Rd | 2 man/set_additive_error_model.Rd | 4 man/set_baseline_effect.Rd | 2 man/set_combined_error_model.Rd | 4 man/set_covariates.Rd | 4 man/set_dataset.Rd | 2 man/set_description.Rd | 2 man/set_direct_effect.Rd | 2 man/set_dtbs_error_model.Rd | 2 man/set_dvid.Rd | 2 man/set_estimation_step.Rd | 2 man/set_evaluation_step.Rd | 2 man/set_first_order_absorption.Rd | 4 man/set_first_order_elimination.Rd | 2 man/set_iiv_on_ruv.Rd | 6 man/set_initial_condition.Rd | 2 man/set_initial_estimates.Rd | 8 man/set_instantaneous_absorption.Rd | 4 man/set_lloq_data.Rd | 4 man/set_lower_bounds.Rd | 2 man/set_michaelis_menten_elimination.Rd | 2 man/set_mixed_mm_fo_elimination.Rd | 2 man/set_n_transit_compartments.Rd |only man/set_name.Rd | 2 man/set_ode_solver.Rd | 21 man/set_peripheral_compartments.Rd | 2 man/set_placebo_model.Rd |only man/set_power_on_ruv.Rd | 6 man/set_property.Rd |only man/set_proportional_error_model.Rd | 4 man/set_reference_values.Rd | 4 man/set_seq_zo_fo_absorption.Rd | 4 man/set_simulation.Rd | 2 man/set_time_varying_error_model.Rd | 2 man/set_tmdd.Rd | 2 man/set_transit_compartments.Rd | 8 man/set_unit.Rd |only man/set_upper_bounds.Rd | 2 man/set_weibull_absorption.Rd | 28 man/set_weighted_error_model.Rd | 2 man/set_zero_order_absorption.Rd | 4 man/set_zero_order_elimination.Rd | 2 man/set_zero_order_input.Rd | 2 man/simplify_expression.Rd | 2 man/solve_ode_system.Rd | 2 man/split_joint_distribution.Rd | 4 man/transform_blq.Rd | 4 man/transform_etas_boxcox.Rd | 4 man/transform_etas_john_draper.Rd | 8 man/transform_etas_tdist.Rd | 4 man/translate_nmtran_time.Rd | 4 man/unconstrain_parameters.Rd | 2 man/undrop_columns.Rd | 4 man/unfix_parameters.Rd | 2 man/unfix_parameters_to.Rd | 2 man/unload_dataset.Rd | 2 man/update_initial_individual_estimates.Rd | 4 man/use_thetas_for_error_stdev.Rd | 2 man/write_csv.Rd | 4 man/write_dataset.Rd |only man/write_model.Rd | 5 205 files changed, 1972 insertions(+), 1511 deletions(-)
Title: ICA-Based Matrix/Tensor Decomposition
Description: Some functions for performing ICA, MICA, Group ICA, and Multilinear ICA are implemented.
ICA, MICA/Group ICA, and Multilinear ICA extract statistically independent components from single matrix, multiple matrices, and single tensor, respectively.
For the details of these methods, see the reference section of GitHub README.md <https://github.com/rikenbit/iTensor>.
Author: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between iTensor versions 1.0.4 dated 2026-05-08 and 1.0.5 dated 2026-05-11
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/ICA.R | 9 +++++---- inst/NEWS | 4 ++++ inst/doc/iTensor-1.html | 6 +++--- inst/doc/iTensor-2.html | 10 +++++----- inst/doc/iTensor-3.html | 6 +++--- 7 files changed, 29 insertions(+), 24 deletions(-)
Title: Local Inferential Feature Significance for Multivariate Kernel
Density Estimation
Description: Local inferential feature significance for multivariate kernel density estimation.
Author: Tarn Duong [aut, cre] ,
Matt Wand [ctb]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between feature versions 1.2.15 dated 2021-02-10 and 1.2.16 dated 2026-05-11
feature-1.2.15/feature/vignettes/earthquake.RData |only feature-1.2.16/feature/DESCRIPTION | 18 - feature-1.2.16/feature/MD5 | 51 +-- feature-1.2.16/feature/R/SiZer.R | 4 feature-1.2.16/feature/R/SignifFeatureData.R | 1 feature-1.2.16/feature/R/SignifFeatureRegion.R | 8 feature-1.2.16/feature/R/addSignifFeatureData.R | 2 feature-1.2.16/feature/R/addSignifFeatureRegion.R | 2 feature-1.2.16/feature/R/dfltBWrange.R | 2 feature-1.2.16/feature/R/dfltCounts.R | 2 feature-1.2.16/feature/R/dfltLabs.R | 2 feature-1.2.16/feature/R/drvkde.R | 11 feature-1.2.16/feature/R/featureSignif.R | 2 feature-1.2.16/feature/R/plot.fs.R | 3 feature-1.2.16/feature/README.md |only feature-1.2.16/feature/build/vignette.rds |binary feature-1.2.16/feature/data/earthquake.RData |binary feature-1.2.16/feature/inst/doc/feature.R | 19 - feature-1.2.16/feature/inst/doc/feature.Rmd | 39 +- feature-1.2.16/feature/inst/doc/feature.html | 301 +++++++++++++--------- feature-1.2.16/feature/inst/pkgdown.yml |only feature-1.2.16/feature/man/SiZer.Rd | 4 feature-1.2.16/feature/man/earthquake.Rd | 5 feature-1.2.16/feature/man/feature-package.Rd | 11 feature-1.2.16/feature/man/featureSignif.Rd | 19 - feature-1.2.16/feature/man/featureSignifGUI.Rd | 5 feature-1.2.16/feature/man/plot.fs.Rd | 2 feature-1.2.16/feature/vignettes/feature.Rmd | 39 +- 28 files changed, 301 insertions(+), 251 deletions(-)
Title: Machine Learning Modelling for Everyone
Description: A minimal library specifically designed to make the estimation of Machine Learning
(ML) techniques as easy and accessible as possible, particularly within the framework of
the Knowledge Discovery in Databases (KDD) process in data mining. The package provides
essential tools to structure and execute each stage of a predictive or classification
modeling workflow, aligning closely with the fundamental steps of the KDD methodology,
from data selection and preparation, through model building and tuning, to the
interpretation and evaluation of results using Sensitivity Analysis. The 'MLwrap' workflow
is organized into four core steps; preprocessing(), build_model(), fine_tuning(), and
sensitivity_analysis(). It also includes global and pairwise interaction analysis based on
Friedman’s H-statistic to support a more detailed interpretation of complex feature
relationships.These steps correspond, respectively, to data preparation and transformation,
model construction, hyperparameter optimizat [...truncated...]
Author: Javier Martinez Garcia [aut] ,
Juan Jose Montano Moreno [ctb] ,
Albert Sese [cre, ctb]
Maintainer: Albert Sese <albert.sese@uib.es>
Diff between MLwrap versions 0.3.0 dated 2025-12-15 and 0.4.0 dated 2026-05-11
DESCRIPTION | 8 - MD5 | 18 +-- R/Bayesian_Optimization.R | 70 ++++++++----- R/GridSearchCV.R | 5 R/Tuners.R | 27 +++++ R/fine_tuning.R | 13 +- R/model_creation.R | 1 R/shap_values.R | 228 ++++++++++++++++++++++++++++---------------- README.md | 236 +++++++++++++++++++++++----------------------- man/fine_tuning.Rd | 5 10 files changed, 362 insertions(+), 249 deletions(-)
Title: Inference Using Simulation
Description: Implements functions for simulation-based inference. In particular, implements functions to perform likelihood inference from data summaries whose distributions are simulated, as described in Rousset et al. (2026) <doi:10.24072/pcjournal.721>.
Author: Francois Rousset [aut, cre, cph]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>
Diff between Infusion versions 2.3.0 dated 2025-07-22 and 2.3.12 dated 2026-05-11
DESCRIPTION | 12 - MD5 | 57 +++--- NAMESPACE | 4 R/HPDint.R | 7 R/MAF_wrappers.R | 117 +++++++++++-- R/MSL.R | 15 - R/SLikSQuant.R | 94 ++++++++-- R/confintLR.SLik.R | 4 R/extractors.R | 120 +++++++++++++ R/jointDens.R | 293 ++++++++++++++++++++++++---------- R/plotProfiles.R | 8 R/project.R | 3 build |only inst/CITATION | 26 ++- inst/NEWS.Rd | 17 + man/C2ST.Rd |only man/Infusion.Rd | 15 + man/MAF.options.Rd | 5 man/MSL.Rd | 4 man/example_raw_proj.Rd | 2 man/get_from.Rd | 4 man/get_nbCluster_range.Rd | 8 man/get_workflow_design.Rd | 14 + man/handling_NAs.Rd | 11 - man/project.Rd | 9 - man/refine.SLik.Rd | 39 +++- man/simulate.SLik_j.Rd | 2 tests/test-all.R | 4 tests/testthat/test-constr_crits.R | 3 tests/testthat/test-reftable.R | 13 + tests/testthat/test-workflow_design.R |only 31 files changed, 694 insertions(+), 216 deletions(-)
Title: Access and Work with HCUP Resources and Datasets
Description: A comprehensive R package for accessing and working with publicly
available and free resources from the Agency for Healthcare Research and Quality
(AHRQ) Healthcare Cost and Utilization Project (HCUP). The package provides
streamlined access to HCUP's Clinical Classifications Software Refined (CCSR)
mapping files and Summary Trend Tables, enabling researchers and analysts to
efficiently map ICD-10-CM diagnosis codes and ICD-10-PCS procedure codes to
CCSR categories and access HCUP statistical reports. Key features include:
direct download from HCUP website, multiple output formats (long/wide/default),
cross-classification support, version management, citation generation, and
intelligent caching. The package does not redistribute HCUP data files but
facilitates direct download from the official HCUP website, ensuring users
always have access to the latest versions and maintain compliance with HCUP
data use policies. This package only accesses free public tools and reports;
it does NOT a [...truncated...]
Author: Vikrant Dev Rathore [aut, cre]
Maintainer: Vikrant Dev Rathore <rathore.vikrant@gmail.com>
Diff between HCUPtools versions 1.0.0 dated 2025-12-10 and 1.0.1 dated 2026-05-11
HCUPtools-1.0.0/HCUPtools/build/vignettes.rds |only HCUPtools-1.0.1/HCUPtools/DESCRIPTION | 9 HCUPtools-1.0.1/HCUPtools/MD5 | 48 - HCUPtools-1.0.1/HCUPtools/NAMESPACE | 1 HCUPtools-1.0.1/HCUPtools/NEWS.md | 13 HCUPtools-1.0.1/HCUPtools/R/ccsr_changelog.R | 5 HCUPtools-1.0.1/HCUPtools/R/ccsr_map.R | 162 +++-- HCUPtools-1.0.1/HCUPtools/R/download_ccsr.R | 31 HCUPtools-1.0.1/HCUPtools/R/download_trend_tables.R | 4 HCUPtools-1.0.1/HCUPtools/R/get_ccsr_description.R | 2 HCUPtools-1.0.1/HCUPtools/R/list_ccsr_versions.R | 10 HCUPtools-1.0.1/HCUPtools/R/read_ccsr.R | 33 - HCUPtools-1.0.1/HCUPtools/R/read_trend_table.R | 36 - HCUPtools-1.0.1/HCUPtools/R/utils.R | 1 HCUPtools-1.0.1/HCUPtools/build/vignette.rds |binary HCUPtools-1.0.1/HCUPtools/inst/CITATION |only HCUPtools-1.0.1/HCUPtools/inst/doc/HCUPtools.R | 34 - HCUPtools-1.0.1/HCUPtools/inst/doc/HCUPtools.Rmd | 38 - HCUPtools-1.0.1/HCUPtools/inst/doc/HCUPtools.html | 483 +++++++-------- HCUPtools-1.0.1/HCUPtools/man/download_trend_tables.Rd | 4 HCUPtools-1.0.1/HCUPtools/man/list_trend_table_sheets.Rd | 5 HCUPtools-1.0.1/HCUPtools/man/read_ccsr.Rd | 29 HCUPtools-1.0.1/HCUPtools/man/read_trend_table.Rd | 31 HCUPtools-1.0.1/HCUPtools/tests/testthat/test-ccsr_map.R | 54 + HCUPtools-1.0.1/HCUPtools/tests/testthat/test-utils.R | 16 HCUPtools-1.0.1/HCUPtools/vignettes/HCUPtools.Rmd | 38 - 26 files changed, 608 insertions(+), 479 deletions(-)
Title: Optimal Graph Partition using the Persistence
Description: Calculate the optimal vertex partition of a graph using the persistence as objective function.
These subroutines have been used in Avellone et al. <doi:10.1007/s10288-023-00559-z>.
Author: Alessandro Avellone [aut, cre],
Paolo Bartesaghi [aut],
Stefano Benati [aut],
Rosanna Grassi [aut]
Maintainer: Alessandro Avellone <alessandro.avellone@unimib.it>
Diff between persistence versions 0.2.0 dated 2025-10-06 and 1.0.0 dated 2026-05-11
persistence-0.2.0/persistence/src/communityMeasure.h |only persistence-0.2.0/persistence/src/louvainMethod.cpp |only persistence-0.2.0/persistence/src/louvainMethod.h |only persistence-0.2.0/persistence/src/matriciCommunity.cpp |only persistence-0.2.0/persistence/src/matriciCommunity.h |only persistence-0.2.0/persistence/src/random.cpp |only persistence-0.2.0/persistence/src/utilita.cpp |only persistence-0.2.0/persistence/src/utilita.h |only persistence-1.0.0/persistence/DESCRIPTION | 8 persistence-1.0.0/persistence/MD5 | 40 persistence-1.0.0/persistence/NAMESPACE | 9 persistence-1.0.0/persistence/R/cluster_milano.R | 240 +++-- persistence-1.0.0/persistence/R/global_persistence.R | 182 ++-- persistence-1.0.0/persistence/R/local_persistence.R | 193 ++-- persistence-1.0.0/persistence/R/persistence-exports.R | 12 persistence-1.0.0/persistence/man/cluster_milano.Rd | 85 +- persistence-1.0.0/persistence/man/global_persistence.Rd | 65 - persistence-1.0.0/persistence/man/local_persistence.Rd | 58 - persistence-1.0.0/persistence/man/persistence-package.Rd | 4 persistence-1.0.0/persistence/src/community_measure.h |only persistence-1.0.0/persistence/src/eccezioni.h | 61 - persistence-1.0.0/persistence/src/grafi.h | 361 +++----- persistence-1.0.0/persistence/src/milano_algorithm.h |only persistence-1.0.0/persistence/src/random.h | 132 ++- persistence-1.0.0/persistence/src/rwrapper.cpp | 623 ++++++++------- persistence-1.0.0/persistence/src/rwrapper.h | 106 ++ 26 files changed, 1219 insertions(+), 960 deletions(-)
Title: Computation of Bayes Factors for Common Biomedical Designs
Description: BAYesian inference for MEDical designs in R. Functions for the
computation of Bayes factors for common biomedical research designs.
Implemented are functions to test the equivalence (equiv_bf),
non-inferiority (infer_bf), and superiority (super_bf) of an experimental
group compared to a control group on a continuous outcome measure, as well
as functions for simulating survival data and calculating a Bayes factor
for Cox proportional hazards models. Bayes factors for these tests can be
computed based on raw data or summary statistics.
Author: Maximilian Linde [aut, cre] ,
Don van Ravenzwaaij [aut] ,
Jorge N. Tendeiro [aut] ,
Quentin F. Gronau [ctb]
Maintainer: Maximilian Linde <maximilian.linde.92@gmail.com>
Diff between baymedr versions 0.1.1 dated 2021-03-27 and 0.2 dated 2026-05-11
baymedr-0.1.1/baymedr/R/zzz.R |only baymedr-0.1.1/baymedr/build |only baymedr-0.1.1/baymedr/inst |only baymedr-0.1.1/baymedr/vignettes |only baymedr-0.2/baymedr/DESCRIPTION | 40 + baymedr-0.2/baymedr/MD5 | 52 +- baymedr-0.2/baymedr/NAMESPACE | 9 baymedr-0.2/baymedr/NEWS.md | 4 baymedr-0.2/baymedr/R/bayes.R |only baymedr-0.2/baymedr/R/baymedr-package.R | 13 baymedr-0.2/baymedr/R/cdf_t.R | 7 baymedr-0.2/baymedr/R/coxph_bf.R |only baymedr-0.2/baymedr/R/coxph_data_sim.R |only baymedr-0.2/baymedr/R/data_sim.R |only baymedr-0.2/baymedr/R/def_classes.R | 42 + baymedr-0.2/baymedr/R/equiv_bf.R | 59 +- baymedr-0.2/baymedr/R/get_bf.R | 37 + baymedr-0.2/baymedr/R/infer_bf.R | 62 +- baymedr-0.2/baymedr/R/methods_show.R | 199 ++++++++ baymedr-0.2/baymedr/R/super_bf.R | 56 +- baymedr-0.2/baymedr/README.md | 347 --------------- baymedr-0.2/baymedr/man/baymedr-package.Rd | 10 baymedr-0.2/baymedr/man/coxph_bf.Rd |only baymedr-0.2/baymedr/man/coxph_data_sim.Rd |only baymedr-0.2/baymedr/man/equiv_bf.Rd | 10 baymedr-0.2/baymedr/man/get_bf.Rd | 22 baymedr-0.2/baymedr/man/infer_bf.Rd | 10 baymedr-0.2/baymedr/man/model-classes.Rd | 15 baymedr-0.2/baymedr/man/super_bf.Rd | 10 baymedr-0.2/baymedr/tests/testthat/test-coxph_bf.R |only baymedr-0.2/baymedr/tests/testthat/test-coxph_data_sim.R |only baymedr-0.2/baymedr/tests/testthat/test-get_bf.R | 30 + 32 files changed, 521 insertions(+), 513 deletions(-)
Title: A Stable Isotope Mixing Model
Description: Fits Stable Isotope Mixing Models (SIMMs) and is meant as a longer term replacement to the previous widely-used package SIAR. SIMMs are used to infer dietary proportions of organisms consuming various food sources from observations on the stable isotope values taken from the organisms' tissue samples. However SIMMs can also be used in other scenarios, such as in sediment mixing or the composition of fatty acids. The main functions are simmr_load() and simmr_mcmc(). The two vignettes contain a quick start and a full listing of all the features. The methods used are detailed in the papers Parnell et al 2010 <doi:10.1371/journal.pone.0009672>, and Parnell et al 2013 <doi:10.1002/env.2221>.
Author: Emma Govan [aut],
Andrew Parnell [cre, aut]
Maintainer: Andrew Parnell <andrew.parnell1@ucd.ie>
Diff between simmr versions 0.5.1.217 dated 2024-10-16 and 0.5.2 dated 2026-05-11
DESCRIPTION | 20 - MD5 | 30 - NAMESPACE | 1 NEWS.md | 4 R/posterior_predictive.simmr_output.R | 36 +- build/vignette.rds |binary inst/doc/advanced_plotting.R | 4 inst/doc/advanced_plotting.html | 205 ++++++------- inst/doc/quick_start.R | 4 inst/doc/quick_start.html | 96 +++--- inst/doc/simmr.R | 230 +++++++------- inst/doc/simmr.Rmd | 4 inst/doc/simmr.html | 528 ++++++++++++++++++---------------- tests/testthat/Rplots.pdf |binary tests/testthat/test-simmr_ffvb.R | 2 vignettes/simmr.Rmd | 4 16 files changed, 627 insertions(+), 541 deletions(-)
Title: Iterative Bias Reduction
Description: Multivariate smoothing using iterative bias reduction with kernel, thin plate splines, Duchon splines or low rank splines.
Author: Pierre-Andre Cornillon [aut, cre],
Nicolas Hengartner [aut],
Eric Matzner-Lober [aut]
Maintainer: Pierre-Andre Cornillon <pierre-andre.cornillon@univ-rennes2.fr>
Diff between ibr versions 2.4-0 dated 2026-05-03 and 2.4-1 dated 2026-05-11
ibr-2.4-0/ibr/README |only ibr-2.4-1/ibr/DESCRIPTION | 8 ++++---- ibr-2.4-1/ibr/MD5 | 5 ++--- ibr-2.4-1/ibr/src/smoother.c | 1 + 4 files changed, 7 insertions(+), 7 deletions(-)
Title: Create Layout Plots of Biological Culture Plates and Microplates
Description: Enables users to create simple plots of biological culture plates as well as microplates. Both continuous and discrete values can be plotted onto the plate layout.
Author: Jan-Philipp Quast [aut, cre]
Maintainer: Jan-Philipp Quast <jpquast.software@gmail.com>
Diff between ggplate versions 0.3.0 dated 2026-05-08 and 0.3.1 dated 2026-05-11
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/plate_plot.R | 55 +++++++++++++++++++++++++++++++------------------------ 4 files changed, 41 insertions(+), 30 deletions(-)
Title: Flexible Simulation Utilities for Pharmacometric Modeling
Description: The goal of 'amp.sim' is to transform 'NONMEM' models into R syntax so they can be used for
simulations using the 'deSolve', 'nlmixr2' or 'mrgsolve' package. Additionally, functionality is included to aid simulations performed
directly in 'NONMEM' and to automatically create shiny apps for simulation models.
Author: Richard Hooijmaijers [aut, cre, cph],
LAPP Consultants [fnd, cph]
Maintainer: Richard Hooijmaijers <richardhooijmaijers@gmail.com>
Diff between amp.sim versions 0.1.0 dated 2026-05-07 and 0.1.1 dated 2026-05-11
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/doc/Vign.01.R_simulations.html | 6 +++--- inst/doc/Vign.02.NONMEM_simulations.html | 12 ++++++------ tests/testthat/test_misc.R | 6 +++--- 6 files changed, 24 insertions(+), 20 deletions(-)
Title: Sampling from Truncated Multivariate Normal and t Distributions
Description: Efficient sampling of truncated multivariate (scale) mixtures of normals under linear inequality constraints is nontrivial due to the analytically intractable normalizing constant. Meanwhile, traditional methods may subject to numerical issues, especially when the dimension is high and dependence is strong. Algorithms proposed by Li and Ghosh (2015) <doi: 10.1080/15598608.2014.996690> are adopted for overcoming difficulties in simulating truncated distributions. Efficient rejection sampling for simulating truncated univariate normal distribution is included in the package, which shows superiority in terms of acceptance rate and numerical stability compared to existing methods and R packages. An efficient function for sampling from truncated multivariate normal distribution subject to convex polytope restriction regions based on Gibbs sampler for conditional truncated univariate distribution is provided. By extending the sampling method, a function for sampling truncated multiv [...truncated...]
Author: Ting Fung Ma [cre, aut],
Sujit K. Ghosh [aut],
Yifang Li [aut]
Maintainer: Ting Fung Ma <tingfung@mailbox.sc.edu>
Diff between tmvmixnorm versions 1.1.1 dated 2020-09-18 and 1.2.0 dated 2026-05-11
tmvmixnorm-1.1.1/tmvmixnorm/R/halfnorm_rejction.R |only tmvmixnorm-1.2.0/tmvmixnorm/DESCRIPTION | 15 ++---- tmvmixnorm-1.2.0/tmvmixnorm/MD5 | 48 ++++++++++---------- tmvmixnorm-1.2.0/tmvmixnorm/NAMESPACE | 22 +++++++-- tmvmixnorm-1.2.0/tmvmixnorm/R/dtuvn.R | 4 + tmvmixnorm-1.2.0/tmvmixnorm/R/exp_acc.R | 7 ++ tmvmixnorm-1.2.0/tmvmixnorm/R/exp_rejection.R | 1 tmvmixnorm-1.2.0/tmvmixnorm/R/halfnorm_acc.R | 4 + tmvmixnorm-1.2.0/tmvmixnorm/R/halfnorm_rejection.R |only tmvmixnorm-1.2.0/tmvmixnorm/R/imp.R | 9 +++ tmvmixnorm-1.2.0/tmvmixnorm/R/imp_acc.R | 2 tmvmixnorm-1.2.0/tmvmixnorm/R/normal_acc.R | 4 + tmvmixnorm-1.2.0/tmvmixnorm/R/normal_rejection.R | 2 tmvmixnorm-1.2.0/tmvmixnorm/R/ptuvn.R | 2 tmvmixnorm-1.2.0/tmvmixnorm/R/rtmvn.R | 2 tmvmixnorm-1.2.0/tmvmixnorm/R/rtmvt.R | 2 tmvmixnorm-1.2.0/tmvmixnorm/R/rtuvn.R | 2 tmvmixnorm-1.2.0/tmvmixnorm/R/unif_acc.R | 4 + tmvmixnorm-1.2.0/tmvmixnorm/R/unif_rejection.R | 2 tmvmixnorm-1.2.0/tmvmixnorm/man/exp_acc_opt.Rd | 1 tmvmixnorm-1.2.0/tmvmixnorm/man/halfnorm_acc.Rd | 40 ++++++++-------- tmvmixnorm-1.2.0/tmvmixnorm/man/halfnorm_rej.Rd | 2 tmvmixnorm-1.2.0/tmvmixnorm/man/norm_acc.Rd | 40 ++++++++-------- tmvmixnorm-1.2.0/tmvmixnorm/man/norm_rej.Rd | 50 ++++++++++----------- tmvmixnorm-1.2.0/tmvmixnorm/man/unif_acc.Rd | 40 ++++++++-------- tmvmixnorm-1.2.0/tmvmixnorm/man/unif_rej.Rd | 50 ++++++++++----------- 26 files changed, 201 insertions(+), 154 deletions(-)
Title: Stepwise Clustered Ensemble
Description: Implementation of Stepwise Clustered Ensemble (SCE) and Stepwise Cluster Analysis (SCA) for multivariate data analysis. The package provides comprehensive tools for feature selection, model training, prediction, and evaluation in hydrological and environmental modeling applications. Key functionalities include recursive feature elimination (RFE), Wilks feature importance analysis, model validation through out-of-bag (OOB) validation, and ensemble prediction capabilities. The package supports both single and multivariate response variables, making it suitable for complex environmental modeling scenarios. For more details see Li et al. (2021) <doi:10.5194/hess-25-4947-2021>.
Author: Kailong Li [aut, cre]
Maintainer: Kailong Li <lkl98509509@gmail.com>
Diff between SCE versions 1.1.3 dated 2026-05-08 and 1.1.4 dated 2026-05-11
DESCRIPTION | 6 - MD5 | 36 +++++----- NEWS.md | 8 ++ R/Model_evaluation.R | 62 +++++++++--------- R/Model_simulation.R | 38 +++++------ R/Prediction.R | 8 +- R/RFE_SCE.R | 52 +++++++-------- R/SCA.R | 110 ++++++++++++++++----------------- R/SCE.R | 135 ++++++++++++++++++++-------------------- R/Training.R | 50 +++++++-------- R/Wilks_importance.R | 4 - README.md | 60 +++++++++--------- man/air_quality.Rd | 108 ++++++++++++++++---------------- man/evaluate.Rd | 8 +- man/importance.Rd | 4 - man/rfe_sce.Rd | 14 ++-- man/sca.Rd | 18 ++--- man/sce.Rd | 22 +++--- man/streamflow.Rd | 170 +++++++++++++++++++++++++-------------------------- 19 files changed, 460 insertions(+), 453 deletions(-)
Title: Cell Type Annotation Using Large Language Models
Description: Automated cell type annotation for single-cell RNA sequencing data
using consensus predictions from multiple large language models. Integrates
with Seurat objects and provides uncertainty quantification for annotations.
Supports various LLM providers including OpenAI, Anthropic, and Google.
For details see Yang et al. (2025) <doi:10.1101/2025.04.10.647852>.
Author: Chen Yang [aut, cre, cph]
Maintainer: Chen Yang <cafferychen777@tamu.edu>
Diff between mLLMCelltype versions 2.0.0 dated 2026-02-08 and 2.0.5 dated 2026-05-11
mLLMCelltype-2.0.0/mLLMCelltype/man/dot-qwen_endpoint_cache.Rd |only mLLMCelltype-2.0.5/mLLMCelltype/DESCRIPTION | 8 mLLMCelltype-2.0.5/mLLMCelltype/MD5 | 129 ++- mLLMCelltype-2.0.5/mLLMCelltype/NAMESPACE | 2 mLLMCelltype-2.0.5/mLLMCelltype/NEWS.md | 56 + mLLMCelltype-2.0.5/mLLMCelltype/R/base_api_processor.R | 5 mLLMCelltype-2.0.5/mLLMCelltype/R/cell_type_annotation.R | 73 +- mLLMCelltype-2.0.5/mLLMCelltype/R/check_consensus.R | 53 + mLLMCelltype-2.0.5/mLLMCelltype/R/compare_model_predictions.R | 197 +++--- mLLMCelltype-2.0.5/mLLMCelltype/R/consensus_annotation.R | 32 mLLMCelltype-2.0.5/mLLMCelltype/R/custom_model_manager.R | 9 mLLMCelltype-2.0.5/mLLMCelltype/R/facilitate_cluster_discussion.R | 50 - mLLMCelltype-2.0.5/mLLMCelltype/R/get_provider.R | 24 mLLMCelltype-2.0.5/mLLMCelltype/R/prompt_templates.R | 101 ++- mLLMCelltype-2.0.5/mLLMCelltype/R/qwen_processor.R | 18 mLLMCelltype-2.0.5/mLLMCelltype/R/response_validation_utils.R |only mLLMCelltype-2.0.5/mLLMCelltype/R/unified_logger.R | 14 mLLMCelltype-2.0.5/mLLMCelltype/R/zhipu_processor.R | 2 mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/advanced-features.R | 60 - mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/advanced-features.Rmd | 60 - mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/advanced-features.html | 64 - mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/consensus-principles.html | 4 mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/contributing-guide.html | 4 mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/faq.Rmd | 52 - mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/faq.html | 104 +-- mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/getting-started.R | 12 mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/getting-started.Rmd | 29 mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/getting-started.html | 35 - mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/installation.R | 2 mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/installation.Rmd | 2 mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/installation.html | 6 mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/introduction.html | 4 mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/mLLMCelltype.R | 54 - mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/mLLMCelltype.Rmd | 72 +- mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/mLLMCelltype.html | 93 +- mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/usage-tutorial.R | 38 - mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/usage-tutorial.Rmd | 74 +- mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/usage-tutorial.html | 98 +-- mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/version-history.html | 4 mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/why-consensus.Rmd | 18 mLLMCelltype-2.0.5/mLLMCelltype/inst/doc/why-consensus.html | 24 mLLMCelltype-2.0.5/mLLMCelltype/man/QwenProcessor.Rd |only mLLMCelltype-2.0.5/mLLMCelltype/man/UnifiedLogger.Rd | 4 mLLMCelltype-2.0.5/mLLMCelltype/man/annotate_cell_types.Rd | 53 - mLLMCelltype-2.0.5/mLLMCelltype/man/compare_model_predictions.Rd | 46 - mLLMCelltype-2.0.5/mLLMCelltype/man/configure_logger.Rd | 4 mLLMCelltype-2.0.5/mLLMCelltype/man/create_annotation_prompt.Rd | 3 mLLMCelltype-2.0.5/mLLMCelltype/man/get_provider.Rd | 22 mLLMCelltype-2.0.5/mLLMCelltype/man/interactive_consensus_annotation.Rd | 6 mLLMCelltype-2.0.5/mLLMCelltype/man/normalize_cluster_gene_list.Rd | 10 mLLMCelltype-2.0.5/mLLMCelltype/man/register_custom_provider.Rd | 2 mLLMCelltype-2.0.5/mLLMCelltype/man/standardize_cell_type_names.Rd | 4 mLLMCelltype-2.0.5/mLLMCelltype/tests/performance/test_api_rate_limits.R | 5 mLLMCelltype-2.0.5/mLLMCelltype/tests/testthat.R |only mLLMCelltype-2.0.5/mLLMCelltype/tests/testthat/helper-integration.R |only mLLMCelltype-2.0.5/mLLMCelltype/tests/testthat/test-cache-core.R | 14 mLLMCelltype-2.0.5/mLLMCelltype/tests/testthat/test-cache-mock.R | 10 mLLMCelltype-2.0.5/mLLMCelltype/tests/testthat/test-cache-performance.R | 4 mLLMCelltype-2.0.5/mLLMCelltype/tests/testthat/test-cache-real-api.R | 152 +--- mLLMCelltype-2.0.5/mLLMCelltype/tests/testthat/test-cache-simple-api.R | 26 mLLMCelltype-2.0.5/mLLMCelltype/tests/testthat/test-input-contract-consistency.R | 323 ++++++++-- mLLMCelltype-2.0.5/mLLMCelltype/vignettes/advanced-features.Rmd | 60 - mLLMCelltype-2.0.5/mLLMCelltype/vignettes/faq.Rmd | 52 - mLLMCelltype-2.0.5/mLLMCelltype/vignettes/getting-started.Rmd | 29 mLLMCelltype-2.0.5/mLLMCelltype/vignettes/installation.Rmd | 2 mLLMCelltype-2.0.5/mLLMCelltype/vignettes/mLLMCelltype.Rmd | 72 +- mLLMCelltype-2.0.5/mLLMCelltype/vignettes/usage-tutorial.Rmd | 74 +- mLLMCelltype-2.0.5/mLLMCelltype/vignettes/why-consensus.Rmd | 18 68 files changed, 1517 insertions(+), 1164 deletions(-)
Title: Optimal Row-Column Designs for Asymmetrical Factorial
Experiments
Description: Constructs and analyzes optimal row-column designs for
mixed-level factorial experiments under square and rectangular field
layouts. For square field layouts, the package implements direct
common-factor constructions by first forming two component treatment
arrays, one for each factor or super-factor, and then combining them
through a symbolic cell-wise product following Gopinath, Parsad and
Mandal (2018) <doi:10.1080/03610926.2017.1376091>. For rectangular
field layouts, the package constructs designs by extracting a balanced
principal block from a mixed-level block design, treating it as the
principal column, taking the complete treatment set as the principal row,
and generating the full row-column design by cyclic modular development.
The package also includes repair utilities for improving disconnected or
partially connected row-column designs through bounded treatment-swap
searches while preserving the row-column layout structure. The package
provides diagnostic tools for co [...truncated...]
Author: Archana A [aut],
Sukanta Dash [aut, cre]
Maintainer: Sukanta Dash <sukanta.iasri@gmail.com>
Diff between MFRCD versions 0.1.0 dated 2026-05-06 and 0.1.1 dated 2026-05-11
MFRCD-0.1.0/MFRCD/man/all_treatment_combinations.Rd |only MFRCD-0.1.0/MFRCD/man/block_balance_score.Rd |only MFRCD-0.1.0/MFRCD/man/check_row_column_balance.Rd |only MFRCD-0.1.0/MFRCD/man/compact_property_checks.Rd |only MFRCD-0.1.0/MFRCD/man/compute_ade_efficiency.Rd |only MFRCD-0.1.0/MFRCD/man/compute_emv_optimality.Rd |only MFRCD-0.1.0/MFRCD/man/connectedness_diagnostics.Rd |only MFRCD-0.1.0/MFRCD/man/connectedness_from_information.Rd |only MFRCD-0.1.0/MFRCD/man/count_connected_components_from_C.Rd |only MFRCD-0.1.0/MFRCD/man/extract_numeric_design.Rd |only MFRCD-0.1.0/MFRCD/man/extract_principal_block_mixedfact.Rd |only MFRCD-0.1.0/MFRCD/man/factor_contrast_basis.Rd |only MFRCD-0.1.0/MFRCD/man/factorial_effect_bases.Rd |only MFRCD-0.1.0/MFRCD/man/format_design.Rd |only MFRCD-0.1.0/MFRCD/man/kronecker_reduce.Rd |only MFRCD-0.1.0/MFRCD/man/labels_to_numeric_array.Rd |only MFRCD-0.1.0/MFRCD/man/level_balance_diagnostics.Rd |only MFRCD-0.1.0/MFRCD/man/make_numeric_array.Rd |only MFRCD-0.1.0/MFRCD/man/make_public_output.Rd |only MFRCD-0.1.0/MFRCD/man/make_row_column_information.Rd |only MFRCD-0.1.0/MFRCD/man/matrix_rank_tol.Rd |only MFRCD-0.1.0/MFRCD/man/mixed_radix_digits.Rd |only MFRCD-0.1.0/MFRCD/man/mod_add_treatment.Rd |only MFRCD-0.1.0/MFRCD/man/parse_treatment_label.Rd |only MFRCD-0.1.0/MFRCD/man/principal_block_to_matrix.Rd |only MFRCD-0.1.0/MFRCD/man/pseudo_inverse_symmetric.Rd |only MFRCD-0.1.0/MFRCD/man/put_zero_treatment_first.Rd |only MFRCD-0.1.0/MFRCD/man/right_shift.Rd |only MFRCD-0.1.0/MFRCD/man/svd_ginv.Rd |only MFRCD-0.1.0/MFRCD/man/symmetrize_matrix.Rd |only MFRCD-0.1.0/MFRCD/man/treatment_index_from_matrix.Rd |only MFRCD-0.1.0/MFRCD/man/treatment_label.Rd |only MFRCD-0.1.0/MFRCD/tests/testthat/test-mfrcd.R |only MFRCD-0.1.1/MFRCD/DESCRIPTION | 56 MFRCD-0.1.1/MFRCD/MD5 | 70 MFRCD-0.1.1/MFRCD/NAMESPACE | 43 MFRCD-0.1.1/MFRCD/NEWS.md |only MFRCD-0.1.1/MFRCD/R/MFRCD.R | 3396 +++++++++++-- MFRCD-0.1.1/MFRCD/man/MFRCD-package.Rd | 8 MFRCD-0.1.1/MFRCD/man/analyse_rcd.Rd |only MFRCD-0.1.1/MFRCD/man/check_rc_factorial_n.Rd | 14 MFRCD-0.1.1/MFRCD/man/make_D2_from_complete_sets.Rd |only MFRCD-0.1.1/MFRCD/man/make_connected_rcd_bounded.Rd |only MFRCD-0.1.1/MFRCD/man/mfrcd.Rd | 38 MFRCD-0.1.1/MFRCD/man/mfrcd_check_repair.Rd |only MFRCD-0.1.1/MFRCD/man/print.mfrcd_check_repair.Rd |only MFRCD-0.1.1/MFRCD/man/print.rcd_analysis.Rd |only MFRCD-0.1.1/MFRCD/man/rc_factorial_n.Rd | 20 MFRCD-0.1.1/MFRCD/man/rc_from_principal_block.Rd | 28 MFRCD-0.1.1/MFRCD/man/rc_method1.Rd | 20 MFRCD-0.1.1/MFRCD/man/rc_method2.Rd | 18 MFRCD-0.1.1/MFRCD/man/rcd_analysis_summary.Rd |only MFRCD-0.1.1/MFRCD/man/rcd_feasibility_check.Rd |only MFRCD-0.1.1/MFRCD/man/summarize_rcd_layout.Rd |only MFRCD-0.1.1/MFRCD/man/tetra_connectedness.Rd |only MFRCD-0.1.1/MFRCD/man/validate_bounded_rcd.Rd |only MFRCD-0.1.1/MFRCD/man/verify_mfrcd.Rd | 23 MFRCD-0.1.1/MFRCD/tests/testthat.R | 24 MFRCD-0.1.1/MFRCD/tests/testthat/test-basic.R |only 59 files changed, 3304 insertions(+), 454 deletions(-)
Title: Weight of Evidence for Quantifying Performance of a Binary
Classifier
Description: The distributions of the weight of evidence (log Bayes factor) favouring case over noncase status in a test dataset (or test folds generated by cross-validation) can be used to quantify the performance of a diagnostic test. This package can be used with any test dataset on which you have computed prior probabilities of case status, posterior probabilities of case status, and you have the observed case-control status. In comparison with the C-statistic (area under ROC curve), the expected weight of evidence (expected information for discrimination) has several advantages as a summary measure of predictive performance. To quantify how the predictor will behave as a risk stratifier, the quantiles of the distributions of weight of evidence in cases and controls can be calculated and plotted.
Author: Paul McKeigue [aut, cre],
Marco Colombo [ctb]
Maintainer: Paul McKeigue <paul.mckeigue@ed.ac.uk>
Diff between wevid versions 0.6.2 dated 2019-09-12 and 0.7.0 dated 2026-05-11
wevid-0.6.2/wevid/data/fitonly.rda |only wevid-0.6.2/wevid/data/pima.rda |only wevid-0.6.2/wevid/inst |only wevid-0.6.2/wevid/man/Wdensities.Rd |only wevid-0.6.2/wevid/man/Wdensities.crude.Rd |only wevid-0.6.2/wevid/man/recalibrate.p.Rd |only wevid-0.6.2/wevid/man/summary-densities.Rd |only wevid-0.6.2/wevid/man/wevid.datasets.Rd |only wevid-0.7.0/wevid/DESCRIPTION | 35 - wevid-0.7.0/wevid/MD5 | 50 +- wevid-0.7.0/wevid/NAMESPACE | 16 wevid-0.7.0/wevid/R/data.R | 48 -- wevid-0.7.0/wevid/R/plots.R | 238 +++++----- wevid-0.7.0/wevid/R/wdists.R | 570 +++++++++---------------- wevid-0.7.0/wevid/R/wevid.R | 71 +-- wevid-0.7.0/wevid/man/Wdensities.fromraw.Rd |only wevid-0.7.0/wevid/man/Wdensities.mix.Rd |only wevid-0.7.0/wevid/man/Wdensities.unadjusted.Rd |only wevid-0.7.0/wevid/man/auroc.model.Rd |only wevid-0.7.0/wevid/man/cleveland.Rd |only wevid-0.7.0/wevid/man/cumfreqs.Rd |only wevid-0.7.0/wevid/man/error.integrals.Rd |only wevid-0.7.0/wevid/man/figures |only wevid-0.7.0/wevid/man/fsmooth.Rd |only wevid-0.7.0/wevid/man/kl.Rd |only wevid-0.7.0/wevid/man/lambda.model.Rd |only wevid-0.7.0/wevid/man/means.densities.Rd |only wevid-0.7.0/wevid/man/plotW.Rd |only wevid-0.7.0/wevid/man/plotWdists.Rd | 37 - wevid-0.7.0/wevid/man/plotcumfreqs.Rd | 15 wevid-0.7.0/wevid/man/plotroc.Rd | 23 - wevid-0.7.0/wevid/man/prop.belowthreshold.Rd | 19 wevid-0.7.0/wevid/man/tobits.Rd |only wevid-0.7.0/wevid/man/weightsofevidence.Rd | 9 wevid-0.7.0/wevid/man/wevid-package.Rd | 65 -- wevid-0.7.0/wevid/man/wtrue.results.Rd |only 36 files changed, 496 insertions(+), 700 deletions(-)
Title: Visualization of Viral Protein Sequence Diversity Dynamics
Description: To ease the visualization of outputs from Diversity Motif Analyser ('DiMA';
<https://github.com/BVU-BILSAB/DiMA>). 'vDiveR' allows visualization of the diversity
motifs (index and its variants – major, minor and unique) for elucidation of
the underlying inherent dynamics. Please refer <https://vdiver-manual.readthedocs.io/en/latest/>
for more information.
Author: Pendy Tok [aut, cre],
Li Chuin Chong [aut],
Evgenia Chikina [aut],
Yin Cheng Chen [aut],
Mohammad Asif Khan [aut]
Maintainer: Pendy Tok <pendytok0518@gmail.com>
This is a re-admission after prior archival of version 2.1.0 dated 2025-09-19
Diff between vDiveR versions 2.1.0 dated 2025-09-19 and 2.2.0 dated 2026-05-11
vDiveR-2.1.0/vDiveR/inst/extdata/city_mapper.csv |only vDiveR-2.2.0/vDiveR/DESCRIPTION | 12 - vDiveR-2.2.0/vDiveR/MD5 | 25 +- vDiveR-2.2.0/vDiveR/NAMESPACE | 10 vDiveR-2.2.0/vDiveR/NEWS.md | 13 - vDiveR-2.2.0/vDiveR/R/json2csv.R | 230 +++++++++++++-------- vDiveR-2.2.0/vDiveR/R/plot_conservation_level.R | 36 +-- vDiveR-2.2.0/vDiveR/R/plot_dynamics_protein.R | 199 ++++++++++-------- vDiveR-2.2.0/vDiveR/R/plot_dynamics_proteome.R | 162 +++++++------- vDiveR-2.2.0/vDiveR/R/plot_entropy.R | 104 +++++++-- vDiveR-2.2.0/vDiveR/R/plot_world_map.R | 28 +- vDiveR-2.2.0/vDiveR/man/plot_dynamics_protein.Rd | 6 vDiveR-2.2.0/vDiveR/man/plot_world_map.Rd | 2 vDiveR-2.2.0/vDiveR/tests/testthat/test-json2csv.R | 5 14 files changed, 501 insertions(+), 331 deletions(-)
Title: Small Sample Size Species Distribution Modeling
Description: Implements a set of distribution modeling methods that are suited to species with small sample sizes (e.g., poorly sampled species or rare species). While these methods can also be used on well-sampled taxa, they are united by the fact that they can be utilized with relatively few data points. More details on the currently implemented methodologies can be found in Maitner et al. (2026) <doi:10.1002/ecog.08112>, Drake and Richards (2018) <doi:10.1002/ecs2.2373>, Drake (2015) <doi:10.1098/rsif.2015.0086>, and Drake (2014) <doi:10.1890/ES13-00202.1>.
Author: Brian S. Maitner [aut, cre] ,
Robert L. Richards [aut],
Ben S. Carlson [aut],
John M. Drake [aut],
Cory Merow [aut]
Maintainer: Brian S. Maitner <bmaitner@usf.edu>
Diff between S4DM versions 0.0.1 dated 2025-01-10 and 0.0.2 dated 2026-05-11
DESCRIPTION | 21 +++--- MD5 | 48 ++++++++------- NAMESPACE | 1 NEWS | 12 +++ R/dr_kliep.R |only R/ensemble_range_map.R | 3 R/evaluate_range_map.R | 20 +++--- R/fit_density_ratio.R | 4 - R/fit_plug_and_play.R | 2 R/get_env_bg.R | 12 +-- R/get_env_pres.R | 2 R/get_response_curves.R | 18 ++--- R/project_plug_and_play.R | 15 ++++ R/stratify_spatial.R | 22 +++---- build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 21 +++++- inst/doc/S4DM.html | 109 +++++++++++++++++------------------ man/dr_kliep.Rd |only man/ensemble_range_map.Rd | 1 man/fit_density_ratio.Rd | 4 - man/fit_plug_and_play.Rd | 2 man/project_plug_and_play.Rd | 4 - man/sample_points.Rd | 48 +++++++-------- tests/testthat/test-dr.R | 38 ++++++++++++ tests/testthat/test-dr_fit_project.R | 2 26 files changed, 245 insertions(+), 164 deletions(-)
Title: Information Bottleneck Methods for Clustering Mixed-Type Data
Description: Implements multiple variants of the Information Bottleneck ('IB') method
for clustering datasets containing continuous, categorical (nominal/ordinal) and mixed-type variables.
The package provides deterministic, agglomerative, generalized,
and standard 'IB' clustering algorithms that preserve relevant information while
forming interpretable clusters. The Deterministic Information Bottleneck is described in
Costa et al. (2026) <doi:10.1016/j.patcog.2026.113580>. The standard 'IB' method
originates from Tishby et al. (2000) <doi:10.48550/arXiv.physics/0004057>,
the agglomerative variant from Slonim and Tishby (1999) <https://papers.nips.cc/paper/1651-agglomerative-information-bottleneck>,
and the generalized 'IB' from Strouse and Schwab (2017) <doi:10.1162/NECO_a_00961>.
Author: Angelos Markos [aut, cre],
Efthymios Costa [aut],
Ioanna Papatsouma [aut]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between IBclust versions 1.2.1 dated 2025-09-19 and 1.3 dated 2026-05-11
DESCRIPTION | 30 +-- MD5 | 65 ++++--- NAMESPACE | 47 ++--- R/AIB.R | 5 R/AIBmix.R | 201 ++++++++++++++++++++++- R/DIBmix.R | 320 +++++++++++++++++++++++++++++++++++-- R/DIBmix_iterate.R | 124 +++----------- R/GIBmix.R | 300 ++++++++++++++++++++++++++++++++--- R/GIBmix_iterate.R | 100 ----------- R/IBclust-package.R |only R/IBmix.R | 293 ++++++++++++++++++++++++++++++++-- R/IBmix_iterate.R | 100 ----------- R/RcppExports.R | 32 +++ R/aibclust-class.R | 6 R/aibclust-methods.R | 97 +++++++++-- R/bw_select.R | 216 ++++++++++++++++++------- R/coord_to_pxy_R.R | 12 - R/coord_to_pxy_nystrom_R.R |only R/gibclust-class.R | 8 R/gibclust-methods.R | 106 ++++++++---- R/importance.R |only R/input_checks.R | 51 +++++ R/make_dendrogram.R | 2 R/qsteps.R |only README.md | 4 build/partial.rdb |binary inst/CITATION | 14 - inst/REFERENCES.bib | 24 +- man/AIBmix.Rd | 106 ++++++------ man/DIBmix.Rd | 122 +++++++++----- man/GIBmix.Rd | 116 +++++++++---- man/IBclust-package.Rd |only man/IBmix.Rd | 117 +++++++++---- src/RcppExports.cpp | 126 ++++++++++++++ src/ib_dist.cpp | 116 +++++++++++++ src/qt_x_step.cpp | 383 +++++++++++++++++++++++++++++++++++++++++++-- 36 files changed, 2498 insertions(+), 745 deletions(-)
Title: Differential Item Functioning in Generalized Partial Credit
Models
Description: Provides a framework to detect Differential Item Functioning (DIF) in Generalized Partial Credit Models (GPCM) and special cases of the GPCM as proposed by Schauberger and Mair (2019) <doi:10.3758/s13428-019-01224-2>. A joint model is set up where DIF is explicitly parametrized and penalized likelihood estimation is used for parameter selection. The big advantage of the method called GPCMlasso is that several variables can be treated simultaneously and that both continuous and categorical variables can be used to detect DIF.
Author: Gunther Schauberger [aut, cre]
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between GPCMlasso versions 0.1-8 dated 2025-07-23 and 0.1-9 dated 2026-05-11
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/get_designX.R | 7 +++++-- man/GPCMlasso-package.Rd | 5 +++++ 4 files changed, 18 insertions(+), 10 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-03-10 0.19.2
2025-07-16 0.19.0
2024-12-12 0.18.1
2024-08-16 0.18.0
2024-05-26 0.17.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-29 0.1.0
Title: Be Nice on the Web
Description: Be responsible when scraping data from websites by following polite principles: introduce yourself, ask for permission, take slowly and never ask twice.
Author: Dmytro Perepolkin [aut, cre]
Maintainer: Dmytro Perepolkin <dperepolkin@gmail.com>
Diff between polite versions 0.1.3 dated 2023-06-30 and 0.1.4 dated 2026-05-11
DESCRIPTION | 15 LICENSE | 4 MD5 | 50 - NAMESPACE | 86 +- NEWS.md | 146 ++-- R/scrape.R | 186 +++-- R/use-manners.R | 4 README.md | 952 ++++++++++++++---------------- inst/templates/polite_template.R | 308 ++++----- man/bow.Rd | 102 +-- man/figures/README-unnamed-chunk-10-1.png |binary man/guess_basename.Rd | 42 - man/html_attrs_dfr.Rd | 82 +- man/nod.Rd | 62 - man/nullcoalesce.Rd | 26 man/pipe.Rd | 24 man/politely.Rd | 82 +- man/print.polite.Rd | 32 - man/rip.Rd | 84 +- man/scrape.Rd | 90 +- man/set_delay.Rd | 60 - man/use_manners.Rd | 32 - tests/testthat.R | 8 tests/testthat/test-scrape.R | 120 +-- tests/testthat/test_bow.R | 64 +- tests/testthat/test_nod.R | 8 26 files changed, 1347 insertions(+), 1322 deletions(-)
Title: Highlight Conserved Edits Across Versions of a Document
Description: Input multiple versions of a source document,
and receive HTML code for a highlighted version of the source document
indicating the frequency of occurrence of phrases in the different versions.
This method is described in Chapter 3 of
Rogers (2024) <https://digitalcommons.unl.edu/dissertations/AAI31240449/>.
Author: Center for Statistics and Applications in Forensic Evidence [aut, cph,
fnd],
Rachel Rogers [aut, cre] ,
Susan VanderPlas [aut]
Maintainer: Rachel Rogers <rrogers.rpackages@gmail.com>
Diff between highlightr versions 2.0.0 dated 2026-04-10 and 2.0.1 dated 2026-05-11
DESCRIPTION | 6 MD5 | 30 - NEWS.md | 7 R/collocation_frequency.R | 2 R/highlighted_text.R | 4 README.md | 5 inst/doc/highlightr.R | 7 inst/doc/highlightr.Rmd | 14 inst/doc/highlightr.html | 121 ++-- inst/doc/wikipedia-highlighter.R | 4 inst/doc/wikipedia-highlighter.Rmd | 4 inst/doc/wikipedia-highlighter.html | 54 - tests/testthat/test-collocation_frequency.R | 778 ++++++++++++++-------------- tests/testthat/test-highlighted_text.R | 15 vignettes/highlightr.Rmd | 14 vignettes/wikipedia-highlighter.Rmd | 4 16 files changed, 571 insertions(+), 498 deletions(-)
Title: Tools to Query the 'Algaebase' Online Database, Standardize
Phytoplankton Taxonomic Data, and Perform Functional Group
Classifications
Description: Functions that facilitate the use of accepted taxonomic nomenclature, collection of
functional trait data, and assignment of functional group classifications to phytoplankton
species. Possible classifications include Morpho-functional group (MFG; Salmaso et al. 2015
<doi:10.1111/fwb.12520>) and CSR (Reynolds 1988; Functional morphology and the
adaptive strategies of phytoplankton. In C.D. Sandgren (ed). Growth and reproductive
strategies of freshwater phytoplankton, 388-433. Cambridge University Press, New York).
Versions 2.0.0 and later includes new functions for querying the
'algaebase' online taxonomic database (www.algaebase.org), however these functions require
a valid API key that must be acquired from the 'algaebase' administrators.
Note that none of the 'algaeClassify' authors are affiliated with 'algaebase' in any way. Taxonomic
names can also be checked against a variety of taxonomic databases using
the 'Global Names Resolver' service via its API (<https://resolver.g [...truncated...]
Author: Vijay Patil [aut, cre],
Torsten Seltmann [aut],
Nico Salmaso [aut],
Orlane Anneville [aut],
Marc Lajeunesse [aut],
Dietmar Straile [aut]
Maintainer: Vijay Patil <vij.patil@gmail.com>
Diff between algaeClassify versions 2.0.5 dated 2025-12-01 and 2.0.6 dated 2026-05-11
DESCRIPTION | 16 +- MD5 | 19 +- NEWS.md | 29 ++++ R/genus_search_itis.r | 257 ++++++++++++++++++++++------------------ R/itis_api.r |only R/itis_search_df.r | 152 ++++++++++------------- R/species_search_itis.r | 286 ++++++++++++++++++++++++--------------------- README.md | 2 man/genus_search_itis.Rd | 2 man/itis_search_df.Rd | 9 - man/species_search_itis.Rd | 2 11 files changed, 417 insertions(+), 357 deletions(-)
Title: Visualization of Design of Experiments from the 'agricolae'
Package
Description: Visualization of Design of Experiments from the 'agricolae' package with 'ggplot2' framework
The user provides an experiment design from the 'agricolae' package, calls the corresponding function and will receive a
visualization with 'ggplot2' based functions that are specific for each design. As there are many different designs, each design is tested on its type.
The output can be modified with standard 'ggplot2' commands or with other packages with 'ggplot2' function extensions.
Author: Jens Harbers [aut, cre]
Maintainer: Jens Harbers <jensharbers@gmail.com>
Diff between agricolaeplotr versions 0.6.1 dated 2025-01-30 and 1.0.0 dated 2026-05-11
DESCRIPTION | 11 MD5 | 222 +++++++-- NAMESPACE | 2 NEWS.md | 8 R/hello.R | 813 ++++++++++++++++++++---------------- README.md | 120 ++--- build/vignette.rds |binary inst/CITATION | 30 - inst/application |only inst/doc/FielDHub.Rmd | 274 ++++++------ inst/doc/FielDHub.html | 810 ++++++++++++++++++------------------ inst/doc/vignette.R | 24 - inst/doc/vignette.Rmd | 782 +++++++++++++++++----------------- inst/doc/vignette.html | 850 +++++++++++++++++++++++++------------- inst/exampleData/DOE_EXP.csv | 602 +++++++++++++------------- man/DOE_obj.Rd | 62 +- man/citations.Rd | 52 +- man/full_control_positions.Rd | 274 ++++++------ man/make_polygons.Rd | 94 ++-- man/plot_alpha.Rd | 126 ++--- man/plot_bib.Rd | 112 ++--- man/plot_cyclic.Rd | 110 ++-- man/plot_dau.Rd | 110 ++-- man/plot_design.factorial_crd.Rd | 122 ++--- man/plot_design.factorial_lsd.Rd | 114 ++--- man/plot_design.factorial_rcbd.Rd | 106 ++-- man/plot_design_crd.Rd | 118 ++--- man/plot_fieldhub.Rd | 180 ++++---- man/plot_graeco.Rd | 118 ++--- man/plot_latin_square.Rd | 112 ++--- man/plot_lattice_simple.Rd | 106 ++-- man/plot_lattice_triple.Rd | 108 ++-- man/plot_longest_diagonal.Rd | 94 ++-- man/plot_split_crd.Rd | 142 +++--- man/plot_split_lsd.Rd | 118 ++--- man/plot_split_rcbd.Rd | 130 ++--- man/plot_strip.Rd | 126 ++--- man/plot_youden.Rd | 112 ++--- man/protective_layers.Rd | 80 +-- man/sample_locations.Rd | 82 +-- man/serpentine.Rd | 52 +- man/summary.Rd | 78 +-- man/test_input_extend.Rd | 42 - man/test_input_ncols.Rd | 42 - man/test_input_nrows.Rd | 42 - man/test_input_reverse.Rd | 42 - man/test_input_shift.Rd | 42 - man/test_name_in_column.Rd | 54 +- man/test_names_design.Rd | 50 +- man/test_string.Rd | 42 - man/theme_gi.Rd | 54 +- man/theme_poster.Rd | 52 +- man/theme_pres.Rd | 52 +- man/to_table.Rd | 90 ++-- tests/testthat.R | 8 tests/testthat/_problems |only tests/testthat/testall.R | 462 +------------------- vignettes/FielDHub.Rmd | 274 ++++++------ vignettes/vignette.Rmd | 782 +++++++++++++++++----------------- 59 files changed, 4927 insertions(+), 4789 deletions(-)
More information about agricolaeplotr at CRAN
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