Title: Matrices for Repeat-Sales Price Indexes
Description: Calculate the matrices in
Shiller (1991, <doi:10.1016/S1051-1377(05)80028-2>) that serve as the
foundation for many repeat-sales price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between rsmatrix versions 0.2.9 dated 2024-12-14 and 0.2.10 dated 2026-05-07
DESCRIPTION | 13 +-- MD5 | 34 ++++---- NEWS.md | 16 ++- R/rs_matrix.R | 27 +++--- R/rs_pairs.R | 14 +-- R/rs_var.R | 8 - README.md | 16 +++ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/rsmatrix.R | 24 ++++- inst/doc/rsmatrix.Rmd | 24 ++++- inst/doc/rsmatrix.html | 126 ++++++++++++++++-------------- man/rs_pairs.Rd | 4 man/rsmatrix-package.Rd | 5 + tests/testthat/test-rs_matrix.R | 166 ++++++++++++++++++++++++++++++---------- tests/testthat/test-rs_pairs.R | 20 ++++ vignettes/rsmatrix.Rmd | 24 ++++- 18 files changed, 349 insertions(+), 174 deletions(-)
Title: Understanding Nonlinear Mixed Effects Modeling for Population
Pharmacokinetics
Description: This shows how NONMEM(R) software works. NONMEM's classical
estimation methods like 'First Order(FO) approximation', 'First Order
Conditional Estimation(FOCE)', and 'Laplacian approximation' are explained.
Additionally, provides functions for post-run processing of NONMEM output
files, generating comprehensive PDF diagnostic reports including objective
function value analysis, parameter estimates, prediction diagnostics,
residual diagnostics, empirical Bayes estimate (EBE) analysis, input data
summary, and individual pharmacokinetic parameter distributions.
Author: Kyun-Seop Bae [aut, cre]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between nmw versions 0.2.0 dated 2026-04-07 and 0.3.0 dated 2026-05-07
nmw-0.2.0/nmw/man/dot-ebe_correlation_tables.Rd |only nmw-0.2.0/nmw/man/dot-ebe_covariate_analysis.Rd |only nmw-0.2.0/nmw/man/dot-ebe_individual_ci.Rd |only nmw-0.2.0/nmw/man/dot-ebe_plot_distributions.Rd |only nmw-0.2.0/nmw/man/dot-ebe_regression_diagnostics.Rd |only nmw-0.3.0/nmw/DESCRIPTION | 6 +- nmw-0.3.0/nmw/MD5 | 48 +++++++++++--------- nmw-0.3.0/nmw/NAMESPACE | 16 ++++++ nmw-0.3.0/nmw/R/nm_helpers.R |only nmw-0.3.0/nmw/inst/NEWS.Rd | 11 ++++ nmw-0.3.0/nmw/man/CalcTaLDForReport.Rd | 18 +------ nmw-0.3.0/nmw/man/CountEXTParams.Rd | 19 +------ nmw-0.3.0/nmw/man/GetCountAllTheta.Rd | 2 nmw-0.3.0/nmw/man/GetCountEps.Rd | 2 nmw-0.3.0/nmw/man/GetCountEta.Rd | 2 nmw-0.3.0/nmw/man/GetCountOmega.Rd | 2 nmw-0.3.0/nmw/man/GetCountPara.Rd | 2 nmw-0.3.0/nmw/man/GetCountUnfixedEps.Rd | 2 nmw-0.3.0/nmw/man/MergeIDStatOFV.Rd | 15 +----- nmw-0.3.0/nmw/man/OFV_SCREEN_LAYOUT.Rd | 13 +---- nmw-0.3.0/nmw/man/PlotDistribution.Rd | 34 +++----------- nmw-0.3.0/nmw/man/ReadEXTFile.Rd | 9 --- nmw-0.3.0/nmw/man/add_crcl_cg.Rd |only nmw-0.3.0/nmw/man/build_dose_records.Rd |only nmw-0.3.0/nmw/man/build_nm_dataset.Rd |only nmw-0.3.0/nmw/man/build_obs_records.Rd |only nmw-0.3.0/nmw/man/code_race.Rd |only nmw-0.3.0/nmw/man/code_sex.Rd |only nmw-0.3.0/nmw/man/crcl_cg.Rd |only nmw-0.3.0/nmw/man/dat2_time_to_posix.Rd |only nmw-0.3.0/nmw/man/locf_value.Rd |only nmw-0.3.0/nmw/man/merge_cov_locf.Rd |only nmw-0.3.0/nmw/man/nm_to_molar.Rd |only nmw-0.3.0/nmw/man/parse_dtc.Rd |only 34 files changed, 88 insertions(+), 113 deletions(-)
Title: Tools for Managing Classes on GitHub
Description: Interface for the GitHub API that enables efficient
management of courses on GitHub. It has a functionality for
managing organizations, teams, repositories, and users on GitHub
and helps automate most of the tedious and repetitive tasks
around creating and distributing assignments.
Author: Colin Rundel [aut, cre],
Mine Cetinkaya-Rundel [aut],
Therese Anders [ctb]
Maintainer: Colin Rundel <rundel@gmail.com>
Diff between ghclass versions 0.3.1 dated 2025-05-06 and 0.4.0 dated 2026-05-07
ghclass-0.3.1/ghclass/R/util_peer.R |only ghclass-0.4.0/ghclass/DESCRIPTION | 8 ghclass-0.4.0/ghclass/MD5 | 125 ++++++++------- ghclass-0.4.0/ghclass/NAMESPACE | 30 +++ ghclass-0.4.0/ghclass/NEWS.md | 44 +++++ ghclass-0.4.0/ghclass/R/action.R | 12 + ghclass-0.4.0/ghclass/R/action_artifacts.R | 23 ++ ghclass-0.4.0/ghclass/R/action_artifacts_download.R | 165 ++++++++++++-------- ghclass-0.4.0/ghclass/R/action_run_logs.R |only ghclass-0.4.0/ghclass/R/action_runs.R | 2 ghclass-0.4.0/ghclass/R/ghclass-internal.R |only ghclass-0.4.0/ghclass/R/github_whoami.R | 4 ghclass-0.4.0/ghclass/R/issue_close.R | 54 +++++- ghclass-0.4.0/ghclass/R/org.R | 30 ++- ghclass-0.4.0/ghclass/R/org_allows_forking.R |only ghclass-0.4.0/ghclass/R/org_create_assignment.R | 34 +++- ghclass-0.4.0/ghclass/R/org_grade_assignment.R |only ghclass-0.4.0/ghclass/R/org_members.R | 2 ghclass-0.4.0/ghclass/R/org_remove.R | 2 ghclass-0.4.0/ghclass/R/org_repo_forking.R |only ghclass-0.4.0/ghclass/R/org_repo_stats.R | 9 - ghclass-0.4.0/ghclass/R/org_repos.R | 2 ghclass-0.4.0/ghclass/R/org_sitrep.R | 7 ghclass-0.4.0/ghclass/R/org_teams_v4.R | 12 - ghclass-0.4.0/ghclass/R/org_user_repos.R |only ghclass-0.4.0/ghclass/R/pages.R | 24 ++ ghclass-0.4.0/ghclass/R/pr.R | 2 ghclass-0.4.0/ghclass/R/repo.R | 27 ++- ghclass-0.4.0/ghclass/R/repo_add_file.R | 6 ghclass-0.4.0/ghclass/R/repo_allows_forking.R |only ghclass-0.4.0/ghclass/R/repo_commits.R | 24 +- ghclass-0.4.0/ghclass/R/repo_contributors.R | 41 ++++ ghclass-0.4.0/ghclass/R/repo_create.R | 4 ghclass-0.4.0/ghclass/R/repo_exists.R | 4 ghclass-0.4.0/ghclass/R/repo_get_file.R | 2 ghclass-0.4.0/ghclass/R/repo_ls.R | 2 ghclass-0.4.0/ghclass/R/repo_mirror.R | 6 ghclass-0.4.0/ghclass/R/repo_mirror_template.R | 2 ghclass-0.4.0/ghclass/R/repo_n_commits.R | 2 ghclass-0.4.0/ghclass/R/repo_put_file.R | 2 ghclass-0.4.0/ghclass/R/repo_set_forking.R |only ghclass-0.4.0/ghclass/R/repo_set_template.R | 2 ghclass-0.4.0/ghclass/R/repo_style.R | 8 ghclass-0.4.0/ghclass/R/user.R | 4 ghclass-0.4.0/ghclass/R/util_args.R | 14 + ghclass-0.4.0/ghclass/R/util_cli.R | 6 ghclass-0.4.0/ghclass/R/util_github.R | 6 ghclass-0.4.0/ghclass/R/util_repo.R | 8 ghclass-0.4.0/ghclass/R/util_safely.R | 10 + ghclass-0.4.0/ghclass/R/util_team.R | 2 ghclass-0.4.0/ghclass/README.md | 4 ghclass-0.4.0/ghclass/man/action.Rd | 66 ++++++-- ghclass-0.4.0/ghclass/man/ghclass-internal.Rd |only ghclass-0.4.0/ghclass/man/github_orgs.Rd | 2 ghclass-0.4.0/ghclass/man/github_whoami.Rd | 2 ghclass-0.4.0/ghclass/man/issue.Rd | 6 ghclass-0.4.0/ghclass/man/org_create_assignment.Rd | 11 - ghclass-0.4.0/ghclass/man/org_details.Rd | 45 ++++- ghclass-0.4.0/ghclass/man/org_grade_assignment.Rd |only ghclass-0.4.0/ghclass/man/org_members.Rd | 6 ghclass-0.4.0/ghclass/man/org_perm.Rd | 18 +- ghclass-0.4.0/ghclass/man/pages.Rd | 6 ghclass-0.4.0/ghclass/man/pr.Rd | 2 ghclass-0.4.0/ghclass/man/repo_core.Rd | 39 +++- ghclass-0.4.0/ghclass/man/repo_details.Rd | 14 + ghclass-0.4.0/ghclass/man/repo_file.Rd | 12 - ghclass-0.4.0/ghclass/man/repo_style.Rd | 8 ghclass-0.4.0/ghclass/man/repo_user.Rd | 4 ghclass-0.4.0/ghclass/man/user.Rd | 4 69 files changed, 734 insertions(+), 288 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor
Analysis-1 (Parafac) model or Parallel Factor Analysis-2 (Parafac2) model fit to
a three-way or four-way data array. See Harshman and Lundy (1994):
<doi:10.1016/0167-9473(94)90132-5>. Classification using principal component
analysis (PCA) fit to a two-way data matrix is also supported. Uses component
weights from one mode of a Parafac, Parafac2, or PCA model as features to tune
parameters for one or more classification methods via a k-fold cross-validation
procedure. Allows for constraints on different tensor modes. Allows for
inclusion of additional features alongside features generated by the component
model. Supports penalized logistic regression, support vector machine, random
forest, feed-forward neural network, regularized discriminant analysis, and
gradient boosting machine. Supports binary and multiclass classification.
Predicts class labels or class probabilities, and calculates multiple
classification performan [...truncated...]
Author: Matthew A. Asisgress [aut, cre]
Maintainer: Matthew A. Asisgress <mattgress@protonmail.ch>
Diff between cpfa versions 1.2-8 dated 2026-04-13 and 1.2-9 dated 2026-05-07
ChangeLog | 20 ++++++++++++++++++++ DESCRIPTION | 36 ++++++++++++++++++++++++++++-------- MD5 | 16 ++++++++-------- R/cpfa.R | 6 ++++-- R/cpm.all.R | 2 +- build/vignette.rds |binary inst/doc/cpfa.Rmd | 29 ++++++++++++++--------------- inst/doc/cpfa.pdf |binary vignettes/cpfa.Rmd | 29 ++++++++++++++--------------- 9 files changed, 89 insertions(+), 49 deletions(-)
Title: Group Lasso and Elastic Net Solver for Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire group lasso and group elastic net regularization path for GLMs, multinomial, the Cox model and multi-task Gaussian models. Similar to the R package 'glmnet' in scope of models, and in computational speed. This package provides R bindings to the C++ code underlying the corresponding Python package 'adelie'. These bindings offer a general purpose group elastic net solver,
a wide range of matrix classes that can exploit special structure
to allow large-scale inputs, and an assortment of
generalized linear model classes for fitting various types of data.
The package is an implementation of Yang, J. and Hastie, T. (2024) <doi:10.48550/arXiv.2405.08631>.
Author: James Yang [aut, cph],
Trevor Hastie [aut, cph, cre],
Balasubramanian Narasimhan [aut]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between adelie versions 1.0.8 dated 2025-07-01 and 1.0.9 dated 2026-05-07
DESCRIPTION | 8 MD5 | 28 NEWS.md | 12 R/solver.R | 11 R/state.R | 2 R/utilities.R | 26 R/wrappers.R | 19 build/partial.rdb |binary build/vignette.rds |binary inst/adelie/adelie/__init__.py | 2 inst/adelie/adelie/src/include/adelie_core/matrix/matrix_naive_kronecker_eye.ipp | 42 inst/adelie/adelie/src/include/adelie_core/solver/solver_base.hpp | 6 inst/adelie/adelie/src/py_decl.hpp | 3 inst/doc/adelie.html | 2169 ++++------ man/predict.grpnet.Rd | 5 15 files changed, 998 insertions(+), 1335 deletions(-)
Title: Bounding Treatment Effects by Limited Information Pooling
Description: Estimation and inference methods for bounding average treatment effects (on the treated) that are valid under an unconfoundedness assumption.
The bounds are designed to be robust in challenging situations, for example, when the conditioning variables take on a large number of different values in the observed sample, or when the overlap condition is violated.
This robustness is achieved by only using limited "pooling" of information across observations.
For more details, see the paper by Lee and Weidner, "Bounding Treatment Effects by Pooling Limited Information across Observations," forthcoming at the Journal of Econometrics, <doi:10.48550/arXiv.2111.05243>.
Author: Sokbae Lee [aut, cre],
Martin Weidner [aut]
Maintainer: Sokbae Lee <sl3841@columbia.edu>
Diff between ATbounds versions 0.1.0 dated 2021-11-24 and 0.1.1 dated 2026-05-07
DESCRIPTION | 11 +- MD5 | 34 ++++---- NEWS.md | 9 ++ R/atebounds.R | 4 - R/attbounds.R | 5 - R/simulation_dgp.R | 12 +-- R/summary.ATbounds.R | 2 README.md | 65 +++++++++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/ATbounds_vignette.R | 152 +++++----------------------------------- inst/doc/ATbounds_vignette.Rmd | 74 ++++++++++--------- inst/doc/ATbounds_vignette.pdf |binary man/atebounds.Rd | 2 man/attbounds.Rd | 2 man/simulation_dgp.Rd | 12 +-- man/summary.ATbounds.Rd | 2 vignettes/ATbounds_vignette.Rmd | 74 ++++++++++--------- 18 files changed, 204 insertions(+), 256 deletions(-)
Title: Complete Stochastic Modelling Solution
Description: Makes univariate, multivariate, or random fields simulations precise and simple. Just select the desired time series or random fields’ properties and it will do the rest. CoSMoS is based on the framework described in Papalexiou (2018, <doi:10.1016/j.advwatres.2018.02.013>), extended for random fields in Papalexiou and Serinaldi (2020, <doi:10.1029/2019WR026331>), and further advanced in Papalexiou et al. (2021, <doi:10.1029/2020WR029466>) to allow fine-scale space-time simulation of storms (or even cyclone-mimicking fields).
Author: Simon Michael Papalexiou [aut],
Francesco Serinaldi [aut],
Filip Strnad [aut],
Yannis Markonis [aut],
Kevin Shook [ctb, cre]
Maintainer: Kevin Shook <kshook@kshook.ca>
Diff between CoSMoS versions 2.1.2 dated 2026-01-27 and 2.2.0 dated 2026-05-07
CoSMoS-2.1.2/CoSMoS/R/AR1.R |only CoSMoS-2.1.2/CoSMoS/R/ARp.R |only CoSMoS-2.1.2/CoSMoS/R/actfInv.r |only CoSMoS-2.1.2/CoSMoS/R/acti.R |only CoSMoS-2.1.2/CoSMoS/R/analyzeTS.R |only CoSMoS-2.1.2/CoSMoS/R/burrIII.R |only CoSMoS-2.1.2/CoSMoS/R/burrXII.R |only CoSMoS-2.1.2/CoSMoS/R/erfc.R |only CoSMoS-2.1.2/CoSMoS/R/errors.R |only CoSMoS-2.1.2/CoSMoS/R/fitACS.R |only CoSMoS-2.1.2/CoSMoS/R/fitDist.R |only CoSMoS-2.1.2/CoSMoS/R/generateMTS.r |only CoSMoS-2.1.2/CoSMoS/R/generateMTSFast.r |only CoSMoS-2.1.2/CoSMoS/R/generateRF.r |only CoSMoS-2.1.2/CoSMoS/R/generateRFFast.r |only CoSMoS-2.1.2/CoSMoS/R/generateTS.R |only CoSMoS-2.1.2/CoSMoS/R/gev.R |only CoSMoS-2.1.2/CoSMoS/R/ggamma.R |only CoSMoS-2.1.2/CoSMoS/R/lmom.R |only CoSMoS-2.1.2/CoSMoS/R/norm.R |only CoSMoS-2.1.2/CoSMoS/R/paretoII.R |only CoSMoS-2.1.2/CoSMoS/R/plotacti.R |only CoSMoS-2.1.2/CoSMoS/R/plotcosmosts.R |only CoSMoS-2.1.2/CoSMoS/R/quickTSPlot.R |only CoSMoS-2.1.2/CoSMoS/R/seasonalACF.R |only CoSMoS-2.1.2/CoSMoS/R/seasonalAR.R |only CoSMoS-2.1.2/CoSMoS/R/stratifyData.R |only CoSMoS-2.1.2/CoSMoS/man/actfdiscreteInv.Rd |only CoSMoS-2.1.2/CoSMoS/man/error.Rd |only CoSMoS-2.2.0/CoSMoS/DESCRIPTION | 21 CoSMoS-2.2.0/CoSMoS/MD5 | 236 - CoSMoS-2.2.0/CoSMoS/NAMESPACE | 36 CoSMoS-2.2.0/CoSMoS/NEWS.md | 65 CoSMoS-2.2.0/CoSMoS/R/CoSMoS.R | 60 CoSMoS-2.2.0/CoSMoS/R/RcppExports.R |only CoSMoS-2.2.0/CoSMoS/R/acs.R | 114 CoSMoS-2.2.0/CoSMoS/R/actf.R | 313 + CoSMoS-2.2.0/CoSMoS/R/advectionF.R | 30 CoSMoS-2.2.0/CoSMoS/R/anisotropyT.R | 18 CoSMoS-2.2.0/CoSMoS/R/ar-models.R |only CoSMoS-2.2.0/CoSMoS/R/checkRF.r | 106 CoSMoS-2.2.0/CoSMoS/R/checkTS.R | 167 CoSMoS-2.2.0/CoSMoS/R/disch.R | 2 CoSMoS-2.2.0/CoSMoS/R/distributions.R |only CoSMoS-2.2.0/CoSMoS/R/ecdf.R | 33 CoSMoS-2.2.0/CoSMoS/R/fitVAR.r | 43 CoSMoS-2.2.0/CoSMoS/R/fitting.R |only CoSMoS-2.2.0/CoSMoS/R/generate-fields.R |only CoSMoS-2.2.0/CoSMoS/R/generate-ts.R |only CoSMoS-2.2.0/CoSMoS/R/getArg.R | 88 CoSMoS-2.2.0/CoSMoS/R/moments.R | 329 - CoSMoS-2.2.0/CoSMoS/R/plot-methods.R |only CoSMoS-2.2.0/CoSMoS/R/population.R | 124 CoSMoS-2.2.0/CoSMoS/R/seasonal.R |only CoSMoS-2.2.0/CoSMoS/R/stcs.r | 8 CoSMoS-2.2.0/CoSMoS/R/utils-internal.R |only CoSMoS-2.2.0/CoSMoS/README.md | 1 CoSMoS-2.2.0/CoSMoS/inst/CITATION | 4 CoSMoS-2.2.0/CoSMoS/inst/doc/vignette.R | 352 + CoSMoS-2.2.0/CoSMoS/inst/doc/vignette.Rmd | 427 +- CoSMoS-2.2.0/CoSMoS/inst/doc/vignette.html | 2513 +++++++++---- CoSMoS-2.2.0/CoSMoS/man/ACSfunctions.Rd | 33 CoSMoS-2.2.0/CoSMoS/man/AR1.Rd | 45 CoSMoS-2.2.0/CoSMoS/man/ARp.Rd | 90 CoSMoS-2.2.0/CoSMoS/man/BurrIII.Rd | 43 CoSMoS-2.2.0/CoSMoS/man/BurrXII.Rd | 44 CoSMoS-2.2.0/CoSMoS/man/CoSMoS-package.Rd | 57 CoSMoS-2.2.0/CoSMoS/man/DHMgenSim.Rd |only CoSMoS-2.2.0/CoSMoS/man/DHMgenSj.Rd |only CoSMoS-2.2.0/CoSMoS/man/ECDF.Rd | 25 CoSMoS-2.2.0/CoSMoS/man/GEV.Rd | 39 CoSMoS-2.2.0/CoSMoS/man/GGamma.Rd | 45 CoSMoS-2.2.0/CoSMoS/man/MSE.Rd |only CoSMoS-2.2.0/CoSMoS/man/N.Rd | 28 CoSMoS-2.2.0/CoSMoS/man/ParetoII.Rd | 40 CoSMoS-2.2.0/CoSMoS/man/PopulationStat.Rd | 32 CoSMoS-2.2.0/CoSMoS/man/YW.Rd | 18 CoSMoS-2.2.0/CoSMoS/man/acs.Rd | 50 CoSMoS-2.2.0/CoSMoS/man/actf.Rd | 13 CoSMoS-2.2.0/CoSMoS/man/actfInv.Rd | 19 CoSMoS-2.2.0/CoSMoS/man/actfdiscrete.Rd | 13 CoSMoS-2.2.0/CoSMoS/man/acti.Rd | 23 CoSMoS-2.2.0/CoSMoS/man/actpnts.Rd | 60 CoSMoS-2.2.0/CoSMoS/man/actpntsB6.Rd |only CoSMoS-2.2.0/CoSMoS/man/actpnts_cpp.Rd |only CoSMoS-2.2.0/CoSMoS/man/advectionF.Rd | 2 CoSMoS-2.2.0/CoSMoS/man/advectionFhyperbolic.Rd | 1 CoSMoS-2.2.0/CoSMoS/man/advectionFradial.Rd | 1 CoSMoS-2.2.0/CoSMoS/man/advectionFrotation.Rd | 1 CoSMoS-2.2.0/CoSMoS/man/advectionFspiral.Rd | 1 CoSMoS-2.2.0/CoSMoS/man/advectionFspiralCE.Rd | 3 CoSMoS-2.2.0/CoSMoS/man/analyzeTS.Rd | 127 CoSMoS-2.2.0/CoSMoS/man/anisotropyT.Rd | 6 CoSMoS-2.2.0/CoSMoS/man/anisotropyTswirl.Rd | 1 CoSMoS-2.2.0/CoSMoS/man/checkRF.Rd | 10 CoSMoS-2.2.0/CoSMoS/man/checkTS.Rd | 27 CoSMoS-2.2.0/CoSMoS/man/disch.Rd | 2 CoSMoS-2.2.0/CoSMoS/man/erfc.Rd | 17 CoSMoS-2.2.0/CoSMoS/man/fitACS.Rd | 43 CoSMoS-2.2.0/CoSMoS/man/fitDist.Rd | 30 CoSMoS-2.2.0/CoSMoS/man/fitVAR.Rd | 23 CoSMoS-2.2.0/CoSMoS/man/fitactf.Rd | 32 CoSMoS-2.2.0/CoSMoS/man/generateMTS.Rd | 46 CoSMoS-2.2.0/CoSMoS/man/generateMTSFast.Rd | 76 CoSMoS-2.2.0/CoSMoS/man/generateRF.Rd | 55 CoSMoS-2.2.0/CoSMoS/man/generateRFFast.Rd | 71 CoSMoS-2.2.0/CoSMoS/man/generateTS.Rd | 138 CoSMoS-2.2.0/CoSMoS/man/getACSArg.Rd | 16 CoSMoS-2.2.0/CoSMoS/man/getDistArg.Rd | 17 CoSMoS-2.2.0/CoSMoS/man/lmom.Rd | 19 CoSMoS-2.2.0/CoSMoS/man/moments.Rd | 48 CoSMoS-2.2.0/CoSMoS/man/optimACS.Rd |only CoSMoS-2.2.0/CoSMoS/man/plot.acti.Rd | 32 CoSMoS-2.2.0/CoSMoS/man/plot.checkTS.Rd | 23 CoSMoS-2.2.0/CoSMoS/man/plot.cosmosts.Rd | 37 CoSMoS-2.2.0/CoSMoS/man/plot.fitACS.Rd | 24 CoSMoS-2.2.0/CoSMoS/man/plot.fitDist.Rd | 21 CoSMoS-2.2.0/CoSMoS/man/quickTSPlot.Rd | 22 CoSMoS-2.2.0/CoSMoS/man/rMSE.Rd |only CoSMoS-2.2.0/CoSMoS/man/regenerateTS.Rd | 34 CoSMoS-2.2.0/CoSMoS/man/sample.moments.Rd | 38 CoSMoS-2.2.0/CoSMoS/man/seasonalACF.Rd | 29 CoSMoS-2.2.0/CoSMoS/man/seasonalAR.Rd | 30 CoSMoS-2.2.0/CoSMoS/man/stcfclayton.Rd | 4 CoSMoS-2.2.0/CoSMoS/man/stcfgneiting14.Rd | 130 CoSMoS-2.2.0/CoSMoS/man/stcfgneiting16.Rd | 128 CoSMoS-2.2.0/CoSMoS/man/stcs.Rd | 4 CoSMoS-2.2.0/CoSMoS/man/stcs2.Rd | 60 CoSMoS-2.2.0/CoSMoS/man/stratifySeasonData.Rd | 24 CoSMoS-2.2.0/CoSMoS/src |only CoSMoS-2.2.0/CoSMoS/tests/testthat/test_acs.R | 19 CoSMoS-2.2.0/CoSMoS/tests/testthat/test_acti.R | 42 CoSMoS-2.2.0/CoSMoS/tests/testthat/test_distribution_fit.R | 28 CoSMoS-2.2.0/CoSMoS/tests/testthat/test_distributions.R | 108 CoSMoS-2.2.0/CoSMoS/tests/testthat/test_get_args.R | 15 CoSMoS-2.2.0/CoSMoS/tests/testthat/test_l_moments.R | 25 CoSMoS-2.2.0/CoSMoS/tests/testthat/test_moments.R | 66 CoSMoS-2.2.0/CoSMoS/tests/testthat/test_ts_gen.R | 7 CoSMoS-2.2.0/CoSMoS/vignettes/figures |only CoSMoS-2.2.0/CoSMoS/vignettes/vignette.Rmd | 427 +- 140 files changed, 5076 insertions(+), 2921 deletions(-)
Title: The Structural Similarity Index Measure for Maps
Description: Extends the classical SSIM method proposed by 'Wang', 'Bovik', 'Sheikh', and 'Simoncelli'(2004) <doi:10.1109/TIP.2003.819861>.
for irregular lattice-based maps and raster images.
The geographical SSIM method incorporates well-developed 'geographically weighted summary statistics'('Brunsdon', 'Fotheringham' and 'Charlton' 2002) <doi:10.1016/S0198-9715(01)00009-6>
with an adaptive bandwidth kernel function for irregular lattice-based maps.
Author: Hui Jeong Ha [aut, cre] ,
Jed Long [aut]
Maintainer: Hui Jeong (Hailyee) Ha <hha24@uwo.ca>
Diff between SSIMmap versions 0.1.1 dated 2023-09-26 and 0.4.0 dated 2026-05-07
SSIMmap-0.1.1/SSIMmap/R/Toronto.R |only SSIMmap-0.1.1/SSIMmap/R/global.R |only SSIMmap-0.1.1/SSIMmap/R/gw_dist.R |only SSIMmap-0.1.1/SSIMmap/R/gw_weight_ad.R |only SSIMmap-0.1.1/SSIMmap/R/gwss_new.R |only SSIMmap-0.1.1/SSIMmap/R/ssim_constant.R |only SSIMmap-0.1.1/SSIMmap/data/Toronto.rda |only SSIMmap-0.1.1/SSIMmap/inst/ex |only SSIMmap-0.1.1/SSIMmap/man/Toronto.Rd |only SSIMmap-0.1.1/SSIMmap/man/ssim_constant.Rd |only SSIMmap-0.4.0/SSIMmap/DESCRIPTION | 19 SSIMmap-0.4.0/SSIMmap/MD5 | 47 SSIMmap-0.4.0/SSIMmap/NAMESPACE | 19 SSIMmap-0.4.0/SSIMmap/NEWS.md |only SSIMmap-0.4.0/SSIMmap/R/data.R |only SSIMmap-0.4.0/SSIMmap/R/ssim_bandwidth.R | 390 +++--- SSIMmap-0.4.0/SSIMmap/R/ssim_polygon.R | 492 ++++--- SSIMmap-0.4.0/SSIMmap/R/ssim_raster.R | 542 +++++++- SSIMmap-0.4.0/SSIMmap/build/vignette.rds |binary SSIMmap-0.4.0/SSIMmap/data/Toronto_SSIM.rda |only SSIMmap-0.4.0/SSIMmap/data/fwi_0816_bc.rda |only SSIMmap-0.4.0/SSIMmap/data/fwi_0818_bc.rda |only SSIMmap-0.4.0/SSIMmap/data/fwi_1101_bc.rda |only SSIMmap-0.4.0/SSIMmap/inst/doc/Introduction_to_SSIMmap.R | 272 +++- SSIMmap-0.4.0/SSIMmap/inst/doc/Introduction_to_SSIMmap.Rmd | 401 +++++- SSIMmap-0.4.0/SSIMmap/inst/doc/Introduction_to_SSIMmap.html | 763 ++++++++---- SSIMmap-0.4.0/SSIMmap/man/Toronto_SSIM.Rd |only SSIMmap-0.4.0/SSIMmap/man/fwi_0816_bc.Rd |only SSIMmap-0.4.0/SSIMmap/man/fwi_0818_bc.Rd |only SSIMmap-0.4.0/SSIMmap/man/fwi_1101_bc.Rd |only SSIMmap-0.4.0/SSIMmap/man/ssim_bandwidth.Rd | 80 - SSIMmap-0.4.0/SSIMmap/man/ssim_polygon.Rd | 106 + SSIMmap-0.4.0/SSIMmap/man/ssim_raster.Rd | 130 +- SSIMmap-0.4.0/SSIMmap/vignettes/Introduction_to_SSIMmap.Rmd | 401 +++++- 34 files changed, 2692 insertions(+), 970 deletions(-)
Title: 'DuckDB' High Throughput Sequencing File Formats Reader
Extension
Description: Bundles the 'duckhts' 'DuckDB' extension for reading High Throughput
Sequencing file formats with 'DuckDB'. The 'DuckDB' C extension API
<https://duckdb.org/docs/stable/clients/c/api> and its 'htslib' dependency are
compiled from vendored sources during package installation. James K Bonfield and co-authors (2021) <doi:10.1093/gigascience/giab007>.
Author: Sounkou Mahamane Toure [aut, cre],
James K Bonfield, John Marshall,Petr Danecek ,Heng Li , Valeriu Ohan,
Andrew Whitwham,Thomas Keane , Robert M Davies [ctb] ,
Brent Pedersen [cph] ,
Giulio Genovese [cph] ,
DuckDB C Extension API Authors [ctb]
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>
Diff between Rduckhts versions 1.1.6-0.0.2 dated 2026-04-09 and 1.2.1-0.1.0 dated 2026-05-07
Rduckhts-1.1.6-0.0.2/Rduckhts/README.md |only Rduckhts-1.2.1-0.1.0/Rduckhts/DESCRIPTION | 10 Rduckhts-1.2.1-0.1.0/Rduckhts/MD5 | 196 +- Rduckhts-1.2.1-0.1.0/Rduckhts/NAMESPACE | 12 Rduckhts-1.2.1-0.1.0/Rduckhts/NEWS.md | 59 Rduckhts-1.2.1-0.1.0/Rduckhts/R/bootstrap.R | 29 Rduckhts-1.2.1-0.1.0/Rduckhts/R/duckhts.R | 792 ++++++++ Rduckhts-1.2.1-0.1.0/Rduckhts/configure | 172 + Rduckhts-1.2.1-0.1.0/Rduckhts/configure.win | 83 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/COPYRIGHT | 6 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/bam_bed_coverage.c |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/bam_bin_counts.c |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/bam_reader.c | 134 + Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/bcf_reader.c | 88 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/cgranges.c |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/cgranges_api.c |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/duckhts.c | 35 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/Makefile | 6 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/NEWS | 48 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/VERSION | 2 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/annot-tsv.1 | 2 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/bgzf.c | 15 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/bgzip.1 | 2 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/configure | 18 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/cram/cram_codecs.c | 101 - Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/cram/cram_decode.c | 141 + Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/cram/cram_encode.c | 32 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/cram/cram_io.c | 8 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/hfile_s3.c | 135 - Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htscodecs/NEWS.md | 14 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htscodecs/htscodecs/arith_dynamic.c | 1 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htscodecs/htscodecs/htscodecs.h | 2 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static32x16pr.c | 44 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c | 101 - Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c | 54 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c | 90 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c | 83 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_static4x16pr.c | 21 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htscodecs/htscodecs/rANS_word.h | 6 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htscodecs/htscodecs/version.h | 2 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htsfile.1 | 2 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htslib-s3-plugin.7 | 2 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htslib/hts.h | 2 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/htslib/kstring.h | 6 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/kstring.c | 137 + Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/ref_cache/ref-cache.1 | 2 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/sam.c | 7 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/tabix.1 | 2 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/htslib/version.sh | 2 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/include/cgranges.h |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/include/khash.h |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/include/wasm_http_hfile.h |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/include/wasm_socket_compat.h |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/interval_udf.c | 74 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/mosdepth_table.c |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/samtools_idxstats_table.c |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/score_udf.c | 934 +++++++--- Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/seq_reader.c | 333 +++ Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/tabix_reader.c | 802 ++++++++ Rduckhts-1.2.1-0.1.0/Rduckhts/inst/duckhts_extension/wasm_http_hfile.c |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/bad.bed |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/big.bam |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/big.bam.csi |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/empty-tids.bam |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/empty-tids.bam.bai |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/empty-tids.bed |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/fixture_mixed.bam |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/fixture_mixed.bam.bai |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/fixture_mixed.cram |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/fixture_mixed.cram.crai |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/fixture_mixed_min_depth_regions.bed |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/fixture_mixed_regions.bed |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/fixture_paired.bam |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/fixture_paired.bam.bai |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/fixture_ref.fa |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/fixture_ref.fa.fai |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/fixture_single.bam |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/fixture_single.bam.bai |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/fixture_unmapped.sam |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/full-fragment-pairs.bam |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/full-fragment-pairs.bam.bai |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/gff_attrs.gff3 |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/gff_strict_extra_field.gff3 |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/gff_strict_invalid.gff3 |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/gff_strict_invalid_attr.gff3 |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/gff_strict_invalid_end.gff3 |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/gff_strict_valid.gff3 |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/gtf_attrs.gtf |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/missing.bed |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/nanopore.bam |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/nanopore.bam.bai |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/nuc_with_n.bed |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/nuc_with_n.fa |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/overlapping-pairs.bam |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/overlapping-pairs.bam.bai |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/ovl.bam |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/ovl.bam.bai |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/score_summaries.list |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/score_summary_CNT.tsv |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/score_summary_dir |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/track.bed |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/extdata/unordered.bed |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/function_catalog/functions.md | 34 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/function_catalog/functions.tsv | 24 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/function_catalog/functions.yaml | 213 ++ Rduckhts-1.2.1-0.1.0/Rduckhts/inst/htslib_config.R.in |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/tinytest/test_bam_bed_coverage.R |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/tinytest/test_basic.R | 101 + Rduckhts-1.2.1-0.1.0/Rduckhts/inst/tinytest/test_bin_counts.R |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/tinytest/test_cgranges_api.R |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/tinytest/test_integration.R | 108 + Rduckhts-1.2.1-0.1.0/Rduckhts/inst/tinytest/test_intervals.R | 33 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/tinytest/test_mosdepth.R |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/tinytest/test_multi.R |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/tinytest/test_samtools_idxstats.R |only Rduckhts-1.2.1-0.1.0/Rduckhts/inst/tinytest/test_score.R | 53 Rduckhts-1.2.1-0.1.0/Rduckhts/inst/tinytest/test_seq_ops.R | 32 Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_bam.Rd | 5 Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_bam_bed_coverage.Rd |only Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_bam_bin_counts.Rd |only Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_bam_multi.Rd |only Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_bcf_multi.Rd |only Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_bed_multi.Rd |only Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_fasta_multi.Rd |only Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_fastq_multi.Rd |only Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_gff.Rd | 11 Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_gff_multi.Rd |only Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_gtf.Rd | 8 Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_gtf_multi.Rd |only Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_mosdepth.Rd |only Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_samtools_idxstats.Rd |only Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_score.Rd | 16 Rduckhts-1.2.1-0.1.0/Rduckhts/man/rduckhts_tabix_multi.Rd |only 133 files changed, 4626 insertions(+), 861 deletions(-)
Title: Conjuntos de Datos para 'Graficas Versatiles con ggplot2'
Description: Una coleccion de conjuntos de datos para el libro
"Graficas versatiles con ggplot: Analisis visuales de datos",
por Raymond L. Tremblay y Julian Hernandez-Serrano. Incluye datos
de ecologia, salud publica, educacion, economia y biodiversidad
para la ensenanza de visualizacion de datos con 'ggplot2'.
Author: Raymond L. Tremblay [aut, cre] ,
Julian Hernandez-Serrano [aut]
Maintainer: Raymond L. Tremblay <raymondtremblay1@mac.com>
Diff between ggversa versions 0.0.1 dated 2017-08-05 and 0.1.1 dated 2026-05-07
DESCRIPTION | 36 +++++++--- MD5 | 105 ++++++++++++++++--------------- NAMESPACE | 2 NEWS.md |only R/ASBESTOS_QUEBEC.R | 38 +++++++---- R/Anolis.R | 83 ++++++++++++------------- R/Camas_Hospital.R | 38 +++++++---- R/Crecimiento_domestico_bruto.R | 52 ++++++++++----- R/CypripediumA.R | 56 ++++++++-------- R/Edu_Salud_Gastos_GDP.R | 38 +++++++---- R/Educacion_Ninas.R | 53 +++++++++------- R/ElphicBirdData.R | 122 +++++++++++++++++++++++++++++-------- R/Godwits.R | 78 +++++++++++------------ R/Internet2.R | 43 ++++++++----- R/LIKERT_DATA.R | 35 ++++++---- R/Lelto.R | 73 +++++++++++----------- R/Morelia_Mich_Tmin.R | 29 ++++---- R/PBI.R | 40 +++++++----- R/PIB_vs_Alfabetismo.R | 23 ++++-- R/PIBvsSalud.R | 28 ++++---- R/PartosInfantes.R | 30 ++++++--- R/Pop_PR.R | 25 ++++--- R/Razon_mortandad.R | 36 ++++++---- R/SparrowsElphick.R | 37 ++++++++++- R/VegSampleV1.R | 56 ++++++++++------ R/caladeniavalida.R | 89 ++++++++++++-------------- R/dipodium.R | 77 ++++++++++------------- R/ggversa-package.R |only R/tiroide.R | 35 +++++----- README.md |only build |only man/ASBESTOS_QUEBEC.Rd | 35 +++++++--- man/Anolis.Rd | 84 ++++++++++++------------- man/Camas_Hospital.Rd | 33 +++++++--- man/Crecimiento_domestico_bruto.Rd | 50 +++++++++++---- man/CypripediumA.Rd | 55 ++++++++-------- man/Edu_Salud_Gastos_GDP.Rd | 34 +++++++--- man/Educacion_Ninas.Rd | 49 +++++++++----- man/ElphickBirdData.Rd | 117 +++++++++++++++++++++++++++++------ man/Godwits.Rd | 73 +++++++++++----------- man/Internet2.Rd | 41 ++++++++---- man/LIKERT_DATA.Rd | 32 ++++++--- man/Lelto.Rd | 73 +++++++++++----------- man/MORELIA.MICH.Tmin.Rd | 31 +++++---- man/PBI.Rd | 43 ++++++++----- man/PIB_vs_Alfabetismo.Rd | 23 ++++-- man/PIB_vs_Salud.Rd | 30 +++++---- man/PartosInfantes.Rd | 30 ++++++--- man/Pop_PR.Rd | 23 ++++-- man/Razon_mortandad.Rd | 36 +++++++--- man/SparrowsElphick.Rd | 38 ++++++++++- man/Tiroide.Rd | 37 +++++------ man/VegSamplesV1.Rd | 57 +++++++++++------ man/caladeniavalida.Rd | 77 +++++++++++------------ man/dipodium.Rd | 74 ++++++++++------------ man/ggversa-package.Rd |only 56 files changed, 1556 insertions(+), 976 deletions(-)
Title: Variable Neighborhood Trust Region Search
Description: Implements the variable neighborhood trust region search (VNTRS)
algorithm for nonlinear global optimization, following Bierlaire et al.
(2009) "A Heuristic for Nonlinear Global Optimization"
<doi:10.1287/ijoc.1090.0343>. The method combines neighborhood
exploration with a trust-region framework to search the solution space
efficiently. It can terminate a local search early when the iterates
converge toward a previously visited local optimum or when further
improvement within the current region is unlikely. The algorithm can also
be used to identify multiple local optima.
Author: Lennart Oelschlaeger [aut, cre]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between vntrs versions 0.2.0 dated 2025-10-25 and 0.2.1 dated 2026-05-07
DESCRIPTION | 27 - MD5 | 20 - NEWS.md | 11 R/vntrs-package.R | 1 R/vntrs.R | 474 ++++++++++++++++----------------- README.md | 34 +- build/partial.rdb |binary man/vntrs-package.Rd | 7 man/vntrs.Rd | 50 +-- src/vntrs.cpp | 10 tests/testthat/test-vntrs.R | 625 +++++++++++++++++++++++++++++--------------- 11 files changed, 729 insertions(+), 530 deletions(-)
Title: Markdown Parser Implemented using the 'MD4C' Library
Description: Provides an R wrapper for the 'MD4C' (Markdown for 'C')
library. Functions exist for parsing markdown ('CommonMark'
compliant) along with support for other common markdown extensions
(e.g. 'GitHub' flavored markdown, 'LaTeX' equation support, etc.). The
package also provides a number of higher level functions for exploring
and manipulating markdown abstract syntax trees as well as translating
and displaying the documents.
Author: Colin Rundel [aut, cre],
Martin Mitas [cph] ,
RStudio, PBC [cph] ,
John MacFarlane [cph]
Maintainer: Colin Rundel <rundel@gmail.com>
Diff between md4r versions 0.5.2.0 dated 2024-02-05 and 0.5.3.0 dated 2026-05-07
DESCRIPTION | 65 MD5 | 53 NAMESPACE | 39 NEWS.md | 30 R/create_block.R |only R/create_span.R |only R/create_text.R |only R/flags.R | 2 R/md_util.R | 2 R/modify_node.R |only R/parse_md.R | 17 R/to_html.R | 5 R/to_md.R | 142 README.md | 33 inst/specs/md4c/regressions.txt | 115 inst/specs/md4c/spec-permissive-autolinks.txt | 24 man/md_block.Rd |only man/md_node_modify.Rd |only man/md_span.Rd |only man/md_text.Rd |only src/markdownparser.cpp | 13 src/md4c.c | 376 tests/testthat/helper-tests.R |only tests/testthat/setup.R | 205 tests/testthat/test-ast-util.R |only tests/testthat/test-create-block.R |only tests/testthat/test-create-span.R |only tests/testthat/test-create-text.R |only tests/testthat/test-input-validation.R |only tests/testthat/test-md-util.R |only tests/testthat/test-modify-node.R |only tests/testthat/test-to_html-gfm.R |10337 +++++++++++++++++++++ tests/testthat/test-to_html-md4c.R |12508 +++++++++++++++++++++++++- tests/testthat/test-to_md-gfm.R | 7318 +++++++++++++++ tests/testthat/test-to_md-md4c.R | 8224 ++++++++++++++++- tests/testthat/test-to_md.R |only 36 files changed, 38721 insertions(+), 787 deletions(-)
Title: J&J Innovative Medicine SDTM Test Data
Description: A set of Study Data Tabulation Model (SDTM) datasets constructed by
modifying the 'pharmaversesdtm' package to meet J&J Innovative Medicine's
standard data structure for Clinical and Statistical Programming.
Author: David Munoz Tord [aut, cre],
Nicholas Masel [aut],
Joe Kovach [aut],
Renfei Mao [ctb],
J&J Innovative Medicine [cph, fnd]
Maintainer: David Munoz Tord <david.munoztord@mailbox.org>
Diff between pharmaversesdtmjnj versions 0.0.1 dated 2025-07-07 and 0.0.4 dated 2026-05-07
DESCRIPTION | 12 ++++++---- MD5 | 44 ++++++++++++++++++++++++++------------ NAMESPACE | 1 NEWS.md | 27 ++++++++++++++++++++--- R/ae.R |only R/ds.R | 5 ++-- R/dv.R |only R/ho.R |only R/ie.R |only R/mh.R | 9 +++++-- R/pharmaversesdtmjnj-package.R | 1 R/suppho.R |only R/ts.R |only README.md | 10 +++++--- data/ae.rda |only data/ds.rda |binary data/dv.rda |only data/ho.rda |only data/ie.rda |only data/mh.rda |binary data/suppho.rda |only data/ts.rda |only inst/WORDLIST | 27 ++++++++++++++++++----- man/ae.Rd |only man/ds.Rd | 4 +-- man/dv.Rd |only man/ho.Rd |only man/ie.Rd |only man/mh.Rd | 8 ++++-- man/pharmaversesdtmjnj-package.Rd | 1 man/suppho.Rd |only man/ts.Rd |only 32 files changed, 108 insertions(+), 41 deletions(-)
More information about pharmaversesdtmjnj at CRAN
Permanent link
Title: J&J Innovative Medicine ADaM Test Data
Description: A set of Analysis Data Model (ADaM) datasets constructed by
modifying the ADaM datasets in the 'pharmaverseadam' package to meet J&J Innovative Medicine's
standard data structure for Clinical and Statistical Programming.
Author: David Munoz Tord [aut, cre],
Nicholas Masel [aut],
Joe Kovach [aut],
Mahesh Divakaran [ctb],
J&J Innovative Medicine [cph, fnd]
Maintainer: David Munoz Tord <david.munoztord@mailbox.org>
Diff between pharmaverseadamjnj versions 0.0.2 dated 2025-12-10 and 0.0.4 dated 2026-05-07
DESCRIPTION | 9 +- MD5 | 81 ++++++++++++----------- NEWS.md | 76 ++++++++++++++++++--- R/adae.R | 74 ++++++++++----------- R/adaeocmq.R | 74 ++++++++++----------- R/adagocmq.R | 2 R/adcm.R | 48 ++++++------- R/addili.R |only R/adeg.R | 69 +++++++++---------- R/adex.R | 138 ++++++++++++++++++++------------------- R/adexsum.R | 2 R/adlb.R | 182 +++++++++++++++++++++++++--------------------------- R/adpc.R | 187 ++++++++++++++++++++++++++--------------------------- R/adsl.R | 70 +++++++++++--------- R/adttesaf.R | 2 R/advs.R | 74 ++++++++++++--------- data/adae.rda |binary data/adaeocmq.rda |binary data/adagocmq.rda |binary data/adcm.rda |binary data/addili.rda |only data/adeg.rda |binary data/adex.rda |binary data/adexsum.rda |binary data/adlb.rda |binary data/adpc.rda |binary data/adsl.rda |binary data/adttesaf.rda |binary data/advs.rda |binary inst/WORDLIST | 147 ++++++++++++++++++++++-------------------- man/adae.Rd | 76 +++++++++++---------- man/adaeocmq.Rd | 76 +++++++++++---------- man/adagocmq.Rd | 4 - man/adcm.Rd | 50 +++++++------- man/addili.Rd |only man/adeg.Rd | 71 ++++++++++---------- man/adex.Rd | 140 ++++++++++++++++++++-------------------- man/adexsum.Rd | 4 - man/adlb.Rd | 184 ++++++++++++++++++++++++++-------------------------- man/adpc.Rd | 189 +++++++++++++++++++++++++++--------------------------- man/adsl.Rd | 72 +++++++++++--------- man/adttesaf.Rd | 4 - man/advs.Rd | 76 ++++++++++++--------- 43 files changed, 1145 insertions(+), 1036 deletions(-)
More information about pharmaverseadamjnj at CRAN
Permanent link
Title: Interface for Masked Autoregressive Flows
Description: Interfaces the 'python' library 'zuko' implementing Masked Autoregressive Flows. See Rozet, Divo and Schnake (2023) <doi:10.5281/zenodo.7625672> and Papamakarios, Pavlakou and Murray (2017) <doi:10.48550/arXiv.1705.07057>.
Author: Jean-Michel Marin [aut, cph],
Francois Rousset [aut, cre, cph]
Maintainer: Francois Rousset <francois.rousset@umontpellier.fr>
Diff between mafR versions 1.1.6 dated 2024-09-26 and 1.1.14 dated 2026-05-07
mafR-1.1.14/mafR/DESCRIPTION | 19 ++++--- mafR-1.1.14/mafR/MD5 | 21 +++++--- mafR-1.1.14/mafR/R/init_py_env.R |only mafR-1.1.14/mafR/R/reticulate_install_1.40.0.R |only mafR-1.1.14/mafR/R/utilities.R | 20 +++++--- mafR-1.1.14/mafR/inst/NEWS.Rd | 7 ++ mafR-1.1.14/mafR/inst/python/GMM.py |only mafR-1.1.14/mafR/inst/python/MAF.py | 60 +++++++++++++++---------- mafR-1.1.14/mafR/man/control_py_env.Rd | 8 ++- mafR-1.1.14/mafR/man/init_py_env.Rd |only mafR-1.1.14/mafR/man/mafR.Rd | 4 - mafR-1.1.14/mafR/man/r_to_torch.Rd | 3 - mafR-1.1.14/mafR/man/utilities.Rd | 26 +++++++--- mafR-1.1.6/mafR/R/install_py_stuff.R |only 14 files changed, 107 insertions(+), 61 deletions(-)
More information about datazoom.social at CRAN
Permanent link
Title: Causal Effect Random Forest of Interaction Trees
Description: Fits a Causal Effect Random Forest of Interaction Trees (CERFIT) which is a modification of the Random Forest algorithm where each split is chosen to maximize subgroup treatment heterogeneity. Doing this allows it to estimate the individualized treatment effect for each observation in either randomized controlled trial (RCT) or observational data. For more information see L. Li, R. A. Levine, and J. Fan (2022) <doi:10.1002/sta4.457>.
Author: Justin Thorp [aut, cre],
Joshua Moffat [aut],
Luo Li [aut],
Juanjuan Fan [aut]
Maintainer: Justin Thorp <jjtthorp@gmail.com>
Diff between CERFIT versions 0.1.1 dated 2025-09-26 and 0.2.0 dated 2026-05-07
DESCRIPTION | 15 +- MD5 | 24 ++-- R/CERFIT.R | 287 +++++++++++++++++++++++++++++++++++++------------- R/data.R | 6 - R/minDepth.R | 6 - R/partition.R | 160 +++++++++++++++++++-------- R/predict.R | 72 +++++++++--- R/predictTree.R | 62 ++++++++++ man/CERFIT.Rd | 103 ++++++++++------- man/MinDepth.Rd | 6 - man/educational.Rd | 2 man/predict.CERFIT.Rd | 20 +-- man/warts.Rd | 4 13 files changed, 542 insertions(+), 225 deletions(-)
Title: Miscellaneous Functions from M. Kohl
Description: Contains several functions for statistical data analysis; e.g. for sample size and power calculations, computation of confidence intervals and tests, and generation of similarity matrices.
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKmisc versions 1.9 dated 2022-11-19 and 2.0 dated 2026-05-07
DESCRIPTION | 13 MD5 | 16 NAMESPACE | 2 NEWS | 7 R/mod.oneway.test.R | 39 - build/vignette.rds |binary inst/doc/MKmisc.R | 14 inst/doc/MKmisc.html | 1775 ++++++++++++++++++++++++++----------------------- man/mod.oneway.test.Rd | 19 9 files changed, 1039 insertions(+), 846 deletions(-)
Title: Automated Multicollinearity Management
Description: Provides a comprehensive and automated workflow for managing multicollinearity in data frames with numeric and/or categorical variables. The package integrates five robust methods into a single function: (1) target encoding of categorical variables based on response values (Micci-Barreca, 2001 (Micci-Barreca, D. 2001 <doi:10.1145/507533.507538>); (2) automated feature prioritization to preserve key predictors during filtering; (3 and 4) pairwise correlation and VIF filtering across all variable types (numeric–numeric, numeric–categorical, and categorical–categorical); (5) adaptive correlation and VIF thresholds. Together, these methods enable a reliable multicollinearity management in most use cases while maintaining model integrity. The package also supports parallel processing and progress tracking via the packages 'future' and 'progressr', and provides seamless integration with the 'tidymodels' ecosystem through a dedicated recipe step.
Author: Blas M. Benito [aut, cre, cph]
Maintainer: Blas M. Benito <blasbenito@gmail.com>
Diff between collinear versions 3.0.0 dated 2025-12-08 and 3.0.1 dated 2026-05-07
collinear-3.0.0/collinear/data/vi.rda |only collinear-3.0.0/collinear/data/vi_predictors.rda |only collinear-3.0.0/collinear/data/vi_predictors_categorical.rda |only collinear-3.0.0/collinear/data/vi_predictors_numeric.rda |only collinear-3.0.0/collinear/data/vi_responses.rda |only collinear-3.0.0/collinear/data/vi_smol.rda |only collinear-3.0.0/collinear/man/figures |only collinear-3.0.0/collinear/man/vi.Rd |only collinear-3.0.0/collinear/man/vi_predictors.Rd |only collinear-3.0.0/collinear/man/vi_predictors_categorical.Rd |only collinear-3.0.0/collinear/man/vi_predictors_numeric.Rd |only collinear-3.0.0/collinear/man/vi_responses.Rd |only collinear-3.0.0/collinear/man/vi_smol.Rd |only collinear-3.0.1/collinear/DESCRIPTION | 11 collinear-3.0.1/collinear/MD5 | 345 ++++------ collinear-3.0.1/collinear/NEWS.md | 20 collinear-3.0.1/collinear/R/collinear.R | 7 collinear-3.0.1/collinear/R/collinear_select.R | 2 collinear-3.0.1/collinear/R/collinear_stats.R | 10 collinear-3.0.1/collinear/R/cor_clusters.R | 2 collinear-3.0.1/collinear/R/cor_df.R | 4 collinear-3.0.1/collinear/R/cor_matrix.R | 4 collinear-3.0.1/collinear/R/cor_select.R | 2 collinear-3.0.1/collinear/R/cor_stats.R | 10 collinear-3.0.1/collinear/R/data.R | 72 -- collinear-3.0.1/collinear/R/drop_geometry_column.R | 2 collinear-3.0.1/collinear/R/f_auto.R | 15 collinear-3.0.1/collinear/R/f_binomial_gam.R | 12 collinear-3.0.1/collinear/R/f_binomial_glm.R | 12 collinear-3.0.1/collinear/R/f_binomial_rf.R | 12 collinear-3.0.1/collinear/R/f_categorical_rf.R | 6 collinear-3.0.1/collinear/R/f_count_gam.R | 6 collinear-3.0.1/collinear/R/f_count_glm.R | 6 collinear-3.0.1/collinear/R/f_count_rf.R | 6 collinear-3.0.1/collinear/R/f_numeric_gam.R | 6 collinear-3.0.1/collinear/R/f_numeric_glm.R | 6 collinear-3.0.1/collinear/R/f_numeric_rf.R | 6 collinear-3.0.1/collinear/R/identify_categorical_variables.R | 2 collinear-3.0.1/collinear/R/identify_logical_variables.R | 2 collinear-3.0.1/collinear/R/identify_numeric_variables.R | 2 collinear-3.0.1/collinear/R/identify_response_type.R | 2 collinear-3.0.1/collinear/R/identify_valid_variables.R | 2 collinear-3.0.1/collinear/R/identify_zero_variance_variables.R | 2 collinear-3.0.1/collinear/R/model_formula.R | 16 collinear-3.0.1/collinear/R/preference_order.R | 16 collinear-3.0.1/collinear/R/score_auc.R | 5 collinear-3.0.1/collinear/R/step_collinear.R | 10 collinear-3.0.1/collinear/R/target_encoding_lab.R | 2 collinear-3.0.1/collinear/R/target_encoding_mean.R | 2 collinear-3.0.1/collinear/R/validate_arg_df.R | 6 collinear-3.0.1/collinear/R/validate_arg_df_not_null.R | 2 collinear-3.0.1/collinear/R/validate_arg_predictors.R | 2 collinear-3.0.1/collinear/R/validate_arg_preference_order.R | 10 collinear-3.0.1/collinear/R/validate_arg_responses.R | 2 collinear-3.0.1/collinear/R/vif.R | 7 collinear-3.0.1/collinear/R/vif_df.R | 2 collinear-3.0.1/collinear/R/vif_select.R | 2 collinear-3.0.1/collinear/R/vif_stats.R | 10 collinear-3.0.1/collinear/R/zzz.R |only collinear-3.0.1/collinear/README.md | 6 collinear-3.0.1/collinear/data/experiment_adaptive_thresholds.rda |binary collinear-3.0.1/collinear/data/experiment_cor_vs_vif.rda |binary collinear-3.0.1/collinear/data/gam_cor_to_vif.rda |binary collinear-3.0.1/collinear/data/prediction_cor_to_vif.rda |binary collinear-3.0.1/collinear/data/toy.rda |binary collinear-3.0.1/collinear/inst/CITATION | 6 collinear-3.0.1/collinear/inst/WORDLIST | 13 collinear-3.0.1/collinear/man/case_weights.Rd | 10 collinear-3.0.1/collinear/man/collinear.Rd | 17 collinear-3.0.1/collinear/man/collinear_select.Rd | 12 collinear-3.0.1/collinear/man/collinear_stats.Rd | 28 collinear-3.0.1/collinear/man/cor_clusters.Rd | 20 collinear-3.0.1/collinear/man/cor_cramer.Rd | 18 collinear-3.0.1/collinear/man/cor_df.Rd | 22 collinear-3.0.1/collinear/man/cor_matrix.Rd | 22 collinear-3.0.1/collinear/man/cor_select.Rd | 12 collinear-3.0.1/collinear/man/cor_stats.Rd | 28 collinear-3.0.1/collinear/man/declare_spatialData.Rd |only collinear-3.0.1/collinear/man/drop_geometry_column.Rd | 26 collinear-3.0.1/collinear/man/experiment_adaptive_thresholds.Rd | 2 collinear-3.0.1/collinear/man/experiment_cor_vs_vif.Rd | 2 collinear-3.0.1/collinear/man/f_auto.Rd | 21 collinear-3.0.1/collinear/man/f_auto_rules.Rd | 6 collinear-3.0.1/collinear/man/f_binomial_gam.Rd | 24 collinear-3.0.1/collinear/man/f_binomial_glm.Rd | 24 collinear-3.0.1/collinear/man/f_binomial_rf.Rd | 24 collinear-3.0.1/collinear/man/f_categorical_rf.Rd | 24 collinear-3.0.1/collinear/man/f_count_gam.Rd | 24 collinear-3.0.1/collinear/man/f_count_glm.Rd | 24 collinear-3.0.1/collinear/man/f_count_rf.Rd | 24 collinear-3.0.1/collinear/man/f_functions.Rd | 6 collinear-3.0.1/collinear/man/f_numeric_gam.Rd | 24 collinear-3.0.1/collinear/man/f_numeric_glm.Rd | 24 collinear-3.0.1/collinear/man/f_numeric_rf.Rd | 24 collinear-3.0.1/collinear/man/gam_cor_to_vif.Rd | 2 collinear-3.0.1/collinear/man/identify_categorical_variables.Rd | 14 collinear-3.0.1/collinear/man/identify_logical_variables.Rd | 14 collinear-3.0.1/collinear/man/identify_numeric_variables.Rd | 14 collinear-3.0.1/collinear/man/identify_response_type.Rd | 14 collinear-3.0.1/collinear/man/identify_valid_variables.Rd | 14 collinear-3.0.1/collinear/man/identify_zero_variance_variables.Rd | 14 collinear-3.0.1/collinear/man/model_formula.Rd | 20 collinear-3.0.1/collinear/man/prediction_cor_to_vif.Rd | 2 collinear-3.0.1/collinear/man/preference_order.Rd | 32 collinear-3.0.1/collinear/man/print.collinear_output.Rd | 8 collinear-3.0.1/collinear/man/print.collinear_selection.Rd | 8 collinear-3.0.1/collinear/man/score_auc.Rd | 10 collinear-3.0.1/collinear/man/score_cramer.Rd | 10 collinear-3.0.1/collinear/man/score_r2.Rd | 10 collinear-3.0.1/collinear/man/step_collinear.Rd | 20 collinear-3.0.1/collinear/man/summary.collinear_output.Rd | 8 collinear-3.0.1/collinear/man/summary.collinear_selection.Rd | 8 collinear-3.0.1/collinear/man/target_encoding_lab.Rd | 6 collinear-3.0.1/collinear/man/target_encoding_methods.Rd | 9 collinear-3.0.1/collinear/man/toy.Rd | 9 collinear-3.0.1/collinear/man/validate_arg_df.Rd | 30 collinear-3.0.1/collinear/man/validate_arg_df_not_null.Rd | 26 collinear-3.0.1/collinear/man/validate_arg_encoding_method.Rd | 24 collinear-3.0.1/collinear/man/validate_arg_f.Rd | 24 collinear-3.0.1/collinear/man/validate_arg_function_name.Rd | 24 collinear-3.0.1/collinear/man/validate_arg_max_cor.Rd | 24 collinear-3.0.1/collinear/man/validate_arg_max_vif.Rd | 24 collinear-3.0.1/collinear/man/validate_arg_predictors.Rd | 26 collinear-3.0.1/collinear/man/validate_arg_preference_order.Rd | 34 collinear-3.0.1/collinear/man/validate_arg_quiet.Rd | 24 collinear-3.0.1/collinear/man/validate_arg_responses.Rd | 26 collinear-3.0.1/collinear/man/vif.Rd | 25 collinear-3.0.1/collinear/man/vif_df.Rd | 20 collinear-3.0.1/collinear/man/vif_select.Rd | 12 collinear-3.0.1/collinear/man/vif_stats.Rd | 28 collinear-3.0.1/collinear/tests/testthat/test-case_weights.R | 2 collinear-3.0.1/collinear/tests/testthat/test-collinear.R | 15 collinear-3.0.1/collinear/tests/testthat/test-collinear_select.R | 10 collinear-3.0.1/collinear/tests/testthat/test-collinear_stats.R | 10 collinear-3.0.1/collinear/tests/testthat/test-cor_clusters.R | 6 collinear-3.0.1/collinear/tests/testthat/test-cor_cramer.R | 2 collinear-3.0.1/collinear/tests/testthat/test-cor_df.R | 8 collinear-3.0.1/collinear/tests/testthat/test-cor_matrix.R | 6 collinear-3.0.1/collinear/tests/testthat/test-cor_select.R | 10 collinear-3.0.1/collinear/tests/testthat/test-cor_stats.R | 10 collinear-3.0.1/collinear/tests/testthat/test-drop_geometry_column.R | 2 collinear-3.0.1/collinear/tests/testthat/test-f_auto.R | 15 collinear-3.0.1/collinear/tests/testthat/test-f_binomial_gam.R | 40 + collinear-3.0.1/collinear/tests/testthat/test-f_binomial_glm.R | 40 + collinear-3.0.1/collinear/tests/testthat/test-f_binomial_rf.R | 40 + collinear-3.0.1/collinear/tests/testthat/test-f_categorical_rf.R | 29 collinear-3.0.1/collinear/tests/testthat/test-f_count_gam.R | 33 collinear-3.0.1/collinear/tests/testthat/test-f_count_glm.R | 29 collinear-3.0.1/collinear/tests/testthat/test-f_count_rf.R | 29 collinear-3.0.1/collinear/tests/testthat/test-f_numeric_gam.R | 33 collinear-3.0.1/collinear/tests/testthat/test-f_numeric_glm.R | 29 collinear-3.0.1/collinear/tests/testthat/test-f_numeric_rf.R | 29 collinear-3.0.1/collinear/tests/testthat/test-identify_categorical_variables.R | 10 collinear-3.0.1/collinear/tests/testthat/test-identify_logical_variables.R | 6 collinear-3.0.1/collinear/tests/testthat/test-identify_numeric_variables.R | 10 collinear-3.0.1/collinear/tests/testthat/test-identify_response_type.R | 2 collinear-3.0.1/collinear/tests/testthat/test-identify_valid_variables.R | 10 collinear-3.0.1/collinear/tests/testthat/test-identify_zero_variance_variables.R | 12 collinear-3.0.1/collinear/tests/testthat/test-model_formula.R | 22 collinear-3.0.1/collinear/tests/testthat/test-preference_order.R | 45 + collinear-3.0.1/collinear/tests/testthat/test-print.collinear_output.R | 9 collinear-3.0.1/collinear/tests/testthat/test-print.collinear_selection.R | 9 collinear-3.0.1/collinear/tests/testthat/test-score_auc.R | 41 + collinear-3.0.1/collinear/tests/testthat/test-score_cramer.R | 2 collinear-3.0.1/collinear/tests/testthat/test-score_r2.R | 2 collinear-3.0.1/collinear/tests/testthat/test-step_collinear.R | 6 collinear-3.0.1/collinear/tests/testthat/test-summary.collinear_output.R | 9 collinear-3.0.1/collinear/tests/testthat/test-summary.collinear_selection.R | 9 collinear-3.0.1/collinear/tests/testthat/test-target_encoding_lab.R | 10 collinear-3.0.1/collinear/tests/testthat/test-target_encoding_loo.R | 2 collinear-3.0.1/collinear/tests/testthat/test-target_encoding_mean.R | 2 collinear-3.0.1/collinear/tests/testthat/test-target_encoding_rank.R | 2 collinear-3.0.1/collinear/tests/testthat/test-validate_arg_df.R | 10 collinear-3.0.1/collinear/tests/testthat/test-validate_arg_df_not_null.R | 2 collinear-3.0.1/collinear/tests/testthat/test-validate_arg_predictors.R | 15 collinear-3.0.1/collinear/tests/testthat/test-validate_arg_preference_order.R | 9 collinear-3.0.1/collinear/tests/testthat/test-validate_arg_responses.R | 2 collinear-3.0.1/collinear/tests/testthat/test-vif.R | 6 collinear-3.0.1/collinear/tests/testthat/test-vif_df.R | 2 collinear-3.0.1/collinear/tests/testthat/test-vif_select.R | 6 collinear-3.0.1/collinear/tests/testthat/test-vif_stats.R | 9 181 files changed, 1518 insertions(+), 1014 deletions(-)
Title: Bayes Factor Design for Two-Arm Binomial Trials
Description: Design and analysis of one- and two-stage two-arm binomial
clinical phase II trials using Bayes factors. Implements Bayes factors
for point-null and directional hypotheses, predictive densities under
different hypotheses, and power and sample size calibration.
Author: Riko Kelter [aut, cre]
Maintainer: Riko Kelter <rkelter@uni-koeln.de>
Diff between bfbin2arm versions 0.1.0 dated 2026-02-24 and 0.1.2 dated 2026-05-07
DESCRIPTION | 24 +- MD5 | 62 +++-- NAMESPACE | 18 + R/bayes_factors.R | 97 +++++--- R/bfbin2arm-package.R | 27 +- R/freq_oc_twoarm_fixed.R |only R/freq_oc_twoarm_helpers.R |only R/globals.R |only R/imports.R |only R/optimal_twostage_2arm.R |only R/plot.R |only R/power_calibration.R | 418 ++++++++++++++++++++++------------- R/predictive_densities.R | 4 build/vignette.rds |binary inst/doc/bfbin2arm-intro.R | 28 +- inst/doc/bfbin2arm-intro.Rmd | 30 +- inst/doc/bfbin2arm-intro.html | 96 +------- inst/doc/bfbin2arm-twostage.R |only inst/doc/bfbin2arm-twostage.Rmd |only inst/doc/bfbin2arm-twostage.html |only man/BFminus1.Rd | 8 man/BFplus1.Rd | 8 man/bfbin2arm.Rd |only man/compute_freq_twostage_oc_2arm.Rd |only man/freq_oc_twostage_twoarm_fixed.Rd |only man/freq_t1e_sup_fixed.Rd |only man/freq_t1e_twostage_twoarm_sup.Rd |only man/optimal_twostage_2arm_bf.Rd |only man/plot_twostage_2arm_bf.Rd |only man/postProbHminus.Rd | 8 man/postProbHplus.Rd | 11 man/powertwoarmbinbf01.Rd | 11 man/priorProbHminus.Rd | 6 man/priorProbHplus.Rd | 6 man/twoarmbinbf01.Rd | 6 man/twoarmbinbf_plus0_direct.Rd |only tests |only vignettes/bfbin2arm-intro.Rmd | 30 +- vignettes/bfbin2arm-twostage.Rmd |only vignettes/figures |only vignettes/references.bib |only 41 files changed, 531 insertions(+), 367 deletions(-)
Title: A Modular Platform for Reproducible Modeling of Species Niches
and Distributions
Description: The 'shiny' application Wallace is a modular platform for
reproducible modeling of species niches and distributions. Wallace
guides users through a complete analysis, from the acquisition of species
occurrence and environmental data to visualizing model predictions on an
interactive map, thus bundling complex workflows into a single,
streamlined interface. An extensive vignette, which guides users through
most package functionality can be found on the package's GitHub Pages
website: <https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html>.
Author: Daniel F. Lopez-Lozano [aut],
Bethany A. Johnson [aut],
Jamie M. Kass [aut],
Gonzalo E. Pinilla-Buitrago [aut],
Andrea Paz [aut],
Valentina Grisales-Betancur [aut],
Dean Attali [aut],
Matthew E. Aiello-Lammens [aut],
Cory Merow [aut],
Mary E. Blair [ [...truncated...]
Maintainer: Mary E. Blair <mblair1@amnh.org>
This is a re-admission after prior archival of version 2.2.0 dated 2025-03-06
Diff between wallace versions 2.2.0 dated 2025-03-06 and 2.2.1 dated 2026-05-07
DESCRIPTION | 30 MD5 | 561 ++-- NAMESPACE | 113 NEWS.md | 457 ++- R/custom_modules.R | 218 - R/envs_ecoClimate.R | 832 +++---- R/envs_userEnvs.R | 176 - R/envs_worldclim.R | 236 +- R/espace_nicheOv.R | 240 +- R/espace_occDens.R | 298 +- R/espace_pca.R | 232 - R/helper_functions.R | 993 ++++---- R/model_bioclim.R | 184 - R/model_maxent.R | 481 ++-- R/occs_paleoDb.R | 294 +- R/occs_queryDb.R | 752 +++--- R/occs_userOccs.R | 360 +-- R/part_partitionOccs.R | 372 +-- R/penvs_bgExtent.R | 252 +- R/penvs_bgMask.R | 204 - R/penvs_bgSample.R | 198 - R/penvs_drawBgExtent.R | 206 - R/penvs_userBgExtent.R | 282 +- R/poccs_removeByID.R | 180 - R/poccs_selectOccs.R | 238 +- R/poccs_thinOccs.R | 210 - R/run_wallace.R | 98 R/utils_leaflet_draw.R |only R/vis_bioclimPlot.R | 218 - R/wallace-package.R | 92 R/xfer_area.R | 292 +- R/xfer_draw.R | 156 - R/xfer_mess.R | 204 - R/xfer_time.R | 298 +- R/xfer_userEnvs.R | 278 +- R/xfer_userExtent.R | 234 +- README.md | 108 inst/CITATION | 64 inst/extdata/Bassaricyon_alleni.csv | 72 inst/extdata/Bassaricyon_alleni_bgPoints.csv | 2002 ++++++++--------- inst/extdata/Bassaricyon_neblina.csv | 38 inst/extdata/Bassaricyon_neblina_bgPoints.csv | 2002 ++++++++--------- inst/extdata/Marmosops_sp.csv | 44 inst/htmlwidgets |only inst/module_skeleton/skeleton.R | 114 inst/module_skeleton/skeleton.Rmd | 18 inst/module_skeleton/skeleton.md | 26 inst/module_skeleton/skeleton.yml | 10 inst/shiny/Rmd/gtext_envs.Rmd | 56 inst/shiny/Rmd/gtext_espace.Rmd | 54 inst/shiny/Rmd/gtext_model.Rmd | 142 - inst/shiny/Rmd/gtext_occs.Rmd | 44 inst/shiny/Rmd/gtext_part.Rmd | 36 inst/shiny/Rmd/gtext_penvs.Rmd | 92 inst/shiny/Rmd/gtext_poccs.Rmd | 28 inst/shiny/Rmd/gtext_rep.Rmd | 58 inst/shiny/Rmd/gtext_vis.Rmd | 34 inst/shiny/Rmd/gtext_xfer.Rmd | 36 inst/shiny/Rmd/references.Rmd | 28 inst/shiny/Rmd/text_about.Rmd | 232 - inst/shiny/Rmd/text_how_to_use.Rmd | 112 inst/shiny/Rmd/text_intro_tab.Rmd | 120 - inst/shiny/Rmd/text_loadsesh.Rmd | 18 inst/shiny/Rmd/text_team.Rmd | 218 - inst/shiny/Rmd/userReport_intro.Rmd | 86 inst/shiny/Rmd/userReport_multSpecies.Rmd | 56 inst/shiny/Rmd/userReport_species.Rmd | 54 inst/shiny/global.R | 352 +-- inst/shiny/helpers.R | 292 +- inst/shiny/modules/envs_ecoclimate.R | 408 +-- inst/shiny/modules/envs_ecoclimate.Rmd | 48 inst/shiny/modules/envs_ecoclimate.md | 38 inst/shiny/modules/envs_ecoclimate.yml | 10 inst/shiny/modules/envs_userEnvs.R | 370 +-- inst/shiny/modules/envs_userEnvs.Rmd | 52 inst/shiny/modules/envs_userEnvs.md | 62 inst/shiny/modules/envs_userEnvs.yml | 10 inst/shiny/modules/envs_worldclim.R | 456 +-- inst/shiny/modules/envs_worldclim.Rmd | 48 inst/shiny/modules/envs_worldclim.md | 84 inst/shiny/modules/envs_worldclim.yml | 10 inst/shiny/modules/espace_nicheOv.R | 302 +- inst/shiny/modules/espace_nicheOv.Rmd | 62 inst/shiny/modules/espace_nicheOv.md | 62 inst/shiny/modules/espace_nicheOv.yml | 10 inst/shiny/modules/espace_occDens.R | 218 - inst/shiny/modules/espace_occDens.Rmd | 36 inst/shiny/modules/espace_occDens.md | 46 inst/shiny/modules/espace_occDens.yml | 10 inst/shiny/modules/espace_pca.R | 528 ++-- inst/shiny/modules/espace_pca.Rmd | 78 inst/shiny/modules/espace_pca.md | 66 inst/shiny/modules/espace_pca.yml | 10 inst/shiny/modules/model_bioclim.R | 240 +- inst/shiny/modules/model_bioclim.Rmd | 26 inst/shiny/modules/model_bioclim.md | 38 inst/shiny/modules/model_bioclim.yml | 10 inst/shiny/modules/model_maxent.R | 590 ++--- inst/shiny/modules/model_maxent.Rmd | 90 inst/shiny/modules/model_maxent.md | 138 - inst/shiny/modules/model_maxent.yml | 10 inst/shiny/modules/occs_paleoDb.R | 282 +- inst/shiny/modules/occs_paleoDb.Rmd | 26 inst/shiny/modules/occs_paleoDb.md | 34 inst/shiny/modules/occs_paleoDb.yml | 10 inst/shiny/modules/occs_queryDb.R | 396 +-- inst/shiny/modules/occs_queryDb.Rmd | 70 inst/shiny/modules/occs_queryDb.md | 60 inst/shiny/modules/occs_queryDb.yml | 10 inst/shiny/modules/occs_userOccs.R | 240 +- inst/shiny/modules/occs_userOccs.Rmd | 32 inst/shiny/modules/occs_userOccs.md | 20 inst/shiny/modules/occs_userOccs.yml | 10 inst/shiny/modules/part_nonSpat.R | 302 +- inst/shiny/modules/part_nonSpat.Rmd | 26 inst/shiny/modules/part_nonSpat.md | 38 inst/shiny/modules/part_nonSpat.yml | 10 inst/shiny/modules/part_spat.R | 322 +- inst/shiny/modules/part_spat.Rmd | 54 inst/shiny/modules/part_spat.md | 30 inst/shiny/modules/part_spat.yml | 10 inst/shiny/modules/penvs_bgExtent.R | 505 ++-- inst/shiny/modules/penvs_bgExtent.Rmd | 58 inst/shiny/modules/penvs_bgExtent.md | 70 inst/shiny/modules/penvs_bgExtent.yml | 10 inst/shiny/modules/penvs_drawBgExtent.R | 509 ++-- inst/shiny/modules/penvs_drawBgExtent.Rmd | 60 inst/shiny/modules/penvs_drawBgExtent.md | 44 inst/shiny/modules/penvs_drawBgExtent.yml | 10 inst/shiny/modules/penvs_userBgExtent.R | 533 ++-- inst/shiny/modules/penvs_userBgExtent.Rmd | 66 inst/shiny/modules/penvs_userBgExtent.md | 18 inst/shiny/modules/penvs_userBgExtent.yml | 10 inst/shiny/modules/poccs_removeByID.R | 223 - 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inst/shiny/modules/vis_bioclimPlot.Rmd | 30 inst/shiny/modules/vis_bioclimPlot.md | 34 inst/shiny/modules/vis_bioclimPlot.yml | 10 inst/shiny/modules/vis_mapPreds.R | 630 ++--- inst/shiny/modules/vis_mapPreds.Rmd | 520 ++-- inst/shiny/modules/vis_mapPreds.md | 54 inst/shiny/modules/vis_mapPreds.yml | 10 inst/shiny/modules/vis_maxentEvalPlot.R | 212 - inst/shiny/modules/vis_maxentEvalPlot.Rmd | 30 inst/shiny/modules/vis_maxentEvalPlot.md | 40 inst/shiny/modules/vis_maxentEvalPlot.yml | 10 inst/shiny/modules/vis_responsePlot.R | 212 - inst/shiny/modules/vis_responsePlot.Rmd | 68 inst/shiny/modules/vis_responsePlot.md | 36 inst/shiny/modules/vis_responsePlot.yml | 10 inst/shiny/modules/xfer_area.R | 893 +++---- inst/shiny/modules/xfer_area.Rmd | 468 ++-- inst/shiny/modules/xfer_area.md | 60 inst/shiny/modules/xfer_area.yml | 10 inst/shiny/modules/xfer_mess.R | 306 +- inst/shiny/modules/xfer_mess.Rmd | 96 inst/shiny/modules/xfer_mess.md | 54 inst/shiny/modules/xfer_mess.yml | 10 inst/shiny/modules/xfer_time.R | 1441 ++++++------ inst/shiny/modules/xfer_time.Rmd | 1606 +++++++------ inst/shiny/modules/xfer_time.md | 68 inst/shiny/modules/xfer_time.yml | 10 inst/shiny/modules/xfer_user.R | 952 ++++---- inst/shiny/modules/xfer_user.Rmd | 752 +++--- inst/shiny/modules/xfer_user.md | 48 inst/shiny/modules/xfer_user.yml | 10 inst/shiny/server.R | 3022 +++++++++++++------------- inst/shiny/ui.R | 1056 ++++----- inst/shiny/www/css/styles.css | 242 +- inst/shiny/www/js/shinyjs-funcs.js | 80 man/addDrawToolbar.Rd |only man/clearAll.Rd | 30 man/create_module.Rd | 60 man/ecoClimate_getdata.Rd | 74 man/ecoClimate_select.Rd | 58 man/ecospat.plot.nicheDEV.Rd | 58 man/editToolbarOptions.Rd |only man/envs_ecoClimate.Rd | 106 man/envs_userEnvs.Rd | 98 man/envs_worldclim.Rd | 112 man/espace_nicheOv.Rd | 188 - man/espace_occDens.Rd | 156 - man/espace_pca.Rd | 184 - man/fmtSpN.Rd | 30 man/getRasterVals.Rd | 34 man/hlSpp.Rd | 30 man/model_bioclim.Rd | 130 - man/model_maxent.Rd | 220 - man/mxNonzeroCoefs.Rd | 36 man/occs_queryDb.Rd | 150 - man/occs_userOccs.Rd | 98 man/part_partitionOccs.Rd | 180 - man/penvs_bgExtent.Rd | 114 man/penvs_bgMask.Rd | 134 - man/penvs_bgSample.Rd | 140 - man/penvs_drawBgExtent.Rd | 152 - man/penvs_userBgExtent.Rd | 152 - man/poccs_removeByID.Rd | 94 man/poccs_selectOccs.Rd | 118 - man/poccs_thinOccs.Rd | 104 man/polyZoom.Rd | 46 man/popUpContent.Rd | 30 man/predictMaxnet.Rd | 42 man/printVecAsis.Rd | 34 man/register_module.Rd | 38 man/remEnvsValsNA.Rd | 42 man/removeDrawToolbar.Rd |only man/reverseLabel.Rd | 34 man/run_wallace.Rd | 68 man/smartProgress.Rd | 44 man/spName.Rd | 32 man/spurious.Rd | 30 man/vis_bioclimPlot.Rd | 138 - man/wallace-package.Rd | 88 man/writeLog.Rd | 38 man/write_csv_robust.Rd | 34 man/xfer_area.Rd | 230 - man/xfer_draw.Rd | 118 - man/xfer_mess.Rd | 142 - man/xfer_time.Rd | 234 +- man/xfer_userEnvs.Rd | 212 - man/xfer_userExtent.Rd | 124 - man/zoom2Occs.Rd | 34 tests/README.txt | 2 tests/testthat.R | 10 tests/testthat/extdata/Marmosops_NA.csv | 44 tests/testthat/extdata/Marmosops_sp.csv | 44 tests/testthat/extdata/Marmosops_wrong.csv | 44 tests/testthat/extdata/Marmosops_wrongSP.csv | 42 tests/testthat/extdata/cerdocyon-thous-2.csv | 82 tests/testthat/test_envs_ecoClimate.R | 124 - tests/testthat/test_envs_userEnvs.R | 102 tests/testthat/test_envs_worldclim.R | 78 tests/testthat/test_espace_nicheOv.R | 126 - tests/testthat/test_espace_occDens.R | 140 - tests/testthat/test_espace_pca.R | 96 tests/testthat/test_model_bioclim.R | 164 - tests/testthat/test_model_maxent.R | 274 +- tests/testthat/test_occs_paleoDb.R | 208 - tests/testthat/test_occs_queryDb.R | 608 ++--- tests/testthat/test_occs_userOccs.R | 186 - tests/testthat/test_part_partitionOccs.R | 286 +- tests/testthat/test_penvs_bgExtent.R | 190 - tests/testthat/test_penvs_bgMask.R | 92 tests/testthat/test_penvs_bgSample.R | 113 tests/testthat/test_penvs_drawBgExtent.R | 136 - tests/testthat/test_penvs_userBgExtent.R | 140 - tests/testthat/test_poccs_removeByID.R | 84 tests/testthat/test_poccs_selectOccs.R | 132 - tests/testthat/test_poccs_thinOccs.R | 82 tests/testthat/test_vis_bioclimPlot.R | 90 tests/testthat/test_xfer_area.R | 106 tests/testthat/test_xfer_draw.R | 70 tests/testthat/test_xfer_mess.R | 64 tests/testthat/test_xfer_time.R | 110 tests/testthat/test_xfer_userEnvs.R | 106 tests/testthat/test_xfer_userExtent.R | 62 280 files changed, 24559 insertions(+), 24424 deletions(-)
Title: Load Configuration Values
Description: A simple approach to configuring R projects with different
parameter values. Configurations are specified using a reduced subset of base
R and parsed accordingly.
Author: Tim Taylor [aut, cre, cph]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ronfig versions 0.0.9 dated 2026-03-16 and 0.0.10 dated 2026-05-07
DESCRIPTION | 8 ++--- MD5 | 10 +++---- NEWS.md | 7 +++++ R/load_config.R | 74 ++++++++++++++++++++++++++++------------------------- build/vignette.rds |binary man/load_config.Rd | 8 ++++- 6 files changed, 62 insertions(+), 45 deletions(-)
Title: Analise multivariada (brazilian portuguese)
Description: Analise multivariada, tendo funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise discriminante linear (LDA) e quadratica (QDA), analise de cluster hierarquico e nao hierarquico, regressao linear simples e multipla, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos, biplot, scatter plot, projection pursuit (PP), grant tour e outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani [aut, cre] ,
Marcelo Angelo Cirillo [aut]
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 2.2.8 dated 2026-04-13 and 2.2.9 dated 2026-05-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/PCA.R | 19 +++++++++++++------ man/MVar.pt-package.Rd | 4 ++-- man/PCA.Rd | 17 ++++++++++------- 5 files changed, 33 insertions(+), 23 deletions(-)
Title: Simplified Legend and Guide Alignment for 'ggplot2'
Description: Provides one-liner functions for common legend and guide operations
in 'ggplot2'. Simplifies legend positioning, styling, wrapping, and
collection across multi-panel plots created with 'patchwork' or 'cowplot'.
Author: Gilles Colling [aut, cre]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between ggguides versions 1.1.6 dated 2026-04-23 and 1.1.10 dated 2026-05-07
DESCRIPTION | 6 MD5 | 56 +- NAMESPACE | 3 NEWS.md | 40 + R/collect_axes.R | 158 +++---- R/legend_position.R | 119 +++-- R/legend_style.R | 421 +++++++++++++++++- README.md | 28 + build/vignette.rds |binary inst/doc/getting-started.html | 4 inst/doc/multiple-legends.R | 70 ++- inst/doc/multiple-legends.Rmd | 99 +++- inst/doc/multiple-legends.html | 199 +++++++- inst/doc/patchwork.html | 4 inst/doc/positioning.html | 4 inst/doc/styling.html | 4 inst/examples/generate_examples.R | 758 ++++++++++++++++++---------------- man/figures/six_legends.svg |only man/ggplotGrob.gg_per_legend_just.Rd |only man/legend_bottom.Rd | 20 man/legend_left.Rd | 43 + man/legend_right.Rd | 30 - man/legend_style.Rd | 9 man/legend_top.Rd | 18 man/print.gg_autofit_legend.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test-legend_multi.R | 135 ++++++ tests/testthat/test-legend_order.R | 17 tests/testthat/test-legend_position.R | 54 ++ vignettes/multiple-legends.Rmd | 99 +++- 30 files changed, 1750 insertions(+), 652 deletions(-)
Title: Generic Implementation of a PK/PD Model
Description: A generic, easy-to-use and expandable implementation of a
pharmacokinetic (PK) / pharmacodynamic (PD) model based on the S4
class system. This package allows the user to read and write
pharmacometric models from and to files, including a JSON-based
interface to import Campsis models defined using a formal JSON schema
distributed with the package. Models can be adapted further on the fly
in the R environment using an intuitive API to add, modify or delete
equations, ordinary differential equations (ODEs), model parameters or
compartment properties (such as infusion duration or rate,
bioavailability and initial values). The package also provides export
facilities for use with the simulation packages 'rxode2' and
'mrgsolve'. The package itself is licensed under the GPL (>= 3); the
JSON schema file shipped in inst/extdata is licensed separately under
the Creative Commons Attribution 4.0 International (CC BY 4.0). This
package is designed and intended to be used with the package
'campsi [...truncated...]
Author: Nicolas Luyckx [aut, cre]
Maintainer: Nicolas Luyckx <nicolas.luyckx@calvagone.com>
Diff between campsismod versions 1.3.1 dated 2026-03-17 and 1.3.2 dated 2026-05-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 3 +++ data/model_suite.rda |binary 4 files changed, 9 insertions(+), 6 deletions(-)
Title: Quantitative Chronology in Archaeology
Description: Simple radiocarbon calibration and chronological analysis.
This package allows the calibration of radiocarbon ages and modern
carbon fraction values using multiple calibration curves. It allows
the calculation of highest density region intervals and credible
intervals. The package also provides tools for visualising results and
estimating statistical summaries.
Author: Nicolas Frerebeau [aut, cre] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between ananke versions 0.1.0 dated 2025-04-18 and 0.2.0 dated 2026-05-07
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Title: Robust Bayesian Meta-Analyses
Description: A framework for Bayesian meta-analysis, including model estimation,
prior specification, model comparison, prediction, summaries, visualizations,
and diagnostics. The package fits single and model-averaged meta-analytic,
meta-regression, multilevel, publication bias adjusted, and generalized linear
mixed models The model-averaged meta-analytic models combine competing models
based on their predictive performance, weight inference by posterior model probabilities,
and test model components using Bayes factors (e.g., effect vs. no effect;
Bartoš et al., 2022, <doi:10.1002/jrsm.1594>; Maier, Bartoš & Wagenmakers, 2022,
<doi:10.1037/met0000405>; Bartoš et al., 2025, <doi:10.1037/met0000737>).
Users can specify flexible prior distributions for effect sizes, heterogeneity,
publication bias (including selection models and PET-PEESE), and moderators.
Author: Frantisek Bartos [aut, cre] ,
Maximilian Maier [aut] ,
Eric-Jan Wagenmakers [ths] ,
Joris Goosen [ctb],
Matthew Denwood [cph] ,
Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
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RoBMA-4.0.0/RoBMA/tests/testthat/test-02-vif.R |only RoBMA-4.0.0/RoBMA/tests/testthat/test-03-bridgesampling.R |only RoBMA-4.0.0/RoBMA/tests/testthat/test-03-loo.R |only RoBMA-4.0.0/RoBMA/tests/testthat/test-03-zplot.R |only RoBMA-4.0.0/RoBMA/tests/testthat/test-cran-smoke.R |only RoBMA-4.0.0/RoBMA/vignettes/_v00-introduction-body.md |only RoBMA-4.0.0/RoBMA/vignettes/_vignette-nowrap.md |only RoBMA-4.0.0/RoBMA/vignettes/v00-introduction.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v01-prior-distributions.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v02-bayesian-meta-analysis.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v03-feature-coverage.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v10-metafor-parity-multilevel.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v11-metafor-parity-publication-bias.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v12-metafor-parity-location-scale.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v13-metafor-parity-glmm.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v20-bayesian-model-averaging.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v21-robust-bayesian-meta-analysis.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v30-tutorial.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v31-robma-metaregression.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v32-robma-multilevel.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v33-robma-multilevel-metaregression.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v34-bma-norm-medicine.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v35-bma-glmm-medicine.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/v36-zplot.Rmd |only RoBMA-4.0.0/RoBMA/vignettes/vignette-cache.R |only 481 files changed, 6145 insertions(+), 6241 deletions(-)
Title: Create Validation Tests for Automated Content Analysis
Description: Intended to create standard human-in-the-loop validity tests for typical automated content analysis such as topic modeling and dictionary-based methods. This package offers a standard workflow with functions to prepare, administer and evaluate a human-in-the-loop validity test. This package provides functions for validating topic models using word intrusion, topic intrusion (Chang et al. 2009, <https://papers.nips.cc/paper/3700-reading-tea-leaves-how-humans-interpret-topic-models>) and word set intrusion (Ying et al. 2021) <doi:10.1017/pan.2021.33> tests. This package also provides functions for generating gold-standard data which are useful for validating dictionary-based methods. The default settings of all generated tests match those suggested in Chang et al. (2009) and Song et al. (2020) <doi:10.1080/10584609.2020.1723752>.
Author: Chung-hong Chan [aut, cre] ,
Marius Saeltzer [aut]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between oolong versions 0.6.1 dated 2024-04-15 and 0.7.0 dated 2026-05-07
DESCRIPTION | 17 ++++++++------- MD5 | 36 ++++++++++++++++---------------- NEWS.md | 9 ++++++++ R/oolong_data_misc.R | 4 +++ R/oolong_summary.R | 16 +++++++------- R/oolong_summary_gs.R | 4 +-- R/oolong_summary_tm.R | 10 ++++----- R/oolong_tm.R | 6 ++--- R/oolong_topicmodels.R | 2 - build/vignette.rds |binary inst/doc/btm.R | 4 +++ inst/doc/btm.html | 2 - inst/doc/deploy.R | 4 +-- inst/doc/deploy.Rmd | 4 +-- inst/doc/deploy.html | 4 +-- inst/doc/overview.R | 42 +++++++++++++++++++------------------- inst/doc/overview.html | 33 +++++++++++++---------------- tests/testthat/_snaps/printing.md | 2 - vignettes/deploy.Rmd | 4 +-- 19 files changed, 109 insertions(+), 94 deletions(-)
Title: Multivariate Analysis
Description: Multivariate analysis, having functions that perform simple correspondence analysis (CA) and multiple correspondence analysis (MCA), principal components analysis (PCA), canonical correlation analysis (CCA), factorial analysis (FA), multidimensional scaling (MDS), linear (LDA) and quadratic discriminant analysis (QDA), hierarchical and non-hierarchical cluster analysis, simple and multiple linear regression, multiple factor analysis (MFA) for quantitative, qualitative, frequency (MFACT) and mixed data, biplot, scatter plot, projection pursuit (PP), grant tour method and other useful functions for the multivariate analysis.
Author: Paulo Cesar Ossani [aut, cre] ,
Marcelo Angelo Cirillo [aut]
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar versions 2.2.8 dated 2026-04-13 and 2.2.9 dated 2026-05-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/PCA_English.R | 15 +++++++++++---- man/MVar-package.Rd | 4 ++-- man/PCA_English.Rd | 5 ++++- 5 files changed, 25 insertions(+), 15 deletions(-)
Title: Omics Data Analysis
Description: Similarity plots based on correlation and median absolute deviation (MAD); adjusting colors for heatmaps; aggregate technical replicates; calculate pairwise fold-changes and log fold-changes; compute one- and two-way ANOVA; simplified interface to package 'limma' (Ritchie et al. (2015), <doi:10.1093/nar/gkv007> ) for moderated t-test and one-way ANOVA; Hamming and Levenshtein (edit) distance of strings as well as optimal alignment scores for global (Needleman-Wunsch) and local (Smith-Waterman) alignments with constant gap penalties (Merkl and Waack (2009), ISBN:978-3-527-32594-8).
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKomics versions 0.7 dated 2021-08-08 and 0.8 dated 2026-05-07
DESCRIPTION | 13 MD5 | 22 - NAMESPACE | 2 NEWS | 15 R/corPlot2.R | 6 R/mod.oneway.test.R | 4 R/mod.t.test.R | 13 build/vignette.rds |binary inst/doc/MKomics.R | 18 - inst/doc/MKomics.html | 768 ++++++++++++++++++++++++++++-------------------- man/0MKomics-package.Rd | 6 man/corPlot.Rd | 8 12 files changed, 519 insertions(+), 356 deletions(-)
Title: Generation and Analysis of 3-Level and 5-Level Factorial Block
Designs
Description: Provides tools to generate and analyze 3-level and 5-level
linear factorial block designs, including complete factorial layouts,
fractional factorial layouts, confounded factorial layouts, and
design-characteristic summaries. The package includes utilities for
recursive construction, defining-contrast identification, alias and
confounding summaries, incidence matrix construction, and selected
design-characteristic diagnostics. The methodological framework follows
foundational work on factorial block designs, including Gupta (1983)
<doi:10.1111/j.2517-6161.1983.tb01253.x>.
Author: Vankudoth Kumar [aut],
Sukanta Dash [aut, cre],
Med Ram Verma [aut]
Maintainer: Sukanta Dash <sukanta.iasri@gmail.com>
Diff between lfebd3 versions 0.1.0 dated 2026-04-24 and 0.2.0 dated 2026-05-07
lfebd3-0.1.0/lfebd3/R/lfebd3.R |only lfebd3-0.1.0/lfebd3/man/lfbd.Rd |only lfebd3-0.1.0/lfebd3/man/lfbd.cf.Rd |only lfebd3-0.1.0/lfebd3/man/lfbd.cf.full.Rd |only lfebd3-0.1.0/lfebd3/man/lfbd.fr.Rd |only lfebd3-0.1.0/lfebd3/man/lfbd_analyze.Rd |only lfebd3-0.1.0/lfebd3/tests |only lfebd3-0.2.0/lfebd3/DESCRIPTION | 37 +-- lfebd3-0.2.0/lfebd3/MD5 | 103 ++++++---- lfebd3-0.2.0/lfebd3/NAMESPACE | 22 +- lfebd3-0.2.0/lfebd3/NEWS.md |only lfebd3-0.2.0/lfebd3/R/lfebd.R |only lfebd3-0.2.0/lfebd3/man/FactChar.Rd | 17 + lfebd3-0.2.0/lfebd3/man/FactChar_fast.Rd |only lfebd3-0.2.0/lfebd3/man/as_blocks_from_cf_full.Rd | 4 lfebd3-0.2.0/lfebd3/man/as_blocks_from_runs.Rd | 2 lfebd3-0.2.0/lfebd3/man/build_block_matrix.Rd | 8 lfebd3-0.2.0/lfebd3/man/build_effect_matrix.Rd | 8 lfebd3-0.2.0/lfebd3/man/build_triplet.Rd | 12 - lfebd3-0.2.0/lfebd3/man/canonical_effect.Rd | 6 lfebd3-0.2.0/lfebd3/man/convert_to_blocks.Rd | 10 lfebd3-0.2.0/lfebd3/man/defining_subgroup.Rd | 4 lfebd3-0.2.0/lfebd3/man/direct_aliases_from_dc.Rd | 6 lfebd3-0.2.0/lfebd3/man/effect_aliases_low_order.Rd | 4 lfebd3-0.2.0/lfebd3/man/effect_label.Rd | 6 lfebd3-0.2.0/lfebd3/man/effect_order.Rd | 4 lfebd3-0.2.0/lfebd3/man/find_defining_contrasts.Rd | 10 lfebd3-0.2.0/lfebd3/man/fractional_confounding_summary.Rd | 6 lfebd3-0.2.0/lfebd3/man/fractional_factorial_5n.Rd |only lfebd3-0.2.0/lfebd3/man/full_factorial_5n.Rd |only lfebd3-0.2.0/lfebd3/man/generate_Tn_full.Rd | 33 +-- lfebd3-0.2.0/lfebd3/man/generate_effect_catalog.Rd | 6 lfebd3-0.2.0/lfebd3/man/get_Tn_square.Rd | 12 - lfebd3-0.2.0/lfebd3/man/is_independent_mod3.Rd | 8 lfebd3-0.2.0/lfebd3/man/lfebd3-package.Rd | 9 lfebd3-0.2.0/lfebd3/man/lfebd3.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd3.cf.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd3.cf.full.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd3.fr.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd3_analyze.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5.cf.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5.cf_independent_confounding.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5.fr.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_all_confounded_effects_from_design.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_all_defining_factors_from_design.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_analyze.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_defining_factors_from_design.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_effect_order.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_effect_word.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_generate_Tn.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_independent_effects_from_design.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_main_effect_aliases_from_design.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_make_selection_matrix.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_make_selection_matrix_cf_stage.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_make_selection_matrix_fr_stage_general.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_make_selection_matrix_stage.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_mod_inv.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_modp.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_normalize_effect.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_nullspace_modp.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_rref_modp.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd5_to_run_table.Rd |only lfebd3-0.2.0/lfebd3/man/lfebd_print_limited.Rd |only lfebd3-0.2.0/lfebd3/man/low_order_aliases_from_subgroup.Rd | 6 lfebd3-0.2.0/lfebd3/man/print.lfebd3_analysis.Rd | 18 + lfebd3-0.2.0/lfebd3/man/print.lfebd3_analyze_result.Rd |only lfebd3-0.2.0/lfebd3/man/print.lfebd3_fr.Rd |only lfebd3-0.2.0/lfebd3/man/print.lfebd5_analyze_result.Rd |only lfebd3-0.2.0/lfebd3/man/print.lfebd5_cf_design.Rd |only lfebd3-0.2.0/lfebd3/man/print.lfebd5_fr_design.Rd |only lfebd3-0.2.0/lfebd3/man/print_generated_design.Rd | 4 lfebd3-0.2.0/lfebd3/man/rank_mod3.Rd | 6 lfebd3-0.2.0/lfebd3/man/reduce_once.Rd | 12 - lfebd3-0.2.0/lfebd3/man/reduce_repeated.Rd | 10 75 files changed, 232 insertions(+), 161 deletions(-)
Title: Models for Correlation Matrices Based on Graphs
Description: Implement some models for
correlation/covariance matrices including two approaches
to model correlation matrices from a graphical structure.
One use latent parent variables as proposed in
Sterrantino et. al. (2024) <doi:10.1007/s10260-025-00788-y>.
The other uses a graph to specify conditional
relations between the variables.
The graphical structure makes correlation matrices
interpretable and avoids the quadratic increase of
parameters as a function of the dimension.
In the first approach a natural sequence of simpler
models along with a complexity penalization is used.
The second penalizes deviations from a base model.
These can be used as prior for model parameters,
considering C code through the 'cgeneric' interface
for the 'INLA' package (<https://www.r-inla.org>).
This allows one to use these models as building
blocks combined and to other latent Gaussian models
in order to build complex data models.
Author: Elias Teixeira Krainski [cre, aut, cph] ,
Denis Rustand [aut, cph] ,
Anna Freni-Sterrantino [aut, cph] ,
Janet van Niekerk [aut, cph] ,
Haavard Rue’ [aut]
Maintainer: Elias Teixeira Krainski <elias.krainski@kaust.edu.sa>
This is a re-admission after prior archival of version 0.1.24 dated 2026-03-23
Diff between graphpcor versions 0.1.24 dated 2026-03-23 and 0.1.25 dated 2026-05-07
DESCRIPTION | 19 ++++++------ MD5 | 71 +++++++++++++++++++++++----------------------- NAMESPACE | 11 ++++--- R/Laplacian.R | 1 R/aaa.R | 13 +++++--- R/basecor.R | 9 ----- R/basecor_utils.R | 24 ++++++++++++++- R/cgeneric_LKJ.R | 33 +++++++++++++-------- R/cgeneric_Wishart.R | 12 +++---- R/cgeneric_graphpcor.R | 65 ++++++++++++++++++++++-------------------- R/cgeneric_pc_correl.R | 49 +++++++++++++++++-------------- R/cgeneric_treepcor.R | 10 +++--- R/edges.R | 3 - R/graphpcor.R | 22 +++++--------- R/numeric_utils.R | 4 -- R/param_utils.R | 2 - R/stan.R | 1 R/treepcor.R | 23 ++++++++------ R/zzz.R |only build/partial.rdb |binary build/vignette.rds |binary demo/LKJ.R | 8 ++--- demo/graphpcor.R | 2 - demo/minimal.R | 17 +++++------ demo/treepcor.R | 20 ++++++------ inst/doc/treepcor.R | 19 +++++------- inst/doc/treepcor.Rmd | 20 +++++------- inst/doc/treepcor.html | 44 ++++++++++++++++++---------- man/basecor-utils.Rd | 11 +++++++ man/cgeneric_LKJ.Rd | 4 +- man/cgeneric_Wishart.Rd | 4 +- man/cgeneric_graphpcor.Rd | 4 +- man/cgeneric_pc_correl.Rd | 4 +- man/cgeneric_treepcor.Rd | 6 +-- man/graphpcor.Rd | 8 ++--- man/treepcor.Rd | 36 ++++++++++++----------- vignettes/treepcor.Rmd | 20 +++++------- 37 files changed, 328 insertions(+), 271 deletions(-)
Title: Robust Bayesian Survival Analysis
Description: A framework for estimating ensembles of parametric survival models
with different parametric families. The RoBSA framework uses Bayesian
model-averaging to combine the competing parametric survival models into
a model ensemble, weights the posterior parameter distributions based on
posterior model probabilities and uses Bayes factors to test for the
presence or absence of the individual predictors or preference for a
parametric family (Bartoš, Aust & Haaf, 2022, <doi:10.1186/s12874-022-01676-9>).
The user can define a wide range of informative priors for all parameters
of interest. The package provides convenient functions for summary, visualizations,
fit diagnostics, and prior distribution calibration.
Author: Frantisek Bartos [aut, cre] ,
Julia M. Haaf [ths] ,
Matthew Denwood [cph] ,
Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between RoBSA versions 1.0.3 dated 2025-03-24 and 1.0.4 dated 2026-05-07
RoBSA-1.0.3/RoBSA/man/contr.meandif.Rd |only RoBSA-1.0.3/RoBSA/man/contr.orthonormal.Rd |only RoBSA-1.0.4/RoBSA/DESCRIPTION | 15 +- RoBSA-1.0.4/RoBSA/MD5 | 25 +-- RoBSA-1.0.4/RoBSA/NAMESPACE | 1 RoBSA-1.0.4/RoBSA/NEWS.md | 16 +- RoBSA-1.0.4/RoBSA/R/check-input-and-settings.R | 160 ++++++++++++++++--------- RoBSA-1.0.4/RoBSA/R/fit-and-marglik.R | 11 - RoBSA-1.0.4/RoBSA/R/plot.R | 68 +++++++--- RoBSA-1.0.4/RoBSA/R/priors.R | 75 ++++++----- RoBSA-1.0.4/RoBSA/R/utilities.R | 5 RoBSA-1.0.4/RoBSA/build/partial.rdb |binary RoBSA-1.0.4/RoBSA/man/RoBSA_control.Rd | 15 ++ RoBSA-1.0.4/RoBSA/man/contr.BayesTools.Rd |only RoBSA-1.0.4/RoBSA/tests/testthat/test-0-CRAN.R | 26 ++-- 15 files changed, 265 insertions(+), 152 deletions(-)
Title: Access and Search MedRxiv and BioRxiv Preprint Data
Description: An increasingly important source of health-related bibliographic
content are preprints - preliminary versions of research articles that have
yet to undergo peer review. The two preprint repositories most relevant to
health-related sciences are medRxiv <https://www.medrxiv.org/> and
bioRxiv, both of which are operated by the Cold
Spring Harbor Laboratory. 'medrxivr' provides programmatic access to the
'Cold Spring Harbour Laboratory (CSHL)' API <https://api.biorxiv.org/>,
allowing users to easily download medRxiv and bioRxiv preprint metadata
(e.g. title, abstract, publication date, author list, etc) into R.
'medrxivr' also provides functions to search the downloaded preprint records
using regular expressions and Boolean logic, as well as helper functions
that allow users to export their search results to a .BIB file for easy
import to a reference manager and to download the full-text PDFs of
preprints matching their search criteria.
Author: Yaoxiang Li [aut, cre] ,
Luke McGuinness [aut],
Lena Schmidt [aut],
Tuija Sonkkila [rev],
Najko Jahn [rev]
Maintainer: Yaoxiang Li <liyaoxiang@outlook.com>
This is a re-admission after prior archival of version 0.1.1 dated 2024-10-04
Diff between medrxivr versions 0.1.1 dated 2024-10-04 and 0.1.3 dated 2026-05-07
DESCRIPTION | 11 + MD5 | 77 ++++++------- NAMESPACE | 1 NEWS.md | 30 +++-- R/helpers.R | 112 +++++++++++++------ R/mx_api.R | 76 +++++++----- R/mx_crosscheck.R | 57 ++++----- R/mx_download.R | 14 +- R/mx_export.R | 6 - R/mx_info.R | 45 ++++--- R/mx_search.R | 173 +++++++++++++++-------------- R/mx_snapshot.R | 223 ++++++++++++++++++++++++++++++++------ R/mx_syntax.R | 9 - README.md | 78 ++++++------- build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/medrxivr.R | 60 +++++----- inst/doc/medrxivr.Rmd | 24 ++-- inst/doc/medrxivr.html | 39 +++--- man/api_page_size.Rd |only man/api_record_count.Rd |only man/figures/hex-medrxivr-wide.png |binary man/figures/logo.png |binary man/inform_snapshot_date.Rd |only man/mx_api_content.Rd | 5 man/mx_api_doi.Rd | 5 man/mx_caps.Rd | 9 - man/mx_crosscheck.Rd | 4 man/mx_download.Rd | 6 - man/mx_export.Rd | 6 - man/mx_info.Rd | 11 + man/mx_search.Rd | 6 - man/mx_snapshot.Rd | 45 ++++--- tests/testthat/helper-fixtures.R |only tests/testthat/test-api.R | 208 ++++++++++++++++++++++++++--------- tests/testthat/test-crosscheck.R | 31 ++++- tests/testthat/test-download.R | 80 +++++-------- tests/testthat/test-export.R | 37 ++---- tests/testthat/test-info.R | 40 ++++++ tests/testthat/test-search.R | 205 +++++++++++++--------------------- tests/testthat/test-snapshot.R |only vignettes/medrxivr.Rmd | 24 ++-- 42 files changed, 1049 insertions(+), 710 deletions(-)
Title: Iota Inter Coder Reliability for Content Analysis
Description: Routines and tools for assessing the quality of content
analysis on the basis of the Iota Reliability Concept. The concept is
inspired by item response theory and can be applied to any kind of
content analysis which uses a standardized coding scheme and discrete
categories. It is also applicable for content analysis conducted by
artificial intelligence. The package provides reliability measures
for a complete scale as well as for every single category. Analysis of
subgroup-invariance and error corrections are implemented. This
information can support the development process of a coding scheme and
allows a detailed inspection of the quality of the generated data.
Equations and formulas working in this package are part of Berding et
al. (2022)<doi:10.3389/feduc.2022.818365> and Berding and Pargmann
(2022) <doi:10.30819/5581>.
Author: Berding Florian [aut, cre] ,
Pargmann Julia [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Diff between iotarelr versions 0.1.8 dated 2026-04-21 and 0.1.9 dated 2026-05-07
DESCRIPTION | 6 - MD5 | 20 ++-- NEWS.md | 4 R/additional_functions.R | 2 README.md | 2 inst/doc/Old_01_How_to_use_Iota1.html | 4 inst/doc/V_02_Estimating_Consequences_for_Subsequent_Analyses.html | 4 inst/doc/V_03_Different_Guidance_Functioning.html | 42 +++++----- inst/doc/V_04_Error_Correction.html | 16 +-- inst/doc/V_05_Test_New_Raters.html | 4 inst/doc/iotarelr.html | 20 ++-- 11 files changed, 64 insertions(+), 60 deletions(-)
Title: Isolate-Detect Method for Multiple Change-Point Detection
Description: The IDetect provides efficient implementation of the ID methodology
for the consistent estimation of the number and location of multiple
change-points in one-dimensional data sequences from the `deterministic
+ noise' model. Currently implemented scenarios are: piecewise-constant signal,
piecewise-constant signal with a heavy-tailed noise, continuous piecewise-linear
signal, continuous piecewise-linear signal with a heavy-tailed noise.
Author: Andreas Anastasiou [aut, cre],
Piotr Fryzlewicz [aut]
Maintainer: Andreas Anastasiou <anastasiou.andreas@ucy.ac.cy>
Diff between IDetect versions 0.1.0 dated 2018-03-09 and 0.1.1 dated 2026-05-07
IDetect-0.1.0/IDetect/man/ID_cplm.Rd |only IDetect-0.1.0/IDetect/man/IDetect.Rd |only IDetect-0.1.0/IDetect/man/cplm_ic.Rd |only IDetect-0.1.0/IDetect/man/cplm_th.Rd |only IDetect-0.1.0/IDetect/man/ht_ID_cplm.Rd |only IDetect-0.1.0/IDetect/man/pcm_ic.Rd |only IDetect-0.1.0/IDetect/man/resid_ID.Rd |only IDetect-0.1.0/IDetect/man/sol_path_cplm.Rd |only IDetect-0.1.0/IDetect/man/win_cplm_th.Rd |only IDetect-0.1.0/IDetect/man/win_pcm_th.Rd |only IDetect-0.1.0/IDetect/tests/testthat/test-ID_cplm.R |only IDetect-0.1.0/IDetect/tests/testthat/test-cplm_ic.R |only IDetect-0.1.0/IDetect/tests/testthat/test-cplm_th.R |only IDetect-0.1.0/IDetect/tests/testthat/test-ht_ID_cplm.R |only IDetect-0.1.0/IDetect/tests/testthat/test-pcm_ic.R |only IDetect-0.1.0/IDetect/tests/testthat/test-resid_ID.R |only IDetect-0.1.0/IDetect/tests/testthat/test-sol_path_cplm.R |only IDetect-0.1.0/IDetect/tests/testthat/test-win_cplm_th.R |only IDetect-0.1.0/IDetect/tests/testthat/test-win_pcm_th.R |only IDetect-0.1.1/IDetect/DESCRIPTION | 34 IDetect-0.1.1/IDetect/MD5 | 80 - IDetect-0.1.1/IDetect/NAMESPACE | 18 IDetect-0.1.1/IDetect/NEWS.md |only IDetect-0.1.1/IDetect/R/Finalised_coding.R | 1079 +++++++------- IDetect-0.1.1/IDetect/R/package-IDetect.R | 19 IDetect-0.1.1/IDetect/inst/CITATION | 11 IDetect-0.1.1/IDetect/man/ID.Rd | 123 - IDetect-0.1.1/IDetect/man/ID_pcm.Rd | 58 IDetect-0.1.1/IDetect/man/ID_plm.Rd |only IDetect-0.1.1/IDetect/man/IDetect-package.Rd |only IDetect-0.1.1/IDetect/man/cpt_ic_pcm.Rd |only IDetect-0.1.1/IDetect/man/cpt_ic_plm.Rd |only IDetect-0.1.1/IDetect/man/cumsum_lin.Rd |only IDetect-0.1.1/IDetect/man/cusum_function.Rd |only IDetect-0.1.1/IDetect/man/cusum_one.Rd |only IDetect-0.1.1/IDetect/man/est_signal.Rd | 29 IDetect-0.1.1/IDetect/man/ht_ID_pcm.Rd | 75 IDetect-0.1.1/IDetect/man/ht_ID_plm.Rd |only IDetect-0.1.1/IDetect/man/linear_contr_one.Rd |only IDetect-0.1.1/IDetect/man/log_lik_slope.Rd |only IDetect-0.1.1/IDetect/man/normalise.Rd | 10 IDetect-0.1.1/IDetect/man/pcm_th.Rd | 58 IDetect-0.1.1/IDetect/man/plm_th.Rd |only IDetect-0.1.1/IDetect/man/resid.Rd |only IDetect-0.1.1/IDetect/man/s_e_points.Rd | 13 IDetect-0.1.1/IDetect/man/sic_pen.Rd |only IDetect-0.1.1/IDetect/man/sol_path_pcm.Rd | 27 IDetect-0.1.1/IDetect/man/sol_path_plm.Rd |only IDetect-0.1.1/IDetect/man/ssic_pen.Rd |only IDetect-0.1.1/IDetect/man/wind_pcm_th.Rd |only IDetect-0.1.1/IDetect/man/wind_plm_th.Rd |only IDetect-0.1.1/IDetect/tests/testthat/test-ID.R | 10 IDetect-0.1.1/IDetect/tests/testthat/test-ID_plm.R |only IDetect-0.1.1/IDetect/tests/testthat/test-cpt_ic_pcm.R |only IDetect-0.1.1/IDetect/tests/testthat/test-cpt_ic_plm.R |only IDetect-0.1.1/IDetect/tests/testthat/test-cusum_one.R | 2 IDetect-0.1.1/IDetect/tests/testthat/test-ht_ID_plm.R |only IDetect-0.1.1/IDetect/tests/testthat/test-plm_th.R |only IDetect-0.1.1/IDetect/tests/testthat/test-resid.R |only IDetect-0.1.1/IDetect/tests/testthat/test-s_e_points.R | 8 IDetect-0.1.1/IDetect/tests/testthat/test-sol_path_pcm.R | 20 IDetect-0.1.1/IDetect/tests/testthat/test-sol_path_plm.R |only IDetect-0.1.1/IDetect/tests/testthat/test-wind_pcm_th.R |only IDetect-0.1.1/IDetect/tests/testthat/test-wind_plm_th.R |only 64 files changed, 901 insertions(+), 773 deletions(-)
Title: Sensitivities of Prices of Financial Options and Implied
Volatilities
Description: Methods to calculate sensitivities of financial option prices for
European, geometric and arithmetic Asian, and American options, with various
payoff functions in the Black Scholes model, and in more general jump diffusion
models. A shiny app to interactively plot the results is included. Furthermore,
methods to compute implied volatilities are provided for a wide range of option
types and custom payoff functions. Classical formulas are implemented for
European options in the Black Scholes Model, as is presented in Hull, J. C.
(2017), Options, Futures, and Other Derivatives.
In the case of Asian options, Malliavin Monte Carlo Greeks are implemented, see
Hudde, A. & Rüschendorf, L. (2023). European and Asian Greeks for exponential
Lévy processes. <doi:10.1007/s11009-023-10014-5>. For American
options, the Binomial Tree Method is implemented, as is presented in Hull,
J. C. (2017).
Author: Anselm Hudde [aut, cre]
Maintainer: Anselm Hudde <anselmhudde@gmx.de>
Diff between greeks versions 1.5.1 dated 2025-11-17 and 1.5.3 dated 2026-05-07
DESCRIPTION | 6 MD5 | 22 - R/BS_European_Greeks.R | 492 ++++--------------------- R/BS_Geometric_Asian_Greeks.R | 240 ------------ R/Binomial_American_Greeks.R | 14 R/RcppExports.R | 8 src/BS_European_Greeks.cpp |only src/BS_Geometric_Asian_Greeks.cpp |only src/Binomial_American_Greeks.cpp | 4 src/RcppExports.cpp | 38 + tests/testthat/test-BS_European_Greeks.R | 60 +++ tests/testthat/test-Binomial_American_Greeks.R | 12 tests/testthat/test-Implied_Volatility.R | 2 13 files changed, 249 insertions(+), 649 deletions(-)
Title: A Blazing Fast Implementation of Random Forest
Description: Yet another implementation of the Random Forest method by Breiman (2001) <doi:10.1023/A:1010933404324>, written in Rust and tailored towards stability, correctness, efficiency and scalability on modern multi-core machines.
Handles both classification and regression, as well as provides permutation feature importance via a novel, highly optimised algorithm.
Author: Miron Bartosz Kursa [aut, cre] ,
Krzysztof Piotr Piwonski [aut]
Maintainer: Miron Bartosz Kursa <m@mbq.me>
Diff between fru versions 0.0.6 dated 2026-04-24 and 0.0.7 dated 2026-05-07
fru-0.0.6/fru/src/fru/vendor.tar.xz |only fru-0.0.7/fru/DESCRIPTION | 7 +++---- fru-0.0.7/fru/MD5 | 11 +++++------ fru-0.0.7/fru/inst/NEWS | 3 +++ fru-0.0.7/fru/src/xrf/Cargo.lock | 2 +- fru-0.0.7/fru/src/xrf/Cargo.toml | 2 +- fru-0.0.7/fru/src/xrf/src/rng.rs | 8 +++++--- 7 files changed, 18 insertions(+), 15 deletions(-)
Title: Data Processing for Aquatic Ecology
Description: Facilitate the analysis of data related to aquatic ecology, specifically the establishment of carbon budget.
Currently, the package allows the below analysis.
(i) the calculation of greenhouse gas flux based on data obtained from trace gas analyzer using the method described in Lin et al. (2024).
(ii) the calculation of Dissolved Oxygen (DO) metabolism based on data obtained from dissolved oxygen data logger using the method described in Staehr et al. (2010).
Yong et al. (2024) <doi:10.5194/bg-21-5247-2024>.
Staehr et al. (2010) <doi:10.4319/lom.2010.8.0628>.
Author: Zhao-Jun Yong [cre, aut]
Maintainer: Zhao-Jun Yong <nuannuan0425@gmail.com>
Diff between aelab versions 1.1.1 dated 2026-02-26 and 1.1.3 dated 2026-05-07
DESCRIPTION | 6 - MD5 | 26 +++---- NAMESPACE | 3 NEWS.md | 16 ++++ R/ghg_flux.R | 49 +++++++++---- R/statistics.R | 75 +++++++++++++++++++- inst/doc/aelab.R | 40 ++++++++++ inst/doc/aelab.Rmd | 57 ++++++++++++++- inst/doc/aelab.html | 142 ++++++++++++++++++++++++++------------- inst/extdata/reference.xlsx |binary man/calculate_regression.Rd | 29 ++++++- man/sig_labels.Rd |only tests/testthat/test-ghg_flux.R | 13 +++ tests/testthat/test-statistics.R |only vignettes/aelab.Rmd | 57 ++++++++++++++- 15 files changed, 415 insertions(+), 98 deletions(-)
Title: Who are You? Bayesian Prediction of Racial Category Using
Surname, First Name, Middle Name, and Geolocation
Description: Predicts individual race/ethnicity using surname, first name,
middle name, geolocation, and other attributes, such as gender and
age. The method utilizes Bayes' Rule (with optional measurement error
correction) to compute the posterior probability of each racial
category for any given individual. The package implements methods
described in Imai and Khanna (2016) "Improving Ecological Inference by
Predicting Individual Ethnicity from Voter Registration Records"
Political Analysis <DOI:10.1093/pan/mpw001> and Imai, Olivella, and
Rosenman (2022) "Addressing census data problems in race imputation
via fully Bayesian Improved Surname Geocoding and name supplements"
<DOI:10.1126/sciadv.adc9824>. The package also incorporates the data
described in Rosenman, Olivella, and Imai (2023) "Race and ethnicity
data for first, middle, and surnames"
<DOI:10.1038/s41597-023-02202-2>.
Author: Kabir Khanna [aut],
Brandon Bertelsen [aut, cre],
Santiago Olivella [aut],
Evan Rosenman [aut],
Alexander Rossell Hayes [aut],
Kosuke Imai [aut],
Noah Dasanaike [aut]
Maintainer: Brandon Bertelsen <brandon@bertelsen.ca>
Diff between wru versions 3.0.3 dated 2024-05-24 and 3.1.0 dated 2026-05-07
DESCRIPTION | 21 +- MD5 | 29 ++- NAMESPACE | 1 R/census_helper_v2.R | 2 R/ebisg_utils.R |only R/predict_race.R | 48 ++++- R/race_prediction_funs.R | 289 ++++++++++++++++++++++++++++++++++ README.md | 87 ++++++++++ man/ebisg.Rd |only man/ebisg_data_preflight.Rd |only man/ebisg_embed_names.Rd |only man/ebisg_model_registry.Rd |only man/ebisg_predict_mlp.Rd |only man/ensure_ebisg_python.Rd |only man/get_ebisg_module.Rd |only man/map_6class_to_5class.Rd |only man/modfuns.Rd | 36 ++++ man/predict_race.Rd | 19 +- man/resolve_ebisg_model.Rd |only man/setup_ebisg.Rd |only tests/testthat/test-ebisg-bug-repro.R |only tests/testthat/test-ebisg.R |only 22 files changed, 504 insertions(+), 28 deletions(-)
Title: Publication-Ready Summary Tables and Forest Plots
Description: A comprehensive framework for descriptive statistics and regression
analysis that produces publication-ready tables and forest plots. Provides a
unified interface from descriptive statistics through multivariable modeling,
with support for linear models, generalized linear models, Cox proportional
hazards, and mixed-effects models. Also includes univariable screening,
multivariate regression, model comparison, and export to multiple formats
including PDF, DOCX, PPTX, 'LaTeX', HTML, and RTF. Built on 'data.table'
for computational efficiency.
Author: Paul Hsin-ti McClelland [aut, cre, cph]
Maintainer: Paul Hsin-ti McClelland <PaulHMcClelland@protonmail.com>
Diff between summata versions 0.11.4 dated 2026-03-20 and 0.11.5 dated 2026-05-07
DESCRIPTION | 10 ++++---- MD5 | 18 +++++++------- NAMESPACE | 1 NEWS.md | 6 ++++ R/imports.R | 5 +++- README.md | 20 ++++++++-------- inst/CITATION | 2 - inst/doc/advanced_workflows.html | 22 ++++++++--------- inst/doc/forest_plots.html | 42 +++++++++++++++++----------------- inst/doc/multivariate_regression.html | 10 ++++---- 10 files changed, 73 insertions(+), 63 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014
<DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic
analysis of functional data through phase and amplitude separation.
Author: J. Derek Tucker [aut, cre] ,
Aymeric Stamm [ctb]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 2.4.3 dated 2026-02-20 and 2.4.4 dated 2026-05-07
DESCRIPTION | 10 ++--- MD5 | 53 ++++++++++++++++--------------- NAMESPACE | 3 + NEWS.md | 3 + R/jointfPCA.R | 4 +- R/pns.R | 25 ++++++++++++++ README.md | 2 - man/beta.Rd | 2 - man/curve2srvf.Rd | 2 - man/discrete2curve.Rd | 2 - man/fastPNSe2s.Rd |only man/fastPNSs2e.Rd |only man/fastpns.Rd |only man/fdasrvf.Rd | 5 ++ man/figures/README-1d_aligned_plot-1.png |binary man/figures/README-1d_aligned_plot-2.png |binary man/figures/README-1d_aligned_plot-3.png |binary man/figures/README-1d_aligned_plot-4.png |binary man/figures/README-1d_aligned_plot-5.png |binary man/figures/README-1d_aligned_plot-6.png |binary man/figures/README-1d_curve_plot-1.png |binary man/growth_vel.Rd | 2 - man/im.Rd | 2 - man/jointFPCAh.Rd | 5 +- man/simu_data.Rd | 2 - man/simu_warp.Rd | 2 - man/simu_warp_median.Rd | 2 - man/toy_data.Rd | 2 - man/toy_warp.Rd | 2 - 29 files changed, 84 insertions(+), 46 deletions(-)
Title: Muscle Near-Infrared Spectroscopy Processing and Analysis
Description: Read, process, and analyse data from muscle near-infrared
spectroscopy (mNIRS) devices. Import raw data from .csv or .xls(x)
files and return time-series data and metadata. Includes standardised
methods for cleaning, filtering, and pre-processing mNIRS data for
subsequent analysis. Also includes a custom plot theme and colour
palette. Intended for mNIRS researchers and practitioners in exercise
physiology, sports science, and clinical rehabilitation with minimal
coding experience required.
Author: Jem Arnold [aut, cre, cph]
Maintainer: Jem Arnold <jem.arnold@gmail.com>
Diff between mnirs versions 0.6.2 dated 2026-04-18 and 0.6.3 dated 2026-05-07
mnirs-0.6.2/mnirs/man/localise_POSIXct.Rd |only mnirs-0.6.2/mnirs/vignettes/_extensions |only mnirs-0.6.3/mnirs/DESCRIPTION | 10 mnirs-0.6.3/mnirs/MD5 | 176 +++---- mnirs-0.6.3/mnirs/NAMESPACE | 1 mnirs-0.6.3/mnirs/NEWS.md | 62 ++ mnirs-0.6.3/mnirs/R/data.R | 10 mnirs-0.6.3/mnirs/R/extract_interval_helpers.R | 54 -- mnirs-0.6.3/mnirs/R/extract_intervals.R | 72 +-- mnirs-0.6.3/mnirs/R/filter_mnirs.R | 18 mnirs-0.6.3/mnirs/R/mnirs_methods.R |only mnirs-0.6.3/mnirs/R/plot.mnirs.R | 163 ++++++- mnirs-0.6.3/mnirs/R/read_mnirs.R | 26 - mnirs-0.6.3/mnirs/R/read_mnirs_helpers.R | 39 + mnirs-0.6.3/mnirs/R/replace_helpers.R | 4 mnirs-0.6.3/mnirs/R/replace_mnirs.R | 28 - mnirs-0.6.3/mnirs/R/resample_mnirs.R | 21 mnirs-0.6.3/mnirs/R/shift_mnirs.R | 6 mnirs-0.6.3/mnirs/R/validate_mnirs.R | 42 + mnirs-0.6.3/mnirs/README.md | 41 - mnirs-0.6.3/mnirs/inst/doc/reading-mnirs-data.R | 5 mnirs-0.6.3/mnirs/inst/doc/reading-mnirs-data.html | 57 +- mnirs-0.6.3/mnirs/inst/doc/reading-mnirs-data.qmd | 7 mnirs-0.6.3/mnirs/inst/extdata/moxy_ramp.xlsx |binary mnirs-0.6.3/mnirs/inst/extdata/portamon-oxcap.xlsx |binary mnirs-0.6.3/mnirs/man/apply_span.Rd | 24 - mnirs-0.6.3/mnirs/man/artinis_intervals.xlsx.Rd | 2 mnirs-0.6.3/mnirs/man/as_plot_data.Rd |only mnirs-0.6.3/mnirs/man/breaks_timespan.Rd | 4 mnirs-0.6.3/mnirs/man/by_time.Rd | 12 mnirs-0.6.3/mnirs/man/compute_helpers.Rd | 10 mnirs-0.6.3/mnirs/man/detect_device_channels.Rd | 2 mnirs-0.6.3/mnirs/man/detect_irregular_samples.Rd | 24 - mnirs-0.6.3/mnirs/man/detect_time_channel.Rd | 34 - mnirs-0.6.3/mnirs/man/device_patterns.Rd | 2 mnirs-0.6.3/mnirs/man/example_mnirs.Rd | 58 +- mnirs-0.6.3/mnirs/man/extract_intervals.Rd | 65 +- mnirs-0.6.3/mnirs/man/extract_start_timestamp.Rd | 24 - mnirs-0.6.3/mnirs/man/figures/README-extract_intervals_distinct-1.png |binary mnirs-0.6.3/mnirs/man/figures/README-extract_intervals_ensemble-1.png |binary mnirs-0.6.3/mnirs/man/figures/README-filter_mnirs-1.png |binary mnirs-0.6.3/mnirs/man/figures/README-pipeline-1.png |binary mnirs-0.6.3/mnirs/man/figures/README-read_mnirs-1.png |binary mnirs-0.6.3/mnirs/man/figures/README-replace_mnirs-1.png |binary mnirs-0.6.3/mnirs/man/figures/README-rescale_mnirs-1.png |binary mnirs-0.6.3/mnirs/man/figures/README-shift_mnirs-1.png |binary mnirs-0.6.3/mnirs/man/figures/lifecycle-deprecated.svg | 42 - mnirs-0.6.3/mnirs/man/figures/lifecycle-experimental.svg | 42 - mnirs-0.6.3/mnirs/man/figures/lifecycle-stable.svg | 58 +- mnirs-0.6.3/mnirs/man/figures/lifecycle-superseded.svg | 42 - mnirs-0.6.3/mnirs/man/filter_ma.Rd | 6 mnirs-0.6.3/mnirs/man/filter_mnirs.Rd | 29 - mnirs-0.6.3/mnirs/man/format_hmmss.Rd | 4 mnirs-0.6.3/mnirs/man/is_empty.Rd | 24 - mnirs-0.6.3/mnirs/man/make_list.Rd | 24 - mnirs-0.6.3/mnirs/man/mnirs_metadata.Rd | 33 - mnirs-0.6.3/mnirs/man/name_channels.Rd | 24 - mnirs-0.6.3/mnirs/man/parse_sample_rate.Rd | 38 - mnirs-0.6.3/mnirs/man/plot.mnirs.Rd | 39 + mnirs-0.6.3/mnirs/man/portamon-oxcap.xlsx.Rd | 8 mnirs-0.6.3/mnirs/man/print.mnirs.Rd |only mnirs-0.6.3/mnirs/man/read_data_table.Rd | 2 mnirs-0.6.3/mnirs/man/read_file.Rd | 24 - mnirs-0.6.3/mnirs/man/read_mnirs.Rd | 4 mnirs-0.6.3/mnirs/man/recycle_span.Rd | 4 mnirs-0.6.3/mnirs/man/rename_duplicates.Rd | 24 - mnirs-0.6.3/mnirs/man/replace_mnirs.Rd | 36 - mnirs-0.6.3/mnirs/man/resample_mnirs.Rd | 8 mnirs-0.6.3/mnirs/man/rescale_mnirs.Rd | 4 mnirs-0.6.3/mnirs/man/shift_mnirs.Rd | 16 mnirs-0.6.3/mnirs/man/validate_mnirs.Rd | 12 mnirs-0.6.3/mnirs/tests/testthat.R | 24 - mnirs-0.6.3/mnirs/tests/testthat/test-extract_intervals.R | 109 +++- mnirs-0.6.3/mnirs/tests/testthat/test-filter_mnirs.R | 4 mnirs-0.6.3/mnirs/tests/testthat/test-plot.mnirs.R | 142 ++++++ mnirs-0.6.3/mnirs/tests/testthat/test-read_mnirs.R | 222 +++++++++- mnirs-0.6.3/mnirs/tests/testthat/test-replace_mnirs.R | 2 mnirs-0.6.3/mnirs/tests/testthat/test-resample_mnirs.R | 36 + mnirs-0.6.3/mnirs/tests/testthat/test-shift_mnirs.R | 2 mnirs-0.6.3/mnirs/tests/testthat/test-validate_mnirs.R | 10 mnirs-0.6.3/mnirs/vignettes/reading-mnirs-data.qmd | 7 81 files changed, 1392 insertions(+), 816 deletions(-)
Title: Kim Filter
Description: 'Rcpp' implementation of the multivariate Kim filter, which combines the Kalman and Hamilton filters for state probability inference.
The filter is designed for state space models and can handle missing values and exogenous data in the observation and state equations.
Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard [aut, cre]
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Diff between kimfilter versions 1.1.0 dated 2025-10-17 and 2.0.0 dated 2026-05-07
kimfilter-1.1.0/kimfilter/man/Rginv.Rd |only kimfilter-1.1.0/kimfilter/man/contains.Rd |only kimfilter-1.1.0/kimfilter/man/gen_inv.Rd |only kimfilter-1.1.0/kimfilter/man/kim_filter_cpp.Rd |only kimfilter-1.1.0/kimfilter/man/self_rbind.Rd |only kimfilter-2.0.0/kimfilter/DESCRIPTION | 10 kimfilter-2.0.0/kimfilter/MD5 | 29 kimfilter-2.0.0/kimfilter/NEWS.md | 6 kimfilter-2.0.0/kimfilter/R/RcppExports.R | 75 kimfilter-2.0.0/kimfilter/R/kim_filter.R | 32 kimfilter-2.0.0/kimfilter/inst/doc/kimfilter_vignette.R | 5 kimfilter-2.0.0/kimfilter/inst/doc/kimfilter_vignette.Rmd | 35 kimfilter-2.0.0/kimfilter/inst/doc/kimfilter_vignette.html | 610 ++--- kimfilter-2.0.0/kimfilter/man/kimfilter-package.Rd | 5 kimfilter-2.0.0/kimfilter/man/ss_prob.Rd | 61 kimfilter-2.0.0/kimfilter/src/RcppExports.cpp | 38 kimfilter-2.0.0/kimfilter/src/kimfilter.cpp | 1549 ++++++++----- kimfilter-2.0.0/kimfilter/vignettes/kimfilter_vignette.Rmd | 35 18 files changed, 1477 insertions(+), 1013 deletions(-)
Title: Chat with Large Language Models
Description: Chat with large language models from a range of providers
including 'Claude' <https://claude.ai>, 'OpenAI'
<https://chatgpt.com>, and more. Supports streaming, asynchronous
calls, tool calling, and structured data extraction.
Author: Hadley Wickham [aut, cre] ,
Joe Cheng [aut],
Aaron Jacobs [aut],
Garrick Aden-Buie [aut] ,
Barret Schloerke [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between ellmer versions 0.4.0 dated 2025-11-15 and 0.4.1 dated 2026-05-07
DESCRIPTION | 39 MD5 | 202 ++-- NAMESPACE | 4 NEWS.md | 26 R/chat-tools.R | 20 R/chat.R | 357 +++++-- R/content.R | 7 R/httr2.R | 44 R/import-standalone-defer.R |only R/otel.R |only R/provider-aws.R | 175 +++ R/provider-claude-tools.R | 22 R/provider-claude.R | 59 - R/provider-databricks.R | 2 R/provider-github.R | 10 R/provider-google-tools.R | 22 R/provider-google.R | 53 - R/provider-groq.R | 43 R/provider-lmstudio.R |only R/provider-ollama.R | 1 R/provider-openai-compatible.R | 91 +- R/provider-openai-tools.R | 11 R/provider-openai.R | 34 R/provider-openrouter.R | 3 R/provider-snowflake.R | 208 ++-- R/provider.R | 21 R/stream-controller.R |only R/sysdata.rda |binary R/tokens.R | 7 R/tools-built-in.R | 7 R/turns.R | 17 R/types.R | 2 R/utils.R | 9 R/zzz.R | 1 build/vignette.rds |binary inst/_vcr/tool.yml | 62 - inst/doc/ellmer.Rmd | 2 inst/doc/ellmer.html | 2 inst/doc/programming.html | 182 ++-- inst/doc/structured-data.Rmd | 2 inst/doc/structured-data.html | 10 inst/doc/tool-calling.html | 46 - man/Chat.Rd | 727 ++++++++-------- man/Content.Rd | 7 man/Turn.Rd | 15 man/chat_anthropic.Rd | 41 man/chat_aws_bedrock.Rd | 82 + man/chat_azure_openai.Rd | 35 man/chat_cloudflare.Rd | 35 man/chat_databricks.Rd | 35 man/chat_deepseek.Rd | 35 man/chat_github.Rd | 42 man/chat_google_gemini.Rd | 38 man/chat_groq.Rd | 42 man/chat_huggingface.Rd | 35 man/chat_lmstudio.Rd |only man/chat_mistral.Rd | 35 man/chat_ollama.Rd | 38 man/chat_openai.Rd | 38 man/chat_openai_compatible.Rd | 42 man/chat_openrouter.Rd | 35 man/chat_perplexity.Rd | 38 man/chat_portkey.Rd | 38 man/chat_vllm.Rd | 3 man/claude_tool_web_fetch.Rd | 10 man/claude_tool_web_search.Rd | 10 man/contents_text.Rd | 2 man/ellmer-package.Rd | 1 man/google_tool_web_fetch.Rd | 10 man/google_tool_web_search.Rd | 10 man/google_upload.Rd | 3 man/openai_tool_web_search.Rd | 10 man/stream_controller.Rd |only man/tool.Rd | 6 man/tool_annotations.Rd | 6 man/tool_reject.Rd | 6 man/type_boolean.Rd | 2 tests/testthat/_snaps/chat.md | 42 tests/testthat/_snaps/provider-aws.md | 2 tests/testthat/_snaps/provider-lmstudio.md |only tests/testthat/_snaps/provider-openrouter.md | 4 tests/testthat/_snaps/tokens.md | 10 tests/testthat/_vcr/aws-bedrock-thinking.yml |only tests/testthat/_vcr/chat-tools-callbacks.yml | 66 - tests/testthat/_vcr/chat-tools-failure.yml | 80 - tests/testthat/_vcr/chat-tools-reject-callback.yml | 70 - tests/testthat/_vcr/chat-tools-reject-tool-function.yml | 68 - tests/testthat/_vcr/chat-tools-sequential.yml | 94 +- tests/testthat/_vcr/openai-v2-web-search.yml | 185 ++-- tests/testthat/helper-provider-aws.R |only tests/testthat/test-chat.R | 205 ++++ tests/testthat/test-otel.R |only tests/testthat/test-provider-aws.R | 171 +++ tests/testthat/test-provider-claude.R | 194 ++++ tests/testthat/test-provider-databricks.R | 14 tests/testthat/test-provider-google.R | 2 tests/testthat/test-provider-groq.R | 8 tests/testthat/test-provider-lmstudio.R |only tests/testthat/test-provider-openai-compatible.R | 137 +++ tests/testthat/test-provider-openai.R | 80 + tests/testthat/test-provider-snowflake.R | 219 ++++ tests/testthat/test-tokens.R | 9 tests/testthat/test-tools-built-in.R |only vignettes/_vcr/tool-calling-inputs-outputs.yml | 68 - vignettes/_vcr/tool-calling-no-tool.yml | 32 vignettes/_vcr/tool-calling-with-tool.yml | 72 - vignettes/ellmer.Rmd | 2 vignettes/structured-data.Rmd | 2 108 files changed, 3436 insertions(+), 1715 deletions(-)
Title: Calculate Metrics for Trauma System Performance
Description: Hospitals, hospital systems, and even trauma systems that
provide care to injured patients may not be aware of robust metrics
that can help gauge the efficacy of their programs in saving the lives
of injured patients. 'traumar' provides robust functions driven by
the academic literature to automate the calculation of relevant
metrics to individuals desiring to measure the performance of their
trauma center or even a trauma system. 'traumar' also provides some
helper functions for the data analysis journey. Users can refer to the
following publications for descriptions of the methods used in
'traumar'. TRISS methodology, including probability of survival, and
the W, M, and Z Scores - Flora (1978)
<doi:10.1097/00005373-197810000-00003>, Boyd et al. (1987,
PMID:3106646), Llullaku et al. (2009) <doi:10.1186/1749-7922-4-2>,
Singh et al. (2011) <doi:10.4103/0974-2700.86626>, Baker et al. (1974,
PMID:4814394), and Champion et al. (1989)
<doi:10.1097/00005373-198905000- [...truncated...]
Author: Nicolas Foss [aut, cre],
Iowa Department of Health and Human Services [cph]
Maintainer: Nicolas Foss <nicolas.foss@hhs.iowa.gov>
Diff between traumar versions 1.2.5 dated 2026-04-16 and 1.2.6 dated 2026-05-07
traumar-1.2.5/traumar/man/validate_character_factor.Rd |only traumar-1.2.5/traumar/man/validate_choice.Rd |only traumar-1.2.5/traumar/man/validate_class.Rd |only traumar-1.2.5/traumar/man/validate_complete.Rd |only traumar-1.2.5/traumar/man/validate_data_pull.Rd |only traumar-1.2.5/traumar/man/validate_data_structure.Rd |only traumar-1.2.5/traumar/man/validate_error_type.Rd |only traumar-1.2.5/traumar/man/validate_length.Rd |only traumar-1.2.5/traumar/man/validate_names.Rd |only traumar-1.2.5/traumar/man/validate_numeric.Rd |only traumar-1.2.5/traumar/man/validate_set.Rd |only traumar-1.2.6/traumar/DESCRIPTION | 16 +-- traumar-1.2.6/traumar/MD5 | 48 ++++------ traumar-1.2.6/traumar/NEWS.md | 16 +++ traumar-1.2.6/traumar/R/pretty_number.r | 8 - traumar-1.2.6/traumar/R/pretty_percent.r | 2 traumar-1.2.6/traumar/R/validate_character_factor.R | 3 traumar-1.2.6/traumar/R/validate_choice.R | 3 traumar-1.2.6/traumar/R/validate_class.R | 3 traumar-1.2.6/traumar/R/validate_complete.R | 3 traumar-1.2.6/traumar/R/validate_data_pull.R | 3 traumar-1.2.6/traumar/R/validate_data_structure.R | 3 traumar-1.2.6/traumar/R/validate_error_type.R | 6 + traumar-1.2.6/traumar/R/validate_length.R | 3 traumar-1.2.6/traumar/R/validate_names.R | 3 traumar-1.2.6/traumar/R/validate_numeric.R | 4 traumar-1.2.6/traumar/R/validate_set.R | 3 traumar-1.2.6/traumar/tests/testthat/test-pretty_number.R | 9 - traumar-1.2.6/traumar/tests/testthat/test-validate_error_type.R |only traumar-1.2.6/traumar/tests/testthat/test-validate_length.R |only traumar-1.2.6/traumar/tests/testthat/test-validate_names.R |only traumar-1.2.6/traumar/tests/testthat/test-validate_numeric.R |only traumar-1.2.6/traumar/tests/testthat/test-validate_set.R |only 33 files changed, 88 insertions(+), 48 deletions(-)
Title: Access to the 'RESOURCECODE' Hindcast Database
Description: Utility functions to download data from the 'RESOURCECODE'
hindcast database of sea-states, time series of sea-state parameters
and time series of 1D and 2D wave spectra. See
<https://resourcecode.ifremer.fr> for more details about the available
data. Also provides facilities to plot and analyse downloaded data,
such as computing the sea-state parameters from both the 1D and 2D
surface elevation variance spectral density.
Author: Nicolas Raillard [aut, cre]
Maintainer: Nicolas Raillard <nicolas.raillard@ifremer.fr>
Diff between resourcecode versions 0.5.3 dated 2026-02-06 and 0.5.4 dated 2026-05-07
resourcecode-0.5.3/resourcecode/data/rscd_dir.rda |only resourcecode-0.5.3/resourcecode/data/rscd_freq.rda |only resourcecode-0.5.3/resourcecode/man/rscd_dir.Rd |only resourcecode-0.5.3/resourcecode/man/rscd_freq.Rd |only resourcecode-0.5.4/resourcecode/DESCRIPTION | 9 -- resourcecode-0.5.4/resourcecode/MD5 | 44 ++++------ resourcecode-0.5.4/resourcecode/NEWS.md | 5 + resourcecode-0.5.4/resourcecode/R/data.R | 24 ----- resourcecode-0.5.4/resourcecode/R/download_data.R | 7 + resourcecode-0.5.4/resourcecode/R/orbital_speed.R | 17 ++- resourcecode-0.5.4/resourcecode/R/plots.R | 13 +- resourcecode-0.5.4/resourcecode/R/resourcecode-package.R | 2 resourcecode-0.5.4/resourcecode/R/specta_data_ploting.R | 11 +- resourcecode-0.5.4/resourcecode/R/sysdata.rda |binary resourcecode-0.5.4/resourcecode/R/utils.R | 8 + resourcecode-0.5.4/resourcecode/R/weather_windows.R | 7 + resourcecode-0.5.4/resourcecode/build/vignette.rds |binary resourcecode-0.5.4/resourcecode/data/rscd_data_example.rda |binary resourcecode-0.5.4/resourcecode/man/compute_orbital_speeds.Rd | 2 resourcecode-0.5.4/resourcecode/man/figures/README-data_fetcher-1.png |binary resourcecode-0.5.4/resourcecode/man/jonswap.Rd | 8 + resourcecode-0.5.4/resourcecode/man/resourcecode-package.Rd | 5 + resourcecode-0.5.4/resourcecode/tests/testthat/test-test_closest_point.R | 21 +++- resourcecode-0.5.4/resourcecode/tests/testthat/test_ww_calc.R | 30 +++++- resourcecode-0.5.4/resourcecode/tests/testthat/tests_download_parameters.R | 13 ++ 25 files changed, 135 insertions(+), 91 deletions(-)
Title: Analyze Multiple Exposure Realizations in Association Studies
Description: Analyze association studies with multiple realizations of a noisy or uncertain exposure. These can be obtained from e.g. a two-dimensional Monte Carlo dosimetry system (Simon et al 2015 <doi:10.1667/RR13729.1>) to characterize exposure uncertainty.
The implemented methods are regression calibration (Carroll et al. 2006 <doi:10.1201/9781420010138>), extended
regression calibration (Little et al. 2023 <doi:10.1038/s41598-023-42283-y>), Monte Carlo maximum
likelihood (Stayner et al. 2007 <doi:10.1667/RR0677.1>), frequentist model averaging (Kwon et al. 2023 <doi:10.1371/journal.pone.0290498>),
and Bayesian model averaging (Kwon et al. 2016 <doi:10.1002/sim.6635>). Supported model families are
Gaussian, binomial, multinomial, Poisson, proportional hazards, and conditional logistic.
Author: Sander Roberti [aut, cre] ,
William Wheeler [aut],
Deukwoo Kwon [aut] ,
Ruth Pfeiffer [ctb] ,
NCI [cph, fnd]
Maintainer: Sander Roberti <sander.roberti@nih.gov>
Diff between ameras versions 0.2.0 dated 2026-04-26 and 0.3.0 dated 2026-05-07
DESCRIPTION | 6 MD5 | 85 +++--- NAMESPACE | 48 +++ NEWS.md | 19 + R/RcppExports.R | 12 R/ameras.R | 29 +- R/amerasfit-class.R | 12 R/check.R | 2 R/likelihoods.R | 54 ++-- R/methods-fma-bma.R | 58 ++-- R/methods-rc-mcml.R | 8 R/plots.R | 32 ++ R/source.R | 54 ---- README.md | 51 ++- inst/doc/confidenceintervals.html | 63 ++-- inst/doc/modelfitting.Rmd | 2 inst/doc/modelfitting.html | 153 +++++------ inst/doc/relativeriskmodels.html | 4 inst/doc/transformations.html | 8 man/ameras-package.Rd | 2 man/ameras.Rd | 18 - man/data.Rd | 2 man/ecdfplot.Rd | 13 - man/figures/README-unnamed-chunk-2-1.png |binary man/print.Rd | 2 src/RcppExports.cpp | 53 ++-- src/ameras.cpp | 403 ++++++++++++++----------------- src/ameras_init.c | 34 ++ tests/testthat.R |only tests/testthat/_snaps/CI.md | 319 +++++++++++++----------- tests/testthat/_snaps/binomial.md | 295 ++++++++++++---------- tests/testthat/_snaps/clogit.md | 142 +++++----- tests/testthat/_snaps/gaussian.md | 173 +++++++------ tests/testthat/_snaps/multinomial.md | 241 ++++++++++-------- tests/testthat/_snaps/poisson.md | 160 ++++++------ tests/testthat/_snaps/prophaz.md | 181 +++++++------ tests/testthat/test-CI.R | 77 ++++- tests/testthat/test-binomial.R | 22 + tests/testthat/test-clogit.R | 11 tests/testthat/test-gaussian.R | 11 tests/testthat/test-multinomial.R | 11 tests/testthat/test-poisson.R | 11 tests/testthat/test-prophaz.R | 13 - vignettes/modelfitting.Rmd | 2 44 files changed, 1561 insertions(+), 1335 deletions(-)
Title: Detect Text Reuse and Document Similarity
Description: Tools for measuring similarity among documents and detecting
passages which have been reused. Implements shingled n-gram, skip n-gram,
and other tokenizers; similarity/dissimilarity functions; pairwise
comparisons; minhash and locality sensitive hashing algorithms; and a
version of the Smith-Waterman local alignment algorithm suitable for
natural language.
Author: Lincoln Mullen [aut] ,
Yaoxiang Li [aut, cre]
Maintainer: Yaoxiang Li <liyaoxiang@outlook.com>
Diff between textreuse versions 0.1.5 dated 2020-05-15 and 1.0.1 dated 2026-05-07
DESCRIPTION | 31 LICENSE | 4 MD5 | 203 NAMESPACE | 210 NEWS.md | 107 R/RcppExports.R | 52 R/TextReuseCorpus.R | 517 R/TextReuseTextDocument.R | 771 R/align_local.R | 499 R/conversion-functions.R | 97 R/filenames.R | 46 R/lsh.R | 333 R/lsh_candidates.R | 78 R/lsh_compare.R | 122 R/lsh_probability.R | 111 R/lsh_query.R | 81 R/lsh_subset.R | 42 R/minhash.R | 128 R/pairwise_candidates.R | 70 R/pairwise_compare.R | 150 R/parallel.R | 28 R/rehash.R | 118 R/similarity.R | 313 R/textreuse-package.r | 102 R/token_index.R |only R/tokenize.R | 164 R/tokenizers.R | 122 R/utils.R | 192 R/wordcount.R | 50 README.md | 493 build/vignette.rds |binary inst/doc/textreuse-alignment.R | 40 inst/doc/textreuse-alignment.Rmd | 84 inst/doc/textreuse-alignment.html | 777 inst/doc/textreuse-introduction.R | 146 inst/doc/textreuse-introduction.Rmd | 322 inst/doc/textreuse-introduction.html | 1188 inst/doc/textreuse-minhash.R | 78 inst/doc/textreuse-minhash.Rmd | 180 inst/doc/textreuse-minhash.html | 920 inst/doc/textreuse-pairwise.R | 50 inst/doc/textreuse-pairwise.Rmd | 108 inst/doc/textreuse-pairwise.html | 785 inst/extdata/ats/calltounconv00baxt.txt |34366 +++++++++++------------ inst/extdata/ats/gospeltruth00whit.txt | 6668 ++-- inst/extdata/ats/lifeofrevrichard00baxt.txt |13362 ++++----- inst/extdata/ats/memoirjamesbrai00ricegoog.txt |36962 ++++++++++++------------- inst/extdata/ats/practicalthought00nev.txt |33602 +++++++++++----------- inst/extdata/ats/remember00palm.txt | 6070 ++-- inst/extdata/ats/remembermeorholy00palm.txt | 6228 ++-- inst/extdata/ats/thoughtsonpopery00nevi.txt |17132 +++++------ inst/extdata/legal/ca1851-match.txt | 160 inst/extdata/legal/ca1851-nomatch.txt | 48 inst/extdata/legal/ny1850-match.txt | 222 man/TextReuseCorpus.Rd | 207 man/TextReuseTextDocument-accessors.Rd | 74 man/TextReuseTextDocument.Rd | 225 man/align_local.Rd | 189 man/as.matrix.textreuse_candidates.Rd | 42 man/filenames.Rd | 54 man/hash_string.Rd | 42 man/lsh.Rd | 151 man/lsh_add.Rd |only man/lsh_candidates.Rd | 56 man/lsh_compare.Rd | 83 man/lsh_probability.Rd | 113 man/lsh_query.Rd | 64 man/lsh_subset.Rd | 60 man/minhash_generator.Rd | 108 man/pairwise_candidates.Rd | 68 man/pairwise_compare.Rd | 110 man/reexports.Rd | 38 man/rehash.Rd | 74 man/similarity-functions.Rd | 208 man/textreuse-package.Rd | 138 man/token_index.Rd |only man/token_index_candidates.Rd |only man/tokenize.Rd | 104 man/tokenizers.Rd | 92 man/wordcount.Rd | 40 src/RcppExports.cpp | 5 src/hash_string.cpp | 1 src/shingle_ngrams.cpp | 1 src/skip_ngrams.cpp | 1 tests/testthat.R | 8 tests/testthat/newman.txt | 56 tests/testthat/test-TextReuseCorpus.R | 246 tests/testthat/test-TextReuseTextDocument.R | 206 tests/testthat/test-alignment.R | 67 tests/testthat/test-candidate_pairs.R | 53 tests/testthat/test-filenames.R | 16 tests/testthat/test-hashing.R | 40 tests/testthat/test-jaccard.R | 62 tests/testthat/test-lsh.R | 136 tests/testthat/test-minhash.R | 62 tests/testthat/test-pairwise_cf.R | 40 tests/testthat/test-ratio_of_matches.R | 62 tests/testthat/test-token_index.R |only tests/testthat/test-tokenizers.R | 146 tests/testthat/test-utils.R | 56 tests/testthat/test-wordcount.R | 36 vignettes/textreuse-alignment.Rmd | 84 vignettes/textreuse-introduction.Rmd | 322 vignettes/textreuse-minhash.Rmd | 180 vignettes/textreuse-pairwise.Rmd | 108 105 files changed, 84880 insertions(+), 84186 deletions(-)
Title: Proteomics Data Analysis and Modeling Tools
Description: A comprehensive, user-friendly package for label-free proteomics data analysis and machine learning-based modeling. Data generated from 'MaxQuant' can be easily used to conduct differential expression analysis, build predictive models with top protein candidates, and assess model performance. promor includes a suite of tools for quality control, visualization, missing data imputation (Lazar et. al. (2016) <doi:10.1021/acs.jproteome.5b00981>), differential expression analysis (Ritchie et. al. (2015) <doi:10.1093/nar/gkv007>), and machine learning-based modeling (Kuhn (2008) <doi:10.18637/jss.v028.i05>).
Author: Chathurani Ranathunge [aut, cre, cph]
Maintainer: Chathurani Ranathunge <caranathunge86@gmail.com>
This is a re-admission after prior archival of version 0.2.2 dated 2025-11-11
Diff between promor versions 0.2.2 dated 2025-11-11 and 0.2.3 dated 2026-05-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ tests/testthat/test-protein_analysis.R | 30 +----------------------------- 4 files changed, 13 insertions(+), 35 deletions(-)
Title: Penalized Synthetic Control Estimation
Description: Estimate penalized synthetic control models
and perform hold-out validation to determine their
penalty parameter. This method is based on the work by
Abadie & L'Hour (2021) <doi:10.1080/01621459.2021.1971535>.
Penalized synthetic controls smoothly interpolate between
one-to-one matching and the synthetic control method.
Author: Erik-Jan van Kesteren [cre, aut] ,
Isaac Slaughter [ctb]
Maintainer: Erik-Jan van Kesteren <erikjanvankesteren@pm.me>
Diff between pensynth versions 0.8.1 dated 2025-10-13 and 0.8.2 dated 2026-05-07
DESCRIPTION | 10 MD5 | 68 +- NAMESPACE | 60 +- R/convex_hull.R | 206 ++++---- R/cv_pensynth.R | 804 +++++++++++++++++------------------ R/examples/example_convex_hull.R | 22 R/examples/example_cv_pensynth.R | 8 R/examples/example_pensynth.R | 50 +- R/examples/example_placebo_test.R | 36 - R/examples/example_showcase.R | 88 +-- R/examples/example_simulate.R | 56 +- R/examples/example_simulate_factor.R | 62 +- R/pensynth.R | 352 +++++++-------- R/placebo_test.R | 348 +++++++-------- R/simulate_data.R | 600 +++++++++++++------------- R/standardization.R | 48 +- man/cv_pensynth.Rd | 140 +++--- man/in_convex_hull.Rd | 110 ++-- man/lambda_sequence.Rd | 72 +-- man/mvrarnorm.Rd | 60 +- man/pensynth.Rd | 176 +++---- man/placebo_test.Rd | 158 +++--- man/plot.cvpensynth.Rd | 50 +- man/plot.pensynthtest.Rd | 52 +- man/predict.cvpensynth.Rd | 62 +- man/predict.pensynth.Rd | 48 +- man/print.cvpensynth.Rd | 38 - man/print.pensynth.Rd | 38 - man/rarnorm.Rd | 56 +- man/simulate_data_factor.Rd | 238 +++++----- tests/testthat/test-convexhull.R | 32 - tests/testthat/test-cvpensynth.R | 62 +- tests/testthat/test-pensynth.R | 54 +- tests/testthat/test-placebo_test.R | 84 +-- tests/testthat/test-simulate_data.R | 98 ++-- 35 files changed, 2223 insertions(+), 2223 deletions(-)
Title: R Client for the Interactive Brokers Client Portal API
Description: Provides a lightweight R interface to the Interactive Brokers (IBKR)
Client Portal REST API. Functions cover session management, account and portfolio
queries, market data retrieval, and order placement and cancellation. Requires a
locally running IBKR Client Portal Gateway.
Author: Nagappan Karuppiah [aut, cre]
Maintainer: Nagappan Karuppiah <sactyr@gmail.com>
Diff between ibkrcp versions 0.1.0 dated 2026-05-06 and 0.1.1 dated 2026-05-07
ibkrcp-0.1.0/ibkrcp/R/account.r |only ibkrcp-0.1.0/ibkrcp/R/market_data.r |only ibkrcp-0.1.0/ibkrcp/R/orders.r |only ibkrcp-0.1.0/ibkrcp/R/session.r |only ibkrcp-0.1.0/ibkrcp/R/utils.r |only ibkrcp-0.1.0/ibkrcp/man/ibkr_get_accounts.Rd |only ibkrcp-0.1.0/ibkrcp/man/ibkr_get_orders.Rd |only ibkrcp-0.1.0/ibkrcp/man/ibkr_get_positions.Rd |only ibkrcp-0.1.0/ibkrcp/man/ibkr_get_summary.Rd |only ibkrcp-0.1.0/ibkrcp/man/ibkr_reauthenticate.Rd |only ibkrcp-0.1.0/ibkrcp/man/ibkr_tickle.Rd |only ibkrcp-0.1.0/ibkrcp/tests/testthat/localhost-5000/v1/api/iserver/orders.json |only ibkrcp-0.1.0/ibkrcp/tests/testthat/localhost-5000/v1/api/iserver/reauthenticate.json |only ibkrcp-0.1.0/ibkrcp/tests/testthat/localhost-5000/v1/api/iserver/secdef/search-5b4185.json |only ibkrcp-0.1.0/ibkrcp/tests/testthat/localhost-5000/v1/api/portfolio/U1234567/positions |only ibkrcp-0.1.0/ibkrcp/tests/testthat/no_orders/localhost-5000/v1/api/iserver/orders.json |only ibkrcp-0.1.0/ibkrcp/tests/testthat/no_positions/localhost-5000/v1/api/portfolio |only ibkrcp-0.1.0/ibkrcp/tests/testthat/test_account.r |only ibkrcp-0.1.0/ibkrcp/tests/testthat/test_session.r |only ibkrcp-0.1.0/ibkrcp/tests/testthat/unauthenticated |only ibkrcp-0.1.1/ibkrcp/DESCRIPTION | 13 ibkrcp-0.1.1/ibkrcp/LICENSE | 4 ibkrcp-0.1.1/ibkrcp/MD5 | 89 +- ibkrcp-0.1.1/ibkrcp/NAMESPACE | 11 ibkrcp-0.1.1/ibkrcp/NEWS.md |only ibkrcp-0.1.1/ibkrcp/R/contracts.R |only ibkrcp-0.1.1/ibkrcp/R/market_data.R |only ibkrcp-0.1.1/ibkrcp/R/orders.R |only ibkrcp-0.1.1/ibkrcp/R/portfolio.R |only ibkrcp-0.1.1/ibkrcp/R/session.R |only ibkrcp-0.1.1/ibkrcp/R/utils.R |only ibkrcp-0.1.1/ibkrcp/build/vignette.rds |binary ibkrcp-0.1.1/ibkrcp/inst/WORDLIST | 3 ibkrcp-0.1.1/ibkrcp/inst/doc/ibkrcp.Rmd | 382 +++++----- ibkrcp-0.1.1/ibkrcp/man/ibkr_auth_status.Rd | 30 ibkrcp-0.1.1/ibkrcp/man/ibkr_cancel_order.Rd | 38 ibkrcp-0.1.1/ibkrcp/man/ibkr_get_price_history.Rd | 48 - ibkrcp-0.1.1/ibkrcp/man/ibkr_get_trading_schedule.Rd | 52 - ibkrcp-0.1.1/ibkrcp/man/ibkr_live_orders.Rd |only ibkrcp-0.1.1/ibkrcp/man/ibkr_ping.Rd |only ibkrcp-0.1.1/ibkrcp/man/ibkr_place_order.Rd | 50 - ibkrcp-0.1.1/ibkrcp/man/ibkr_portfolio_accounts.Rd |only ibkrcp-0.1.1/ibkrcp/man/ibkr_portfolio_positions.Rd |only ibkrcp-0.1.1/ibkrcp/man/ibkr_portfolio_summary.Rd |only ibkrcp-0.1.1/ibkrcp/man/ibkr_search_contracts.Rd | 46 - ibkrcp-0.1.1/ibkrcp/tests/testthat.R | 24 ibkrcp-0.1.1/ibkrcp/tests/testthat/localhost-5000/v1/api/iserver/account/U1234567/order/1001.json | 8 ibkrcp-0.1.1/ibkrcp/tests/testthat/localhost-5000/v1/api/iserver/account/U1234567/orders-50e22c-POST.json | 12 ibkrcp-0.1.1/ibkrcp/tests/testthat/localhost-5000/v1/api/iserver/account/orders-b2e57e.json |only ibkrcp-0.1.1/ibkrcp/tests/testthat/localhost-5000/v1/api/iserver/auth/status.json | 14 ibkrcp-0.1.1/ibkrcp/tests/testthat/localhost-5000/v1/api/iserver/marketdata/history-45530b.json | 12 ibkrcp-0.1.1/ibkrcp/tests/testthat/localhost-5000/v1/api/iserver/secdef/search-82afae-POST.json |only ibkrcp-0.1.1/ibkrcp/tests/testthat/localhost-5000/v1/api/portfolio/U1234567/summary.json | 34 ibkrcp-0.1.1/ibkrcp/tests/testthat/localhost-5000/v1/api/portfolio/accounts.json | 16 ibkrcp-0.1.1/ibkrcp/tests/testthat/localhost-5000/v1/api/portfolio2 |only ibkrcp-0.1.1/ibkrcp/tests/testthat/localhost-5000/v1/api/tickle.json | 20 ibkrcp-0.1.1/ibkrcp/tests/testthat/localhost-5000/v1/api/trsrv/secdef/schedule-c1b48e.json | 34 ibkrcp-0.1.1/ibkrcp/tests/testthat/no_history/localhost-5000/v1/api/iserver/marketdata/history-45530b.json | 6 ibkrcp-0.1.1/ibkrcp/tests/testthat/no_orders/localhost-5000/v1/api/iserver/account |only ibkrcp-0.1.1/ibkrcp/tests/testthat/no_positions/localhost-5000/v1/api/portfolio2 |only ibkrcp-0.1.1/ibkrcp/tests/testthat/test_market_data.R | 140 +-- ibkrcp-0.1.1/ibkrcp/tests/testthat/test_orders.R | 130 +-- ibkrcp-0.1.1/ibkrcp/tests/testthat/test_portfolio.R |only ibkrcp-0.1.1/ibkrcp/tests/testthat/test_session.R |only ibkrcp-0.1.1/ibkrcp/vignettes/ibkrcp.Rmd | 382 +++++----- 65 files changed, 787 insertions(+), 811 deletions(-)
Title: Functional Guilds, Invasion Status, Endemism, and Rarity of Ants
Description: Provides functions for the analysis of ant communities, aiming to
standardize workflows in myrmecology. The package automates the assignment
of species to functional guilds based on trophic strategies, feeding
habits, and foraging behavior, using established classification frameworks
(Silva et al., 2015 <doi:10.7476/9788574554419>; Silvestre et al., 2003
<isbn:9588151236>; Delabie et al., 2000
<https://www.researchgate.net/publication/44961742_Sampling_Ground-Dwelling_Ants_Case_Studies_from_the_World%27s_Rain_Forests>),
and also includes a novel classification system implemented within the
package, developed from ant species occurring in urban environments.
It also includes routines to flag exotic species of Brazil (Vieira, 2025,
unpublished master's thesis), identify endemic species (Silva et al., 2025
<doi:10.37885/250920259>), and classify species rarity and rarity forms
of the Atlantic Forest (Silva et al., 2024 <doi:10.1016/j.biocon.2024.110640>).
The [...truncated...]
Author: Debora C. O. Goncalves [aut, cre],
Nathalia S. Silva [aut],
Rony P. S. Almeida [aut],
Livia P. Prado [aut],
Maria S. C. Morini [aut]
Maintainer: Debora C. O. Goncalves <debora_cog@outlook.com>
Diff between AntClassify versions 0.1.0 dated 2026-04-09 and 0.2.1 dated 2026-05-07
DESCRIPTION | 43 MD5 | 47 NAMESPACE | 9 R/antclassify.R | 104 + R/antclassify_community.R |only R/assign_guild_ants.R | 71 - R/check_endemic_atlantic_ants.R | 123 +- R/check_exotic_ants.R | 118 +- R/check_rarity_atlantic_ants.R | 120 +- R/globals.R |only R/sysdata.rda |binary R/validate_species_names.R |only build/vignette.rds |binary data/ant_community.rda |only data/data.R | 2 inst/WORDLIST | 1 inst/doc/antclassify_workflow.R | 30 inst/doc/antclassify_workflow.Rmd | 66 - inst/doc/antclassify_workflow.html | 1988 ++++++++++++++++++++----------------- man/ant_community.Rd |only man/antclassify.Rd | 30 man/antclassify_community.Rd |only man/assign_guild_ants.Rd | 34 man/check_endemic_atlantic_ants.Rd | 37 man/check_exotic_ants.Rd | 37 man/check_rarity_atlantic_ants.Rd | 37 man/validate_species_names.Rd |only vignettes/antclassify_workflow.Rmd | 66 - 28 files changed, 1707 insertions(+), 1256 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-04-18 0.11.1
2026-04-03 0.10.0
2026-03-20 0.8.5
2026-03-03 0.8.4
2025-12-22 0.8.3
2025-12-03 0.7.2
2025-11-15 0.6.2
2025-09-22 0.5.1
2025-08-26 0.3.1
Title: Genetic Relatedness Between Polyclonal Infections
Description: An implementation of Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent (IBD) based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. The package includes functions that format and preprocess the data, implement the method, and visualize the results.
Gerlovina et al. (2022) <doi:10.1093/genetics/iyac126>.
Author: Inna Gerlovina [aut, cre]
Maintainer: Inna Gerlovina <innager@berkeley.edu>
Diff between dcifer versions 1.5.0 dated 2025-11-11 and 1.5.2 dated 2026-05-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/ibd.R | 8 ++++++++ R/prep.R | 2 +- build/vignette.rds |binary inst/doc/vignetteDcifer.pdf |binary 6 files changed, 18 insertions(+), 10 deletions(-)
Title: Multi-Way Component Analysis
Description: For single tensor data, any matrix factorization method can be specified the matricised tensor in each dimension by Multi-way Component Analysis (MWCA). An originally extended MWCA is also implemented to specify and decompose multiple matrices and tensors simultaneously (CoupledMWCA). See the reference section of GitHub README.md <https://github.com/rikenbit/mwTensor>, for details of the methods.
Author: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between mwTensor versions 1.1.0 dated 2023-07-06 and 1.2.2 dated 2026-05-07
mwTensor-1.1.0/mwTensor/R/CoupledMWCA_Check.R |only mwTensor-1.2.2/mwTensor/DESCRIPTION | 9 mwTensor-1.2.2/mwTensor/MD5 | 51 +++-- mwTensor-1.2.2/mwTensor/NAMESPACE | 14 + mwTensor-1.2.2/mwTensor/R/AllClasses.R | 28 ++ mwTensor-1.2.2/mwTensor/R/AllGenerics.R | 14 + mwTensor-1.2.2/mwTensor/R/CoupledMWCA_Check_common.R | 79 +------ mwTensor-1.2.2/mwTensor/R/CoupledMWCA_Check_specific.R | 99 ++-------- mwTensor-1.2.2/mwTensor/R/MWCAProgram.R |only mwTensor-1.2.2/mwTensor/R/checkCoupledMWCA.R |only mwTensor-1.2.2/mwTensor/R/compileMWCAProgram.R |only mwTensor-1.2.2/mwTensor/R/executeMWCAProgram.R |only mwTensor-1.2.2/mwTensor/R/initCoupledMWCA.R |only mwTensor-1.2.2/mwTensor/R/mwTensor-internal.R | 76 +++++++ mwTensor-1.2.2/mwTensor/R/refineFactor.R |only mwTensor-1.2.2/mwTensor/build/partial.rdb |binary mwTensor-1.2.2/mwTensor/build/vignette.rds |only mwTensor-1.2.2/mwTensor/inst/NEWS | 55 +++++ mwTensor-1.2.2/mwTensor/inst/doc |only mwTensor-1.2.2/mwTensor/man/CoupledMWCA.Rd | 8 mwTensor-1.2.2/mwTensor/man/CoupledMWCAInit-class.Rd |only mwTensor-1.2.2/mwTensor/man/MWCAProgram.Rd |only mwTensor-1.2.2/mwTensor/man/RefinedFactor-class.Rd |only mwTensor-1.2.2/mwTensor/man/checkCoupledMWCA.Rd |only mwTensor-1.2.2/mwTensor/man/compileMWCAProgram.Rd |only mwTensor-1.2.2/mwTensor/man/defaultCoupledMWCAParams.Rd | 2 mwTensor-1.2.2/mwTensor/man/executeMWCAProgram.Rd |only mwTensor-1.2.2/mwTensor/man/initCoupledMWCA.Rd |only mwTensor-1.2.2/mwTensor/man/mwTensor-package.Rd | 2 mwTensor-1.2.2/mwTensor/man/refineFactor.Rd |only mwTensor-1.2.2/mwTensor/man/validateMWCAProgram.Rd |only mwTensor-1.2.2/mwTensor/tests/testthat.R | 4 mwTensor-1.2.2/mwTensor/tests/testthat/test_MWCAProgram.R |only mwTensor-1.2.2/mwTensor/tests/testthat/test_checkCoupledMWCA.R |only mwTensor-1.2.2/mwTensor/tests/testthat/test_initCoupledMWCA.R |only mwTensor-1.2.2/mwTensor/tests/testthat/test_refineFactor.R |only mwTensor-1.2.2/mwTensor/vignettes |only 37 files changed, 281 insertions(+), 160 deletions(-)
Title: Publication-Quality 'ggplot2' Visualisation
Description: Wrapper 'ggplot2' functions for publication-quality visualisation.
Aligned with 'ggplot2' and 'tidyverse'. Covers much of what 'ggplot2' does.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggblanket versions 12.4.0 dated 2025-06-03 and 20.0.0 dated 2026-05-07
ggblanket-12.4.0/ggblanket/R/aes.R |only ggblanket-12.4.0/ggblanket/R/annotate_axis_line.R |only ggblanket-12.4.0/ggblanket/R/bind_each_all.R |only ggblanket-12.4.0/ggblanket/R/colour.R |only ggblanket-12.4.0/ggblanket/R/dark_mode.R |only ggblanket-12.4.0/ggblanket/R/flex_mode.R |only ggblanket-12.4.0/ggblanket/R/get_base.R |only ggblanket-12.4.0/ggblanket/R/gg_area.R |only ggblanket-12.4.0/ggblanket/R/gg_bar.R |only ggblanket-12.4.0/ggblanket/R/gg_bin_2d.R |only ggblanket-12.4.0/ggblanket/R/gg_blanket.R |only ggblanket-12.4.0/ggblanket/R/gg_boxplot.R |only ggblanket-12.4.0/ggblanket/R/gg_col.R |only ggblanket-12.4.0/ggblanket/R/gg_contour.R |only ggblanket-12.4.0/ggblanket/R/gg_contour_filled.R |only ggblanket-12.4.0/ggblanket/R/gg_crossbar.R |only ggblanket-12.4.0/ggblanket/R/gg_density.R |only ggblanket-12.4.0/ggblanket/R/gg_density_2d.R |only ggblanket-12.4.0/ggblanket/R/gg_density_2d_filled.R |only ggblanket-12.4.0/ggblanket/R/gg_errorbar.R |only ggblanket-12.4.0/ggblanket/R/gg_freqpoly.R |only ggblanket-12.4.0/ggblanket/R/gg_function.R |only ggblanket-12.4.0/ggblanket/R/gg_hex.R |only ggblanket-12.4.0/ggblanket/R/gg_histogram.R |only ggblanket-12.4.0/ggblanket/R/gg_jitter.R |only ggblanket-12.4.0/ggblanket/R/gg_label.R |only ggblanket-12.4.0/ggblanket/R/gg_line.R |only ggblanket-12.4.0/ggblanket/R/gg_linerange.R |only ggblanket-12.4.0/ggblanket/R/gg_path.R |only ggblanket-12.4.0/ggblanket/R/gg_point.R |only ggblanket-12.4.0/ggblanket/R/gg_pointrange.R |only ggblanket-12.4.0/ggblanket/R/gg_polygon.R |only ggblanket-12.4.0/ggblanket/R/gg_qq.R |only ggblanket-12.4.0/ggblanket/R/gg_quantile.R |only ggblanket-12.4.0/ggblanket/R/gg_raster.R |only ggblanket-12.4.0/ggblanket/R/gg_rect.R |only ggblanket-12.4.0/ggblanket/R/gg_ribbon.R |only ggblanket-12.4.0/ggblanket/R/gg_rug.R |only ggblanket-12.4.0/ggblanket/R/gg_segment.R |only ggblanket-12.4.0/ggblanket/R/gg_sf.R |only ggblanket-12.4.0/ggblanket/R/gg_smooth.R |only 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Title: Advanced Continuous Glucose Monitoring Analysis with
High-Performance C++ Backend
Description: Tools for advanced analysis of continuous glucose monitoring (CGM)
time-series, implementing GRID (Glucose Rate Increase Detector) and GRID-based
algorithms for postprandial peak detection, and detection of hypoglycemic and
hyperglycemic episodes (Levels 1/2/Extended) aligned with international consensus
CGM metrics. Core algorithms are implemented in optimized C++ using 'Rcpp' to
provide accurate and fast analysis on large datasets.
Author: Sang Ho Park [aut, cre],
Rosa Oh [aut, ctb],
Sang-Man Jin [aut, ctb]
Maintainer: Sang Ho Park <shstat1729@gmail.com>
Diff between cgmguru versions 0.1.0 dated 2025-11-05 and 0.2.0 dated 2026-05-07
DESCRIPTION | 6 MD5 | 161 +++--- NEWS.md | 18 R/cgmguru-functions-docs.R | 635 ++++++++++++++----------- R/cgmguru-package.R | 32 - R/function_overrides.R | 155 ++++++ inst/doc/detect_all_events.R | 4 inst/doc/detect_all_events.Rmd | 5 inst/doc/detect_all_events.html | 25 inst/doc/detect_between_maxima.html | 9 inst/doc/detect_hyperglycemic_events.html | 345 ++++++------- inst/doc/detect_hypoglycemic_events.html | 279 +++++----- inst/doc/examples.R | 2 inst/doc/examples.Rmd | 2 inst/doc/examples.html | 197 +++---- inst/doc/excursion.Rmd | 2 inst/doc/excursion.html | 3 inst/doc/find_local_maxima.html | 1 inst/doc/find_max_after_hours.html | 15 inst/doc/find_max_before_hours.html | 15 inst/doc/find_min_after_hours.html | 15 inst/doc/find_min_before_hours.html | 15 inst/doc/find_new_maxima.html | 5 inst/doc/grid.html | 23 inst/doc/intro.R | 32 - inst/doc/intro.Rmd | 36 - inst/doc/intro.html | 253 ++++----- inst/doc/maxima_grid.html | 1 inst/doc/mod_grid.html | 1 inst/doc/orderfast.html | 1 inst/doc/start_finder.Rmd | 2 inst/doc/start_finder.html | 15 inst/doc/transform_df.html | 29 - inst/examples/detect_hyperglycemic_events.R | 18 inst/examples/detect_hypoglycemic_events.R | 15 inst/examples/find_max_after_hours.R | 14 inst/examples/find_max_before_hours.R | 14 inst/examples/find_min_after_hours.R | 14 inst/examples/find_min_before_hours.R | 14 inst/examples/start_finder.R | 8 inst/examples/transform_df.R | 4 man/cgmguru-package.Rd | 32 - man/detect_all_events.Rd | 2 man/detect_between_maxima.Rd | 10 man/detect_hyperglycemic_events.Rd | 139 +++-- man/detect_hypoglycemic_events.Rd | 127 +++-- man/excursion.Rd | 6 man/find_max_after_hours.Rd | 28 - man/find_max_before_hours.Rd | 26 - man/find_min_after_hours.Rd | 24 man/find_min_before_hours.Rd | 24 man/find_new_maxima.Rd | 12 man/grid.Rd | 2 man/maxima_grid.Rd | 9 man/mod_grid.Rd | 13 man/start_finder.Rd | 16 man/transform_df.Rd | 30 - src/detect_all_events.cpp | 27 - src/detect_hyperglycemic_events.cpp | 147 +++-- src/detect_hypoglycemic_events.cpp | 14 src/excursion.cpp | 2 src/find_max_after_hours.cpp | 6 src/find_max_before_hours.cpp | 6 src/find_min_after_hours.cpp | 6 src/find_min_before_hours.cpp | 6 src/find_new_maxima.cpp | 6 src/grid.cpp | 2 src/mod_grid.cpp | 2 src/start_finder.cpp | 2 tests/testthat/test-events.R | 31 + tests/testthat/test-find_local_maxima.R | 4 tests/testthat/test-find_new_maxima-branches.R | 4 tests/testthat/test-function_overrides.R | 4 tests/testthat/test-pre-recovery-events.R |only tests/testthat/test-start_finder.R | 4 tests/testthat/test-transform-between.R | 2 tests/testthat/test-windowing.R | 24 vignettes/detect_all_events.Rmd | 5 vignettes/examples.Rmd | 2 vignettes/excursion.Rmd | 2 vignettes/intro.Rmd | 36 - vignettes/start_finder.Rmd | 2 82 files changed, 1853 insertions(+), 1433 deletions(-)
Title: Non-Parametric Causal Effects of Feasible Interventions Based on
Modified Treatment Policies
Description: Non-parametric estimators for casual effects based on longitudinal modified treatment
policies as described in Diaz, Williams, Hoffman, and Schenck <doi:10.1080/01621459.2021.1955691>, traditional point treatment,
and traditional longitudinal effects. Continuous, binary, categorical treatments, and multivariate treatments are allowed as well are
censored outcomes. The treatment mechanism is estimated via a density ratio classification procedure
irrespective of treatment variable type. For both continuous and binary outcomes, additive treatment effects
can be calculated and relative risks and odds ratios may be calculated for binary outcomes.
Supports survival outcomes with competing risks (Diaz, Hoffman, and Hejazi; <doi:10.1007/s10985-023-09606-7>).
Author: Nicholas Williams [aut, cre, cph] ,
Ivan Diaz [aut, cph] ,
Beaudan Campbell-Brown [ctb]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>
Diff between lmtp versions 1.5.3 dated 2025-07-24 and 1.5.4 dated 2026-05-07
DESCRIPTION | 14 +++++++------- MD5 | 20 +++++++++++--------- NAMESPACE | 1 - NEWS.md | 13 +++++++++++++ R/contrasts.R | 10 ++++++++-- R/lmtp-package.R | 1 - R/make_folds.R |only R/sl.R | 6 ++++++ build/partial.rdb |binary man/lmtp-package.Rd | 2 +- tests/testthat/test-checks.R | 13 +++++++++++++ tests/testthat/test-make_folds.R |only 12 files changed, 59 insertions(+), 21 deletions(-)