Title: Estimating Disease Prevalence from Registry Data
Description: Estimates disease prevalence for a given index date using existing
registry data extended with Monte Carlo simulations following the method of Crouch et al (2014) <doi: 10.1016/j.canep.2014.02.005>.
Author: Stuart Lacy [cre, aut],
Simon Crouch [aut],
Stephanie Lax [aut]
Maintainer: Stuart Lacy <stuart.lacy@york.ac.uk>
Diff between rprev versions 1.0.5 dated 2021-05-04 and 1.0.6 dated 2025-06-27
rprev-1.0.5/rprev/R/rprev.R |only rprev-1.0.5/rprev/man/rprev.Rd |only rprev-1.0.6/rprev/DESCRIPTION | 11 rprev-1.0.6/rprev/MD5 | 29 rprev-1.0.6/rprev/NAMESPACE | 2 rprev-1.0.6/rprev/NEWS.md | 8 rprev-1.0.6/rprev/R/fixedcure.R | 12 rprev-1.0.6/rprev/R/flexsurv.R | 5 rprev-1.0.6/rprev/R/rprev-package.R |only rprev-1.0.6/rprev/R/test_custom_models.R | 4 rprev-1.0.6/rprev/README.md | 7 rprev-1.0.6/rprev/build/partial.rdb |only rprev-1.0.6/rprev/build/vignette.rds |binary rprev-1.0.6/rprev/inst/doc/diagnostics.R | 14 rprev-1.0.6/rprev/inst/doc/diagnostics.html | 797 ++++++++++++++----- rprev-1.0.6/rprev/inst/doc/user_guide.R | 106 +- rprev-1.0.6/rprev/inst/doc/user_guide.html | 1141 +++++++++++++++++++--------- rprev-1.0.6/rprev/man/rprev-package.Rd |only 18 files changed, 1490 insertions(+), 646 deletions(-)
Title: Exploratory Data Analysis, Group Comparison Tools, and Other
Procedures
Description: Provides a comprehensive set of tools for descriptive statistics,
graphical data exploration, outlier detection, homoscedasticity testing, and
multiple comparison procedures. Includes manual implementations of Levene's test,
Bartlett's test, and the Fligner-Killeen test, as well as post hoc comparison
methods such as Tukey, Scheffé, Games-Howell, Brunner-Munzel, and others.
This version introduces two new procedures: the Jonckheere-Terpstra trend test
and the Jarque-Bera test with Glinskiy's (2024) correction. Designed for use in
teaching, applied statistical analysis, and reproducible research.
Author: Carlos Jimenez-Gallardo [aut, cre]
Maintainer: Carlos Jimenez-Gallardo <carlos.jimenez@ufrontera.cl>
Diff between Analitica versions 1.8.1 dated 2025-06-14 and 1.8.5 dated 2025-06-27
DESCRIPTION | 22 +++++++++++++--------- MD5 | 10 +++++++--- NAMESPACE | 4 ++++ R/JarqueBera_GTest.R |only R/JonckheereTest.R |only inst/doc/Analitica-intro.html | 4 ++-- man/JBGTest.Rd |only man/JT_Test.Rd |only 8 files changed, 26 insertions(+), 14 deletions(-)
Title: Group Sequential Design with Non-Constant Effect
Description: The goal of 'gsDesign2' is to enable fixed or group sequential
design under non-proportional hazards. To enable highly flexible enrollment,
time-to-event and time-to-dropout assumptions, 'gsDesign2' offers piecewise
constant enrollment, failure rates, and dropout rates for a stratified
population. This package includes three methods for designs:
average hazard ratio, weighted logrank tests in Yung and Liu (2019)
<doi:10.1111/biom.13196>, and MaxCombo tests.
Substantial flexibility on top of what is in the 'gsDesign' package
is intended for selecting boundaries.
Author: Keaven Anderson [aut],
Yujie Zhao [aut, cre],
Yilong Zhang [aut],
John Blischak [aut],
Yihui Xie [aut],
Nan Xiao [aut],
Jianxiao Yang [aut],
Amin Shirazi [ctb],
Ruixue Wang [ctb],
Yi Cui [ctb],
Ping Yang [ctb],
Xin Tong Li [ctb],
Chenxiang Li [ctb],
[...truncated...]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between gsDesign2 versions 1.1.4 dated 2025-06-06 and 1.1.5 dated 2025-06-27
DESCRIPTION | 6 MD5 | 10 NEWS.md | 8 R/to_integer.R | 16 inst/doc/gsDesign2.html | 770 ++++++++++++++--------------- tests/testthat/test-developer-to_integer.R | 24 6 files changed, 431 insertions(+), 403 deletions(-)
Title: General Bivariate Copula Theory and Many Utility Functions
Description: Extensive functions for bivariate copula (bicopula) computations and related operations
for bicopula theory. The lower, upper, product, and select other bicopula are implemented along
with operations including the diagonal, survival copula, dual of a copula, co-copula, and
numerical bicopula density. Level sets, horizontal and vertical sections are supported. Numerical
derivatives and inverses of a bicopula are provided through which simulation is implemented.
Bicopula composition, convex combination, asymmetry extension, and products also are provided.
Support extends to the Kendall Function as well as the Lmoments thereof. Kendall Tau,
Spearman Rho and Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer-
Wolff Sigma, tail dependency, tail order, skewness, and bivariate Lmoments are implemented, and
positive/negative quadrant dependency, left (right) increasing (decreasing) are available.
Other features include Kullback-Leibler Divergence, Vuong Procedure, spectral measure, [...truncated...]
Author: William Asquith [aut, cre]
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between copBasic versions 2.2.7 dated 2025-01-25 and 2.2.8 dated 2025-06-27
DESCRIPTION | 11 ++-- MD5 | 32 ++++++------ NEWS | 13 ++++- R/level.curvesCOP.R | 9 +++ R/level.curvesCOP2.R | 9 +++ build/partial.rdb |binary man/FGMcop.Rd | 62 ++++++++++++------------ man/FRcop.Rd | 2 man/GHcop.Rd | 2 man/GLcop.Rd | 6 +- man/HRcop.Rd | 2 man/LzCOPpermsym.Rd | 124 ++++++++++++++++++++++++++++++++++++------------ man/RAYcop.Rd | 4 - man/hoefCOP.Rd | 14 +---- man/kullCOP.Rd | 1 man/level.curvesCOP.Rd | 2 man/level.curvesCOP2.Rd | 2 17 files changed, 190 insertions(+), 105 deletions(-)
Title: Read/Write, Analyze, and Visualize 'BIOM' Data
Description: A toolkit for working with Biological Observation Matrix ('BIOM') files.
Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and
beta diversity (including 'UniFrac'). Summarize counts by taxonomic level.
Subset based on metadata. Generate visualizations and statistical analyses.
CPU intensive operations are coded in C for speed.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between rbiom versions 2.2.0 dated 2025-04-04 and 2.2.1 dated 2025-06-27
DESCRIPTION | 11 ++++++----- LICENSE | 4 ++-- MD5 | 35 ++++++++++++++++++----------------- R/bdiv_heatmap.r | 22 +++------------------- R/bdiv_ord_plot.r | 1 + R/corrplot_stats.r | 10 ++++++++-- R/data.r | 2 +- R/geom_dendro.r | 7 ++++++- R/plot_wrap.r |only R/rare_multiplot.r | 23 ++--------------------- R/taxa_heatmap.r | 20 ++------------------ R/taxa_stacked.r | 18 ++---------------- R/utils.r | 1 + README.md | 5 +++-- build/partial.rdb |binary man/figures/README-bdiv-1.png |binary man/figures/README-bdiv-3.png |binary man/figures/README-taxa-1.png |binary man/hmp50.Rd | 2 +- 19 files changed, 56 insertions(+), 105 deletions(-)
Title: Bayesian Longitudinal Regularized Quantile Mixed Model
Description: With high-dimensional omics features, repeated measure ANOVA leads to longitudinal gene-environment interaction studies that have intra-cluster correlations, outlying observations and structured sparsity arising from the ANOVA design. In this package, we have developed robust sparse Bayesian mixed effect models tailored for the above studies (Fan et al. (2025) <doi:10.1093/jrsssc/qlaf027>). An efficient Gibbs sampler has been developed to facilitate fast computation. The Markov chain Monte Carlo algorithms of the proposed and alternative methods are efficiently implemented in 'C++'. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Kun Fan [aut, cre],
Cen Wu [aut]
Maintainer: Kun Fan <kfan@ksu.edu>
Diff between mixedBayes versions 0.1.8 dated 2025-05-15 and 0.1.9 dated 2025-06-27
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/LONBGLSS.R | 2 +- R/LONRBGLSS.R | 2 +- README.md | 2 +- build/partial.rdb |binary 7 files changed, 17 insertions(+), 13 deletions(-)
Title: Grouped Hyper Data Frame: An Extension of Hyper Data Frame
Description: An S3 class 'groupedHyperframe' that
inherits from hyper data frame. Batch
processes on point-pattern hyper column.
Aggregation of function-value-table hyper
column(s) and numeric hyper column(s) over a
nested grouping structure.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [aut]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe versions 0.2.3 dated 2025-06-05 and 0.2.4 dated 2025-06-27
DESCRIPTION | 7 - MD5 | 38 ++++----- R/aggregate_fv.R | 1 R/aggregate_num.R | 1 R/cash_set.R | 3 R/data_doc.R | 2 R/mc_identical_by.R | 1 R/onLoad_parallel.R | 12 ++ R/op_ppplist.R | 1 build/vignette.rds |binary inst/doc/groupedHyperframe.R | 20 ++-- inst/doc/groupedHyperframe.html | 162 ++++++++++++++++++++++++++-------------- inst/doc/groupedHyperframe.qmd | 56 ++++++++++--- man/aggregate_fv.Rd | 3 man/aggregate_num.Rd | 3 man/mc_identical_by.Rd | 3 man/op_ppplist.Rd | 3 man/wrobel_lung.Rd | 2 vignettes/groupedHyperframe.bib | 34 ++++++++ vignettes/groupedHyperframe.qmd | 56 ++++++++++--- 20 files changed, 275 insertions(+), 133 deletions(-)
More information about groupedHyperframe at CRAN
Permanent link
Title: 'ForLion' Algorithm to Find D-Optimal Designs for Experiments
Description: Designing experimental plans that involve both discrete and continuous factors with general parametric statistical models using the 'ForLion' algorithm and 'EW ForLion' algorithm. The algorithms will search for locally optimal designs and EW optimal designs under the D-criterion. Reference: Huang, Y., Li, K., Mandal, A., & Yang, J., (2024)<doi:10.1007/s11222-024-10465-x>.
Author: Yifei Huang [aut],
Siting Lin [aut, cre],
Jie Yang [aut]
Maintainer: Siting Lin <slin95@uic.edu>
Diff between ForLion versions 0.2.0 dated 2025-06-10 and 0.3.0 dated 2025-06-27
DESCRIPTION | 11 - MD5 | 86 ++++---- R/EW_ForLion_GLM_Optimal.R | 136 ++++++------- R/EW_ForLion_MLM_Optimal.R | 92 +++++---- R/EW_Xw_maineffects_self.R | 8 R/EW_design_initial_GLM.R | 20 +- R/EW_design_initial_MLM.R | 10 - R/EW_liftoneDoptimal_GLM_func.R | 4 R/EW_liftoneDoptimal_MLM_func.R | 4 R/EW_liftoneDoptimal_log_GLM_func.R | 4 R/ForLion_GLM_Optimal.R | 72 +++---- R/ForLion_MLM_Optimal.R | 86 ++++---- R/GLM_Exact_Design.R | 23 +- R/MLM_Exact_Design.R | 11 - R/design_initial_self.R | 18 - R/liftoneDoptimal_GLM_func.R | 4 R/liftoneDoptimal_MLM_func.R | 4 R/liftoneDoptimal_log_GLM_func.R | 4 R/print.design_output.R | 70 +++++-- inst/doc/Intro_to_ForLion.R | 24 +- inst/doc/Intro_to_ForLion.Rmd | 27 +- inst/doc/Intro_to_ForLion.html | 322 ++++++++++++++++----------------- man/EW_ForLion_GLM_Optimal.Rd | 42 ++-- man/EW_ForLion_MLM_Optimal.Rd | 243 ++++++++++++------------ man/EW_Xw_maineffects_self.Rd | 130 ++++++------- man/EW_design_initial_GLM.Rd | 130 ++++++------- man/EW_design_initial_MLM.Rd | 146 +++++++------- man/EW_dprime_func_self.Rd | 80 ++++---- man/EW_liftoneDoptimal_GLM_func.Rd | 152 +++++++-------- man/EW_liftoneDoptimal_MLM_func.Rd | 158 ++++++++-------- man/EW_liftoneDoptimal_log_GLM_func.Rd | 154 +++++++-------- man/ForLion-package.Rd | 4 man/ForLion_GLM_Optimal.Rd | 175 +++++++++-------- man/ForLion_MLM_Optimal.Rd | 249 ++++++++++++------------- man/GLM_Exact_Design.Rd | 223 +++++++++++----------- man/MLM_Exact_Design.Rd | 163 ++++++++-------- man/design_initial_self.Rd | 14 - man/liftoneDoptimal_GLM_func.Rd | 4 man/liftoneDoptimal_MLM_func.Rd | 4 man/liftoneDoptimal_log_GLM_func.Rd | 4 man/polynomial_sol_J3.Rd | 50 ++--- man/polynomial_sol_J4.Rd | 54 ++--- man/polynomial_sol_J5.Rd | 56 ++--- vignettes/Intro_to_ForLion.Rmd | 27 +- 44 files changed, 1676 insertions(+), 1626 deletions(-)
Title: Calculate Persistent Homology with Ripser-Based Engines
Description: Ports the Ripser <doi:10.48550/arXiv.1908.02518>
and Cubical Ripser <doi:10.48550/arXiv.2005.12692>
persistent homology calculation engines from C++.
Can be used as a rapid calculation tool in topological data analysis
pipelines.
Author: Raoul R. Wadhwa [aut] ,
Matt Piekenbrock [aut],
Jason Cory Brunson [aut, cre] ,
Xinyi Zhang [aut],
Alice Zhang [aut] ,
Kent Phipps [aut],
Sean Hershkowitz [aut],
Emily Noble [ctb],
Aymeric Stamm [ctb] ,
Aidan Bryant [ctb],
James Golabek [ctb],
Jacob [...truncated...]
Maintainer: Jason Cory Brunson <cornelioid@gmail.com>
Diff between ripserr versions 0.3.0 dated 2025-04-06 and 1.0.0 dated 2025-06-27
ripserr-0.3.0/ripserr/src/ripser_short.cpp |only ripserr-1.0.0/ripserr/DESCRIPTION | 92 - ripserr-1.0.0/ripserr/MD5 | 37 ripserr-1.0.0/ripserr/NEWS.md | 8 ripserr-1.0.0/ripserr/R/RcppExports.R | 8 ripserr-1.0.0/ripserr/R/data.r | 63 ripserr-1.0.0/ripserr/R/utility.R | 32 ripserr-1.0.0/ripserr/R/vietoris_rips.R | 142 + ripserr-1.0.0/ripserr/data/powehi.rda |only ripserr-1.0.0/ripserr/data/sagAstar.rda |only ripserr-1.0.0/ripserr/inst/doc/cubical.html | 353 +++- ripserr-1.0.0/ripserr/inst/doc/modeling-disease-using-PH.R | 5 ripserr-1.0.0/ripserr/inst/doc/modeling-disease-using-PH.Rmd | 5 ripserr-1.0.0/ripserr/inst/doc/modeling-disease-using-PH.html | 751 +++++++--- ripserr-1.0.0/ripserr/inst/doc/vietoris-rips.html | 395 ++++- ripserr-1.0.0/ripserr/man/aegypti.Rd | 5 ripserr-1.0.0/ripserr/man/blackholes.Rd |only ripserr-1.0.0/ripserr/man/ripserr.Rd | 14 ripserr-1.0.0/ripserr/man/vietoris_rips.Rd | 8 ripserr-1.0.0/ripserr/src/RcppExports.cpp | 29 ripserr-1.0.0/ripserr/src/ripser.cpp |only ripserr-1.0.0/ripserr/vignettes/modeling-disease-using-PH.Rmd | 5 22 files changed, 1452 insertions(+), 500 deletions(-)
Title: Test Helpers for 'httr2'
Description: Testing and documenting code that communicates with remote servers
can be painful. This package helps with writing tests for packages that
use 'httr2'. It enables testing all of the logic
on the R sides of the API without requiring access to the
remote service, and it also allows recording real API responses to use as
test fixtures. The ability to save responses and load them offline also
enables writing vignettes and other dynamic documents that can be
distributed without access to a live server.
Author: Neal Richardson [aut, cre] ,
Jonathan Keane [ctb],
Maelle Salmon [ctb]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httptest2 versions 1.1.0 dated 2024-04-26 and 1.2.0 dated 2025-06-27
DESCRIPTION | 13 +++--- MD5 | 36 ++++++++--------- NEWS.md | 7 ++- R/build-mock-url.R | 68 +++++++++++++++++++-------------- R/redactor.R | 2 build/vignette.rds |binary inst/doc/httptest2.Rmd | 7 +-- inst/doc/httptest2.html | 14 +++--- inst/doc/redacting.Rmd | 4 - inst/doc/redacting.html | 9 +--- inst/doc/vignettes.Rmd | 2 inst/doc/vignettes.html | 9 +--- man/expect_request_header.Rd | 4 - man/set_redactor.Rd | 2 tests/testthat/test-capture-requests.R | 22 ++++++++++ tests/testthat/test-mock-api.R | 8 ++- vignettes/httptest2.Rmd | 7 +-- vignettes/redacting.Rmd | 4 - vignettes/vignettes.Rmd | 2 19 files changed, 132 insertions(+), 88 deletions(-)
Title: Archaeological Synchronism
Description: Estimation of unknown historical or archaeological dates subject to relationships with other relative dates and absolute constraints, derived as marginal densities from the full joint conditional, using a two-stage Gibbs sampler with consistent batch means to assess convergence. Features reporting on Monte Carlo standard errors, as well as tools for rule-based estimation of dates of production and use of artifact types, aligning and checking relative sequences, and evaluating the impact of the omission of relative/absolute events upon one another.
Author: Stephen A. Collins-Elliott [aut, cre]
Maintainer: Stephen A. Collins-Elliott <sce@utk.edu>
Diff between eratosthenes versions 0.0.2 dated 2024-09-20 and 0.0.9 dated 2025-06-27
DESCRIPTION | 14 MD5 | 48 NAMESPACE | 29 R/RcppExports.R | 36 R/eratosthenes.R | 1732 +++++++++++++++--- README.md | 440 +++- build/partial.rdb |only inst/CITATION | 8 inst/REFERENCES.bib | 53 inst/doc/aligning-relative-sequences.html | 28 inst/doc/gibbs-sampling-for-archaeological-dates.R | 2 inst/doc/gibbs-sampling-for-archaeological-dates.Rmd | 4 inst/doc/gibbs-sampling-for-archaeological-dates.html | 58 man/finds_d2l.Rd |only man/finds_l2d.Rd |only man/gibbs_ad.Rd | 67 man/gibbs_ad_use.Rd |only man/histogram.Rd |only man/ids_of_types.Rd |only man/msd.Rd |only man/quae_antea.Rd | 7 man/quae_postea.Rd | 2 man/seq_check.Rd | 5 man/sq_disp.Rd |only man/synth_rank.Rd | 2 man/tidy_marginals.Rd |only man/traceplot.Rd |only src/RcppExports.cpp | 93 src/eratosthenes.cpp | 583 ++++++ vignettes/gibbs-sampling-for-archaeological-dates.Rmd | 4 30 files changed, 2818 insertions(+), 397 deletions(-)
Title: R Interface to RESTful Web Services
Description: Models a RESTful service as if it were a nested R list.
Author: Michael Lawrence [aut, cre]
Maintainer: Michael Lawrence <michafla@gene.com>
Diff between restfulr versions 0.0.15 dated 2022-06-16 and 0.0.16 dated 2025-06-27
DESCRIPTION | 14 +++++++++----- MD5 | 6 +++--- R/HTTP-class.R | 2 +- man/RestUri-class.Rd | 4 +++- 4 files changed, 16 insertions(+), 10 deletions(-)
Title: Just a Rather Bayesian Evidence Synthesis
Description: Provides a new class of Bayesian meta-analysis models that incorporates a model for internal and external validity bias. In this way, it is possible to combine studies of diverse quality and different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS).
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>
Diff between jarbes versions 2.2.5 dated 2025-03-28 and 2.3.0 dated 2025-06-27
ChangeLog | 13 + DESCRIPTION | 10 - MD5 | 67 ++++---- NAMESPACE | 11 + R/b3lmeta.R | 75 ++++++--- R/bcdpmeta.R | 83 ++++++---- R/bchmr.R | 56 ++++-- R/bcmeta.R | 75 ++++++--- R/bcmixmeta.R | 171 +++++++++++++-------- R/bmeta.R | 63 +++++-- R/caterplot_compare.R |only R/diagnostic.bcmeta.R | 4 R/diagnostic.bcmixmeta.R | 6 R/dpmeta.R | 80 ++++++--- R/dpmetareg.R | 75 ++++++--- R/dpmmeta.R | 74 ++++++--- R/dummy.R | 2 R/hmr.R | 377 +++++++++++++++++++++++++++-------------------- R/jarbes-package.R | 10 - R/metarisk.R | 57 +++++-- R/plot.simData.R |only R/simData.R |only R/summary.simData.R |only man/b3lmeta.Rd | 5 man/bcdpmeta.Rd | 5 man/bchmr.Rd | 5 man/bcmeta.Rd | 5 man/bcmixmeta.Rd | 5 man/bmeta.Rd | 5 man/caterplot_compare.Rd |only man/dpmeta.Rd | 9 - man/dpmetareg.Rd | 5 man/dpmmeta.Rd | 5 man/hmr.Rd | 109 +++++++++---- man/metarisk.Rd | 7 man/plot.simData.Rd |only man/print.simData.Rd |only man/simData.Rd |only man/summary.simData.Rd |only 39 files changed, 980 insertions(+), 494 deletions(-)
Title: Semiparametric Likelihood Estimation with Errors in Variables
Description: Efficient regression analysis under general two-phase sampling, where Phase I includes error-prone data and Phase II contains validated data on a subset.
Author: Sarah Lotspeich [aut],
Ran Tao [aut, cre],
Joey Sherrill [prg],
Jiangmei Xiong [ctb]
Maintainer: Ran Tao <r.tao@vanderbilt.edu>
Diff between sleev versions 1.1.3 dated 2025-06-12 and 1.1.4 dated 2025-06-27
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- R/cv_linear2ph.R | 29 +++++++++++++++++++++++++++++ R/cv_logistic2ph.R | 31 +++++++++++++++++++++++++++++++ R/linear2ph.R | 14 ++++++++++++++ R/logistic2ph.R | 15 +++++++++++++++ build/vignette.rds |binary inst/doc/sleev_vignette_file.Rnw | 2 +- inst/doc/sleev_vignette_file.pdf |binary man/cv_linear2ph.Rd | 29 +++++++++++++++++++++++++++++ man/cv_logistic2ph.Rd | 31 +++++++++++++++++++++++++++++++ man/linear2ph.Rd | 15 +++++++++++++++ man/logistic2ph.Rd | 16 ++++++++++++++++ vignettes/sleev_vignette.pdf |binary vignettes/sleev_vignette_file.Rnw | 2 +- 15 files changed, 199 insertions(+), 19 deletions(-)
Title: Some Utilities for Developing Data Science Software
Description: A collection of general-purpose helper functions that I (and maybe
others) find useful when developing data science software. Includes tools
for simulation, data transformation, input validation, and more.
Author: Lennart Oelschlaeger [aut, cre]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between oeli versions 0.7.3 dated 2025-05-19 and 0.7.4 dated 2025-06-27
DESCRIPTION | 12 +- MD5 | 37 ++++--- NAMESPACE | 18 +++ NEWS.md | 6 + R/check_missing.R | 7 + R/occurrence_info.R |only R/oeli-package.R | 164 ++++++++++++++++++---------------- R/simulator.R |only man/Simulator.Rd |only man/check_missing.Rd | 9 + man/correlated_regressors.Rd | 1 man/ddirichlet.Rd | 1 man/delete_columns_data.frame.Rd | 1 man/dmvnorm.Rd | 1 man/dtnorm.Rd | 1 man/dwishart.Rd | 1 man/group_data.frame.Rd | 1 man/occurrence_info.Rd |only man/round_data.frame.Rd | 3 man/simulate_markov_chain.Rd | 1 tests/testthat/_snaps/simulator.md |only tests/testthat/test-occurrence_info.R |only tests/testthat/test-simulator.R |only 23 files changed, 167 insertions(+), 97 deletions(-)
Title: Non Linear Least Squares with Inequality Constraints
Description: We solve non linear least squares problems with optional
equality and/or inequality constraints. Non linear iterations are
globalized with back-tracking method. Linear problems are solved by
dense QR decomposition from 'LAPACK' which can limit the size of
treated problems. On the other side, we avoid condition number
degradation which happens in classical quadratic programming approach.
Inequality constraints treatment on each non
linear iteration is based on 'NNLS' method (by Lawson and Hanson).
We provide an original function 'lsi_ln' for solving linear least squares
problem with inequality constraints in least norm sens. Thus if Jacobian of
the problem is rank deficient a solution still can be provided.
However, truncation errors are probable in this case.
Equality constraints are treated by using a basis of Null-space.
User defined function calculating residuals must return a list having
residual vector (not their squared sum) and Jacobian. If Jacobian is
not in the returned list, [...truncated...]
Author: Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between nlsic versions 1.1.0 dated 2025-05-16 and 1.1.1 dated 2025-06-27
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/nlsic.R | 28 ++++++++++++++++++++++++---- inst/unitTests/runit.nlsic.R | 18 +++++++++++++++--- man/ls_ln.Rd | 2 +- 6 files changed, 52 insertions(+), 16 deletions(-)
Title: Generalized Additive Models with Hyper Column
Description: Generalized additive models with a numeric hyper column
tabulated on a common grid. Sign-adjustment based on the
correlation of model prediction and a selected slice of the
hyper column. Visualization of the integrand surface over the
hyper column.
Author: Tingting Zhan [aut, cre] ,
Inna Chervoneva [aut] ,
Erjia Cui [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between hyper.gam versions 0.1.1 dated 2025-05-27 and 0.1.2 dated 2025-06-27
hyper.gam-0.1.1/hyper.gam/R/onLoad.R |only hyper.gam-0.1.2/hyper.gam/DESCRIPTION | 7 hyper.gam-0.1.2/hyper.gam/MD5 | 24 - hyper.gam-0.1.2/hyper.gam/R/integrandSurface.R | 10 hyper.gam-0.1.2/hyper.gam/R/kfoldPredict.R | 13 hyper.gam-0.1.2/hyper.gam/R/onLoad_parallel.R |only hyper.gam-0.1.2/hyper.gam/build/partial.rdb |binary hyper.gam-0.1.2/hyper.gam/build/vignette.rds |binary hyper.gam-0.1.2/hyper.gam/inst/doc/applications.R | 20 - hyper.gam-0.1.2/hyper.gam/inst/doc/applications.html | 297 +++++++++------- hyper.gam-0.1.2/hyper.gam/inst/doc/applications.qmd | 161 +++++--- hyper.gam-0.1.2/hyper.gam/man/kfoldPredict.hyper_gam.Rd | 7 hyper.gam-0.1.2/hyper.gam/vignettes/applications.qmd | 161 +++++--- hyper.gam-0.1.2/hyper.gam/vignettes/hypergam.bib | 96 ++++- 14 files changed, 506 insertions(+), 290 deletions(-)
Title: 'ggplot2' Based Publication Ready Plots
Description: The 'ggplot2' package is excellent and flexible for elegant data
visualization in R. However the default generated plots requires some formatting
before we can send them for publication. Furthermore, to customize a 'ggplot',
the syntax is opaque and this raises the level of difficulty for researchers
with no advanced R programming skills. 'ggpubr' provides some easy-to-use
functions for creating and customizing 'ggplot2'- based publication ready plots.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggpubr versions 0.6.0 dated 2023-02-10 and 0.6.1 dated 2025-06-27
DESCRIPTION | 20 - MD5 | 138 +++++----- NEWS.md | 35 ++ R/add_summary.R | 17 - R/geom_bracket.R | 3 R/geom_exec.R | 6 R/geom_pwc.R | 7 R/ggadd.R | 19 + R/ggboxplot.R | 9 R/ggline.R | 35 ++ R/ggpar.R | 6 R/grids.R | 4 R/shared_docs.R |only R/stat_anova_test.R | 1 R/stat_central_tendency.R | 1 R/stat_chull.R | 1 R/stat_compare_means.R | 31 -- R/stat_conf_ellipse.R | 1 R/stat_cor.R | 1 R/stat_friedman_test.R | 1 R/stat_kruskal_test.R | 1 R/stat_mean.R | 1 R/stat_overlay_normal_density.R | 1 R/stat_pvalue_manual.R | 15 - R/stat_regline_equation.R | 26 + R/stat_stars.R | 1 R/stat_welch_anova_test.R | 1 R/theme_pubr.R | 6 R/utilities.R | 2 R/utils_stat_test_label.R | 44 +++ README.md | 88 ++---- man/add_summary.Rd | 3 man/geom_bracket.Rd | 49 ++- man/geom_pwc.Rd | 51 ++- man/ggadd.Rd | 12 man/ggadjust_pvalue.Rd | 2 man/ggbarplot.Rd | 16 - man/ggboxplot.Rd | 8 man/ggerrorplot.Rd | 16 - man/ggline.Rd | 27 + man/ggpubr-common-params.Rd |only man/ggviolin.Rd | 20 + man/stat_anova_test.Rd | 48 ++- man/stat_central_tendency.Rd | 48 ++- man/stat_chull.Rd | 81 ++++- man/stat_compare_means.Rd | 48 ++- man/stat_conf_ellipse.Rd | 79 ++++- man/stat_cor.Rd | 48 ++- man/stat_friedman_test.Rd | 48 ++- man/stat_kruskal_test.Rd | 48 ++- man/stat_mean.Rd | 48 ++- man/stat_overlay_normal_density.Rd | 48 ++- man/stat_pvalue_manual.Rd | 10 man/stat_regline_equation.Rd | 54 ++- man/stat_stars.Rd | 48 ++- man/stat_welch_anova_test.Rd | 48 ++- tests/testthat/test-convert_label_dotdot_notation_to_after_stat.R |only tests/testthat/test-gghistogram.R | 12 tests/testthat/test-stat_pvalue_manual.R |only tools/README-cleveland-dot-plots-1.png |binary tools/README-deviation-graphs-1.png |binary tools/README-deviation-graphs-horizontal-1.png |binary tools/README-ggpubr-1.png |binary tools/README-ggpubr-2.png |binary tools/README-ggpubr-box-plot-dot-plots-strip-charts-1.png |binary tools/README-ggpubr-box-plot-dot-plots-strip-charts-2.png |binary tools/README-ggpubr-box-plot-dot-plots-strip-charts-3.png |binary tools/README-lollipop-chart-1.png |binary tools/README-lollipop-chart-deviation-1.png |binary tools/README-lollipop-chart-rotate-1.png |binary tools/README-ordered-bar-plots-1.png |binary tools/README-ordered-bar-plots-by-groups-1.png |binary 72 files changed, 991 insertions(+), 451 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality
Data
Description: Collection of functions to help retrieve U.S. Geological Survey
and U.S. Environmental Protection Agency water quality and
hydrology data from web services.
Author: Laura DeCicco [aut, cre] ,
Robert Hirsch [aut] ,
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Platt [ctb],
David Watkins [aut] ,
David Blodgett [aut] ,
Mike Johnson [aut] ,
Aliesha Krall [ctb] ,
Lee Stanish [ctb] ,
Joeseph Zemm [...truncated...]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.18 dated 2025-02-27 and 2.7.19 dated 2025-06-27
dataRetrieval-2.7.18/dataRetrieval/R/read_USGS_samples.R |only dataRetrieval-2.7.18/dataRetrieval/man/check_param.Rd |only dataRetrieval-2.7.18/dataRetrieval/man/construct_USGS_sample_request.Rd |only dataRetrieval-2.7.18/dataRetrieval/man/read_USGS_samples.Rd |only dataRetrieval-2.7.18/dataRetrieval/man/summarize_USGS_samples.Rd |only dataRetrieval-2.7.18/dataRetrieval/tests/manual |only dataRetrieval-2.7.19/dataRetrieval/DESCRIPTION | 46 dataRetrieval-2.7.19/dataRetrieval/MD5 | 160 +- dataRetrieval-2.7.19/dataRetrieval/NAMESPACE | 13 dataRetrieval-2.7.19/dataRetrieval/NEWS | 9 dataRetrieval-2.7.19/dataRetrieval/R/AAA.R | 19 dataRetrieval-2.7.19/dataRetrieval/R/checkWQPdates.R | 4 dataRetrieval-2.7.19/dataRetrieval/R/citations.R | 4 dataRetrieval-2.7.19/dataRetrieval/R/constructNWISURL.R | 205 +- dataRetrieval-2.7.19/dataRetrieval/R/construct_api_requests.R |only dataRetrieval-2.7.19/dataRetrieval/R/dataRetrievals-package.R | 28 dataRetrieval-2.7.19/dataRetrieval/R/findNLDI.R | 38 dataRetrieval-2.7.19/dataRetrieval/R/getWebServiceData.R | 11 dataRetrieval-2.7.19/dataRetrieval/R/importNGWMN_wml2.R | 14 dataRetrieval-2.7.19/dataRetrieval/R/importRDB1.R | 13 dataRetrieval-2.7.19/dataRetrieval/R/importWQP.R | 16 dataRetrieval-2.7.19/dataRetrieval/R/importWaterML1.R | 6 dataRetrieval-2.7.19/dataRetrieval/R/readNGWMNdata.R | 16 dataRetrieval-2.7.19/dataRetrieval/R/readNWISdata.R | 96 - dataRetrieval-2.7.19/dataRetrieval/R/readNWISdv.R | 52 dataRetrieval-2.7.19/dataRetrieval/R/readNWISpCode.R | 13 dataRetrieval-2.7.19/dataRetrieval/R/readNWISsite.R | 27 dataRetrieval-2.7.19/dataRetrieval/R/readNWISunit.R | 115 - dataRetrieval-2.7.19/dataRetrieval/R/readWQPdata.R | 104 - dataRetrieval-2.7.19/dataRetrieval/R/readWQPdots.R | 2 dataRetrieval-2.7.19/dataRetrieval/R/readWQPqw.R | 20 dataRetrieval-2.7.19/dataRetrieval/R/read_waterdata.R |only dataRetrieval-2.7.19/dataRetrieval/R/read_waterdata_daily.R |only dataRetrieval-2.7.19/dataRetrieval/R/read_waterdata_latest_continuous.R |only dataRetrieval-2.7.19/dataRetrieval/R/read_waterdata_monitoring_location.R |only dataRetrieval-2.7.19/dataRetrieval/R/read_waterdata_samples.R |only dataRetrieval-2.7.19/dataRetrieval/R/read_waterdata_ts_meta.R |only dataRetrieval-2.7.19/dataRetrieval/R/renameColumns.R | 6 dataRetrieval-2.7.19/dataRetrieval/R/setAccess.R | 8 dataRetrieval-2.7.19/dataRetrieval/R/walk_pages.R |only dataRetrieval-2.7.19/dataRetrieval/R/whatNWISdata.R | 60 dataRetrieval-2.7.19/dataRetrieval/R/whatNWISsites.R | 60 dataRetrieval-2.7.19/dataRetrieval/R/whatWQPdata.R | 91 - dataRetrieval-2.7.19/dataRetrieval/R/whatWQPsites.R | 46 dataRetrieval-2.7.19/dataRetrieval/build/vignette.rds |binary dataRetrieval-2.7.19/dataRetrieval/inst/CITATION | 26 dataRetrieval-2.7.19/dataRetrieval/inst/doc/dataRetrieval.R | 224 --- dataRetrieval-2.7.19/dataRetrieval/inst/doc/dataRetrieval.Rmd | 278 +-- dataRetrieval-2.7.19/dataRetrieval/inst/doc/dataRetrieval.html | 725 ++++------ dataRetrieval-2.7.19/dataRetrieval/inst/extdata/temperatureAndFlow.RData |binary dataRetrieval-2.7.19/dataRetrieval/inst/templates |only dataRetrieval-2.7.19/dataRetrieval/man/addWaterYear.Rd | 6 dataRetrieval-2.7.19/dataRetrieval/man/check_OGC_requests.Rd |only dataRetrieval-2.7.19/dataRetrieval/man/check_waterdata_sample_params.Rd |only dataRetrieval-2.7.19/dataRetrieval/man/construct_api_requests.Rd |only dataRetrieval-2.7.19/dataRetrieval/man/construct_waterdata_sample_request.Rd |only dataRetrieval-2.7.19/dataRetrieval/man/countyCd.Rd | 5 dataRetrieval-2.7.19/dataRetrieval/man/findNLDI.Rd | 10 dataRetrieval-2.7.19/dataRetrieval/man/importWQP.Rd | 2 dataRetrieval-2.7.19/dataRetrieval/man/importWaterML1.Rd | 4 dataRetrieval-2.7.19/dataRetrieval/man/pcode_to_name.Rd | 4 dataRetrieval-2.7.19/dataRetrieval/man/readNWISdata.Rd | 55 dataRetrieval-2.7.19/dataRetrieval/man/readNWISdv.Rd | 44 dataRetrieval-2.7.19/dataRetrieval/man/readNWISgwl.Rd | 9 dataRetrieval-2.7.19/dataRetrieval/man/readNWISmeas.Rd | 2 dataRetrieval-2.7.19/dataRetrieval/man/readNWISpCode.Rd | 22 dataRetrieval-2.7.19/dataRetrieval/man/readNWISpeak.Rd | 4 dataRetrieval-2.7.19/dataRetrieval/man/readNWISrating.Rd | 2 dataRetrieval-2.7.19/dataRetrieval/man/readNWISsite.Rd | 90 - dataRetrieval-2.7.19/dataRetrieval/man/readNWISstat.Rd | 2 dataRetrieval-2.7.19/dataRetrieval/man/readNWISuv.Rd | 8 dataRetrieval-2.7.19/dataRetrieval/man/readWQPdata.Rd | 79 - dataRetrieval-2.7.19/dataRetrieval/man/readWQPqw.Rd | 12 dataRetrieval-2.7.19/dataRetrieval/man/readWQPsummary.Rd | 6 dataRetrieval-2.7.19/dataRetrieval/man/read_waterdata.Rd |only dataRetrieval-2.7.19/dataRetrieval/man/read_waterdata_daily.Rd |only dataRetrieval-2.7.19/dataRetrieval/man/read_waterdata_latest_continuous.Rd |only dataRetrieval-2.7.19/dataRetrieval/man/read_waterdata_monitoring_location.Rd |only dataRetrieval-2.7.19/dataRetrieval/man/read_waterdata_samples.Rd |only dataRetrieval-2.7.19/dataRetrieval/man/read_waterdata_ts_meta.Rd |only dataRetrieval-2.7.19/dataRetrieval/man/renameNWISColumns.Rd | 2 dataRetrieval-2.7.19/dataRetrieval/man/stateCd.Rd | 5 dataRetrieval-2.7.19/dataRetrieval/man/summarize_waterdata_samples.Rd |only dataRetrieval-2.7.19/dataRetrieval/man/whatNWISdata.Rd | 36 dataRetrieval-2.7.19/dataRetrieval/man/whatNWISsites.Rd | 9 dataRetrieval-2.7.19/dataRetrieval/man/whatWQPdata.Rd | 16 dataRetrieval-2.7.19/dataRetrieval/man/wqpSpecials.Rd | 6 dataRetrieval-2.7.19/dataRetrieval/man/wqp_check_status.Rd | 4 dataRetrieval-2.7.19/dataRetrieval/tests/testthat/tests_general.R | 364 ++--- dataRetrieval-2.7.19/dataRetrieval/tests/testthat/tests_nldi.R | 333 ++-- dataRetrieval-2.7.19/dataRetrieval/tests/testthat/tests_samples.R | 38 dataRetrieval-2.7.19/dataRetrieval/tests/testthat/tests_userFriendly_fxns.R | 152 +- dataRetrieval-2.7.19/dataRetrieval/vignettes/Wide_data_example.xlsx |only dataRetrieval-2.7.19/dataRetrieval/vignettes/dataRetrieval.Rmd | 278 +-- 94 files changed, 2021 insertions(+), 2143 deletions(-)
Title: Likelihood Based Inference for ARIMA Modeling
Description: Estimating and analyzing auto regressive integrated moving average
(ARIMA) models. The primary function in this package is arima(), which fits
an ARIMA model to univariate time series data using a random restart
algorithm. This approach frequently leads to models that have model
likelihood greater than or equal to that of the likelihood obtained by
fitting the same model using the arima() function from the 'stats' package.
This package enables proper optimization of model likelihoods, which is a
necessary condition for performing likelihood ratio tests. This package
relies heavily on the source code of the arima() function of the 'stats'
package. For more information, please see Jesse Wheeler and Edward L.
Ionides (2023) <doi:10.48550/arXiv.2310.01198>.
Author: Jesse Wheeler [aut, cre, cph],
Noel McAllister [aut],
Dhajanae Sylvertooth [aut],
Edward Ionides [ctb],
Brian Ripley [ctb] ,
R Core Team [cph]
Maintainer: Jesse Wheeler <jeswheel@umich.edu>
Diff between arima2 versions 3.3.0 dated 2024-08-19 and 3.4.0 dated 2025-06-27
DESCRIPTION | 8 - MD5 | 18 +-- NEWS.md | 6 + R/arima.R | 18 +++ R/sample_ARMA_coef.R | 153 +++++++++++++++++++++++++------ README.md | 12 +- man/arima.Rd | 19 +++ man/figures/README-PlotARMAresults-2.png |binary man/sample_ARMA_coef.Rd | 30 ++++-- tests/testthat/test-sample_ARMA_coef.R | 61 +++++++++++- 10 files changed, 262 insertions(+), 63 deletions(-)
Title: Generate UpSet Plots of VP and HP Based on the ASV Concept
Description: Using matrix layout to visualize the unique, common, or individual contribution of each predictor (or matrix of predictors) towards explained variation on different models. These contributions were derived from variation partitioning (VP) and hierarchical partitioning (HP), applying the algorithm of "Lai et al. (2022) Generalizing hierarchical and variation partitioning in multiple regression and canonical analyses using the rdacca.hp R package.Methods in Ecology and Evolution, 13: 782-788 <doi:10.1111/2041-210X.13800>".
Author: Jiangshan Lai [aut, cre] ,
Yao Liu [aut],
Bangken Ying [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between upset.hp versions 0.0.1 dated 2025-06-04 and 0.0.2 dated 2025-06-27
DESCRIPTION | 13 - MD5 | 7 R/upset.hp.r | 588 +++++++++++++++++++++++++++++++++++++++++--------------- R/zzz.r |only man/upset.hp.Rd | 9 5 files changed, 458 insertions(+), 159 deletions(-)
Title: Time-Varying Minimum Variance Portfolio
Description: Provides the estimation of a time-dependent covariance matrix of returns with the intended use for portfolio optimization. The package offers methods for determining the optimal number of factors to be used in the covariance estimation, a hypothesis test of time-varying covariance, and user-friendly functions for portfolio optimization and rolling window evaluation. The local PCA method, method for determining the number of factors, and associated hypothesis test are based on Su and Wang (2017) <doi:10.1016/j.jeconom.2016.12.004>. The approach to time-varying portfolio optimization follows Fan et al. (2024) <doi:10.1016/j.jeconom.2022.08.007>. The regularisation applied to the residual covariance matrix adopts the technique introduced by Chen et al. (2019) <doi:10.1016/j.jeconom.2019.04.025>.
Author: Erik Lillrank [aut, cre] ,
Yukai Yang [aut]
Maintainer: Erik Lillrank <erik.lillrank@gmail.com>
Diff between TVMVP versions 1.0.4 dated 2025-05-29 and 1.0.5 dated 2025-06-27
TVMVP-1.0.4/TVMVP/man/rolling_time_varying_mvp.Rd |only TVMVP-1.0.5/TVMVP/DESCRIPTION | 10 TVMVP-1.0.5/TVMVP/LICENSE | 2 TVMVP-1.0.5/TVMVP/MD5 | 39 +- TVMVP-1.0.5/TVMVP/NAMESPACE | 18 - TVMVP-1.0.5/TVMVP/NEWS.md |only TVMVP-1.0.5/TVMVP/R/R6class.R | 6 TVMVP-1.0.5/TVMVP/R/R6rollingmvp.R | 11 TVMVP-1.0.5/TVMVP/R/TVMVP.R | 4 TVMVP-1.0.5/TVMVP/R/forecasting_functions.R | 108 +++---- TVMVP-1.0.5/TVMVP/R/globals.R |only TVMVP-1.0.5/TVMVP/README.md | 44 +- TVMVP-1.0.5/TVMVP/inst/doc/TVMVP_overview.R | 9 TVMVP-1.0.5/TVMVP/inst/doc/TVMVP_overview.Rmd | 16 - TVMVP-1.0.5/TVMVP/inst/doc/TVMVP_overview.html | 154 +++++----- TVMVP-1.0.5/TVMVP/inst/doc/thesis.pdf |binary TVMVP-1.0.5/TVMVP/man/TVMVP-package.Rd | 4 TVMVP-1.0.5/TVMVP/man/TVMVP.Rd | 6 TVMVP-1.0.5/TVMVP/man/expanding_tvmvp.Rd |only TVMVP-1.0.5/TVMVP/man/figures |only TVMVP-1.0.5/TVMVP/tests/testthat/test-rolling_time_varying_mvp.R | 6 TVMVP-1.0.5/TVMVP/vignettes/TVMVP_overview.Rmd | 16 - TVMVP-1.0.5/TVMVP/vignettes/thesis_body.pdf |binary 23 files changed, 247 insertions(+), 206 deletions(-)
Title: Mapping Averaged Pairwise Information
Description: Mapping Averaged Pairwise Information (MAPI) is an
exploratory method providing graphical representations summarizing the
spatial variation of pairwise metrics (eg. distance, similarity
coefficient, ...) computed between georeferenced samples.
Author: Sylvain Piry [aut, cre] ,
Thomas Campolunghi [aut],
Florent Cestier [aut],
Karine Berthier [aut]
Maintainer: Sylvain Piry <sylvain.piry@inrae.fr>
Diff between mapi versions 1.0.5 dated 2022-01-19 and 1.1.3 dated 2025-06-27
mapi-1.0.5/mapi/R/mapi.R |only mapi-1.0.5/mapi/README.md |only mapi-1.0.5/mapi/src/MAPI.cpp |only mapi-1.0.5/mapi/src/code.cpp |only mapi-1.1.3/mapi/DESCRIPTION | 25 mapi-1.1.3/mapi/MD5 | 68 +- mapi-1.1.3/mapi/NAMESPACE | 21 mapi-1.1.3/mapi/NEWS.md | 28 - mapi-1.1.3/mapi/R/MAPI_CheckData.R | 131 ++-- mapi-1.1.3/mapi/R/MAPI_EstimateHalfwidth.R | 34 - mapi-1.1.3/mapi/R/MAPI_GridAuto.R | 20 mapi-1.1.3/mapi/R/MAPI_GridHexagonal.R | 221 ++++---- mapi-1.1.3/mapi/R/MAPI_Plot.R | 92 +-- mapi-1.1.3/mapi/R/MAPI_Plot2.R | 72 +- mapi-1.1.3/mapi/R/MAPI_RunAuto.R | 12 mapi-1.1.3/mapi/R/MAPI_RunOnGrid.R | 699 ++++++++++++++++---------- mapi-1.1.3/mapi/R/MAPI_Tails.R | 153 +++-- mapi-1.1.3/mapi/R/MAPI_Varicell.R |only mapi-1.1.3/mapi/R/RcppExports.R | 42 + mapi-1.1.3/mapi/R/mapi-package.R |only mapi-1.1.3/mapi/build/partial.rdb |binary mapi-1.1.3/mapi/data/metric.rda |binary mapi-1.1.3/mapi/data/samples.rda |binary mapi-1.1.3/mapi/inst/CITATION | 17 mapi-1.1.3/mapi/inst/WORDLIST | 16 mapi-1.1.3/mapi/man/MAPI_CheckData.Rd | 2 mapi-1.1.3/mapi/man/MAPI_EstimateHalfwidth.Rd | 2 mapi-1.1.3/mapi/man/MAPI_GridAuto.Rd | 12 mapi-1.1.3/mapi/man/MAPI_GridHexagonal.Rd | 15 mapi-1.1.3/mapi/man/MAPI_RunAuto.Rd | 4 mapi-1.1.3/mapi/man/MAPI_RunOnGrid.Rd | 23 mapi-1.1.3/mapi/man/MAPI_Varicell.Rd |only mapi-1.1.3/mapi/man/mapi.Rd | 35 - mapi-1.1.3/mapi/src/RcppExports.cpp | 17 mapi-1.1.3/mapi/src/mapi.cpp |only mapi-1.1.3/mapi/tests |only 36 files changed, 1053 insertions(+), 708 deletions(-)
Title: Transformed and Relative Lorenz Curves for Survey Weighted Data
Description: Functions for constructing Transformed and Relative Lorenz curves with survey sampling weights. Given a variable of interest measured in two groups with scaled survey weights so that their hypothetical populations are of equal size, tlorenz() computes the proportion of members of the group with smaller values (ordered from smallest to largest) needed for their sum to match the sum of the top qth percentile of the group with higher values. rlorenz() shows the fraction of the total value of the group with larger values held by the pth percentile of those in the group with smaller values. Fd() is a survey weighted cumulative distribution function and Eps() is a survey weighted inverse cdf used in rlorenz(). Ramos, Graubard, and Gastwirth (2025) <doi:10.1093/jrsssa/qnaf044>.
Author: Mark Ramos [aut, cre, cph]
Maintainer: Mark Ramos <mlr6219@psu.edu>
Diff between glorenz versions 0.1.0 dated 2025-06-04 and 0.1.1 dated 2025-06-27
DESCRIPTION | 6 +- MD5 | 4 - R/tlorenz.R | 148 +++++++++++++++++++++++++++++------------------------------- 3 files changed, 78 insertions(+), 80 deletions(-)
Title: Conditional Method Agreement Trees (COAT)
Description: Agreement of continuously scaled measurements made by two techniques, devices or methods is usually
evaluated by the well-established Bland-Altman analysis or plot. Conditional method agreement trees (COAT),
proposed by Karapetyan, Zeileis, Henriksen, and Hapfelmeier (2023) <doi:10.48550/arXiv.2306.04456>,
embed the Bland-Altman analysis in the framework of recursive partitioning to explore heterogeneous method
agreement in dependence of covariates. COAT can also be used to perform a Bland-Altman test for differences
in method agreement.
Author: Alexander Hapfelmeier [aut, cre] ,
Siranush Karapetyan [aut] ,
Achim Zeileis [aut]
Maintainer: Alexander Hapfelmeier <Alexander.Hapfelmeier@mri.tum.de>
Diff between coat versions 0.2.0 dated 2023-07-11 and 0.2.1 dated 2025-06-27
DESCRIPTION | 19 ++++--- MD5 | 12 ++-- NAMESPACE | 126 +++++++++++++++++++++------------------------------- NEWS.md | 4 + R/coat-methods.R | 93 +++----------------------------------- build/partial.rdb |binary man/coat-methods.Rd | 31 +----------- 7 files changed, 84 insertions(+), 201 deletions(-)
Title: Graphical Diagnostics for Pharmacometric Models: Extension to
'nlmixr2'
Description: Extension to 'xpose' to support 'nlmixr2'. Provides functions to import 'nlmixr2' fit data into an 'xpose' data object, allowing the use of 'xpose' for 'nlmixr2' model diagnostics.
Author: Justin Wilkins [aut, cre, cph],
Matthew Fidler [aut, cph],
Benjamin Guiastrennec [aut],
Andrew C. Hooker [aut],
Anna Olofsson [aut, cph],
Sebastian Ueckert [aut],
Ron Keizer [aut],
Kajsa Harling [ctb],
Mike K. Smith [ctb],
Elodie Plan [ctb],
Mats O. [...truncated...]
Maintainer: Justin Wilkins <justin.wilkins@occams.com>
Diff between xpose.nlmixr2 versions 0.4.0 dated 2022-06-08 and 0.4.1 dated 2025-06-27
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/summarise_nlmixr_model.R | 2 +- R/xpose_data_nlmixr.R | 6 +++--- 5 files changed, 19 insertions(+), 15 deletions(-)
Title: Assertion and Message Functions
Description: Enhanced message functions (cat() / message() / warning() / error())
using wrappers around sprintf(). Also, multiple assertion functions
(e.g. to check class, length, values, files, arguments, etc.).
Author: Florian Prive [aut, cre]
Maintainer: Florian Prive <florian.prive.21@gmail.com>
Diff between bigassertr versions 0.1.6 dated 2023-01-10 and 0.1.7 dated 2025-06-27
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 1 + R/assert.R | 12 ++++++++++++ man/assert.Rd | 5 +++++ tests/testthat/test-assert.R | 5 +++++ 6 files changed, 33 insertions(+), 10 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014
<DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic
analysis of functional data through phase and amplitude separation.
Author: J. Derek Tucker [aut, cre] ,
Aymeric Stamm [ctb]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 2.3.6 dated 2025-02-17 and 2.4.0 dated 2025-06-27
fdasrvf-2.3.6/fdasrvf/R/curve_karcher_cov.R |only fdasrvf-2.3.6/fdasrvf/R/curve_karcher_mean.R |only fdasrvf-2.3.6/fdasrvf/R/curve_principal_directions.R |only fdasrvf-2.3.6/fdasrvf/R/curve_srvf_align.R |only fdasrvf-2.3.6/fdasrvf/man/curve_karcher_cov.Rd |only fdasrvf-2.3.6/fdasrvf/man/curve_karcher_mean.Rd |only fdasrvf-2.3.6/fdasrvf/man/curve_principal_directions.Rd |only fdasrvf-2.3.6/fdasrvf/man/curve_srvf_align.Rd |only fdasrvf-2.4.0/fdasrvf/DESCRIPTION | 15 fdasrvf-2.4.0/fdasrvf/MD5 | 88 +- fdasrvf-2.4.0/fdasrvf/NAMESPACE | 14 fdasrvf-2.4.0/fdasrvf/NEWS.md | 9 fdasrvf-2.4.0/fdasrvf/R/calc_shape_dist.R | 6 fdasrvf-2.4.0/fdasrvf/R/curve_boxplot.R | 12 fdasrvf-2.4.0/fdasrvf/R/curve_functions.R | 65 + fdasrvf-2.4.0/fdasrvf/R/curve_pair_align.R | 30 fdasrvf-2.4.0/fdasrvf/R/geometry.R | 196 ++++ fdasrvf-2.4.0/fdasrvf/R/kmeans.R | 4 fdasrvf-2.4.0/fdasrvf/R/multiple_align_multivariate.R |only fdasrvf-2.4.0/fdasrvf/R/multivariate_karcher_cov.R |only fdasrvf-2.4.0/fdasrvf/R/multivariate_karcher_mean.R | 107 +- fdasrvf-2.4.0/fdasrvf/R/multivariate_pca.R |only fdasrvf-2.4.0/fdasrvf/R/plot.curve_pca.R |only fdasrvf-2.4.0/fdasrvf/R/plot.fdacurve.R |only fdasrvf-2.4.0/fdasrvf/R/pns.R |only fdasrvf-2.4.0/fdasrvf/R/predict.curve_pca.R |only fdasrvf-2.4.0/fdasrvf/R/predict.hfpca.R | 2 fdasrvf-2.4.0/fdasrvf/R/predict.jfpca.R | 4 fdasrvf-2.4.0/fdasrvf/R/predict.jfpcah.R | 2 fdasrvf-2.4.0/fdasrvf/R/predict.vfpca.R | 2 fdasrvf-2.4.0/fdasrvf/R/rotation.R |only fdasrvf-2.4.0/fdasrvf/R/sample_shapes.R | 17 fdasrvf-2.4.0/fdasrvf/R/shape_CI.R | 4 fdasrvf-2.4.0/fdasrvf/R/utils-pointwise.R | 2 fdasrvf-2.4.0/fdasrvf/R/utils.R | 644 ++++++++------- fdasrvf-2.4.0/fdasrvf/README.md | 2 fdasrvf-2.4.0/fdasrvf/man/calc_shape_dist.Rd | 6 fdasrvf-2.4.0/fdasrvf/man/curve_boxplot.Rd | 4 fdasrvf-2.4.0/fdasrvf/man/curve_dist.Rd | 2 fdasrvf-2.4.0/fdasrvf/man/curvebox_data.Rd | 2 fdasrvf-2.4.0/fdasrvf/man/gam_to_h.Rd | 2 fdasrvf-2.4.0/fdasrvf/man/gam_to_psi.Rd |only fdasrvf-2.4.0/fdasrvf/man/gam_to_v.Rd | 2 fdasrvf-2.4.0/fdasrvf/man/multiple_align_multivariate.Rd |only fdasrvf-2.4.0/fdasrvf/man/multivariate_karcher_cov.Rd |only fdasrvf-2.4.0/fdasrvf/man/multivariate_karcher_mean.Rd | 4 fdasrvf-2.4.0/fdasrvf/man/multivariate_pca.Rd |only fdasrvf-2.4.0/fdasrvf/man/predict.curve_pca.Rd |only fdasrvf-2.4.0/fdasrvf/man/predict.hfpca.Rd | 2 fdasrvf-2.4.0/fdasrvf/man/predict.jfpca.Rd | 2 fdasrvf-2.4.0/fdasrvf/man/predict.jfpcah.Rd | 2 fdasrvf-2.4.0/fdasrvf/man/predict.vfpca.Rd | 2 fdasrvf-2.4.0/fdasrvf/man/psi_to_gam.Rd |only fdasrvf-2.4.0/fdasrvf/man/rotation_pca.Rd |only fdasrvf-2.4.0/fdasrvf/man/sample_shapes.Rd | 6 fdasrvf-2.4.0/fdasrvf/man/v_to_curve.Rd |only fdasrvf-2.4.0/fdasrvf/src/fdasrsf/dp_grid.h | 2 57 files changed, 816 insertions(+), 447 deletions(-)
Title: Distributional Instrumental Variable (DIV) Model
Description: Distributional instrumental variable (DIV) model
for estimation of the interventional distribution of the outcome Y under a
do-intervention on the treatment X. Instruments, predictors and targets can
be univariate or multivariate. Functionality includes estimation of the (conditional)
interventional mean and quantiles, as well as sampling from the fitted (conditional)
interventional distribution.
Author: Anastasiia Holovchak [aut, cre, ctb],
Sorawit Saengkyongam [aut, ctb],
Nicolai Meinshausen [aut, ctb],
Xinwei Shen [aut, ctb]
Maintainer: Anastasiia Holovchak <anastasiia.holovchak@stat.math.ethz.ch>
Diff between DistributionIV versions 0.1.0 dated 2025-02-27 and 0.1.2 dated 2025-06-27
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 2 ++ R/div.R | 5 ++++- R/predict.DIV.R | 5 ++++- R/print.DIV.R | 4 +++- R/zzz.R | 7 +------ man/div.Rd | 5 ++++- man/energyloss.Rd | 6 +++--- man/energylossbeta.Rd | 4 ++-- man/predict.DIV.Rd | 19 ++++++++++--------- man/print.DIV.Rd | 4 +++- 12 files changed, 51 insertions(+), 40 deletions(-)
More information about DistributionIV at CRAN
Permanent link
Title: UNHCR 'ggplot2' Theme and Colour Palettes
Description: A 'ggplot2' theme and color palettes following
the United Nations High Commissioner for Refugees (UNHCR) Data Visualization Guidelines recommendations.
Author: Cedric Vidonne [aut, cre],
Ahmadou Dicko [aut],
UNHCR [cph]
Maintainer: Cedric Vidonne <cedric@vidonne.me>
Diff between unhcrthemes versions 0.6.3 dated 2025-01-16 and 0.7.0 dated 2025-06-27
DESCRIPTION | 6 MD5 | 36 +- NEWS.md | 12 R/display_unhcr_pal.R | 32 +- R/palettes.R | 39 +- R/scales.R | 108 ++++--- R/sysdata.rda |binary R/theme_unhcr.R | 491 ++++++++++++++++++++-------------- README.md | 3 build/vignette.rds |binary inst/doc/unhcrthemes.html | 18 - man/figures/README-base-plot-1.png |binary man/figures/README-geom-plot-1.png |binary man/figures/README-palette-all-1.png |binary man/figures/README-palette-blue-1.png |binary man/figures/README-scale-plot-1.png |binary man/rmdfragments/unhcr_tools.Rmd | 2 man/unhcr_pal.Rd | 2 man/unhcr_scale.Rd | 18 - 19 files changed, 467 insertions(+), 300 deletions(-)
Title: Mixed-Effect Models, with or without Spatial Random Effects
Description: Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models (Rousset and Ferdy 2014 <doi:10.1111/ecog.00566>), and Markov random field models on irregular grids (as considered in the 'INLA' package, <https://www.r-inla.org>), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) are also implemented.
Author: Francois Rousset [aut, cre, cph] ,
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [aut]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 4.5.0 dated 2024-06-09 and 4.6.1 dated 2025-06-27
spaMM-4.5.0/spaMM/man/libraries.Rd |only spaMM-4.6.1/spaMM/DESCRIPTION | 27 spaMM-4.6.1/spaMM/MD5 | 373 ++++---- spaMM-4.6.1/spaMM/NAMESPACE | 13 spaMM-4.6.1/spaMM/R/Beta.R | 4 spaMM-4.6.1/spaMM/R/COMPoisson.R | 21 spaMM-4.6.1/spaMM/R/GLM.fit.R | 5 spaMM-4.6.1/spaMM/R/HLCor_body.R | 10 spaMM-4.6.1/spaMM/R/HLFactorList.R | 448 +++++++--- spaMM-4.6.1/spaMM/R/HLfit.R | 2 spaMM-4.6.1/spaMM/R/HLfit_Internals.R | 266 ++++- spaMM-4.6.1/spaMM/R/HLfit_b_internals.R | 43 spaMM-4.6.1/spaMM/R/HLfit_body.R | 55 - spaMM-4.6.1/spaMM/R/HLfit_loop.R | 17 spaMM-4.6.1/spaMM/R/HLframes.R | 2 spaMM-4.6.1/spaMM/R/IRLS_internals.R | 2 spaMM-4.6.1/spaMM/R/LLM.R | 35 spaMM-4.6.1/spaMM/R/LR.R | 40 spaMM-4.6.1/spaMM/R/LevM_internals.R | 2 spaMM-4.6.1/spaMM/R/LevM_v_h.R | 2 spaMM-4.6.1/spaMM/R/LevM_v_h_spprec.R | 2 spaMM-4.6.1/spaMM/R/MakeCovEst.R | 26 spaMM-4.6.1/spaMM/R/PAIRfn.R |only spaMM-4.6.1/spaMM/R/RcppExports.R | 4 spaMM-4.6.1/spaMM/R/X.GCA.R | 8 spaMM-4.6.1/spaMM/R/ZAL_class.R | 30 spaMM-4.6.1/spaMM/R/betabin.R | 6 spaMM-4.6.1/spaMM/R/betaresp.R | 2 spaMM-4.6.1/spaMM/R/calc_logdisp_cov.R | 259 +++-- spaMM-4.6.1/spaMM/R/combinepar.R | 21 spaMM-4.6.1/spaMM/R/corrHLfit-internals.R | 68 + spaMM-4.6.1/spaMM/R/corrHLfit_body.R | 1 spaMM-4.6.1/spaMM/R/cov_new_fix.R | 13 spaMM-4.6.1/spaMM/R/determine_spprec.R | 35 spaMM-4.6.1/spaMM/R/emmeans.R |only spaMM-4.6.1/spaMM/R/extractors.R | 144 ++- spaMM-4.6.1/spaMM/R/fit_as_ZX.R | 17 spaMM-4.6.1/spaMM/R/fit_as_sparsePrecision.R | 4 spaMM-4.6.1/spaMM/R/fitme.R | 13 spaMM-4.6.1/spaMM/R/fitme_body.R | 1 spaMM-4.6.1/spaMM/R/fitmecorrHLfit_body_internals.R | 108 ++ spaMM-4.6.1/spaMM/R/fitmv_body.R | 8 spaMM-4.6.1/spaMM/R/generateName.R | 1 spaMM-4.6.1/spaMM/R/geo_info.R | 11 spaMM-4.6.1/spaMM/R/get_inits_by_glm.R | 5 spaMM-4.6.1/spaMM/R/goftest.R |only spaMM-4.6.1/spaMM/R/inverse.Gamma.R | 76 - spaMM-4.6.1/spaMM/R/locoptim.R | 6 spaMM-4.6.1/spaMM/R/mapMM.R | 119 +- spaMM-4.6.1/spaMM/R/negbin1.R | 4 spaMM-4.6.1/spaMM/R/negbin2.R | 34 spaMM-4.6.1/spaMM/R/numInfo.R | 2 spaMM-4.6.1/spaMM/R/plot_effects.R | 27 spaMM-4.6.1/spaMM/R/pois4mlogit.R |only spaMM-4.6.1/spaMM/R/poisson.R | 6 spaMM-4.6.1/spaMM/R/postfit_internals.R | 121 +- spaMM-4.6.1/spaMM/R/predict.R | 71 - spaMM-4.6.1/spaMM/R/predict_marg.R | 6 spaMM-4.6.1/spaMM/R/predict_mv.R | 191 +--- spaMM-4.6.1/spaMM/R/preprocess.R | 86 + spaMM-4.6.1/spaMM/R/preprocess_MV.R | 68 - spaMM-4.6.1/spaMM/R/preprocess_internals.R | 172 ++- spaMM-4.6.1/spaMM/R/profile.R | 18 spaMM-4.6.1/spaMM/R/sXaug_EigenDense_QRP_Chol_scaled.R | 8 spaMM-4.6.1/spaMM/R/sXaug_Matrix_CHM_Hess.R | 41 spaMM-4.6.1/spaMM/R/sXaug_Matrix_QRP_CHM.R | 68 - spaMM-4.6.1/spaMM/R/sXaug_sparsePrecisions.R | 36 spaMM-4.6.1/spaMM/R/safe_opt.R | 6 spaMM-4.6.1/spaMM/R/save.R | 2 spaMM-4.6.1/spaMM/R/separator.R | 52 - spaMM-4.6.1/spaMM/R/simulate.HL.R | 5 spaMM-4.6.1/spaMM/R/spaMM.data.R | 53 - spaMM-4.6.1/spaMM/R/spaMM_boot.R | 42 spaMM-4.6.1/spaMM/R/summary.HL.R | 23 spaMM-4.6.1/spaMM/R/utils.R | 30 spaMM-4.6.1/spaMM/build/partial.rdb |binary spaMM-4.6.1/spaMM/inst/NEWS.Rd | 59 + spaMM-4.6.1/spaMM/man/AIC.Rd | 1 spaMM-4.6.1/spaMM/man/COMPoisson.Rd | 2 spaMM-4.6.1/spaMM/man/HLCor.Rd | 2 spaMM-4.6.1/spaMM/man/HLfit.Rd | 8 spaMM-4.6.1/spaMM/man/IMRF.Rd | 3 spaMM-4.6.1/spaMM/man/MaternCorr.Rd | 2 spaMM-4.6.1/spaMM/man/MaternIMRF.Rd | 4 spaMM-4.6.1/spaMM/man/PAIRfn.Rd |only spaMM-4.6.1/spaMM/man/R2.Rd | 5 spaMM-4.6.1/spaMM/man/WinterWheat.Rd | 1 spaMM-4.6.1/spaMM/man/ZAXlist.Rd | 1 spaMM-4.6.1/spaMM/man/aliases.Rd |only spaMM-4.6.1/spaMM/man/anova.HLfit.Rd | 4 spaMM-4.6.1/spaMM/man/beta_resp.Rd | 2 spaMM-4.6.1/spaMM/man/betabin.Rd | 2 spaMM-4.6.1/spaMM/man/corMatern.Rd | 2 spaMM-4.6.1/spaMM/man/diallel.Rd | 3 spaMM-4.6.1/spaMM/man/dopar.Rd | 12 spaMM-4.6.1/spaMM/man/extractors.Rd | 12 spaMM-4.6.1/spaMM/man/fitme.Rd | 4 spaMM-4.6.1/spaMM/man/fitmv.Rd | 5 spaMM-4.6.1/spaMM/man/fixed.Rd | 5 spaMM-4.6.1/spaMM/man/get_inits_from_fit.Rd | 2 spaMM-4.6.1/spaMM/man/gof.Rd |only spaMM-4.6.1/spaMM/man/good-practice.Rd | 4 spaMM-4.6.1/spaMM/man/how.Rd | 2 spaMM-4.6.1/spaMM/man/is_separated.Rd | 2 spaMM-4.6.1/spaMM/man/llm.fit.Rd | 6 spaMM-4.6.1/spaMM/man/mapMM.Rd | 8 spaMM-4.6.1/spaMM/man/method.Rd | 2 spaMM-4.6.1/spaMM/man/multinomial.Rd | 6 spaMM-4.6.1/spaMM/man/mv.Rd | 4 spaMM-4.6.1/spaMM/man/options.Rd | 3 spaMM-4.6.1/spaMM/man/phi-resid.model.Rd | 4 spaMM-4.6.1/spaMM/man/plot.HL.Rd | 2 spaMM-4.6.1/spaMM/man/plot_effect.Rd | 13 spaMM-4.6.1/spaMM/man/pois4mlogit.Rd |only spaMM-4.6.1/spaMM/man/poisson.Rd | 6 spaMM-4.6.1/spaMM/man/post-fit.Rd | 5 spaMM-4.6.1/spaMM/man/predVar.Rd | 4 spaMM-4.6.1/spaMM/man/predict.Rd | 10 spaMM-4.6.1/spaMM/man/resid.model.Rd | 2 spaMM-4.6.1/spaMM/man/residVar.Rd | 18 spaMM-4.6.1/spaMM/man/residuals.HLfit.Rd | 16 spaMM-4.6.1/spaMM/man/scotlip.Rd | 2 spaMM-4.6.1/spaMM/man/spaMM-S3.Rd | 8 spaMM-4.6.1/spaMM/man/spaMM.Rd | 4 spaMM-4.6.1/spaMM/man/spaMM.filled.contour.Rd | 2 spaMM-4.6.1/spaMM/man/spaMM_boot.Rd | 2 spaMM-4.6.1/spaMM/man/summary.HL.Rd | 2 spaMM-4.6.1/spaMM/man/vcov.Rd | 15 spaMM-4.6.1/spaMM/src/PLS.cpp | 24 spaMM-4.6.1/spaMM/src/RcppExports.cpp | 13 spaMM-4.6.1/spaMM/src/internals.cpp | 9 spaMM-4.6.1/spaMM/tests/test-all.R | 16 spaMM-4.6.1/spaMM/tests/testthat/extralong/test-composite-extra.R | 105 +- spaMM-4.6.1/spaMM/tests/testthat/extralong/test-mv-corrFamily.R | 8 spaMM-4.6.1/spaMM/tests/testthat/extralong/test-mv-extra.R | 102 +- spaMM-4.6.1/spaMM/tests/testthat/test-ANOVA-&-lmerTest.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-AR1.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-CAR.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-COMPoisson.R | 4 spaMM-4.6.1/spaMM/tests/testthat/test-GxE_variance_stability.R | 4 spaMM-4.6.1/spaMM/tests/testthat/test-HLCor.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-HLfit.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-IMRF.R | 4 spaMM-4.6.1/spaMM/tests/testthat/test-Infusion.R | 4 spaMM-4.6.1/spaMM/tests/testthat/test-IsoriX-new.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-LLM.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-LRT-boot.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-MSFDR.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-Nugget.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-Rasch.R | 4 spaMM-4.6.1/spaMM/tests/testthat/test-X.GCA.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-adjacency-corrMatrix.R | 6 spaMM-4.6.1/spaMM/tests/testthat/test-adjacency-long.R | 4 spaMM-4.6.1/spaMM/tests/testthat/test-augZXy.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-blackbox.R | 4 spaMM-4.6.1/spaMM/tests/testthat/test-cAIC.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-cloglog.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-composite.R | 96 +- spaMM-4.6.1/spaMM/tests/testthat/test-confint.R | 19 spaMM-4.6.1/spaMM/tests/testthat/test-corMatern.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-corrFamilies.R | 22 spaMM-4.6.1/spaMM/tests/testthat/test-corrFamily-doc-examples.R | 14 spaMM-4.6.1/spaMM/tests/testthat/test-covStruct.R |only spaMM-4.6.1/spaMM/tests/testthat/test-dhglm.R | 6 spaMM-4.6.1/spaMM/tests/testthat/test-distMatrix.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-extractors-spprec.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-filled.mapMM.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-fixedLRT.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-inverse.Gamma.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-mm.R |only spaMM-4.6.1/spaMM/tests/testthat/test-more-predict.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-multinomial.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-mv.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-negbin1.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-nested-geostat.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-numInfo.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-obsInfo.R | 7 spaMM-4.6.1/spaMM/tests/testthat/test-pdep-effects.R | 4 spaMM-4.6.1/spaMM/tests/testthat/test-pedigree.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-pois4mlogit.R |only spaMM-4.6.1/spaMM/tests/testthat/test-poly.R | 12 spaMM-4.6.1/spaMM/tests/testthat/test-predVar-Matern-corrMatrix.R | 10 spaMM-4.6.1/spaMM/tests/testthat/test-predVar.R | 8 spaMM-4.6.1/spaMM/tests/testthat/test-prior.weights.R |only spaMM-4.6.1/spaMM/tests/testthat/test-ranCoefs.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-random-slope.R | 4 spaMM-4.6.1/spaMM/tests/testthat/test-rank.R | 6 spaMM-4.6.1/spaMM/tests/testthat/test-salamander.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-simulate.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-spaMM.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-spaMM.filled.contour.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-spaMM_glm.R | 2 spaMM-4.6.1/spaMM/tests/testthat/test-truncated.R | 19 spaMM-4.6.1/spaMM/tests/testthat/test_init_NaN.R | 2 194 files changed, 2806 insertions(+), 1620 deletions(-)
Title: Bayesian Hierarchical Analysis of Cognitive Models of Choice
Description: Fit Bayesian (hierarchical) cognitive models
using a linear modeling language interface using particle Metropolis Markov
chain Monte Carlo sampling with Gibbs steps. The diffusion decision model (DDM),
linear ballistic accumulator model (LBA), racing diffusion model (RDM), and the lognormal
race model (LNR) are supported. Additionally, users can specify their own likelihood
function and/or choose for non-hierarchical
estimation, as well as for a diagonal, blocked or full multivariate normal
group-level distribution to test individual differences. Prior specification
is facilitated through methods that visualize the (implied) prior.
A wide range of plotting functions assist in assessing model convergence and
posterior inference. Models can be easily evaluated using functions
that plot posterior predictions or using relative model comparison metrics
such as information criteria or Bayes factors.
References: Stevenson et al. (2024) <doi:10.31234/osf.io/2e4dq>.
Author: Niek Stevenson [aut, cre] ,
Michelle Donzallaz [aut],
Andrew Heathcote [aut],
Steven Miletic [ctb],
Raphael Hartmann [ctb],
Karl C. Klauer [ctb],
Steven G. Johnson [ctb],
Jean M. Linhart [ctb],
Brian Gough [ctb],
Gerard Jungman [ctb],
Rudolf Schuerer [...truncated...]
Maintainer: Niek Stevenson <niek.stevenson@gmail.com>
Diff between EMC2 versions 3.1.1 dated 2025-04-06 and 3.2.0 dated 2025-06-27
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Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>;
Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>;
Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings
and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank mo [...truncated...]
Author: Oystein Sorensen [aut, cre] ,
Waldir Leoncio [aut],
Valeria Vitelli [aut] ,
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut],
Anja Stein [aut]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 2.2.4 dated 2025-06-13 and 2.2.5 dated 2025-06-27
DESCRIPTION | 6 ++--- MD5 | 28 ++++++++++++++------------- NEWS.md | 4 +++ R/data.R | 14 +++++++++++++ build/partial.rdb |binary build/vignette.rds |binary data/sounds.rda |only man/beach_preferences.Rd | 1 man/bernoulli_data.Rd | 1 man/cluster_data.Rd | 1 man/potato_true_ranking.Rd | 1 man/potato_visual.Rd | 1 man/potato_weighing.Rd | 1 man/sounds.Rd |only man/sushi_rankings.Rd | 3 +- tests/testthat/test-smc_update_correctness.R | 6 ----- 16 files changed, 44 insertions(+), 23 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xintong Li [ctb] ,
Xihang Chen [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 1.4.0 dated 2025-05-30 and 1.4.1 dated 2025-06-27
DESCRIPTION | 6 MD5 | 24 +-- NEWS.md | 4 R/addIntersect.R | 133 ++++++++++---------- R/addObservationPeriodId.R | 4 inst/doc/cohort-intersect.html | 98 +++++++-------- inst/doc/concept-intersect.html | 94 +++++++------- inst/doc/demographics.html | 238 ++++++++++++++++++------------------- inst/doc/summarise.html | 152 +++++++++++------------ inst/doc/table-intersect.html | 86 ++++++------- man/addObservationPeriodId.Rd | 2 man/addObservationPeriodIdQuery.Rd | 2 tests/testthat/test-addIntersect.R | 6 13 files changed, 428 insertions(+), 421 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: GCC Estimation of the Multilevel Factor Model
Description: Provides methods for model selection, estimation, inference, and simulation for the
multilevel factor model, based on the principal component estimation and generalised
canonical correlation approach. Details can be found in "Generalised Canonical Correlation
Estimation of the Multilevel Factor Model." Lin and Shin (2025) <doi:10.2139/ssrn.4295429>.
Author: Rui Lin [aut, cre],
Yongcheol Shin [aut]
Maintainer: Rui Lin <ruilin1081@gmail.com>
Diff between GCCfactor versions 1.0.1 dated 2023-10-30 and 1.1.0 dated 2025-06-27
GCCfactor-1.0.1/GCCfactor/R/bootstrap_functions.R |only GCCfactor-1.0.1/GCCfactor/man/AsymCI_local_loading.Rd |only GCCfactor-1.0.1/GCCfactor/man/BS_global_comp.Rd |only GCCfactor-1.0.1/GCCfactor/man/BS_global_factor.Rd |only GCCfactor-1.0.1/GCCfactor/man/BS_global_loading.Rd |only GCCfactor-1.0.1/GCCfactor/man/BS_local_comp.Rd |only GCCfactor-1.0.1/GCCfactor/man/BS_local_factor.Rd |only GCCfactor-1.0.1/GCCfactor/man/Bartlett.Rd |only GCCfactor-1.0.1/GCCfactor/man/dwBS.Rd |only GCCfactor-1.0.1/GCCfactor/man/get_bw.Rd |only GCCfactor-1.1.0/GCCfactor/DESCRIPTION | 14 +- GCCfactor-1.1.0/GCCfactor/MD5 | 31 ++-- GCCfactor-1.1.0/GCCfactor/NAMESPACE | 15 -- GCCfactor-1.1.0/GCCfactor/R/main_functions.R | 20 +-- GCCfactor-1.1.0/GCCfactor/R/utility_functions.R | 113 ------------------ GCCfactor-1.1.0/GCCfactor/R/vcov_functions.R |only GCCfactor-1.1.0/GCCfactor/man/GCC.Rd | 12 - GCCfactor-1.1.0/GCCfactor/man/check_data.Rd | 2 GCCfactor-1.1.0/GCCfactor/man/multilevel.Rd | 8 - GCCfactor-1.1.0/GCCfactor/man/vcov_global_comp.Rd |only GCCfactor-1.1.0/GCCfactor/man/vcov_global_factor.Rd |only GCCfactor-1.1.0/GCCfactor/man/vcov_global_loading.Rd |only GCCfactor-1.1.0/GCCfactor/man/vcov_local_comp.Rd |only GCCfactor-1.1.0/GCCfactor/man/vcov_local_factor.Rd |only GCCfactor-1.1.0/GCCfactor/man/vcov_local_loading.Rd |only 25 files changed, 47 insertions(+), 168 deletions(-)
Title: Estimate Time Varying Reproduction Numbers from Epidemic Curves
Description: Tools to quantify transmissibility throughout
an epidemic from the analysis of time series of incidence as described in
Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004)
<doi:10.1093/aje/kwh255>.
Author: Anne Cori [aut, cre] ,
Simon Cauchemez [ctb],
Neil M. Ferguson [ctb] ,
Christophe Fraser [ctb] ,
Elisabeth Dahlqwist [ctb] ,
P. Alex Demarsh [ctb],
Thibaut Jombart [ctb] ,
Zhian N. Kamvar [ctb] ,
Justin Lessler [ctb] ,
Shikun Li [ctb],
Jonathan A. Po [...truncated...]
Maintainer: Anne Cori <a.cori@imperial.ac.uk>
Diff between EpiEstim versions 2.2-4.1 dated 2025-06-23 and 2.2-5 dated 2025-06-27
DESCRIPTION | 8 MD5 | 80 +-- R/coarse2estim.R | 10 R/data.R | 2 R/estimate_R_plots.R | 2 R/estimate_r.R | 71 +-- R/init_mcmc_params.R | 20 R/make_config.R | 135 +++--- R/make_mcmc_control.R | 23 - R/overall_infectivity.R | 8 R/plot.R | 58 +- R/utilities.R | 2 R/wallinga_teunis.R | 55 +- build/vignette.rds |binary data/Flu1918.rda |binary data/Flu2009.rda |binary data/Measles1861.rda |binary data/MockRotavirus.rda |binary data/SARS2003.rda |binary data/Smallpox1972.rda |binary data/flu_2009_NYC_school.rda |binary data/mers_2014_15.rda |binary inst/doc/demo.Rmd | 2 inst/doc/demo.html | 927 +++++++++++++++++++------------------------ man/Flu1918.Rd | 6 man/Flu2009.Rd | 6 man/Measles1861.Rd | 6 man/MockRotavirus.Rd | 6 man/SARS2003.Rd | 6 man/Smallpox1972.Rd | 6 man/coarse2estim.Rd | 10 man/estimate_R.Rd | 75 +-- man/flu_2009_NYC_school.Rd | 8 man/init_mcmc_params.Rd | 20 man/make_config.Rd | 134 ++---- man/make_mcmc_control.Rd | 23 - man/mers_2014_15.Rd | 6 man/overall_infectivity.Rd | 8 man/plot.estimate_R.Rd | 58 +- man/wallinga_teunis.Rd | 54 +- vignettes/demo.Rmd | 2 41 files changed, 899 insertions(+), 938 deletions(-)
Title: Response Quality Indicators for Survey Research
Description: Calculate common survey data quality indicators for multi-item scales
and matrix questions. Currently supports the calculation of
response style indicators and response distribution indicators.
For an overview on response quality indicators see Bhaktha N,
Henning S, Clemens L (2024). 'Characterizing response quality
in surveys with multi-item scales: A unified framework'
<https://osf.io/9gs67/>.
Author: Matthias Roth [aut, cre, cph] ,
Nivedita Bhaktha [aut, ctb],
Matthias Bluemke [aut, ctb],
Thomas Knopf [aut, ctb],
Fabienne Kraemer [aut, ctb],
Clemens Lechner [aut, ctb],
Cagla Yildiz [aut, ctb]
Maintainer: Matthias Roth <matthias.roth@gesis.org>
Diff between resquin versions 0.0.2 dated 2024-09-11 and 0.1.1 dated 2025-06-27
resquin-0.0.2/resquin/R/resp_times.R |only resquin-0.1.1/resquin/DESCRIPTION | 15 resquin-0.1.1/resquin/MD5 | 59 - resquin-0.1.1/resquin/NAMESPACE | 17 resquin-0.1.1/resquin/NEWS.md | 33 resquin-0.1.1/resquin/R/data.R |only resquin-0.1.1/resquin/R/flag_resp.R |only resquin-0.1.1/resquin/R/resp_distributions.R | 68 + resquin-0.1.1/resquin/R/resp_nondifferentiation.R |only resquin-0.1.1/resquin/R/resp_patterns.R | 232 ++++ resquin-0.1.1/resquin/R/resp_styles.R | 45 resquin-0.1.1/resquin/R/s3_methods.R |only resquin-0.1.1/resquin/R/util.R | 106 +- resquin-0.1.1/resquin/README.md | 171 ++- resquin-0.1.1/resquin/build/vignette.rds |binary resquin-0.1.1/resquin/data |only resquin-0.1.1/resquin/inst/doc/flagging_respondents.R |only resquin-0.1.1/resquin/inst/doc/flagging_respondents.Rmd |only resquin-0.1.1/resquin/inst/doc/flagging_respondents.html |only resquin-0.1.1/resquin/inst/doc/getting_started_with_resquin.R | 74 + resquin-0.1.1/resquin/inst/doc/getting_started_with_resquin.Rmd | 198 ++++ resquin-0.1.1/resquin/inst/doc/getting_started_with_resquin.html | 469 +++++++++- resquin-0.1.1/resquin/man/figures |only resquin-0.1.1/resquin/man/flag_resp.Rd |only resquin-0.1.1/resquin/man/nep.Rd |only resquin-0.1.1/resquin/man/plot.resp_indicator.Rd |only resquin-0.1.1/resquin/man/resp_distributions.Rd | 29 resquin-0.1.1/resquin/man/resp_nondifferentiation.Rd |only resquin-0.1.1/resquin/man/resp_patterns.Rd |only resquin-0.1.1/resquin/man/resp_styles.Rd | 35 resquin-0.1.1/resquin/man/summary.flag_resp.Rd |only resquin-0.1.1/resquin/man/summary.resp_indicator.Rd |only resquin-0.1.1/resquin/tests/testthat/Rplots.pdf |only resquin-0.1.1/resquin/tests/testthat/_snaps |only resquin-0.1.1/resquin/tests/testthat/test-flag_resp.R |only resquin-0.1.1/resquin/tests/testthat/test-resp_distributions.R | 15 resquin-0.1.1/resquin/tests/testthat/test-resp_nondifferentiation.R |only resquin-0.1.1/resquin/tests/testthat/test-resp_patterns.R |only resquin-0.1.1/resquin/tests/testthat/test-resp_styles.R | 134 +- resquin-0.1.1/resquin/tests/testthat/test-s3_methods.R |only resquin-0.1.1/resquin/vignettes/flagging_respondents.Rmd |only resquin-0.1.1/resquin/vignettes/getting_started_with_resquin.Rmd | 198 ++++ resquin-0.1.1/resquin/vignettes/references.bib |only 43 files changed, 1678 insertions(+), 220 deletions(-)
Title: Functions to Support Data Management and Processing Using the
Maelstrom Research Approach
Description: Functions to support data cleaning, evaluation, and description,
developed for integration with Maelstrom Research software tools. 'madshapR'
provides functions primarily to evaluate and manipulate datasets and
data dictionaries in preparation for data harmonization with the package
'Rmonize' and to facilitate integration and transfer between RStudio servers
and secure Opal environments. 'madshapR' functions can be used independently
but are optimized in conjunction with ‘Rmonize’ functions for streamlined
and coherent harmonization processing.
Author: Guillaume Fabre [aut, cre] ,
Maelstrom Research [aut, fnd, cph]
Maintainer: Guillaume Fabre <guijoseph.fabre@gmail.com>
Diff between madshapR versions 1.1.0 dated 2024-04-23 and 2.0.0 dated 2025-06-27
madshapR-1.1.0/madshapR/build/partial.rdb |only madshapR-1.1.0/madshapR/data/madshapR_DEMO.rda |only madshapR-1.1.0/madshapR/man/deprecated.Rd |only madshapR-1.1.0/madshapR/man/madshapR_DEMO.Rd |only madshapR-2.0.0/madshapR/DESCRIPTION | 50 madshapR-2.0.0/madshapR/MD5 | 178 madshapR-2.0.0/madshapR/NAMESPACE | 199 madshapR-2.0.0/madshapR/NEWS.md | 777 +- madshapR-2.0.0/madshapR/R/01-utils.R | 74 madshapR-2.0.0/madshapR/R/02-dictionaries_functions.R | 1782 +++--- madshapR-2.0.0/madshapR/R/03-dataset_functions.R | 324 - madshapR-2.0.0/madshapR/R/04-catalogue_functions.R | 766 +- madshapR-2.0.0/madshapR/R/05-unit_checks.R | 780 +- madshapR-2.0.0/madshapR/R/06-data_evaluate.R | 957 ++- madshapR-2.0.0/madshapR/R/07-data_summarize.R | 2730 +++++----- madshapR-2.0.0/madshapR/R/08-data_visualize.R | 2230 +++----- madshapR-2.0.0/madshapR/R/deprecated.R | 52 madshapR-2.0.0/madshapR/R/experimental.R | 793 ++ madshapR-2.0.0/madshapR/README.md | 28 madshapR-2.0.0/madshapR/data/color_palette_maelstrom.rda |only madshapR-2.0.0/madshapR/data/madshapR_examples.rda |only madshapR-2.0.0/madshapR/data/valueType_list.rda |binary madshapR-2.0.0/madshapR/inst/WORDLIST | 14 madshapR-2.0.0/madshapR/inst/doc/madshapR-vignette.R | 23 madshapR-2.0.0/madshapR/inst/doc/madshapR-vignette.Rmd | 26 madshapR-2.0.0/madshapR/inst/doc/madshapR-vignette.html | 34 madshapR-2.0.0/madshapR/man/as_category.Rd | 37 madshapR-2.0.0/madshapR/man/as_data_dict.Rd | 106 madshapR-2.0.0/madshapR/man/as_data_dict_mlstr.Rd | 123 madshapR-2.0.0/madshapR/man/as_data_dict_shape.Rd | 90 madshapR-2.0.0/madshapR/man/as_dataset.Rd | 102 madshapR-2.0.0/madshapR/man/as_dossier.Rd | 114 madshapR-2.0.0/madshapR/man/as_taxonomy.Rd | 85 madshapR-2.0.0/madshapR/man/as_valueType.Rd | 103 madshapR-2.0.0/madshapR/man/check_data_dict_categories.Rd | 87 madshapR-2.0.0/madshapR/man/check_data_dict_missing_categories.Rd | 85 madshapR-2.0.0/madshapR/man/check_data_dict_valueType.Rd | 105 madshapR-2.0.0/madshapR/man/check_data_dict_variables.Rd | 81 madshapR-2.0.0/madshapR/man/check_dataset_categories.Rd | 124 madshapR-2.0.0/madshapR/man/check_dataset_valueType.Rd | 132 madshapR-2.0.0/madshapR/man/check_dataset_variables.Rd | 107 madshapR-2.0.0/madshapR/man/check_name_standards.Rd | 74 madshapR-2.0.0/madshapR/man/col_id.Rd | 19 madshapR-2.0.0/madshapR/man/color_palette_maelstrom.Rd |only madshapR-2.0.0/madshapR/man/data_dict_apply.Rd | 119 madshapR-2.0.0/madshapR/man/data_dict_collapse.Rd | 134 madshapR-2.0.0/madshapR/man/data_dict_evaluate.Rd | 126 madshapR-2.0.0/madshapR/man/data_dict_expand.Rd | 137 madshapR-2.0.0/madshapR/man/data_dict_extract.Rd | 131 madshapR-2.0.0/madshapR/man/data_dict_filter.Rd | 156 madshapR-2.0.0/madshapR/man/data_dict_group_by.Rd | 119 madshapR-2.0.0/madshapR/man/data_dict_group_split.Rd | 133 madshapR-2.0.0/madshapR/man/data_dict_list_nest.Rd | 115 madshapR-2.0.0/madshapR/man/data_dict_match_dataset.Rd | 142 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Title: Lorenz and Penalized Lorenz Regressions
Description: Inference for the Lorenz and penalized Lorenz regressions. More broadly, the package proposes functions to assess inequality and graphically represent it. The Lorenz Regression procedure is introduced in Heuchenne and Jacquemain (2022) <doi:10.1016/j.csda.2021.107347> and in Jacquemain, A., C. Heuchenne, and E. Pircalabelu (2024) <doi:10.1214/23-EJS2200>.
Author: Alexandre Jacquemain [aut, cre] ,
Xingjie Shi [ctb]
Maintainer: Alexandre Jacquemain <aljacquemain@gmail.com>
Diff between LorenzRegression versions 2.1.0 dated 2024-10-11 and 2.2.0 dated 2025-06-27
LorenzRegression-2.1.0/LorenzRegression/src/PLR_derivative.cpp |only LorenzRegression-2.1.0/LorenzRegression/src/PLR_loss.cpp |only LorenzRegression-2.2.0/LorenzRegression/DESCRIPTION | 16 LorenzRegression-2.2.0/LorenzRegression/MD5 | 99 ++-- LorenzRegression-2.2.0/LorenzRegression/NAMESPACE | 23 - LorenzRegression-2.2.0/LorenzRegression/NEWS.md | 13 LorenzRegression-2.2.0/LorenzRegression/R/FABS-estimation.R | 28 + LorenzRegression-2.2.0/LorenzRegression/R/GA-call.R | 9 LorenzRegression-2.2.0/LorenzRegression/R/GA-estimation.R | 32 + LorenzRegression-2.2.0/LorenzRegression/R/GA-suggestions.R |only LorenzRegression-2.2.0/LorenzRegression/R/Gini-coefficient.R | 11 LorenzRegression-2.2.0/LorenzRegression/R/LR-confint.R | 3 LorenzRegression-2.2.0/LorenzRegression/R/LR-plot.R | 71 ++- LorenzRegression-2.2.0/LorenzRegression/R/LR-predict.R | 43 +- LorenzRegression-2.2.0/LorenzRegression/R/LR-summary.R | 3 LorenzRegression-2.2.0/LorenzRegression/R/Lorenz-bootstrap-combine.R | 11 LorenzRegression-2.2.0/LorenzRegression/R/Lorenz-bootstrap.R | 206 ++++++---- LorenzRegression-2.2.0/LorenzRegression/R/Lorenz-curve.R | 23 - LorenzRegression-2.2.0/LorenzRegression/R/Lorenz-graphs.R | 95 +++- LorenzRegression-2.2.0/LorenzRegression/R/Lorenz-regression.R | 86 +--- LorenzRegression-2.2.0/LorenzRegression/R/PLR-CV.R | 90 +--- LorenzRegression-2.2.0/LorenzRegression/R/PLR-coef.R | 5 LorenzRegression-2.2.0/LorenzRegression/R/PLR-confint.R | 5 LorenzRegression-2.2.0/LorenzRegression/R/PLR-fit.R |only LorenzRegression-2.2.0/LorenzRegression/R/PLR-ineqExplained.R | 5 LorenzRegression-2.2.0/LorenzRegression/R/PLR-plot.R | 99 ++++ LorenzRegression-2.2.0/LorenzRegression/R/PLR-predict.R | 70 +++ LorenzRegression-2.2.0/LorenzRegression/R/RcppExports.R | 26 + LorenzRegression-2.2.0/LorenzRegression/R/Rearrangement-estimation.R | 112 +++-- LorenzRegression-2.2.0/LorenzRegression/R/SCADFABS-estimation.R | 57 +- LorenzRegression-2.2.0/LorenzRegression/R/globals.R | 5 LorenzRegression-2.2.0/LorenzRegression/R/ineqExplained.R | 50 ++ LorenzRegression-2.2.0/LorenzRegression/man/Lorenz.GA.Rd | 5 LorenzRegression-2.2.0/LorenzRegression/man/Lorenz.Reg.Rd | 8 LorenzRegression-2.2.0/LorenzRegression/man/Lorenz.Suggestions.Rd |only LorenzRegression-2.2.0/LorenzRegression/man/Lorenz.boot.Rd | 189 ++++----- LorenzRegression-2.2.0/LorenzRegression/man/Lorenz.curve.Rd | 9 LorenzRegression-2.2.0/LorenzRegression/man/Lorenz.ga.call.Rd | 3 LorenzRegression-2.2.0/LorenzRegression/man/Lorenz.graphs.Rd | 2 LorenzRegression-2.2.0/LorenzRegression/man/PLR.CV.Rd | 22 - LorenzRegression-2.2.0/LorenzRegression/man/PLR.fit.Rd |only LorenzRegression-2.2.0/LorenzRegression/man/Rearrangement.estimation.Rd | 54 ++ LorenzRegression-2.2.0/LorenzRegression/man/autoplot.LR.Rd | 17 LorenzRegression-2.2.0/LorenzRegression/man/autoplot.PLR.Rd | 23 - LorenzRegression-2.2.0/LorenzRegression/man/dot-frac_rank_cpp.Rd |only LorenzRegression-2.2.0/LorenzRegression/man/ineqExplained.lm.Rd |only LorenzRegression-2.2.0/LorenzRegression/man/predict.LR.Rd | 6 LorenzRegression-2.2.0/LorenzRegression/man/predict.PLR.Rd | 12 LorenzRegression-2.2.0/LorenzRegression/man/residuals.LR.Rd |only LorenzRegression-2.2.0/LorenzRegression/man/residuals.PLR.Rd |only LorenzRegression-2.2.0/LorenzRegression/src/GA_fitness.cpp | 24 - LorenzRegression-2.2.0/LorenzRegression/src/GA_meanrank.cpp | 49 -- LorenzRegression-2.2.0/LorenzRegression/src/PLR_derivative_m.cpp |only LorenzRegression-2.2.0/LorenzRegression/src/PLR_derivative_zero.cpp |only LorenzRegression-2.2.0/LorenzRegression/src/PLR_loss_m.cpp |only LorenzRegression-2.2.0/LorenzRegression/src/PLR_loss_zero.cpp |only LorenzRegression-2.2.0/LorenzRegression/src/RcppExports.cpp | 76 +++ LorenzRegression-2.2.0/LorenzRegression/src/frac_rank.cpp |only 58 files changed, 1156 insertions(+), 639 deletions(-)
More information about LorenzRegression at CRAN
Permanent link
Title: DEFLATE Compression and Static Library
Description: Whole-buffer DEFLATE-based compression and
decompression of raw vectors using the 'libdeflate' library
(see <https://github.com/ebiggers/libdeflate>). Provides the user with additional
control over the speed and the quality of DEFLATE compression
compared to the fixed level of compression offered in R's
'memCompress()' function. Also provides the 'libdeflate' static library and
'C' headers along with a 'CMake' target and 'package‑config' file that
ease linking of 'libdeflate' in packages that compile and statically link
bundled libraries using 'CMake'.
Author: Tyler Morgan-Wall [aut, cre] ,
Eric Biggers [aut, cph],
Google LLC [cph],
Kevin Ushey [cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between libdeflate versions 1.24-2 dated 2025-06-24 and 1.24-3 dated 2025-06-27
DESCRIPTION | 6 MD5 | 8 - src/Makevars.in | 14 - src/Makevars.win.in | 14 - tools/config/configure.R | 341 ++++++++++++++++++++++++----------------------- 5 files changed, 201 insertions(+), 182 deletions(-)
Title: Affinity in Co-Occurrence Data
Description: Computes a novel metric of affinity between two entities based on their co-occurrence
(using binary presence/absence data). The metric and its MLE, alpha hat, were advanced in
Mainali, Slud, et al, 2021 <doi:10.1126/sciadv.abj9204>. Various types of confidence intervals and median interval
were developed in Mainali and Slud, 2022 <doi:10.1101/2022.11.01.514801>. The `finches` dataset is now
bundled internally (no longer pulled via the cooccur package, which has been dropped).
Author: Kumar Mainali [aut, cre],
Eric Slud [aut]
Maintainer: Kumar Mainali <kpmainali@gmail.com>
Diff between CooccurrenceAffinity versions 1.0 dated 2023-05-03 and 1.0.2 dated 2025-06-27
DESCRIPTION | 15 +-- MD5 | 22 ++-- NEWS.md |only R/CovrgPlot.R | 2 R/finches-data.R |only README.md | 62 +++++++----- data |only inst/examples/CovrgPlot_example.R | 24 ++-- inst/examples/affinity_example.R | 184 +++++++++++++++++--------------------- inst/examples/plotgg_example.R | 171 +++++++++++++++-------------------- man/CovrgPlot.Rd | 26 ++--- man/affinity.Rd | 184 +++++++++++++++++--------------------- man/finches.Rd |only man/plotgg.Rd | 171 +++++++++++++++-------------------- 14 files changed, 407 insertions(+), 454 deletions(-)
More information about CooccurrenceAffinity at CRAN
Permanent link
Title: Linguistic Fuzzy Logic
Description: Various algorithms related to linguistic fuzzy logic: mining for linguistic fuzzy association
rules, composition of fuzzy relations, performing perception-based logical deduction (PbLD),
and forecasting time-series using fuzzy rule-based ensemble (FRBE). The package also contains basic
fuzzy-related algebraic functions capable of handling missing values in different styles (Bochvar,
Sobocinski, Kleene etc.), computation of Sugeno integrals and fuzzy transform.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between lfl versions 2.2.1 dated 2024-10-22 and 2.3.0 dated 2025-06-27
DESCRIPTION | 13 +++--- MD5 | 43 ++++++++++++----------- NAMESPACE | 4 +- NEWS.md | 8 ++++ R/algebra.R | 1 R/algebraNA.R | 54 +++++++++++++++++++++++++++-- R/evalfrbe.R | 1 R/fcut.R | 13 +----- R/frbe.R | 12 ------ R/fsets.R | 33 ++++++++++++++++- R/ft.R | 1 R/ftinv.R | 1 R/lcut.R | 2 - R/lfl-package.R | 27 +++++++++++++- R/quantifier.R | 16 ++++---- R/rollapply.R |only README.md | 10 +++-- build/vignette.rds |binary configure.ac | 1 man/algebraNA.Rd | 31 ++++++++++++++++ man/lcut.Rd | 2 - man/quantifier.Rd | 16 ++++---- man/str.fsets.Rd |only tests/testthat/test-algebraNA-lowerBound.R |only 24 files changed, 209 insertions(+), 80 deletions(-)