Title: Time-to-Event Data Analysis with Missing Survival Times
Description: Fits a pseudo Cox proprotional hazards model when survival times are missing for control groups.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Diff between coxphm versions 0.1.0 dated 2024-09-23 and 0.2.0 dated 2025-04-11
coxphm-0.1.0/coxphm/R/01.n_ps_pll.R.R |only coxphm-0.2.0/coxphm/DESCRIPTION | 10 ++--- coxphm-0.2.0/coxphm/MD5 | 10 ++--- coxphm-0.2.0/coxphm/NAMESPACE | 2 - coxphm-0.2.0/coxphm/R/01.n_ps_pll.R |only coxphm-0.2.0/coxphm/R/coxphm.R | 61 ++++++++++++++++++++-------------- coxphm-0.2.0/coxphm/man/coxphm.Rd | 40 +++++++++++----------- 7 files changed, 67 insertions(+), 56 deletions(-)
Title: Extra Analysis Results Data Utilities
Description: Create extra Analysis Results Data (ARD) summary objects.
The package supplements the simple ARD functions from the 'cards'
package, exporting functions to put statistical results in the ARD
format. These objects are used and re-used to construct summary
tables, visualizations, and written reports.
Author: Daniel D. Sjoberg [aut, cre] ,
Abinaya Yogasekaram [aut],
Emily de la Rua [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cardx versions 0.2.3 dated 2025-02-18 and 0.2.4 dated 2025-04-11
DESCRIPTION | 16 MD5 | 55 +- NAMESPACE | 4 NEWS.md | 18 R/ard_emmeans_mean_difference.R | 143 +++-- R/ard_regression.R | 35 + R/ard_regression_basic.R | 61 ++ R/ard_stats_mantelhaen_test.R |only R/ard_stats_prop_test.R | 2 R/ard_survival_survfit.R | 78 ++- R/construction_helpers.R | 4 R/import-standalone-check_pkg_installed.R | 14 R/import-standalone-forcats.R | 20 README.md | 3 inst/WORDLIST | 3 man/ard_emmeans_mean_difference.Rd | 2 man/ard_regression.Rd | 40 + man/ard_regression_basic.Rd | 49 +- man/ard_stats_anova.Rd | 2 man/ard_stats_mantelhaen_test.Rd |only man/ard_survival_survfit.Rd | 8 man/construction_helpers.Rd | 2 tests/testthat/_snaps/ard_emmeans_mean_difference.md |only tests/testthat/_snaps/ard_regression.md | 3 tests/testthat/_snaps/ard_stats_mantelhaen_test.md |only tests/testthat/_snaps/ard_survival_survfit.md | 459 +++++++++---------- tests/testthat/test-ard_emmeans_mean_difference.R | 23 tests/testthat/test-ard_regression.R | 18 tests/testthat/test-ard_regression_basic.R | 9 tests/testthat/test-ard_stats_mantelhaen_test.R |only tests/testthat/test-ard_survival_survfit.R | 50 ++ 31 files changed, 763 insertions(+), 358 deletions(-)
Title: Statistical Reporting with 'Quarto'
Description: Provides statistical components, tables, and graphs
that are useful in 'Quarto' and 'RMarkdown' reports and that produce 'Quarto'
elements for special formatting such as tabs and marginal notes and graphs.
Some of the functions produce entire report sections with tabs, e.g.,
the missing data report created by missChk(). Functions for inserting
variables and tables inside 'graphviz' and 'mermaid' diagrams are included,
and so are special clinical trial graphics for adverse event reporting.
Author: Frank Harrell [aut, cre]
Maintainer: Frank Harrell <fh@fharrell.com>
Diff between qreport versions 1.0-1 dated 2024-05-26 and 1.0-2 dated 2025-04-11
DESCRIPTION | 17 +++++++++++------ MD5 | 10 ++++++---- NEWS | 4 ++++ R/makegvflow.r |only R/reptools.r | 23 +++++++++++++++++++++-- man/makegvflow.Rd |only man/missChk.Rd | 2 +- 7 files changed, 43 insertions(+), 13 deletions(-)
Title: Mixed Effect Model with the Box-Cox Transformation
Description: Inference on the marginal model of the mixed effect model with
the Box-Cox transformation and on the model median differences between
treatment groups for longitudinal randomized clinical trials. These
statistical methods are proposed by Maruo et al. (2017)
<doi:10.1002/sim.7279>.
Author: Kazushi Maruo [aut, cre],
Ryota Ishii [aut],
Yusuke Yamaguchi [ctb],
Masahiko Gosho [ctb]
Maintainer: Kazushi Maruo <kazushi.maruo@gmail.com>
Diff between bcmixed versions 0.1.4 dated 2020-03-31 and 0.1.5 dated 2025-04-11
bcmixed-0.1.4/bcmixed/R/bcmixed.R |only bcmixed-0.1.4/bcmixed/man/bcmixed.Rd |only bcmixed-0.1.5/bcmixed/DESCRIPTION | 8 +-- bcmixed-0.1.5/bcmixed/MD5 | 44 ++++++++--------- bcmixed-0.1.5/bcmixed/NAMESPACE | 4 + bcmixed-0.1.5/bcmixed/NEWS.md | 4 + bcmixed-0.1.5/bcmixed/R/aidscd4.R | 6 +- bcmixed-0.1.5/bcmixed/R/bcmarg.R | 34 +++++++++++-- bcmixed-0.1.5/bcmixed/R/bcmixed-package.R |only bcmixed-0.1.5/bcmixed/R/bcmmrm.R | 4 - bcmixed-0.1.5/bcmixed/R/bcreg.R | 2 bcmixed-0.1.5/bcmixed/R/bct.R | 2 bcmixed-0.1.5/bcmixed/R/bct.v.R | 6 +- bcmixed-0.1.5/bcmixed/R/summary.bcmmrm.R | 6 +- bcmixed-0.1.5/bcmixed/README.md | 6 -- bcmixed-0.1.5/bcmixed/build |only bcmixed-0.1.5/bcmixed/inst |only bcmixed-0.1.5/bcmixed/man/aidscd4.Rd | 12 ++-- bcmixed-0.1.5/bcmixed/man/bcmarg.Rd | 6 +- bcmixed-0.1.5/bcmixed/man/bcmixed-package.Rd |only bcmixed-0.1.5/bcmixed/man/bcmmrm.Rd | 4 - bcmixed-0.1.5/bcmixed/man/bcreg.Rd | 2 bcmixed-0.1.5/bcmixed/man/bct.Rd | 2 bcmixed-0.1.5/bcmixed/man/bct.v.Rd | 2 bcmixed-0.1.5/bcmixed/man/figures/README-example-1.png |binary bcmixed-0.1.5/bcmixed/man/summary.bcmmrm.Rd | 6 +- 26 files changed, 97 insertions(+), 63 deletions(-)
Title: Testing for Shiny Applications
Description: Automated unit testing of Shiny applications through a headless 'Chromium' browser.
Author: Barret Schloerke [cre, aut] ,
Posit Software, PBC [cph, fnd],
Winston Chang [ctb] ,
Gabor Csardi [ctb] ,
Hadley Wickham [ctb] ,
Mango Solutions [cph, ccp]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between shinytest2 versions 0.4.0 dated 2025-04-10 and 0.4.1 dated 2025-04-11
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 9 +++++++-- R/app-driver.R | 2 +- man/AppDriver.Rd | 2 +- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Export Domain Logic from Shiny using Meta-Programming
Description: Provides tools for capturing logic in a Shiny app and exposing it as code that can be run outside of Shiny (e.g., from an R console). It also provides tools for bundling both the code and results to the end user.
Author: Joe Cheng [aut],
Carson Sievert [cre, aut] ,
RStudio [cph]
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between shinymeta versions 0.2.0.3 dated 2021-11-17 and 0.2.1 dated 2025-04-11
DESCRIPTION | 8 ++--- MD5 | 32 +++++++++++------------ NAMESPACE | 2 - NEWS.md | 10 ++++++- R/archive.R | 1 R/display.R | 4 +- R/imports.R | 1 R/metareactive.R | 17 ++++++------ R/observe.R | 16 +++++------ R/render.R | 2 - README.md | 17 +++++------- man/displayCodeModal.Rd | 11 +++++--- man/expandChain.Rd | 66 ++++++++++++++++++++++++++++++++---------------- man/metaObserve.Rd | 16 +++++------ man/metaReactive.Rd | 13 +++++---- man/metaRender.Rd | 2 - man/outputCodeButton.Rd | 2 - 17 files changed, 127 insertions(+), 93 deletions(-)
Title: Managing and Building of Quarterly Life Tables
Description: Manages, builds and computes statistics and datasets for the
construction of quarterly (sub-annual) life tables by exploiting micro-data from
either a general or an insured population.
References:
Pavía and Lledó (2022) <doi:10.1111/rssa.12769>.
Pavía and Lledó (2023) <doi:10.1017/asb.2023.16>.
Pavía and Lledó (2025) <doi:10.1371/journal.pone.0315937>.
Acknowledgements:
The authors wish to thank Conselleria de Educación, Universidades y Empleo, Generalitat Valenciana (grants AICO/2021/257; CIAICO/2024/031), Ministerio de Ciencia e Innovación (grant PID2021-128228NB-I00) and Fundación Mapfre (grant 'Modelización espacial e intra-anual de la mortalidad en España. Una herramienta automática para el calculo de productos de vida') for supporting this research.
Author: Jose M. Pavia [aut, cre] ,
Josep Lledo [aut]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Diff between qlifetable versions 0.0.2-5 dated 2024-06-28 and 0.0.2-6 dated 2025-04-11
DESCRIPTION | 9 +++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 5 +++++ R/annual2quarterly.R | 1 + R/compute_SAI.R | 1 + R/coord_age.R | 1 + R/coord_time.R | 1 + R/exact_age.R | 1 + man/annual2quarterly.Rd | 2 ++ man/compute_SAI.Rd | 2 ++ man/coord_age.Rd | 2 ++ man/coord_time.Rd | 2 ++ man/exact_age.Rd | 2 ++ 13 files changed, 37 insertions(+), 16 deletions(-)
More information about clinDataReview at CRAN
Permanent link
Title: Simulation of Populations by Sampling Waiting-Time Distributions
Description: Constructs a virtual population from fertility and mortality rates for any country,
calendar year and birth cohort in the Human Mortality Database <https://www.mortality.org> and the Human Fertility Database <https://www.humanfertility.org>. Fertility histories are simulated for every individual and their offspring, producing a multi-generation virtual population.
Author: Frans Willekens [aut, cre] ,
Tim Riffe [ctb]
Maintainer: Frans Willekens <willekens@nidi.nl>
Diff between VirtualPop versions 2.0.2 dated 2024-03-18 and 2.1.0 dated 2025-04-11
DESCRIPTION | 10 MD5 | 46 NAMESPACE | 2 NEWS.md | 2 R/BuildViP.R | 12 R/Children.R | 1 R/GetGenerations.R | 6 R/PartnerSearch.R | 112 + R/VirtualPop-package.R | 2 build/vignette.rds |binary data/dLH.rda |binary data/rates.rda |binary data/ratesC.rda |binary inst/doc/MultistateLH.R | 16 inst/doc/MultistateLH.Rmd | 18 inst/doc/MultistateLH.html | 2069 +++++++++++++++++++++++++++++++++++- inst/doc/Piecewise_exponential.html | 56 inst/doc/Tutorial.R | 31 inst/doc/Tutorial.Rmd | 35 inst/doc/Tutorial.html | 125 +- man/PartnerSearch.Rd | 15 vignettes/MultistateLH.Rmd | 18 vignettes/References.bib | 4 vignettes/Tutorial.Rmd | 35 24 files changed, 2343 insertions(+), 272 deletions(-)
Title: Efficient Bayesian Inference for Dynamic Survival Models with
Shrinkage
Description: Efficient Markov chain Monte Carlo (MCMC) algorithms for fully
Bayesian estimation of dynamic survival models with shrinkage priors.
Details on the algorithms used are provided in Wagner (2011) <doi:10.1007/s11222-009-9164-5>,
Bitto and Frühwirth-Schnatter (2019) <doi:10.1016/j.jeconom.2018.11.006> and
Cadonna et al. (2020) <doi:10.3390/econometrics8020020>.
Author: Daniel Winkler [aut, cre],
Peter Knaus [aut]
Maintainer: Daniel Winkler <daniel.winkler@wu.ac.at>
Diff between shrinkDSM versions 0.2.0 dated 2022-11-15 and 1.0.0 dated 2025-04-11
DESCRIPTION | 11 MD5 | 24 NAMESPACE | 2 R/Imports.R | 2 R/RcppExports.R | 22 R/shrinkDSM.R | 1498 ++++++++++++++++++++-------------------- R/utilities_shrinkDSM.R | 827 +++++++++++----------- man/plot.mcmc.dsm.tvp.Rd | 4 man/reexports.Rd |only man/shrinkDSM.Rd | 30 src/Makevars | 2 src/Makevars.win | 2 tests/testthat/Rplots.pdf |only tests/testthat/test_shrinkDSM.R | 52 - 14 files changed, 1274 insertions(+), 1202 deletions(-)
Title: Ecological Inference by Linear Programming under Homogeneity
Description: Provides a bunch of algorithms based on linear programming for estimating, under
the homogeneity hypothesis, RxC ecological contingency tables (or vote transition matrices)
using mainly aggregate data (from voting units).
References:
Pavía and Romero (2024) <doi:10.1177/00491241221092725>.
Pavía and Romero (2024) <doi:10.1093/jrsssa/qnae013>.
Pavía (2023) <doi:10.1007/s43545-023-00658-y>.
Pavía (2024) <doi:10.1080/0022250X.2024.2423943>.
Pavía (2024) <doi:10.1177/07591063241277064>.
Pavía and Penadés (2024). A bottom-up approach for ecological inference.
Romero, Pavía, Martín and Romero (2020) <doi:10.1080/02664763.2020.1804842>.
Acknowledgements:
The authors wish to thank Consellería de Educación, Universidades y Empleo, Generalitat Valenciana (grants AICO/2021/257, CIAICO/2023/031) and Ministerio de Economía e Innovación (grant PID2021-128228NB-I00) for supporting this research.
Author: Jose M. Pavia [aut, cre] ,
Rafael Romero [aut]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Diff between lphom versions 0.3.5-5 dated 2024-03-03 and 0.3.5-6 dated 2025-04-11
DESCRIPTION | 15 +++++++------- MD5 | 52 ++++++++++++++++++++++++------------------------- NEWS.md | 4 +++ R/adjust2integers.R | 2 - R/lclphom.R | 5 ++-- R/lphom.R | 1 R/lphom_dual.R | 2 - R/lphom_joint.R | 2 - R/nslphom.R | 3 +- R/nslphom_dual.R | 2 - R/nslphom_joint.R | 2 - R/rslphom.R | 2 - R/tslphom.R | 5 ++-- R/tslphom_dual.R | 2 - R/tslphom_joint.R | 2 - man/adjust2integers.Rd | 2 - man/lclphom.Rd | 6 +++-- man/lphom.Rd | 2 + man/lphom_dual.Rd | 2 - man/lphom_joint.Rd | 2 - man/nslphom.Rd | 4 ++- man/nslphom_dual.Rd | 2 - man/nslphom_joint.Rd | 2 - man/rslphom.Rd | 2 - man/tslphom.Rd | 4 ++- man/tslphom_dual.Rd | 2 - man/tslphom_joint.Rd | 2 - 27 files changed, 75 insertions(+), 58 deletions(-)
Title: Analysis Results Data
Description: Construct CDISC (Clinical Data Interchange Standards
Consortium) compliant Analysis Results Data objects. These objects are
used and re-used to construct summary tables, visualizations, and
written reports. The package also exports utilities for working with
these objects and creating new Analysis Results Data objects.
Author: Daniel D. Sjoberg [aut, cre] ,
Becca Krouse [aut],
Emily de la Rua [aut],
F. Hoffmann-La Roche AG [cph, fnd],
GlaxoSmithKline Research & Development Limited [cph]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cards versions 0.5.1 dated 2025-03-01 and 0.6.0 dated 2025-04-11
cards-0.5.1/cards/R/shift_ard_columns.R |only cards-0.5.1/cards/man/dot-is_list_column_of_scalars.Rd |only cards-0.5.1/cards/man/dot-pair_columns.Rd |only cards-0.5.1/cards/man/dot-shift_column_pair.Rd |only cards-0.5.1/cards/tests/testthat/_snaps/shift_ard_columns.md |only cards-0.5.1/cards/tests/testthat/test-shift_ard_columns.R |only cards-0.6.0/cards/DESCRIPTION | 6 cards-0.6.0/cards/MD5 | 70 - cards-0.6.0/cards/NAMESPACE | 4 cards-0.6.0/cards/NEWS.md | 30 cards-0.6.0/cards/R/ard_formals.R |only cards-0.6.0/cards/R/ard_stack_hierarchical.R | 10 cards-0.6.0/cards/R/cards-package.R | 4 cards-0.6.0/cards/R/deprecated.R | 9 cards-0.6.0/cards/R/filter_ard_hierarchical.R |only cards-0.6.0/cards/R/import-standalone-check_pkg_installed.R | 14 cards-0.6.0/cards/R/import-standalone-forcats.R | 22 cards-0.6.0/cards/R/rename_ard_columns.R |only cards-0.6.0/cards/R/shuffle_ard.R | 64 - cards-0.6.0/cards/R/sort_ard_hierarchical.R |only cards-0.6.0/cards/R/tidy_as_ard.R | 4 cards-0.6.0/cards/R/unlist_ard_columns.R |only cards-0.6.0/cards/R/utils.R | 4 cards-0.6.0/cards/README.md | 425 -------- cards-0.6.0/cards/inst/WORDLIST | 3 cards-0.6.0/cards/man/ard_formals.Rd |only cards-0.6.0/cards/man/dot-detect_msgs.Rd | 3 cards-0.6.0/cards/man/filter_ard_hierarchical.Rd |only cards-0.6.0/cards/man/rename_ard_columns.Rd | 41 cards-0.6.0/cards/man/sort_ard_hierarchical.Rd |only cards-0.6.0/cards/man/tidy_as_ard.Rd | 4 cards-0.6.0/cards/man/unlist_ard_columns.Rd |only cards-0.6.0/cards/tests/testthat/_snaps/ard_formals.md |only cards-0.6.0/cards/tests/testthat/_snaps/ard_stack_hierarchical.md | 30 cards-0.6.0/cards/tests/testthat/_snaps/filter_ard_hierarchical.md |only cards-0.6.0/cards/tests/testthat/_snaps/rename_ard_columns.md | 62 - cards-0.6.0/cards/tests/testthat/_snaps/shuffle_ard.md | 531 +--------- cards-0.6.0/cards/tests/testthat/_snaps/sort_ard_hierarchical.md |only cards-0.6.0/cards/tests/testthat/test-ard_formals.R |only cards-0.6.0/cards/tests/testthat/test-ard_stack.R | 3 cards-0.6.0/cards/tests/testthat/test-ard_stack_hierarchical.R | 141 +- cards-0.6.0/cards/tests/testthat/test-filter_ard_hierarchical.R |only cards-0.6.0/cards/tests/testthat/test-nest_for_ard.R | 10 cards-0.6.0/cards/tests/testthat/test-rename_ard_columns.R | 47 cards-0.6.0/cards/tests/testthat/test-shuffle_ard.R | 60 - cards-0.6.0/cards/tests/testthat/test-sort_ard_hierarchical.R |only cards-0.6.0/cards/tests/testthat/test-unlist_ard_columns.R |only 47 files changed, 420 insertions(+), 1181 deletions(-)
Title: Bayesian Longitudinal Regularized Quantile Mixed Model
Description: In longitudinal studies, the same subjects are measured repeatedly over time, leading to correlations among the repeated measurements. Properly accounting for the intra-cluster correlations in the presence of data heterogeneity and long tailed distributions of the disease phenotype is challenging, especially in the context of high dimensional regressions. In this package, we developed a Bayesian quantile mixed effects model with spike- and -slab priors to dissect important gene - environment interactions under longitudinal genomics studies. An efficient Gibbs sampler has been developed to facilitate fast computation. The Markov chain Monte Carlo algorithms of the proposed and alternative methods are efficiently implemented in 'C++'. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Kun Fan [aut, cre],
Cen Wu [aut]
Maintainer: Kun Fan <kfan@ksu.edu>
Diff between mixedBayes versions 0.1.5 dated 2025-02-11 and 0.1.6 dated 2025-04-11
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NEWS.md |only R/mixedBayes-package.R | 3 ++- R/mixedBayes.R | 2 +- README.md | 29 +++++------------------------ build/partial.rdb |binary man/mixedBayes-package.Rd | 3 ++- man/mixedBayes.Rd | 2 +- 9 files changed, 23 insertions(+), 39 deletions(-)
Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival
Analysis
Description: This model fitting tool incorporates cyclic coordinate descent and
majorization-minimization approaches to fit a variety of regression models
found in large-scale observational healthcare data. Implementations focus
on computational optimization and fine-scale parallelization to yield
efficient inference in massive datasets. Please see:
Suchard, Simpson, Zorych, Ryan and Madigan (2013) <doi:10.1145/2414416.2414791>.
Author: Marc A. Suchard [aut, cre],
Martijn J. Schuemie [aut],
Trevor R. Shaddox [aut],
Yuxi Tian [aut],
Jianxiao Yang [aut],
Eric Kawaguchi [aut],
Sushil Mittal [ctb],
Observational Health Data Sciences and Informatics [cph],
Marcus Geelnard [cph, ctb] ,
Ru [...truncated...]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between Cyclops versions 3.5.0 dated 2024-12-01 and 3.5.1 dated 2025-04-11
Cyclops-3.5.0/Cyclops/build |only Cyclops-3.5.0/Cyclops/man/Cyclops-package.Rd |only Cyclops-3.5.0/Cyclops/tests/testthat/save.R |only Cyclops-3.5.0/Cyclops/tests/testthat/test-recenter.R |only Cyclops-3.5.1/Cyclops/DESCRIPTION | 6 Cyclops-3.5.1/Cyclops/MD5 | 52 +- Cyclops-3.5.1/Cyclops/NAMESPACE | 5 Cyclops-3.5.1/Cyclops/NEWS.md | 9 Cyclops-3.5.1/Cyclops/R/Cyclops-package.R | 2 Cyclops-3.5.1/Cyclops/R/ModelFit.R | 51 +- Cyclops-3.5.1/Cyclops/R/Predict.R | 25 - Cyclops-3.5.1/Cyclops/R/RcppExports.R | 24 + Cyclops-3.5.1/Cyclops/R/Residuals.R |only Cyclops-3.5.1/Cyclops/inst/CITATION | 2 Cyclops-3.5.1/Cyclops/man/confint.cyclopsFit.Rd | 3 Cyclops-3.5.1/Cyclops/man/cyclops.Rd | 2 Cyclops-3.5.1/Cyclops/man/getCyclopsProfileLogLikelihood.Rd | 2 Cyclops-3.5.1/Cyclops/man/residuals.cyclopsFit.Rd |only Cyclops-3.5.1/Cyclops/man/testProportionality.Rd |only Cyclops-3.5.1/Cyclops/src/RcppCyclopsInterface.cpp | 156 ++++++ Cyclops-3.5.1/Cyclops/src/RcppCyclopsInterface.h | 3 Cyclops-3.5.1/Cyclops/src/RcppExports.cpp | 75 +++ Cyclops-3.5.1/Cyclops/src/cyclops/CyclicCoordinateDescent.cpp | 29 + Cyclops-3.5.1/Cyclops/src/cyclops/CyclicCoordinateDescent.h | 9 Cyclops-3.5.1/Cyclops/src/cyclops/engine/AbstractModelSpecifics.h | 11 Cyclops-3.5.1/Cyclops/src/cyclops/engine/ModelSpecifics.h | 18 Cyclops-3.5.1/Cyclops/src/cyclops/engine/ModelSpecifics.hpp | 240 ++++++++++ Cyclops-3.5.1/Cyclops/tests/testthat/test-profileLikelihood.R | 2 Cyclops-3.5.1/Cyclops/tests/testthat/test-residuals.R |only Cyclops-3.5.1/Cyclops/tests/testthat/test-smallCLR.R | 19 Cyclops-3.5.1/Cyclops/tests/testthat/test-smallCox.R | 19 31 files changed, 710 insertions(+), 54 deletions(-)
Title: Analysis of Coarsely Observed Data
Description: Functions to analyze coarse data.
Specifically, it contains functions to (1) fit parametric accelerated
failure time models to interval-censored survival time data, and (2)
estimate the case-fatality ratio in scenarios with under-reporting.
This package's development was motivated by applications to infectious
disease: in particular, problems with estimating the incubation period and
the case fatality ratio of a given disease. Sample data files are included
in the package. See Reich et al. (2009) <doi:10.1002/sim.3659>,
Reich et al. (2012) <doi:10.1111/j.1541-0420.2011.01709.x>, and
Lessler et al. (2009) <doi:10.1016/S1473-3099(09)70069-6>.
Author: Nicholas G. Reich [aut, cre],
Justin Lessler [aut],
Andrew Azman [aut],
Zhian N. Kamvar [ctb],
Hugo Gruson [ctb]
Maintainer: Nicholas G. Reich <nick@umass.edu>
Diff between coarseDataTools versions 0.6-6 dated 2021-12-09 and 0.7.2 dated 2025-04-11
coarseDataTools-0.6-6/coarseDataTools/vignettes/CFR_vignette_cache/html/runAnalysis_99f06cae14587f14b5c5ebde7e5454ea.RData |only coarseDataTools-0.6-6/coarseDataTools/vignettes/CFR_vignette_cache/html/runAnalysis_99f06cae14587f14b5c5ebde7e5454ea.rdb |only coarseDataTools-0.6-6/coarseDataTools/vignettes/CFR_vignette_cache/html/runAnalysis_99f06cae14587f14b5c5ebde7e5454ea.rdx |only coarseDataTools-0.7.2/coarseDataTools/ChangeLog | 10 coarseDataTools-0.7.2/coarseDataTools/DESCRIPTION | 20 coarseDataTools-0.7.2/coarseDataTools/MD5 | 54 coarseDataTools-0.7.2/coarseDataTools/NEWS.md |only coarseDataTools-0.7.2/coarseDataTools/R/CFR_estimation.R | 642 ++--- coarseDataTools-0.7.2/coarseDataTools/R/S4stuff.R | 81 coarseDataTools-0.7.2/coarseDataTools/R/coarseDataTools-package.R | 20 coarseDataTools-0.7.2/coarseDataTools/R/dic.fit.R | 1189 +++++----- coarseDataTools-0.7.2/coarseDataTools/R/dic.fit.mcmc.R | 559 ++-- coarseDataTools-0.7.2/coarseDataTools/R/get.obs.type.R | 16 coarseDataTools-0.7.2/coarseDataTools/R/sampleSizeSimulation.R | 263 +- coarseDataTools-0.7.2/coarseDataTools/README.md | 3 coarseDataTools-0.7.2/coarseDataTools/build/partial.rdb |only coarseDataTools-0.7.2/coarseDataTools/build/vignette.rds |binary coarseDataTools-0.7.2/coarseDataTools/inst/CITATION | 32 coarseDataTools-0.7.2/coarseDataTools/inst/doc/CFR_vignette.R | 28 coarseDataTools-0.7.2/coarseDataTools/inst/doc/CFR_vignette.Rmd | 28 coarseDataTools-0.7.2/coarseDataTools/inst/doc/CFR_vignette.html | 436 +-- coarseDataTools-0.7.2/coarseDataTools/man/EMforCFR.Rd | 51 coarseDataTools-0.7.2/coarseDataTools/man/dic.fit.Rd | 6 coarseDataTools-0.7.2/coarseDataTools/man/dic.fit.mcmc.Rd | 4 coarseDataTools-0.7.2/coarseDataTools/man/exp.win.lengths.Rd | 2 coarseDataTools-0.7.2/coarseDataTools/man/fluA.inc.per.Rd | 2 coarseDataTools-0.7.2/coarseDataTools/man/nycH1N1.Rd | 2 coarseDataTools-0.7.2/coarseDataTools/vignettes/CFR_vignette.Rmd | 28 coarseDataTools-0.7.2/coarseDataTools/vignettes/CFR_vignette_cache/html/__packages | 6 coarseDataTools-0.7.2/coarseDataTools/vignettes/CFR_vignette_cache/html/runAnalysis_6f65817ffbd024efda42a802d57ff206.RData |only coarseDataTools-0.7.2/coarseDataTools/vignettes/CFR_vignette_cache/html/runAnalysis_6f65817ffbd024efda42a802d57ff206.rdb |only coarseDataTools-0.7.2/coarseDataTools/vignettes/CFR_vignette_cache/html/runAnalysis_6f65817ffbd024efda42a802d57ff206.rdx |only 32 files changed, 1725 insertions(+), 1757 deletions(-)
More information about coarseDataTools at CRAN
Permanent link
Title: Spatial Dynamic Panel Data Modeling
Description: Spatial model calculation for static and dynamic panel data models, weights matrix creation and Bayesian model comparison.
Bayesian model comparison methods were described by 'LeSage' (2014) <doi:10.1016/j.spasta.2014.02.002>.
The 'Lee'-'Yu' transformation approach is described in 'Yu', 'De Jong' and 'Lee' (2008) <doi:10.1016/j.jeconom.2008.08.002>, 'Lee' and 'Yu' (2010) <doi:10.1016/j.jeconom.2009.08.001> and 'Lee' and 'Yu' (2010) <doi:10.1017/S0266466609100099>.
Author: Rozeta Simonovska [aut, cre]
Maintainer: Rozeta Simonovska <simonovska.r@gmail.com>
Diff between SDPDmod versions 0.0.5 dated 2024-04-13 and 0.0.6 dated 2025-04-11
DESCRIPTION | 8 +-- MD5 | 34 ++++++------- NEWS.md | 4 + R/SDPDm.R | 56 +++++++++++++++------- R/SharedBMat.R | 3 - R/logdet.R | 10 +++- R/mOrdNbr.R | 3 - R/rownor.R | 3 - build/vignette.rds |binary inst/doc/spatial_matrices.html | 4 - inst/doc/spatial_model.R | 4 + inst/doc/spatial_model.Rmd | 4 + inst/doc/spatial_model.html | 101 +++++++++++++++++++++-------------------- man/SDPDm.Rd | 56 +++++++++++++++------- man/SharedBMat.Rd | 3 - man/mOrdNbr.Rd | 3 - man/rownor.Rd | 3 - vignettes/spatial_model.Rmd | 4 + 18 files changed, 184 insertions(+), 119 deletions(-)
Title: Syntactically Awesome Style Sheets ('Sass')
Description: An 'SCSS' compiler, powered by the 'LibSass' library. With this,
R developers can use variables, inheritance, and functions to generate
dynamic style sheets. The package uses the 'Sass CSS' extension language,
which is stable, powerful, and CSS compatible.
Author: Joe Cheng [aut],
Timothy Mastny [aut],
Richard Iannone [aut] ,
Barret Schloerke [aut] ,
Carson Sievert [aut, cre] ,
Christophe Dervieux [ctb] ,
RStudio [cph, fnd],
Sass Open Source Foundation [ctb, cph] ,
Greter Marcel [ctb, cph] ,
Mifsud Michael [ct [...truncated...]
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between sass versions 0.4.9 dated 2024-03-15 and 0.4.10 dated 2025-04-11
sass-0.4.10/sass/DESCRIPTION | 8 +-- sass-0.4.10/sass/MD5 | 29 +++++------ sass-0.4.10/sass/NEWS.md | 6 ++ sass-0.4.10/sass/R/file_cache.R | 14 ++--- sass-0.4.10/sass/R/fonts.R | 24 +++++++-- sass-0.4.10/sass/README.md | 4 - sass-0.4.10/sass/build/vignette.rds |binary sass-0.4.10/sass/inst/doc/sass.R | 2 sass-0.4.10/sass/inst/doc/sass.html | 13 ++-- sass-0.4.10/sass/man/FileCache.Rd | 11 ---- sass-0.4.10/sass/src/Makevars | 18 ++++-- sass-0.4.10/sass/src/compile.c | 4 - sass-0.4.10/sass/tests/testthat/_snaps/font-objects.md | 12 ++++ sass-0.4.10/sass/tests/testthat/_snaps/font-objects/font-css | 6 +- sass-0.4.10/sass/tests/testthat/test-font-objects.R | 7 +- sass-0.4.9/sass/src/Makevars.win |only 16 files changed, 93 insertions(+), 65 deletions(-)
Title: An Automatic Suite for Estimation of Various Effect Size
Measures
Description: Automatically estimate 11 effect size measures from a well-formatted dataset. Various other functions can help, for example, removing dependency between several effect sizes, or identifying differences between two datasets.
This package is mainly designed to assist in conducting a systematic review with a meta-analysis but can be useful to any researcher interested in estimating an effect size.
Author: Corentin J. Gosling [aut, cre],
Samuele Cortese [aut],
Marco Solmi [aut],
Belen Haza [aut],
Eduard Vieta [aut],
Richard Delorme [aut],
Paolo Fusar-Poli [aut],
Joaquim Radua [aut]
Maintainer: Corentin J. Gosling <corentin.gosling@parisnanterre.fr>
Diff between metaConvert versions 1.0.2 dated 2024-11-17 and 1.0.3 dated 2025-04-11
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ R/es_from_PAIRED_MC.R | 1 - R/es_from_PAIRED_MEANS.R | 8 ++++---- R/es_from_stand_RR.R | 1 - R/functions_summary.R | 4 ++-- R/internal_generate_df.R | 7 +++++-- R/main_convert_df.R | 6 +++--- R/zzz.R | 9 +++------ inst/CITATION | 2 +- inst/doc/Tutorial.html | 16 ++++++++-------- 12 files changed, 44 insertions(+), 42 deletions(-)
Title: Tools for Outbreak Investigation/Infectious Disease Surveillance
Description: Create epicurves or epigantt charts in 'ggplot2'. Prepare
data for visualisation or other reporting for infectious disease
surveillance and outbreak investigation. Includes tidy functions to solve
date based transformations for common reporting tasks, like
(A) seasonal date alignment for respiratory disease surveillance,
(B) date-based case binning based on specified time intervals like
isoweek, epiweek, month and more, (C) automated detection and marking
of the new year based on the date/datetime axis of the 'ggplot2'.
An introduction on how to use epicurves can be found on the US CDC website
(2012, <https://www.cdc.gov/training/quicklearns/epimode/index.html>).
Author: Alexander Bartel [aut, cre]
Maintainer: Alexander Bartel <alexander.bartel@fu-berlin.de>
Diff between ggsurveillance versions 0.2.0 dated 2025-03-02 and 0.3.0 dated 2025-04-11
ggsurveillance-0.2.0/ggsurveillance/man/figures/ggepicurve_plot_readme.png |only ggsurveillance-0.3.0/ggsurveillance/DESCRIPTION | 16 ggsurveillance-0.3.0/ggsurveillance/MD5 | 67 ++- ggsurveillance-0.3.0/ggsurveillance/NAMESPACE | 18 - ggsurveillance-0.3.0/ggsurveillance/NEWS.md | 20 - ggsurveillance-0.3.0/ggsurveillance/R/align_dates_seasonal.R | 39 +- ggsurveillance-0.3.0/ggsurveillance/R/geom_epicurve.R | 6 ggsurveillance-0.3.0/ggsurveillance/R/geom_epigantt.R | 13 ggsurveillance-0.3.0/ggsurveillance/R/geom_vline_year.R | 131 ++++++- ggsurveillance-0.3.0/ggsurveillance/R/ggplot_theme_helpers.R |only ggsurveillance-0.3.0/ggsurveillance/R/reexport-tidyr.R | 10 ggsurveillance-0.3.0/ggsurveillance/R/scale_cases_5er.R | 44 +- ggsurveillance-0.3.0/ggsurveillance/R/utils.R | 25 + ggsurveillance-0.3.0/ggsurveillance/README.md | 46 +- ggsurveillance-0.3.0/ggsurveillance/inst/WORDLIST | 2 ggsurveillance-0.3.0/ggsurveillance/inst/doc/Epigantt_with_ggsurveillance.R | 7 ggsurveillance-0.3.0/ggsurveillance/inst/doc/Epigantt_with_ggsurveillance.Rmd | 7 ggsurveillance-0.3.0/ggsurveillance/inst/doc/Epigantt_with_ggsurveillance.html | 9 ggsurveillance-0.3.0/ggsurveillance/inst/doc/align_dates_seasonal.R | 5 ggsurveillance-0.3.0/ggsurveillance/inst/doc/align_dates_seasonal.Rmd | 9 ggsurveillance-0.3.0/ggsurveillance/inst/doc/align_dates_seasonal.html | 15 ggsurveillance-0.3.0/ggsurveillance/man/align_dates_seasonal.Rd | 6 ggsurveillance-0.3.0/ggsurveillance/man/figures/epigantt_plot_readme.png |only ggsurveillance-0.3.0/ggsurveillance/man/figures/logo_github_social_media.png |only ggsurveillance-0.3.0/ggsurveillance/man/geom_epicurve.Rd | 4 ggsurveillance-0.3.0/ggsurveillance/man/geom_epigantt.Rd | 5 ggsurveillance-0.3.0/ggsurveillance/man/geom_vline_year.Rd | 37 +- ggsurveillance-0.3.0/ggsurveillance/man/scale_y_cases_5er.Rd | 12 ggsurveillance-0.3.0/ggsurveillance/man/theme_mod_disable_legend.Rd |only ggsurveillance-0.3.0/ggsurveillance/man/theme_mod_remove_minor_grid.Rd |only ggsurveillance-0.3.0/ggsurveillance/man/theme_mod_rotate_axis_labels.Rd |only ggsurveillance-0.3.0/ggsurveillance/man/uncount.Rd | 5 ggsurveillance-0.3.0/ggsurveillance/tests/testthat/test-align_and_bin_dates_seasonal.R | 61 +++ ggsurveillance-0.3.0/ggsurveillance/tests/testthat/test-geom_epicurve.R | 18 - ggsurveillance-0.3.0/ggsurveillance/tests/testthat/test-geom_epigantt.R | 25 + ggsurveillance-0.3.0/ggsurveillance/tests/testthat/test-geom_vline_year.R | 177 +++++++++- ggsurveillance-0.3.0/ggsurveillance/vignettes/Epigantt_with_ggsurveillance.Rmd | 7 ggsurveillance-0.3.0/ggsurveillance/vignettes/align_dates_seasonal.Rmd | 9 38 files changed, 644 insertions(+), 211 deletions(-)
More information about ggsurveillance at CRAN
Permanent link
Title: Translate English Sentence into Chinese, or Translate Chinese
Sentence into English
Description: If translate English or Chinese sentence, there is a faster
way for R user. You can pass in an English or Chinese sentence, ecce
package support both English and Chinese translation. It also support
browse translation results in website. In addition, also support obtain
the pinyin of the Chinese character, you can more easily understand
the pronunciation of the Chinese character.
Author: Xinyuan Chu [aut, cre]
Maintainer: Xinyuan Chu <chuxinyuan@outlook.com>
Diff between ecce versions 3.0.2 dated 2024-06-27 and 3.0.3 dated 2025-04-11
DESCRIPTION | 14 LICENSE | 4 MD5 | 18 - R/pinyin.R | 334 ++++++++++---------- README.md | 122 +++---- build/vignette.rds |binary inst/doc/ecce.R | 92 ++--- inst/doc/ecce.Rmd | 168 +++++----- inst/doc/ecce.html | 883 ++++++++++++++++++++++++++--------------------------- vignettes/ecce.Rmd | 168 +++++----- 10 files changed, 902 insertions(+), 901 deletions(-)
Title: Install R Packages or Download File from GitHub via the Proxy
Site
Description: When you want to install R package or download file from GitHub,
but you can't access GitHub, this package helps you install R packages or
download file from GitHub via the proxy website <https://gh-proxy.com/>
or <https://ghfast.top/>, which is in real-time sync with GitHub.
Author: Xinyuan Chu [aut, cre]
Maintainer: Xinyuan Chu <chuxinyuan@outlook.com>
Diff between ipkg versions 1.1.2 dated 2025-02-27 and 1.1.3 dated 2025-04-11
DESCRIPTION | 12 +-- LICENSE | 4 - MD5 | 10 +- R/download_file.R | 190 ++++++++++++++++++++++++++--------------------------- R/install_github.R | 140 +++++++++++++++++++-------------------- README.md | 82 +++++++++++----------- 6 files changed, 219 insertions(+), 219 deletions(-)
Title: Get Basic Information from Chinese ID Number
Description: The Chinese ID number contains a lot of information,
this package helps you get the region, date of birth, age,
age based on year, gender, zodiac, constellation information from
the Chinese ID number.
Author: Xinyuan Chu [aut, cre]
Maintainer: Xinyuan Chu <chuxinyuan@outlook.com>
Diff between CNID versions 2.1.0 dated 2025-03-17 and 2.1.1 dated 2025-04-11
DESCRIPTION | 12 - MD5 | 22 +- R/age.R | 56 +++--- R/age_by_year.R | 56 +++--- R/birth_date.R | 56 +++--- R/check_id.R | 56 +++--- R/cnid_info.R | 468 ++++++++++++++++++++++++++++---------------------------- R/cstl.R | 56 +++--- R/gender.R | 56 +++--- R/region.R | 56 +++--- R/zodiac.R | 56 +++--- README.md | 4 12 files changed, 477 insertions(+), 477 deletions(-)
Title: Style Your Code Fast
Description: Provides a set of functions
that allow users for styling their R code according to
the 'tidyverse' style guide. The package uses a native
Rust implementation to ensure the highest performance.
Learn more about 'tergo' at <https://rtergo.pagacz.io>.
Author: Konrad Pagacz [aut, cre],
Maciej Nasinski [ctb],
The authors of the dependency Rust crates [ctb]
Maintainer: Konrad Pagacz <konrad.pagacz@gmail.com>
Diff between tergo versions 0.1.8 dated 2025-02-05 and 0.1.9 dated 2025-04-11
tergo-0.1.8/tergo/src/Makevars.ucrt |only tergo-0.1.9/tergo/DESCRIPTION | 13 tergo-0.1.9/tergo/LICENSE.note | 198 ------------ tergo-0.1.9/tergo/MD5 | 53 +-- tergo-0.1.9/tergo/R/extendr-wrappers.R | 7 tergo-0.1.9/tergo/R/styling.R | 109 +++++- tergo-0.1.9/tergo/build/vignette.rds |binary tergo-0.1.9/tergo/configure | 86 ----- tergo-0.1.9/tergo/configure.win | 67 ---- tergo-0.1.9/tergo/inst/AUTHORS | 125 +------ tergo-0.1.9/tergo/inst/doc/styling_with_tergo.Rmd | 1 tergo-0.1.9/tergo/inst/doc/styling_with_tergo.html | 6 tergo-0.1.9/tergo/man/get_default_config.Rd | 7 tergo-0.1.9/tergo/man/is_in_ignored_paths.Rd |only tergo-0.1.9/tergo/man/style.Rd | 1 tergo-0.1.9/tergo/man/style_file.Rd | 6 tergo-0.1.9/tergo/man/style_file_internal.Rd |only tergo-0.1.9/tergo/man/style_pkg.Rd | 1 tergo-0.1.9/tergo/man/style_text.Rd | 10 tergo-0.1.9/tergo/man/truncate_error.Rd |only tergo-0.1.9/tergo/src/Makevars.in | 55 ++- tergo-0.1.9/tergo/src/Makevars.win.in | 53 +-- tergo-0.1.9/tergo/src/rust/Cargo.lock | 331 +++------------------ tergo-0.1.9/tergo/src/rust/Cargo.toml | 11 tergo-0.1.9/tergo/src/rust/src/lib.rs | 271 ++++++++++------- tergo-0.1.9/tergo/src/rust/vendor-config.toml |only tergo-0.1.9/tergo/src/rust/vendor.tar.xz |binary tergo-0.1.9/tergo/tests |only tergo-0.1.9/tergo/tools/config.R |only tergo-0.1.9/tergo/tools/msrv.R |only tergo-0.1.9/tergo/vignettes/styling_with_tergo.Rmd | 1 31 files changed, 471 insertions(+), 941 deletions(-)
Title: DBI/RJDBC Interface to H2 Database
Description: DBI/RJDBC interface to h2 database. h2 version 2.3.232 is included.
Author: G. Grothendieck [aut],
"David M. Kaplan" [cre]
Maintainer: "David M. Kaplan" <dmkaplan2000@gmail.com>
Diff between RH2 versions 0.2.4 dated 2018-03-14 and 0.2.5 dated 2025-04-11
RH2-0.2.4/RH2/inst/java/h2-1.3.175.jar |only RH2-0.2.5/RH2/DESCRIPTION | 25 +++++++++++++++++-------- RH2-0.2.5/RH2/MD5 | 14 +++++++------- RH2-0.2.5/RH2/NAMESPACE | 16 +++++++++++++--- RH2-0.2.5/RH2/NEWS | 6 ++++++ RH2-0.2.5/RH2/README.md | 2 +- RH2-0.2.5/RH2/inst/java/h2-2.3.232.jar |only RH2-0.2.5/RH2/java/README | 6 +++++- RH2-0.2.5/RH2/man/H2Connection-class.Rd | 4 ++-- 9 files changed, 51 insertions(+), 22 deletions(-)
Title: International Geomagnetic Reference Field
Description: The 14th generation International Geomagnetic Reference Field (IGRF).
A standard spherical harmonic representation of the Earth's main field.
Author: Koen Hufkens [aut, cre] ,
BlueGreen Labs [cph, fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between igrf versions 1.0 dated 2022-01-07 and 2.0 dated 2025-04-11
igrf-1.0/igrf/src/igrf13.f |only igrf-2.0/igrf/DESCRIPTION | 17 - igrf-2.0/igrf/MD5 | 21 - igrf-2.0/igrf/R/igrf.R | 8 igrf-2.0/igrf/build/vignette.rds |binary igrf-2.0/igrf/inst/CITATION |only igrf-2.0/igrf/inst/doc/igrf.R | 4 igrf-2.0/igrf/inst/doc/igrf.Rmd | 4 igrf-2.0/igrf/inst/doc/igrf.html | 462 ++++++++++++++++++++++++++++----------- igrf-2.0/igrf/src/Makevars | 6 igrf-2.0/igrf/src/igrf14.f |only igrf-2.0/igrf/src/wrapper.c | 10 igrf-2.0/igrf/vignettes/igrf.Rmd | 4 13 files changed, 373 insertions(+), 163 deletions(-)
Title: Easy Study of Patient DICOM Data in Oncology
Description: Exploitation, processing and 2D-3D visualization of DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, in a patient-oriented perspective.
Author: Cathy Fontbonne [aut, cre] ,
Jean-Marc Fontbonne [aut] ,
Nathan Azemar [ctb]
Maintainer: Cathy Fontbonne <contact.espadon@lpccaen.in2p3.fr>
Diff between espadon versions 1.10.0 dated 2025-02-05 and 1.11.0 dated 2025-04-11
DESCRIPTION | 6 MD5 | 66 ++-- NAMESPACE | 2 R/bin_from_roi.R | 6 R/dicom_browser.R | 23 - R/dicom_parser.R | 44 -- R/dicom_patient_anonymiser.R | 16 - R/dicom_raw_data_anonymizer.R | 411 +++++++++++++++++++------- R/dicom_viewer.R | 2 R/err_metrics_from_roi.R | 112 +++++-- R/espadon_hidden.R | 4 R/export.R | 72 ---- R/load_Rdcm_raw_data.R | 4 R/struct_update_roiinfo.R |only R/study_deployment.R | 2 build/partial.rdb |binary build/stage23.rdb |binary build/vignette.rds |binary inst/doc/espadon_overview.Rmd | 2 inst/doc/espadon_overview.html | 42 +- man/dicom.patient.anonymiser.Rd | 12 man/dicom.raw.data.anonymizer.Rd | 12 man/err.metrics.from.roi.Rd | 30 + man/struct.update_roiinfo.Rd |only src/RcppExports.cpp | 2 src/dicombrowser.cpp | 601 +++++++++++++++++++++++++++++++++------ src/fantovoxelC.cpp | 2 src/gammaindex.cpp | 2 src/labelbrowser.cpp | 2 src/mdcC.cpp | 2 src/meshinfront.cpp | 2 src/ouline2voxC.cpp | 2 src/ptinpolygonC.cpp | 2 src/ptnearestC.cpp | 2 vignettes/espadon_overview.Rmd | 2 35 files changed, 1076 insertions(+), 413 deletions(-)
Title: Visualizing the Elements Within Bio-Sequences
Description: Visualizing the types and distribution of elements within
bio-sequences. At the same time, We have developed a geom layer,
geom_rrect(), that can generate rounded rectangles. No external references
are used in the development of this package.
Author: Shiqi Zhao [aut, cre, cph]
Maintainer: Shiqi Zhao <zhaosq89@163.com>
Diff between BioVizSeq versions 1.0.2 dated 2025-03-20 and 1.0.3 dated 2025-04-11
BioVizSeq-1.0.2/BioVizSeq/inst/extdata/meme.xml |only BioVizSeq-1.0.3/BioVizSeq/DESCRIPTION | 8 BioVizSeq-1.0.3/BioVizSeq/MD5 | 51 ++- BioVizSeq-1.0.3/BioVizSeq/NAMESPACE | 4 BioVizSeq-1.0.3/BioVizSeq/NEWS.md | 7 BioVizSeq-1.0.3/BioVizSeq/R/combi_plot.R | 60 ++- BioVizSeq-1.0.3/BioVizSeq/R/globalvariables.R | 3 BioVizSeq-1.0.3/BioVizSeq/R/meme_plot.R | 14 BioVizSeq-1.0.3/BioVizSeq/R/plantcare_plot.R | 167 +++++++++- BioVizSeq-1.0.3/BioVizSeq/README.md | 17 - BioVizSeq-1.0.3/BioVizSeq/inst/extdata/group_class.csv |only BioVizSeq-1.0.3/BioVizSeq/inst/shinyapp/app.R | 9 BioVizSeq-1.0.3/BioVizSeq/inst/shinyapp/global.R | 2 BioVizSeq-1.0.3/BioVizSeq/inst/shinyapp/script/mod_advplot2.R |only BioVizSeq-1.0.3/BioVizSeq/inst/shinyapp/script/mod_plantcareplot.R | 2 BioVizSeq-1.0.3/BioVizSeq/inst/shinyapp/script/mod_plantcareplot2.R |only BioVizSeq-1.0.3/BioVizSeq/inst/shinyapp/www/html/README.html | 23 - BioVizSeq-1.0.3/BioVizSeq/man/figures |only BioVizSeq-1.0.3/BioVizSeq/man/meme_plot.Rd | 7 BioVizSeq-1.0.3/BioVizSeq/man/meme_seq.Rd | 4 BioVizSeq-1.0.3/BioVizSeq/man/meme_to_loc.Rd | 3 BioVizSeq-1.0.3/BioVizSeq/man/plantcare_plot1.Rd |only BioVizSeq-1.0.3/BioVizSeq/man/plantcare_plot2.Rd |only BioVizSeq-1.0.3/BioVizSeq/man/plantcare_plot3.Rd |only 24 files changed, 299 insertions(+), 82 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-18 0.1.6
2022-03-01 0.1.5
2022-01-24 0.1.4
Title: Acoustic Template Detection in R
Description: Acoustic template detection and monitoring database interface. Create, modify, save, and use templates for detection of animal vocalizations. View, verify, and extract results. Upload a MySQL schema to a existing instance, manage survey metadata, write and read templates and detections locally or to the database.
Author: Sasha D. Hafner [aut, cre] ,
Jon Katz [aut],
Jerome Sueur [aut] ),
Thierry Aubin [aut] ),
Caroline Simonis [aut] ),
Uwe Ligges [aut] used in
monitoR)),
Therese Donovan [ctb]
Maintainer: Sasha D. Hafner <sasha.hafner@bce.au.dk>
Diff between monitoR versions 1.0.7 dated 2018-02-14 and 1.2 dated 2025-04-11
monitoR-1.0.7/monitoR/NEWS |only monitoR-1.0.7/monitoR/README |only monitoR-1.2/monitoR/ChangeLog | 17 + monitoR-1.2/monitoR/DESCRIPTION | 54 +++ monitoR-1.2/monitoR/MD5 | 153 ++++----- monitoR-1.2/monitoR/NAMESPACE | 2 monitoR-1.2/monitoR/NEWS.md |only monitoR-1.2/monitoR/R/Classes.R | 56 +-- monitoR-1.2/monitoR/R/Methods-index.R | 6 monitoR-1.2/monitoR/R/Methods-plot.R | 114 +++---- monitoR-1.2/monitoR/R/Methods-show.R | 28 - monitoR-1.2/monitoR/R/batchBinMatch.R | 28 - monitoR-1.2/monitoR/R/batchCorMatch.R | 30 - monitoR-1.2/monitoR/R/binMatch.R | 11 monitoR-1.2/monitoR/R/bindEvents.R | 22 - monitoR-1.2/monitoR/R/changeSampRate.R | 16 - monitoR-1.2/monitoR/R/collapseClips.R | 10 monitoR-1.2/monitoR/R/combineBinTemplates.R | 9 monitoR-1.2/monitoR/R/combineCorTemplates.R | 11 monitoR-1.2/monitoR/R/compareTemplates.R | 18 - monitoR-1.2/monitoR/R/corMatch.R | 61 +-- monitoR-1.2/monitoR/R/cutWave.R | 30 + monitoR-1.2/monitoR/R/dbDownloadCardRecorderID.R | 8 monitoR-1.2/monitoR/R/dbDownloadResult.R | 32 +- monitoR-1.2/monitoR/R/dbDownloadSurvey.R | 18 - monitoR-1.2/monitoR/R/dbDownloadTemplate.R | 33 +- monitoR-1.2/monitoR/R/dbSchema.R | 22 - monitoR-1.2/monitoR/R/dbUploadAnno.R | 16 - monitoR-1.2/monitoR/R/dbUploadResult.R | 26 - monitoR-1.2/monitoR/R/dbUploadSurvey.R | 32 +- monitoR-1.2/monitoR/R/dbUploadTemplate.R | 20 - monitoR-1.2/monitoR/R/eventEval.R | 27 - monitoR-1.2/monitoR/R/fileCopyRename.R | 54 +-- monitoR-1.2/monitoR/R/findDetections.R | 10 monitoR-1.2/monitoR/R/findPeaks.R | 20 - monitoR-1.2/monitoR/R/getClip.R | 37 +- monitoR-1.2/monitoR/R/getDetections.R | 6 monitoR-1.2/monitoR/R/getPeaks.R | 6 monitoR-1.2/monitoR/R/getTemplates.R | 6 monitoR-1.2/monitoR/R/makeBinTemplate.R | 312 ++++++++++---------- monitoR-1.2/monitoR/R/makeCorTemplate.R | 107 +++--- monitoR-1.2/monitoR/R/mp3Subsamp.R | 46 +- monitoR-1.2/monitoR/R/readBinTemplates.R | 20 - monitoR-1.2/monitoR/R/readCorTemplates.R | 20 - monitoR-1.2/monitoR/R/readMP3.R | 14 monitoR-1.2/monitoR/R/readOneBinTemplate.R | 2 monitoR-1.2/monitoR/R/readOneCorTemplate.R | 2 monitoR-1.2/monitoR/R/showPeaks.R | 98 +++--- monitoR-1.2/monitoR/R/specCols.R | 10 monitoR-1.2/monitoR/R/spectro.R | 2 monitoR-1.2/monitoR/R/templateComment.R | 2 monitoR-1.2/monitoR/R/templateCutoff.R | 4 monitoR-1.2/monitoR/R/templateNames.R | 2 monitoR-1.2/monitoR/R/templatePath.R | 2 monitoR-1.2/monitoR/R/timeAlign.R | 17 - monitoR-1.2/monitoR/R/viewSpec.R | 218 ++++++------- monitoR-1.2/monitoR/R/writeBinTemplates.R | 10 monitoR-1.2/monitoR/R/writeCorTemplates.R | 10 monitoR-1.2/monitoR/R/writeOneBinTemplate.R | 66 ++-- monitoR-1.2/monitoR/R/writeOneCorTemplate.R | 64 ++-- monitoR-1.2/monitoR/build/vignette.rds |binary monitoR-1.2/monitoR/data/btnw.rda |binary monitoR-1.2/monitoR/data/oven.rda |binary monitoR-1.2/monitoR/data/survey.rda |binary monitoR-1.2/monitoR/data/survey_anno.rda |binary monitoR-1.2/monitoR/inst/CITATION | 8 monitoR-1.2/monitoR/inst/doc/monitoR_QuickStart.R | 8 monitoR-1.2/monitoR/inst/doc/monitoR_QuickStart.pdf |binary monitoR-1.2/monitoR/man/TemplateList-class.Rd | 2 monitoR-1.2/monitoR/man/bindEvents.Rd | 2 monitoR-1.2/monitoR/man/combineTemplates.Rd | 2 monitoR-1.2/monitoR/man/dbSchema.Rd | 2 monitoR-1.2/monitoR/man/fileCopyRename.Rd | 4 monitoR-1.2/monitoR/man/makeTemplate.Rd | 5 monitoR-1.2/monitoR/man/monitoR-package.Rd | 2 monitoR-1.2/monitoR/man/mp3Subsamp.Rd | 2 monitoR-1.2/monitoR/man/readMP3.Rd | 4 monitoR-1.2/monitoR/man/templateMatching.Rd | 2 monitoR-1.2/monitoR/man/viewSpec.Rd | 2 79 files changed, 1101 insertions(+), 1021 deletions(-)
Title: Censored Regression with Smooth Terms
Description: Implementation of Tobit type I and type II families for censored regression using the 'mgcv' package, based on methods detailed in Woods (2016) <doi:10.1080/01621459.2016.1180986>.
Author: Zhou Fang [aut, cre]
Maintainer: Zhou Fang <zhou.fang@bioss.ac.uk>
Diff between cenGAM versions 0.5.3 dated 2017-08-30 and 0.5.4 dated 2025-04-11
DESCRIPTION | 16 ++++++++++------ MD5 | 6 +++--- man/tobit1.Rd | 4 ++-- man/tobit2.Rd | 2 +- 4 files changed, 16 insertions(+), 12 deletions(-)
Title: Clinical Trial Style Data Readout Listings
Description: Listings are often part of the submission of clinical trial
data in regulatory settings. We provide a framework for the specific
formatting features often used when displaying large datasets in that
context.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Joe Zhu [aut, cre] ,
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [ctb] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between rlistings versions 0.2.10 dated 2025-01-08 and 0.2.11 dated 2025-04-11
DESCRIPTION | 25 +- MD5 | 49 ++-- NEWS.md | 5 R/rlistings.R | 161 ++++++++++++- R/rlistings_methods.R | 42 ++- build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/col_formatting.html | 90 +++---- inst/doc/large_list.R |only inst/doc/large_list.Rmd |only inst/doc/large_list.html |only inst/doc/pagination.html | 6 inst/doc/ref_footnotes.html | 6 inst/doc/rlistings.html | 32 +- man/listing_methods.Rd | 14 + man/listings.Rd | 13 + man/make_row_df-listing_df-method.Rd | 7 man/matrix_form-listing_df-method.Rd | 7 man/rlistings-package.Rd | 6 man/vec_nlines.Rd | 16 + tests/testthat/_snaps/paginate_listing.md | 360 ++++++++++++++++++++++++++++-- tests/testthat/_snaps/print.md | 13 + tests/testthat/setup.R | 8 tests/testthat/test-listings.R | 69 +++++ tests/testthat/test-paginate_listing.R | 83 ++++++ tests/testthat/test-print.R | 106 ++++++++ vignettes/large_list.Rmd |only vignettes/rlisting_time.png |only 28 files changed, 959 insertions(+), 163 deletions(-)
Title: The Residual-Based Predictiveness Curve
Description: The RBP curve is a visual tool to assess the
performance of prediction models.
Author: Giuseppe Casalicchio [cre, aut]
,
Bernd Bischl [ctb]
Maintainer: Giuseppe Casalicchio <giuseppe.casalicchio@stat.uni-muenchen.de>
Diff between RBPcurve versions 1.2 dated 2017-05-15 and 1.3 dated 2025-04-11
DESCRIPTION | 22 +++-- MD5 | 16 +-- R/addWellCalib.R | 228 ++++++++++++++++++++++++++-------------------------- README.md | 19 ++-- man/addGoodCalib.Rd | 10 +- man/addPEV.Rd | 9 +- man/addRates.Rd | 10 +- man/addWellCalib.Rd | 11 +- man/plotRBPCurve.Rd | 18 +++- 9 files changed, 191 insertions(+), 152 deletions(-)
Title: Vegetation Phenological Cycle and Anomaly Detection using Remote
Sensing Data
Description: Calculates phenological cycle and anomalies using a non-parametric
approach applied to time series of vegetation indices derived from remote sensing data
or field measurements. The package implements basic and high-level functions for
manipulating vector data (numerical series) and raster data (satellite derived products).
Processing of very large raster files is supported. For more information, please check
the following paper:
Chávez et al. (2023) <doi:10.3390/rs15010073>.
Author: Roberto O. Chavez [aut] ,
Sergio A. Estay [aut] ,
Jose A. Lastra [cre, ctb] ,
Carlos G. Riquelme [ctb]
Maintainer: Jose A. Lastra <jose.lastra@pucv.cl>
Diff between npphen versions 2.0.0 dated 2023-10-12 and 2.0.1 dated 2025-04-11
DESCRIPTION | 22 ++++++++++++++++------ MD5 | 18 +++++++++--------- R/ExtremeAnoMap.R | 4 ++-- R/ExtremeAnom.R | 4 ++-- R/PhenKplot.R | 4 ++-- man/ExtremeAnoMap.Rd | 12 ++++++------ man/ExtremeAnom.Rd | 4 ++-- man/Phen.Rd | 2 +- man/PhenKplot.Rd | 10 +++++----- man/npphen.Rd | 4 ++-- 10 files changed, 47 insertions(+), 37 deletions(-)
Title: Visualisations for Generalized Additive Models
Description: Extension of the 'mgcv' package, providing visual tools for Generalized Additive Models that exploit the additive structure of such models, scale to large data sets and can be used in conjunction with a wide range of response distributions. The focus is providing visual methods for better understanding the model output and for aiding model checking and development beyond simple exponential family regression. The graphical framework is based on the layering system provided by 'ggplot2'.
Author: Matteo Fasiolo [aut, cre],
Raphael Nedellec [aut],
Yannig Goude [ctb],
Christian Capezza [ctb],
Simon N. Wood [ctb]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between mgcViz versions 0.1.11 dated 2023-10-06 and 0.2.0 dated 2025-04-11
mgcViz-0.1.11/mgcViz/R/I_prepareInnerSI.R |only mgcViz-0.1.11/mgcViz/R/I_prepareNested.R |only mgcViz-0.2.0/mgcViz/DESCRIPTION | 12 +-- mgcViz-0.2.0/mgcViz/MD5 | 86 ++++++++++++------------- mgcViz-0.2.0/mgcViz/NAMESPACE | 2 mgcViz-0.2.0/mgcViz/R/I_getDataTypeY.R | 2 mgcViz-0.2.0/mgcViz/R/I_getResTypeAndMethod.R | 16 ++-- mgcViz-0.2.0/mgcViz/R/I_prepareInnerNested.R |only mgcViz-0.2.0/mgcViz/R/I_prepareOuterNested.R |only mgcViz-0.2.0/mgcViz/R/L_ciBar.R | 2 mgcViz-0.2.0/mgcViz/R/L_ciLine.R | 2 mgcViz-0.2.0/mgcViz/R/L_ciPoly.R | 3 mgcViz-0.2.0/mgcViz/R/L_dens1D.R | 4 - mgcViz-0.2.0/mgcViz/R/L_dens2D.R | 3 mgcViz-0.2.0/mgcViz/R/L_fitBar.R | 2 mgcViz-0.2.0/mgcViz/R/L_fitContour.R | 2 mgcViz-0.2.0/mgcViz/R/L_fitLine.R | 2 mgcViz-0.2.0/mgcViz/R/L_fitPoints.R | 2 mgcViz-0.2.0/mgcViz/R/L_fitRaster.R | 2 mgcViz-0.2.0/mgcViz/R/L_glyphs2D.R | 2 mgcViz-0.2.0/mgcViz/R/L_hist.R | 4 - mgcViz-0.2.0/mgcViz/R/L_points.R | 5 - mgcViz-0.2.0/mgcViz/R/L_rug.R | 4 - mgcViz-0.2.0/mgcViz/R/check2D.R | 2 mgcViz-0.2.0/mgcViz/R/check_gamViz.R | 6 + mgcViz-0.2.0/mgcViz/R/getViz.R | 2 mgcViz-0.2.0/mgcViz/R/listLayers.R | 2 mgcViz-0.2.0/mgcViz/R/plotRGL_mgcv_smooth_2D.R | 2 mgcViz-0.2.0/mgcViz/R/plotRGL_mgcv_smooth_MD.R | 2 mgcViz-0.2.0/mgcViz/R/plot_gamViz.R | 2 mgcViz-0.2.0/mgcViz/R/plot_mgamViz.R | 2 mgcViz-0.2.0/mgcViz/R/plot_mgcv_smooth_2D.R | 14 +++- mgcViz-0.2.0/mgcViz/R/plot_nested1D.R |only mgcViz-0.2.0/mgcViz/R/plot_sos_smooth.R | 2 mgcViz-0.2.0/mgcViz/R/postSim.R | 6 - mgcViz-0.2.0/mgcViz/R/print_plotGam.R | 5 - mgcViz-0.2.0/mgcViz/R/qq_gamViz.R | 2 mgcViz-0.2.0/mgcViz/R/simulate_gam.R | 4 - mgcViz-0.2.0/mgcViz/R/sm.R | 4 - mgcViz-0.2.0/mgcViz/inst/doc/mgcviz.html | 30 ++++---- mgcViz-0.2.0/mgcViz/man/getViz.Rd | 2 mgcViz-0.2.0/mgcViz/man/l_glyphs2D.Rd | 4 - mgcViz-0.2.0/mgcViz/man/plot.gamViz.Rd | 2 mgcViz-0.2.0/mgcViz/man/plot.mgamViz.Rd | 2 mgcViz-0.2.0/mgcViz/man/plot.nested1D.Rd |only mgcViz-0.2.0/mgcViz/man/postSim.Rd | 6 - mgcViz-0.2.0/mgcViz/man/simulate.gam.Rd | 4 - 47 files changed, 143 insertions(+), 121 deletions(-)
Title: Easily Downloads a Gene Expression Dataset from a GEO Code and
Retrieves the Gene Symbols of Its Probesets
Description: A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, <doi:10.1007/978-1-0716-1839-4_12>.
Author: Davide Chicco [aut, cre]
Maintainer: Davide Chicco <davidechicco@davidechicco.it>
Diff between geneExpressionFromGEO versions 0.9 dated 2021-12-16 and 1.2 dated 2025-04-11
DESCRIPTION | 11 +- MD5 | 12 +- R/geneExpressionFromGEO.r | 18 +++- build/vignette.rds |binary inst/doc/geneExpressionFromGEOvignette.R | 2 inst/doc/geneExpressionFromGEOvignette.html | 117 ++++++++++++++++++---------- man/getGeneExpressionFromGEO.Rd | 2 7 files changed, 104 insertions(+), 58 deletions(-)
More information about geneExpressionFromGEO at CRAN
Permanent link
Title: Ecological Inference of RxC Tables by Overdispersed-Multinomial
Models
Description: Estimates RxC (R by C) vote transfer matrices (ecological contingency tables) from aggregate data using the model described in Forcina et al. (2012), as extension of the model proposed in Brown and Payne (1986). Allows incorporation of covariates.
References:
Brown, P. and Payne, C. (1986). ''Aggregate data, ecological regression and voting transitions''. Journal of the American Statistical Association, 81, 453–460. <DOI:10.1080/01621459.1986.10478290>.
Forcina, A., Gnaldi, M. and Bracalente, B. (2012). ''A revised Brown and Payne model of voting behaviour applied to the 2009 elections in Italy''. Statistical Methods & Applications, 21, 109–119. <DOI:10.1007/s10260-011-0184-x>.
Author: Antonio Forcina [aut] ,
Jose M. Pavia [aut, cre]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Diff between eiCircles versions 0.0.1-7 dated 2024-03-24 and 0.0.1-12 dated 2025-04-11
DESCRIPTION | 8 - MD5 | 18 ++- NAMESPACE | 5 + NEWS.md | 11 +- R/BPF.R | 79 ++++++++++++----- R/auxiliary_functions.R | 174 ++++++++++++++++++++++++++++++++++++-- R/simula_BPF.R |only R/simula_BPF_with_deviations.R |only build/partial.rdb |binary man/BPF.Rd | 39 +++++--- man/simula_BPF.Rd |only man/simula_BPF_with_deviations.Rd |only 12 files changed, 278 insertions(+), 56 deletions(-)
Title: A Copula-Based Clustering Algorithm
Description: A copula based clustering algorithm that finds clusters according to the complex multivariate dependence structure of the data generating process. The updated version of the algorithm is described in Di Lascio, F.M.L. and Giannerini, S. (2019). "Clustering dependent observations with copula functions". Statistical Papers, 60, p.35-51. <doi:10.1007/s00362-016-0822-3>.
Author: Francesca Marta Lilja Di Lascio [aut, cre],
Simone Giannerini [aut]
Maintainer: Francesca Marta Lilja Di Lascio <marta.dilascio@unibz.it>
Diff between CoClust versions 0.3-2 dated 2017-12-17 and 1.0-0 dated 2025-04-11
ChangeLog | 5 +++ DESCRIPTION | 22 +++++++++++----- MD5 | 14 +++++----- R/CoClust.R | 17 +++++++------ R/Internal_functions.R | 3 +- inst/CITATION | 64 +++++++++++++++++++++++-------------------------- man/CoClust-class.Rd | 29 ++++++++++------------ man/CoClust.Rd | 19 +++++++------- 8 files changed, 94 insertions(+), 79 deletions(-)
Title: Course-Dependent Skill Structures
Description: Deriving skill structures from skill assignment
data for courses (sets of learning objects).
Author: Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between CDSS versions 0.2-0 dated 2023-10-08 and 0.3-0 dated 2025-04-11
CDSS-0.2-0/CDSS/R/binary_matrix_product.R |only CDSS-0.2-0/CDSS/R/close_ar.R |only CDSS-0.2-0/CDSS/R/read_skll_assignments_csv.R |only CDSS-0.2-0/CDSS/R/read_skll_assignments_ods.R |only CDSS-0.2-0/CDSS/R/read_skll_assignments_xlsx.R |only CDSS-0.2-0/CDSS/R/reduce_sf.R |only CDSS-0.2-0/CDSS/man/binary_matrix_product.Rd |only CDSS-0.2-0/CDSS/man/close_ar.Rd |only CDSS-0.2-0/CDSS/man/read_skill_assignment_csv.Rd |only CDSS-0.2-0/CDSS/man/read_skill_assignment_ods.Rd |only CDSS-0.2-0/CDSS/man/read_skill_assignment_xlsx.Rd |only CDSS-0.2-0/CDSS/man/reduce_sf.Rd |only CDSS-0.3-0/CDSS/Changelog | 4 CDSS-0.3-0/CDSS/DESCRIPTION | 10 +- CDSS-0.3-0/CDSS/MD5 | 56 ++++++----- CDSS-0.3-0/CDSS/NAMESPACE | 17 ++- CDSS-0.3-0/CDSS/R/CDSS-package.R | 4 CDSS-0.3-0/CDSS/R/cdss_binary_matrix_product.R |only CDSS-0.3-0/CDSS/R/cdss_close_ar.R |only CDSS-0.3-0/CDSS/R/cdss_lo_csma2sf.R |only CDSS-0.3-0/CDSS/R/cdss_lo_sa2af.R |only CDSS-0.3-0/CDSS/R/cdss_lo_sa2ar.R |only CDSS-0.3-0/CDSS/R/cdss_read_skll_assignments_csv.R |only CDSS-0.3-0/CDSS/R/cdss_read_skll_assignments_ods.R |only CDSS-0.3-0/CDSS/R/cdss_read_skll_assignments_xlsx.R |only CDSS-0.3-0/CDSS/R/cdss_reduce_sf.R |only CDSS-0.3-0/CDSS/R/cdss_sa2ar_skill.R | 84 ++++++++--------- CDSS-0.3-0/CDSS/R/cdss_wf_read_skill_assignment.R |only CDSS-0.3-0/CDSS/inst/extdata/KST-Intro.ods |binary CDSS-0.3-0/CDSS/inst/extdata/KST.ods |binary CDSS-0.3-0/CDSS/man/CDSS.Rd | 4 CDSS-0.3-0/CDSS/man/cdss_binary_matrix_product.Rd |only CDSS-0.3-0/CDSS/man/cdss_close_ar.Rd |only CDSS-0.3-0/CDSS/man/cdss_lo_csma2sf.Rd |only CDSS-0.3-0/CDSS/man/cdss_lo_sa2af.Rd |only CDSS-0.3-0/CDSS/man/cdss_lo_sa2ar.Rd |only CDSS-0.3-0/CDSS/man/cdss_read_skill_assignment_csv.Rd |only CDSS-0.3-0/CDSS/man/cdss_read_skill_assignment_ods.Rd |only CDSS-0.3-0/CDSS/man/cdss_read_skill_assignment_xlsx.Rd |only CDSS-0.3-0/CDSS/man/cdss_reduce_sf.Rd |only CDSS-0.3-0/CDSS/man/cdss_sa2ar_skill.Rd | 3 CDSS-0.3-0/CDSS/man/cdss_sa2sma.Rd | 2 CDSS-0.3-0/CDSS/man/cdss_sa_describes_sr.Rd | 1 CDSS-0.3-0/CDSS/man/cdss_tables2sa.Rd | 2 CDSS-0.3-0/CDSS/man/cdss_wf_read_skill_assignment.Rd |only 45 files changed, 105 insertions(+), 82 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre2' (BSD license, see <https://github.com/PCRE2Project/pcre2/blob/master/LICENCE.md>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stephanie Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb],
Marius Bertram [ctb],
Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.6.6 dated 2025-03-30 and 0.6.7 dated 2025-04-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/doc/vignette.html | 4 ++-- src/cwb/cl/makecomps.c | 9 ++++++++- src/cwb/definitions.mk | 2 +- src/cwb/utils/cwb-huffcode.c | 7 +++++++ 6 files changed, 27 insertions(+), 13 deletions(-)
Title: Demographic Modelling Using Projection Matrices
Description: Tools for modelling populations and demography using matrix projection models,
with deterministic and stochastic model implementations. Includes population projection,
indices of short- and long-term population size and growth, perturbation analysis,
convergence to stability or stationarity, and diagnostic and manipulation tools.
Author: Iain Stott [aut, cre],
Dave Hodgson [aut],
Stuart Townley [aut],
Stephen Ellner [ctb]
Maintainer: Iain Stott <iainmstott@gmail.com>
Diff between popdemo versions 1.3-1 dated 2021-11-16 and 1.3-2 dated 2025-04-11
popdemo-1.3-1/popdemo/data/Pbear.R |only popdemo-1.3-1/popdemo/data/Tort.R |only popdemo-1.3-2/popdemo/ChangeLog | 1 popdemo-1.3-2/popdemo/DESCRIPTION | 8 popdemo-1.3-2/popdemo/MD5 | 42 ++-- popdemo-1.3-2/popdemo/NAMESPACE | 1 popdemo-1.3-2/popdemo/R/S3-plot.tfam.R | 2 popdemo-1.3-2/popdemo/R/popdemo-deprecated.R | 1 popdemo-1.3-2/popdemo/R/popdemo-onAttach.R | 2 popdemo-1.3-2/popdemo/R/popdemo-package.R | 2 popdemo-1.3-2/popdemo/R/tfa_inertia.R | 2 popdemo-1.3-2/popdemo/R/tfs_inertia&tfsm_inertia.R | 6 popdemo-1.3-2/popdemo/build/vignette.rds |binary popdemo-1.3-2/popdemo/data/Pbear.rda |only popdemo-1.3-2/popdemo/data/Tort.rda |only popdemo-1.3-2/popdemo/inst/doc/popdemo.R | 22 +- popdemo-1.3-2/popdemo/inst/doc/popdemo.Rmd | 4 popdemo-1.3-2/popdemo/inst/doc/popdemo.html | 185 ++++++++++----------- popdemo-1.3-2/popdemo/man/plot.tfam.Rd | 2 popdemo-1.3-2/popdemo/man/popdemo-deprecated.Rd | 1 popdemo-1.3-2/popdemo/man/popdemo-package.Rd | 2 popdemo-1.3-2/popdemo/man/tfa_inertia.Rd | 2 popdemo-1.3-2/popdemo/man/tfs_inertia.Rd | 6 popdemo-1.3-2/popdemo/vignettes/popdemo.Rmd | 4 24 files changed, 141 insertions(+), 154 deletions(-)
Title: Double Machine Learning in R
Description: Implementation of the double/debiased machine learning framework of
Chernozhukov et al. (2018) <doi:10.1111/ectj.12097> for partially linear
regression models, partially linear instrumental variable regression models,
interactive regression models and interactive instrumental variable
regression models. 'DoubleML' allows estimation of the nuisance parts in
these models by machine learning methods and computation of the Neyman
orthogonal score functions. 'DoubleML' is built on top of 'mlr3' and the
'mlr3' ecosystem. The object-oriented implementation of 'DoubleML' based on
the 'R6' package is very flexible. More information available in the
publication in the Journal of Statistical Software: <doi:10.18637/jss.v108.i03>.
Author: Philipp Bach [aut, cre],
Victor Chernozhukov [aut],
Malte S. Kurz [aut],
Martin Spindler [aut],
Klaassen Sven [aut]
Maintainer: Philipp Bach <philipp.bach@uni-hamburg.de>
Diff between DoubleML versions 1.0.1 dated 2024-06-05 and 1.0.2 dated 2025-04-11
DESCRIPTION | 14 - MD5 | 104 ++++++----- NAMESPACE | 4 R/datasets.R | 114 ++++++++++++ R/double_ml.R | 14 - R/double_ml_data.R | 125 +++++++++++-- R/double_ml_iivm.R | 3 R/double_ml_irm.R | 5 R/double_ml_pliv.R | 11 - R/double_ml_plr.R | 2 R/double_ml_ssm.R |only R/helper.R | 43 ++++ R/zzz.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction_to_DoubleML.html | 4 inst/doc/getstarted.R | 22 +- inst/doc/getstarted.Rmd | 20 +- inst/doc/getstarted.html | 24 +- inst/doc/install.R | 8 man/DoubleML.Rd | 5 man/DoubleMLClusterData.Rd | 4 man/DoubleMLData.Rd | 7 man/DoubleMLIIVM.Rd | 3 man/DoubleMLIRM.Rd | 5 man/DoubleMLPLIV.Rd | 5 man/DoubleMLPLR.Rd | 5 man/DoubleMLSSM.Rd |only man/double_ml_data_from_data_frame.Rd | 4 man/double_ml_data_from_matrix.Rd | 4 man/make_ssm_data.Rd |only tests/testthat/helper-03-dgp.R | 35 +++ tests/testthat/helper-04-simdata.R | 33 +++ tests/testthat/helper-05-ml-learner.R | 50 +++++ tests/testthat/helper-17-dml_ssm.R |only tests/testthat/print_outputs/dml_cluster_data.txt | 1 tests/testthat/print_outputs/dml_data.txt | 1 tests/testthat/print_outputs/dml_pliv.txt | 1 tests/testthat/print_outputs/dml_plr.txt | 1 tests/testthat/test-double_ml_active_bindings.R | 3 tests/testthat/test-double_ml_cluster_not_implemented.R | 3 tests/testthat/test-double_ml_data.R | 145 ++++++++++++---- tests/testthat/test-double_ml_data_active_bindings.R | 69 +++++-- tests/testthat/test-double_ml_data_cluster.R |only tests/testthat/test-double_ml_datasets.R | 29 +++ tests/testthat/test-double_ml_pliv_exception_handling.R | 6 tests/testthat/test-double_ml_pliv_partial_x.R | 8 tests/testthat/test-double_ml_pliv_partial_xz.R | 8 tests/testthat/test-double_ml_pliv_partial_z.R | 8 tests/testthat/test-double_ml_plr_classifier.R | 3 tests/testthat/test-double_ml_plr_exception_handling.R | 3 tests/testthat/test-double_ml_set_sample_splitting.R | 9 tests/testthat/test-double_ml_ssm_mar.R |only tests/testthat/test-double_ml_ssm_nonignorable.R |only tests/testthat/test-double_ml_ssm_tuning.R |only tests/testthat_regression_tests.R | 1 vignettes/getstarted.Rmd | 20 +- 57 files changed, 765 insertions(+), 233 deletions(-)
Title: Stability-enHanced Approaches using Resampling Procedures
Description: In stability selection (N Meinshausen, P Bühlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>) and consensus clustering (S Monti et al (2003) <doi:10.1023/A:1023949509487>), resampling techniques are used to enhance the reliability of the results. In this package (B Bodinier et al (2025) <doi:10.18637/jss.v112.i05>), hyper-parameters are calibrated by maximising model stability, which is measured under the null hypothesis that all selection (or co-membership) probabilities are identical (B Bodinier et al (2023a) <doi:10.1093/jrsssc/qlad058> and B Bodinier et al (2023b) <doi:10.1093/bioinformatics/btad635>). Functions are readily implemented for the use of LASSO regression, sparse PCA, sparse (group) PLS or graphical LASSO in stability selection, and hierarchical clustering, partitioning around medoids, K means or Gaussian mixture models in consensus clustering.
Author: Barbara Bodinier [aut, cre]
Maintainer: Barbara Bodinier <barbara.bodinier@gmail.com>
Diff between sharp versions 1.4.6 dated 2024-02-03 and 1.4.7 dated 2025-04-11
sharp-1.4.6/sharp/build/vignette.rds |only sharp-1.4.6/sharp/inst/doc |only sharp-1.4.6/sharp/vignettes |only sharp-1.4.7/sharp/DESCRIPTION | 16 +++-- sharp-1.4.7/sharp/MD5 | 54 ++++++++---------- sharp-1.4.7/sharp/NEWS.md | 4 + sharp-1.4.7/sharp/R/clustering.R | 4 + sharp-1.4.7/sharp/R/graphical_model.R | 4 + sharp-1.4.7/sharp/R/s3_plot.R | 8 +- sharp-1.4.7/sharp/R/selection_performance.R | 16 ++--- sharp-1.4.7/sharp/R/sharp-package.R | 6 +- sharp-1.4.7/sharp/R/structural_equation_modelling.R | 4 + sharp-1.4.7/sharp/R/variable_selection.R | 4 + sharp-1.4.7/sharp/README.md | 45 ++++++++------- sharp-1.4.7/sharp/build/partial.rdb |binary sharp-1.4.7/sharp/inst/CITATION |only sharp-1.4.7/sharp/inst/REFERENCES.bib | 60 ++++++++++++-------- sharp-1.4.7/sharp/inst/WORDLIST | 3 + sharp-1.4.7/sharp/man/Clustering.Rd | 4 + sharp-1.4.7/sharp/man/ClusteringPerformance.Rd | 2 sharp-1.4.7/sharp/man/GraphComparison.Rd | 4 - sharp-1.4.7/sharp/man/GraphicalModel.Rd | 4 + sharp-1.4.7/sharp/man/SelectionPerformance.Rd | 6 +- sharp-1.4.7/sharp/man/SelectionPerformanceGraph.Rd | 4 - sharp-1.4.7/sharp/man/StructuralModel.Rd | 4 + sharp-1.4.7/sharp/man/VariableSelection.Rd | 4 + sharp-1.4.7/sharp/man/plot.clustering.Rd | 2 sharp-1.4.7/sharp/man/plot.roc_band.Rd | 6 +- sharp-1.4.7/sharp/man/sharp-package.Rd | 6 +- 29 files changed, 157 insertions(+), 117 deletions(-)
Title: Reporting Tables
Description: Reporting tables often have structure that goes beyond simple
rectangular data. The 'rtables' package provides a framework for
declaring complex multi-level tabulations and then applying them to
data. This framework models both tabulation and the resulting tables
as hierarchical, tree-like objects which support sibling sub-tables,
arbitrary splitting or grouping of data in row and column dimensions,
cells containing multiple values, and the concept of contextual
summary computations. A convenient pipe-able interface is provided for
declaring table layouts and the corresponding computations, and then
applying them to data.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Daniel Sabanes Bove [ctb],
Maximilian Mordig [ctb],
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [ctb] ,
Joe Zhu [aut, cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between rtables versions 0.6.11 dated 2025-01-09 and 0.6.12 dated 2025-04-11
rtables-0.6.11/rtables/tests/testthat/Rplots.pdf |only rtables-0.6.12/rtables/DESCRIPTION | 32 rtables-0.6.12/rtables/MD5 | 111 +- rtables-0.6.12/rtables/NEWS.md | 27 rtables-0.6.12/rtables/R/as_html.R | 5 rtables-0.6.12/rtables/R/colby_constructors.R | 14 rtables-0.6.12/rtables/R/default_split_funs.R | 5 rtables-0.6.12/rtables/R/format_rcell.R | 5 rtables-0.6.12/rtables/R/tree_accessors.R | 11 rtables-0.6.12/rtables/R/tt_as_df.R | 226 +++- rtables-0.6.12/rtables/R/tt_compare_tables.R | 11 rtables-0.6.12/rtables/R/tt_dotabulation.R | 32 rtables-0.6.12/rtables/R/tt_pos_and_access.R | 78 + rtables-0.6.12/rtables/R/tt_sort.R | 50 rtables-0.6.12/rtables/R/tt_toString.R | 42 rtables-0.6.12/rtables/build/vignette.rds |binary rtables-0.6.12/rtables/inst/WORDLIST | 4 rtables-0.6.12/rtables/inst/doc/advanced_usage.html | 6 rtables-0.6.12/rtables/inst/doc/ard_how_to.html | 524 ++++------ rtables-0.6.12/rtables/inst/doc/baseline.html | 6 rtables-0.6.12/rtables/inst/doc/clinical_trials.html | 6 rtables-0.6.12/rtables/inst/doc/col_counts.html | 6 rtables-0.6.12/rtables/inst/doc/custom_appearance.html | 6 rtables-0.6.12/rtables/inst/doc/example_analysis_coxreg.html | 6 rtables-0.6.12/rtables/inst/doc/exploratory_analysis.html | 8 rtables-0.6.12/rtables/inst/doc/format_precedence.html | 6 rtables-0.6.12/rtables/inst/doc/introspecting_tables.html | 6 rtables-0.6.12/rtables/inst/doc/manual_table_construction.html | 6 rtables-0.6.12/rtables/inst/doc/rtables.html | 8 rtables-0.6.12/rtables/inst/doc/sorting_pruning.html | 10 rtables-0.6.12/rtables/inst/doc/split_functions.html | 6 rtables-0.6.12/rtables/inst/doc/subsetting_tables.html | 6 rtables-0.6.12/rtables/inst/doc/tabulation_concepts.html | 2 rtables-0.6.12/rtables/inst/doc/tabulation_dplyr.html | 6 rtables-0.6.12/rtables/inst/doc/title_footer.html | 6 rtables-0.6.12/rtables/man/additional_fun_params.Rd | 7 rtables-0.6.12/rtables/man/analyze.Rd | 9 rtables-0.6.12/rtables/man/brackets.Rd | 2 rtables-0.6.12/rtables/man/data.frame_export.Rd | 13 rtables-0.6.12/rtables/man/format_rcell.Rd | 5 rtables-0.6.12/rtables/man/formatters_methods.Rd | 4 rtables-0.6.12/rtables/man/gfc.Rd | 14 rtables-0.6.12/rtables/man/matrix_form-VTableTree-method.Rd | 7 rtables-0.6.12/rtables/man/prune_table.Rd | 6 rtables-0.6.12/rtables/man/rtables-package.Rd | 6 rtables-0.6.12/rtables/man/sort_at_path.Rd | 28 rtables-0.6.12/rtables/man/tostring.Rd | 7 rtables-0.6.12/rtables/tests/testthat/test-accessors.R | 8 rtables-0.6.12/rtables/tests/testthat/test-as_html.R | 10 rtables-0.6.12/rtables/tests/testthat/test-default_split_funs.R | 38 rtables-0.6.12/rtables/tests/testthat/test-exporters.R | 39 rtables-0.6.12/rtables/tests/testthat/test-formatting.R | 13 rtables-0.6.12/rtables/tests/testthat/test-printing.R | 58 - rtables-0.6.12/rtables/tests/testthat/test-result_data_frame.R | 122 ++ rtables-0.6.12/rtables/tests/testthat/test-sort-prune.R | 65 + rtables-0.6.12/rtables/tests/testthat/test-subset-access.R | 101 + rtables-0.6.12/rtables/tests/testthat/test-tab_afun_cfun.R | 22 57 files changed, 1321 insertions(+), 546 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
mikefc [cph] ,
Yann Collet [cph] ,
Posit, PBC [cph, fnd]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between rlang versions 1.1.5 dated 2025-01-17 and 1.1.6 dated 2025-04-11
rlang-1.1.5/rlang/src/internal/init.c |only rlang-1.1.6/rlang/DESCRIPTION | 19 rlang-1.1.6/rlang/MD5 | 435 ++++----- rlang-1.1.6/rlang/NEWS.md | 19 rlang-1.1.6/rlang/R/aaa-topics.R | 60 - rlang-1.1.6/rlang/R/aaa.R | 2 rlang-1.1.6/rlang/R/arg.R | 38 rlang-1.1.6/rlang/R/attr.R | 6 rlang-1.1.6/rlang/R/bytes.R | 16 rlang-1.1.6/rlang/R/c-lib.R | 6 rlang-1.1.6/rlang/R/call.R | 64 - rlang-1.1.6/rlang/R/cnd-abort.R | 112 +- rlang-1.1.6/rlang/R/cnd-entrace.R | 10 rlang-1.1.6/rlang/R/cnd-handlers.R | 12 rlang-1.1.6/rlang/R/cnd-last.R | 5 rlang-1.1.6/rlang/R/cnd-message.R | 22 rlang-1.1.6/rlang/R/cnd-signal.R | 104 +- rlang-1.1.6/rlang/R/cnd.R | 118 +- rlang-1.1.6/rlang/R/deparse.R | 70 - rlang-1.1.6/rlang/R/doc-data-masking.R | 2 rlang-1.1.6/rlang/R/dots-ellipsis.R | 58 - rlang-1.1.6/rlang/R/dots.R | 48 - rlang-1.1.6/rlang/R/env-binding.R | 41 rlang-1.1.6/rlang/R/env-special.R | 19 rlang-1.1.6/rlang/R/env.R | 45 rlang-1.1.6/rlang/R/eval-tidy.R | 21 rlang-1.1.6/rlang/R/expr.R | 7 rlang-1.1.6/rlang/R/fn.R | 81 + rlang-1.1.6/rlang/R/lifecycle-deprecated.R | 131 +- rlang-1.1.6/rlang/R/node.R | 2 rlang-1.1.6/rlang/R/nse-defuse.R | 108 +- rlang-1.1.6/rlang/R/nse-inject.R | 14 rlang-1.1.6/rlang/R/obj.R | 15 rlang-1.1.6/rlang/R/quo.R | 31 rlang-1.1.6/rlang/R/session.R | 113 +- rlang-1.1.6/rlang/R/stack.R | 14 rlang-1.1.6/rlang/R/standalone-cli.R | 265 +++-- rlang-1.1.6/rlang/R/standalone-downstream-deps.R | 46 rlang-1.1.6/rlang/R/standalone-lazyeval.R | 28 rlang-1.1.6/rlang/R/standalone-lifecycle.R | 72 - 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rlang-1.1.6/rlang/man/topic-error-chaining.Rd | 7 rlang-1.1.6/rlang/src/Makevars | 1 rlang-1.1.6/rlang/src/internal/arg.c | 1 rlang-1.1.6/rlang/src/internal/call.c | 2 rlang-1.1.6/rlang/src/internal/decl/vec-decl.h | 6 rlang-1.1.6/rlang/src/internal/dots-ellipsis.c | 11 rlang-1.1.6/rlang/src/internal/dots.c | 1 rlang-1.1.6/rlang/src/internal/dots.h | 4 rlang-1.1.6/rlang/src/internal/encoding.c | 14 rlang-1.1.6/rlang/src/internal/env-binding.c | 76 - rlang-1.1.6/rlang/src/internal/env.c | 11 rlang-1.1.6/rlang/src/internal/eval-tidy.c | 3 rlang-1.1.6/rlang/src/internal/eval.c | 1 rlang-1.1.6/rlang/src/internal/exported.c | 61 - rlang-1.1.6/rlang/src/internal/fn.c | 1 rlang-1.1.6/rlang/src/internal/internal.c | 327 ++++++ rlang-1.1.6/rlang/src/internal/internal.h | 6 rlang-1.1.6/rlang/src/internal/names.c | 3 rlang-1.1.6/rlang/src/internal/nse-defuse.c | 1 rlang-1.1.6/rlang/src/internal/squash.c | 4 rlang-1.1.6/rlang/src/internal/utils.c | 2 rlang-1.1.6/rlang/src/internal/vec.c | 1 rlang-1.1.6/rlang/src/internal/weakref.c | 3 rlang-1.1.6/rlang/src/rlang/altrep.h | 3 rlang-1.1.6/rlang/src/rlang/arg.h | 3 rlang-1.1.6/rlang/src/rlang/attrib.h | 5 rlang-1.1.6/rlang/src/rlang/c-utils.h | 5 rlang-1.1.6/rlang/src/rlang/call.h | 4 rlang-1.1.6/rlang/src/rlang/cnd.h | 5 rlang-1.1.6/rlang/src/rlang/debug.h | 3 rlang-1.1.6/rlang/src/rlang/decl/env-decl.h | 3 rlang-1.1.6/rlang/src/rlang/df.h | 4 rlang-1.1.6/rlang/src/rlang/dict.h | 4 rlang-1.1.6/rlang/src/rlang/dyn-array.h | 5 rlang-1.1.6/rlang/src/rlang/dyn-list-of.h | 4 rlang-1.1.6/rlang/src/rlang/env-binding.h | 3 rlang-1.1.6/rlang/src/rlang/env.c | 72 - rlang-1.1.6/rlang/src/rlang/env.h | 69 + rlang-1.1.6/rlang/src/rlang/eval.h | 5 rlang-1.1.6/rlang/src/rlang/export.h | 6 rlang-1.1.6/rlang/src/rlang/fn.h | 4 rlang-1.1.6/rlang/src/rlang/formula.h | 3 rlang-1.1.6/rlang/src/rlang/globals.h | 3 rlang-1.1.6/rlang/src/rlang/node.h | 3 rlang-1.1.6/rlang/src/rlang/obj.h | 5 rlang-1.1.6/rlang/src/rlang/parse.h | 3 rlang-1.1.6/rlang/src/rlang/quo.h | 3 rlang-1.1.6/rlang/src/rlang/rlang-types.h | 10 rlang-1.1.6/rlang/src/rlang/rlang.c | 28 rlang-1.1.6/rlang/src/rlang/rlang.h | 13 rlang-1.1.6/rlang/src/rlang/session.h | 3 rlang-1.1.6/rlang/src/rlang/stack.h | 3 rlang-1.1.6/rlang/src/rlang/state.h | 8 rlang-1.1.6/rlang/src/rlang/sym.h | 3 rlang-1.1.6/rlang/src/rlang/vec-chr.h | 5 rlang-1.1.6/rlang/src/rlang/vec-lgl.h | 4 rlang-1.1.6/rlang/src/rlang/vec.h | 10 rlang-1.1.6/rlang/src/rlang/vendor.h | 2 rlang-1.1.6/rlang/src/rlang/walk.h | 5 rlang-1.1.6/rlang/src/version.c | 2 rlang-1.1.6/rlang/tests/sink.R | 1 rlang-1.1.6/rlang/tests/testthat/_snaps/4.5_and_older |only rlang-1.1.6/rlang/tests/testthat/_snaps/arg.md | 170 +-- rlang-1.1.6/rlang/tests/testthat/_snaps/attr.md | 10 rlang-1.1.6/rlang/tests/testthat/_snaps/c-api.md | 14 rlang-1.1.6/rlang/tests/testthat/_snaps/cnd-abort.md | 82 - rlang-1.1.6/rlang/tests/testthat/_snaps/cnd-handlers.md | 17 rlang-1.1.6/rlang/tests/testthat/_snaps/cnd-message.md | 10 rlang-1.1.6/rlang/tests/testthat/_snaps/cnd-signal.md | 20 rlang-1.1.6/rlang/tests/testthat/_snaps/cnd.md | 29 rlang-1.1.6/rlang/tests/testthat/_snaps/current/cnd-abort.md | 10 rlang-1.1.6/rlang/tests/testthat/_snaps/dots-ellipsis.md | 25 rlang-1.1.6/rlang/tests/testthat/_snaps/dots.md | 10 rlang-1.1.6/rlang/tests/testthat/_snaps/env-binding.md | 10 rlang-1.1.6/rlang/tests/testthat/_snaps/eval-tidy.md | 10 rlang-1.1.6/rlang/tests/testthat/_snaps/fn.md | 40 rlang-1.1.6/rlang/tests/testthat/_snaps/friendly-type.md | 5 rlang-1.1.6/rlang/tests/testthat/_snaps/nse-inject.md | 50 - rlang-1.1.6/rlang/tests/testthat/_snaps/s3.md | 10 rlang-1.1.6/rlang/tests/testthat/_snaps/session.md | 131 +- rlang-1.1.6/rlang/tests/testthat/_snaps/standalone-types-check.md | 6 rlang-1.1.6/rlang/tests/testthat/_snaps/trace.md | 96 -- rlang-1.1.6/rlang/tests/testthat/_snaps/types.md | 15 rlang-1.1.6/rlang/tests/testthat/fixtures/error-backtrace-conditionMessage.R | 1 rlang-1.1.6/rlang/tests/testthat/fixtures/error-backtrace-empty.R | 1 rlang-1.1.6/rlang/tests/testthat/fixtures/error-backtrace-parent.R | 1 rlang-1.1.6/rlang/tests/testthat/fixtures/error-backtrace-rethrown.R | 1 rlang-1.1.6/rlang/tests/testthat/fixtures/error-entrace.R | 4 rlang-1.1.6/rlang/tests/testthat/fixtures/rlanglibtest/tests/testthat/test-quo-accessors.R | 5 rlang-1.1.6/rlang/tests/testthat/helper-c-api.R | 13 rlang-1.1.6/rlang/tests/testthat/helper-cli.R | 8 rlang-1.1.6/rlang/tests/testthat/helper-cnd.R | 81 + rlang-1.1.6/rlang/tests/testthat/helper-locale.R | 8 rlang-1.1.6/rlang/tests/testthat/helper-package.R |only rlang-1.1.6/rlang/tests/testthat/helper-print.R | 1 rlang-1.1.6/rlang/tests/testthat/helper-rlang.R | 7 rlang-1.1.6/rlang/tests/testthat/helper-trace.R | 11 rlang-1.1.6/rlang/tests/testthat/setup-tests.R | 1 rlang-1.1.6/rlang/tests/testthat/teardown-tests.R | 1 rlang-1.1.6/rlang/tests/testthat/test-arg.R | 98 +- rlang-1.1.6/rlang/tests/testthat/test-attr.R | 31 rlang-1.1.6/rlang/tests/testthat/test-bytes.R | 2 rlang-1.1.6/rlang/tests/testthat/test-c-api.R | 91 + rlang-1.1.6/rlang/tests/testthat/test-call.R | 157 ++- rlang-1.1.6/rlang/tests/testthat/test-cnd-abort.R | 108 +- rlang-1.1.6/rlang/tests/testthat/test-cnd-entrace.R | 156 ++- rlang-1.1.6/rlang/tests/testthat/test-cnd-handlers.R | 4 rlang-1.1.6/rlang/tests/testthat/test-cnd-message.R | 117 +- rlang-1.1.6/rlang/tests/testthat/test-cnd-signal.R | 112 +- rlang-1.1.6/rlang/tests/testthat/test-cnd.R | 28 rlang-1.1.6/rlang/tests/testthat/test-deparse.R | 479 ++++++++-- rlang-1.1.6/rlang/tests/testthat/test-deprecated-vec-squash.R | 51 - rlang-1.1.6/rlang/tests/testthat/test-deprecated.R | 83 + rlang-1.1.6/rlang/tests/testthat/test-dots-ellipsis.R | 90 + rlang-1.1.6/rlang/tests/testthat/test-dots.R | 89 + rlang-1.1.6/rlang/tests/testthat/test-encoding.R | 2 rlang-1.1.6/rlang/tests/testthat/test-env-binding.R | 124 +- rlang-1.1.6/rlang/tests/testthat/test-env.R | 81 - rlang-1.1.6/rlang/tests/testthat/test-eval-tidy.R | 125 +- rlang-1.1.6/rlang/tests/testthat/test-eval.R | 1 rlang-1.1.6/rlang/tests/testthat/test-expr.R | 42 rlang-1.1.6/rlang/tests/testthat/test-fn.R | 90 + rlang-1.1.6/rlang/tests/testthat/test-formula.R | 10 rlang-1.1.6/rlang/tests/testthat/test-friendly-type.R | 413 +++++--- rlang-1.1.6/rlang/tests/testthat/test-lifecycle.R | 7 rlang-1.1.6/rlang/tests/testthat/test-names.R | 25 rlang-1.1.6/rlang/tests/testthat/test-node.R | 19 rlang-1.1.6/rlang/tests/testthat/test-nse-defuse.R | 155 ++- rlang-1.1.6/rlang/tests/testthat/test-nse-inject.R | 382 +++++-- rlang-1.1.6/rlang/tests/testthat/test-obj.R | 5 rlang-1.1.6/rlang/tests/testthat/test-operators.R | 5 rlang-1.1.6/rlang/tests/testthat/test-parse.R | 26 rlang-1.1.6/rlang/tests/testthat/test-quo.R | 33 rlang-1.1.6/rlang/tests/testthat/test-raw.R | 5 rlang-1.1.6/rlang/tests/testthat/test-s3.R | 11 rlang-1.1.6/rlang/tests/testthat/test-session.R | 152 +-- rlang-1.1.6/rlang/tests/testthat/test-stack.R | 4 rlang-1.1.6/rlang/tests/testthat/test-standalone-cli.R | 180 ++- rlang-1.1.6/rlang/tests/testthat/test-standalone-downstream-deps.R | 20 rlang-1.1.6/rlang/tests/testthat/test-standalone-obj-type.R | 13 rlang-1.1.6/rlang/tests/testthat/test-standalone-purrr.R | 36 rlang-1.1.6/rlang/tests/testthat/test-standalone-s3-register.R | 6 rlang-1.1.6/rlang/tests/testthat/test-standalone-types-check.R | 15 rlang-1.1.6/rlang/tests/testthat/test-standalone-vctrs.R | 2 rlang-1.1.6/rlang/tests/testthat/test-standalone-zeallot.R | 1 rlang-1.1.6/rlang/tests/testthat/test-standalone.R | 72 + rlang-1.1.6/rlang/tests/testthat/test-trace.R | 108 +- rlang-1.1.6/rlang/tests/testthat/test-types.R | 37 rlang-1.1.6/rlang/tests/testthat/test-utils.R | 4 rlang-1.1.6/rlang/tests/testthat/test-vec-new.R | 51 - rlang-1.1.6/rlang/tests/testthat/test-vec.R | 2 rlang-1.1.6/rlang/tests/testthat/test-weakref.R | 14 220 files changed, 5561 insertions(+), 3361 deletions(-)
Title: Easily Access US Census Bureau Survey and Geographic Data
Description: The key function 'get_vintage_data()' returns a dataframe and is
the window into the Census Bureau API requiring just a dataset name,
vintage(year), and vector of variable names for survey estimates/percentages.
Other functions assist in searching for available datasets, geographies,
group/variable concepts of interest. Also provided are functions to access
and layer (via standard piping) displayable geometries for the US, states,
counties, blocks/tracts, roads, landmarks, places, and bodies of water.
Joining survey data with many of the geometry functions is built-in to
produce choropleth maps.
Author: Rick Dean [aut, cre, cph]
Maintainer: Rick Dean <deanr3@bardstown.com>
Diff between RcensusPkg versions 0.1.4 dated 2025-03-15 and 0.1.5 dated 2025-04-11
RcensusPkg-0.1.4/RcensusPkg/R/check_response.R |only RcensusPkg-0.1.4/RcensusPkg/R/get_dt.R |only RcensusPkg-0.1.4/RcensusPkg/R/parse_response.R |only RcensusPkg-0.1.4/RcensusPkg/man/dot-check_response.Rd |only RcensusPkg-0.1.4/RcensusPkg/man/dot-get_dt.Rd |only RcensusPkg-0.1.4/RcensusPkg/man/dot-parse_response.Rd |only RcensusPkg-0.1.4/RcensusPkg/tests/testthat/Rplots.pdf |only RcensusPkg-0.1.4/RcensusPkg/tests/testthat/_snaps/remove_area_water.md |only RcensusPkg-0.1.4/RcensusPkg/tests/testthat/test-remove_area_water.R |only RcensusPkg-0.1.5/RcensusPkg/DESCRIPTION | 14 RcensusPkg-0.1.5/RcensusPkg/MD5 | 187 ++++------ RcensusPkg-0.1.5/RcensusPkg/NAMESPACE | 10 RcensusPkg-0.1.5/RcensusPkg/NEWS.md | 5 RcensusPkg-0.1.5/RcensusPkg/R/get_dataset_names.R | 87 ++-- RcensusPkg-0.1.5/RcensusPkg/R/get_geography.R | 34 - RcensusPkg-0.1.5/RcensusPkg/R/get_groups.R | 37 - RcensusPkg-0.1.5/RcensusPkg/R/get_idb_data.R | 54 +- RcensusPkg-0.1.5/RcensusPkg/R/get_multi_vintage_data.R | 51 +- RcensusPkg-0.1.5/RcensusPkg/R/get_variable_names.R | 46 +- RcensusPkg-0.1.5/RcensusPkg/R/get_vintage_data.R | 125 ++++-- RcensusPkg-0.1.5/RcensusPkg/R/join_it.R | 2 RcensusPkg-0.1.5/RcensusPkg/R/long_to_wide.R | 2 RcensusPkg-0.1.5/RcensusPkg/R/plot_us_data.R | 10 RcensusPkg-0.1.5/RcensusPkg/R/remove_area_water.R | 11 RcensusPkg-0.1.5/RcensusPkg/R/send_tiger_url.R | 80 +--- RcensusPkg-0.1.5/RcensusPkg/R/tiger_block_groups_sf.R | 37 + RcensusPkg-0.1.5/RcensusPkg/R/tiger_blocks_sf.R | 19 - RcensusPkg-0.1.5/RcensusPkg/R/tiger_cbsa_sf.R | 49 +- RcensusPkg-0.1.5/RcensusPkg/R/tiger_counties_sf.R | 39 +- RcensusPkg-0.1.5/RcensusPkg/R/tiger_county_subsection_sf.R | 38 +- RcensusPkg-0.1.5/RcensusPkg/R/tiger_landmarks_sf.R | 20 - RcensusPkg-0.1.5/RcensusPkg/R/tiger_places_sf.R | 21 - RcensusPkg-0.1.5/RcensusPkg/R/tiger_roads_sf.R | 37 + RcensusPkg-0.1.5/RcensusPkg/R/tiger_states_sf.R | 37 + RcensusPkg-0.1.5/RcensusPkg/R/tiger_tracts_sf.R | 37 + RcensusPkg-0.1.5/RcensusPkg/R/tiger_urban_area_sf.R | 27 - RcensusPkg-0.1.5/RcensusPkg/R/tiger_water_sf.R | 37 + RcensusPkg-0.1.5/RcensusPkg/R/tiger_zctas_sf.R | 31 - RcensusPkg-0.1.5/RcensusPkg/R/wide_to_long.R | 2 RcensusPkg-0.1.5/RcensusPkg/README.md | 2 RcensusPkg-0.1.5/RcensusPkg/man/get_dataset_names.Rd | 5 RcensusPkg-0.1.5/RcensusPkg/man/get_geography.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/get_groups.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/get_idb_data.Rd | 3 RcensusPkg-0.1.5/RcensusPkg/man/get_multi_vintage_data.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/get_variable_names.Rd | 3 RcensusPkg-0.1.5/RcensusPkg/man/get_vintage_data.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/join_it.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/long_to_wide.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/plot_us_data.Rd | 8 RcensusPkg-0.1.5/RcensusPkg/man/remove_area_water.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/tiger_block_groups_sf.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/tiger_blocks_sf.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/tiger_cbsa_sf.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/tiger_counties_sf.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/tiger_county_subsection_sf.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/tiger_landmarks_sf.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/tiger_places_sf.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/tiger_roads_sf.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/tiger_states_sf.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/tiger_tracts_sf.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/tiger_urban_area_sf.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/tiger_water_sf.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/tiger_zctas_sf.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/man/wide_to_long.Rd | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/_snaps/get_multi_vintage_data.md | 24 - RcensusPkg-0.1.5/RcensusPkg/tests/testthat/_snaps/get_variable_names.md | 25 + RcensusPkg-0.1.5/RcensusPkg/tests/testthat/_snaps/tiger_block_groups_sf.md | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/_snaps/tiger_cbsa_sf.md | 3 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/_snaps/tiger_counties_sf.md | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/_snaps/tiger_county_subsection_sf.md | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/_snaps/tiger_landmarks_sf.md | 3 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/_snaps/tiger_places_sf.md | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/_snaps/tiger_roads_sf.md | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/_snaps/tiger_states_sf.md | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/_snaps/tiger_tracts_sf.md | 3 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/_snaps/tiger_urban_area_sf.md | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/_snaps/tiger_water_sf.md | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/_snaps/tiger_zctas_sf.md | 3 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-get_dataset_names.R | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-get_geography.R | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-get_groups.R | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-get_idb_data.R | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-get_multi_vintage_data.R | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-get_variable_names.R | 8 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-get_vintage_data.R | 2 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-plot_us_data.R | 3 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-tiger_block_groups_sf.R | 5 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-tiger_cbsa_sf.R | 5 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-tiger_counties_sf.R | 7 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-tiger_county_subsection_sf.R | 5 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-tiger_landmarks_sf.R | 5 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-tiger_places_sf.R | 5 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-tiger_roads_sf.R | 5 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-tiger_states_sf.R | 5 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-tiger_tracts_sf.R | 5 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-tiger_urban_area_sf.R | 5 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-tiger_water_sf.R | 5 RcensusPkg-0.1.5/RcensusPkg/tests/testthat/test-tiger_zctas_sf.R | 5 99 files changed, 740 insertions(+), 671 deletions(-)
Title: Parametric Time-Dependent Receiver Operating Characteristic
Description: Producing the time-dependent receiver operating characteristic (ROC) curve through parametric approaches. Tools for
generating random data, fitting, predicting and check goodness of fit are prepared. The methods are
developed from the theoretical framework of proportional hazard model and copula functions.
Using this package, users can now simulate parametric time-dependent ROC and run experiment
to understand the behavior of the curve under different scenario.
Author: Faiz Azhar [aut, cre, cph] ,
Adina Najwa Kamarudin [cph, ths]
,
Universiti Teknologi Malaysia, UTM [cph]
Maintainer: Faiz Azhar <faiz.azhar241@gmail.com>
Diff between parTimeROC versions 0.1.0 dated 2024-06-14 and 0.1.1 dated 2025-04-11
DESCRIPTION | 29 MD5 | 66 - NAMESPACE | 5 NEWS.md | 7 R/get.distributions.R | 86 ++ R/ipcw.R |only R/parTimeROC-package.R | 3 R/preprocessors.R | 2 R/print.R | 16 R/rate_change.R | 3 R/rtimeroc.R | 8 R/timeroc_auc.R | 2 R/timeroc_fit.R | 275 +++++--- R/timeroc_gof.R | 107 ++- R/timeroc_predict.R | 131 +++ R/utils.R | 28 README.md | 1259 ++++++++++++++++++++++++++++++++++++- inst/WORDLIST | 1 inst/stan/ph.stan | 2 man/figures/README-example10-1.png |binary man/figures/README-example11-1.png |binary man/figures/README-example2-1.png |binary man/figures/README-example4-1.png |binary man/figures/README-example5-1.png |binary man/figures/README-example8-1.png |binary man/figures/README-example9-1.png |binary man/figures/parTimeROC.png |only man/get.distributions.Rd | 2 man/rate_change.Rd | 3 man/timeroc_auc.Rd | 2 man/timeroc_fit.Rd | 14 man/timeroc_gof.Rd | 22 man/timeroc_predict.Rd | 3 src/Makevars.win | 2 src/stanExports_ph.h | 6 35 files changed, 1840 insertions(+), 244 deletions(-)
Title: Dynamic (Longitudinal) Network Datasets
Description: A collection of dynamic network data sets from various sources and multiple authors represented as 'networkDynamic'-formatted objects.
Author: Skye Bender-deMoll [cre, aut],
Martina Morris [ctb],
Li Wang [ctb],
Gerhard van de Bunt [ctb],
Goele Bossaert [ctb],
Nadine Meidert [ctb],
SocioPatterns.org [ctb],
Tore Opsahi [ctb],
Radoslaw Michalski, [ctb],
Allison Davis, [ctb],
C.E. Priebe, [c [...truncated...]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between networkDynamicData versions 0.2.1 dated 2016-01-11 and 0.3.0 dated 2025-04-11
ChangeLog | 4 +++- DESCRIPTION | 14 +++++++------- MD5 | 19 ++++++++++--------- build |only man/concurrencyComparisonNets.Rd | 6 +++--- man/davisDyn.Rd | 4 ++-- man/harry_potter.Rd | 8 ++++---- man/hospital.Rd | 6 +++--- man/manufacturingEmails.Rd | 2 +- man/onlineNet.Rd | 8 ++++---- man/vanDeBunt_students.Rd | 8 ++++---- 11 files changed, 41 insertions(+), 38 deletions(-)
More information about networkDynamicData at CRAN
Permanent link
Title: Mixed-Effects Modeling for Growth Data
Description: Simple and user-friendly wrappers to the 'saemix' package for
performing linear and non-linear mixed-effects regression modeling for
growth data to account for clustering or longitudinal analysis via repeated
measurements. The package allows users to fit a variety of growth
models, including linear, exponential, logistic, and 'Gompertz'
functions. For non-linear models, starting values are automatically
calculated using initial least-squares estimates. The package includes
functions for summarizing models, visualizing data and results,
calculating doubling time and other key statistics, and generating model
diagnostic plots and residual summary statistics. It also provides
functions for generating publication-ready summary tables for reports.
Additionally, users can fit linear and non-linear least-squares
regression models if clustering is not applicable. The mixed-effects
modeling methods in this package are based on Comets, Lavenu, and
Lavielle (2017) <doi:10.18637/jss.v080.i03&g [...truncated...]
Author: Anand Panigrahy [aut, cre] ,
Sonam Bhatia [ctb] ,
Thomas Quinn [dtc],
Aniket Shetty [rev],
Keith Ligon [fnd] ,
Center for Patient-Derived Models Dana-Farber Cancer Institute [cph]
Maintainer: Anand Panigrahy <anand_panigrahy@dfci.harvard.edu>
Diff between GrowthCurveME versions 0.1.0 dated 2024-12-17 and 0.1.11 dated 2025-04-11
DESCRIPTION | 6 +-- MD5 | 41 +++++++++++++++------------ NEWS.md | 3 + R/growth_curve_model_fit.R | 2 + R/growth_model_residual_plots.R | 2 + R/growth_model_summary_table.R | 2 + R/growth_vs_time_plot.R | 2 + R/linear_mixed_model.R | 2 + R/summarize_growth_model.R | 2 + R/summarize_growth_model_mixed.R | 2 + README.md | 13 +++++--- man/figures/README-diagnostics-1.svg |only man/figures/README-example-data-1.svg |only man/figures/README-plots-1.svg |only man/figures/README-plots-2.svg |only man/figures/README-sim_curve-1.svg |only man/growth_curve_model_fit.Rd | 2 + man/growth_model_residual_plots.Rd | 2 + man/growth_model_summary_table.Rd | 2 + man/growth_vs_time_plot.Rd | 2 + man/linear_mixed_model.Rd | 2 + man/summarize_growth_model.Rd | 2 + man/summarize_growth_model_mixed.Rd | 2 + tests/testthat/test-growth_curve_model_fit.R | 23 +++++---------- 24 files changed, 73 insertions(+), 41 deletions(-)
Title: Global Fishery and Aquaculture Statistics
Description: The Food and Agriculture Organization of the United Nations (FAO)
FishStat database is the leading source of global fishery and aquaculture
statistics and provides unique information for sector analysis and monitoring.
This package provides the global production data from all fisheries and
aquaculture in R format, ready for analysis.
Author: Arni Magnusson [aut, cre],
Rishi Sharma [aut],
FAO [cph]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Diff between fishstat versions 2024.1.0.1 dated 2025-02-17 and 2025.1.0.0 dated 2025-04-11
DESCRIPTION | 8 ++--- MD5 | 68 ++++++++++++++++++++++++------------------------ NEWS.md | 7 ++++ R/aquaculture.R | 12 ++++---- R/area.R | 19 ++++++------- R/capture.R | 10 +++---- R/country.R | 12 ++++---- R/environment.R | 8 ++--- R/fishstat-package.R | 3 +- R/measure.R | 8 ++--- R/production.R | 9 +++--- R/source.R | 8 ++--- R/species.R | 23 ++++++++-------- R/status.R | 8 ++--- data/aquaculture.RData |binary data/area.RData |binary data/capture.RData |binary data/country.RData |binary data/environment.RData |binary data/measure.RData |binary data/production.RData |binary data/source.RData |binary data/species.RData |binary data/status.RData |binary man/aquaculture.Rd | 12 ++++---- man/area.Rd | 19 ++++++------- man/capture.Rd | 10 +++---- man/country.Rd | 12 ++++---- man/environment.Rd | 8 ++--- man/fishstat-package.Rd | 3 +- man/measure.Rd | 8 ++--- man/production.Rd | 9 +++--- man/source.Rd | 8 ++--- man/species.Rd | 23 ++++++++-------- man/status.Rd | 8 ++--- 35 files changed, 167 insertions(+), 156 deletions(-)
Title: Causally Interpretable Meta-Analysis
Description: Provides robust and efficient methods for estimating causal effects in a target population using a multi-source dataset, including those of Dahabreh et al. (2019) <doi:10.1111/biom.13716>, Robertson et al. (2021) <doi:10.48550/arXiv.2104.05905>, and Wang et al. (2024) <doi:10.48550/arXiv.2402.02684>. The multi-source data can be a collection of trials, observational studies, or a combination of both, which have the same data structure (outcome, treatment, and covariates). The target population can be based on an internal dataset or an external dataset where only covariate information is available. The causal estimands available are average treatment effects and subgroup treatment effects. See Wang et al. (2025) <doi:10.1017/rsm.2025.5> for a detailed guide on using the package.
Author: Yi Lian [aut],
Guanbo Wang [aut],
Sean McGrath [aut, cre] ,
Issa Dahabreh [aut]
Maintainer: Sean McGrath <sean.mcgrath514@gmail.com>
Diff between CausalMetaR versions 0.1.2 dated 2024-06-04 and 0.1.3 dated 2025-04-11
DESCRIPTION | 16 ++-- MD5 | 22 ++--- NEWS.md | 4 + R/ATE_external.R | 2 R/ATE_internal.R | 2 R/STE_external.R | 2 R/STE_internal.R | 2 README.md | 191 ++++++++++++++++++++++++++++++++++++++++++++++++++-- man/ATE_external.Rd | 2 man/ATE_internal.Rd | 2 man/STE_external.Rd | 2 man/STE_internal.Rd | 2 12 files changed, 218 insertions(+), 31 deletions(-)
Title: A Robust Interface to ArcGIS 'Geocoding Services'
Description: A very fast and robust interface to ArcGIS 'Geocoding
Services'. Provides capabilities for reverse geocoding, finding
address candidates, character-by-character search autosuggestion, and
batch geocoding. The public 'ArcGIS World Geocoder' is accessible for
free use via 'arcgisgeocode' for all services except batch geocoding.
'arcgisgeocode' also integrates with 'arcgisutils' to provide access
to custom locators or private 'ArcGIS World Geocoder' hosted on
'ArcGIS Enterprise'. Learn more in the 'Geocode service' API reference
<https://developers.arcgis.com/rest/geocode/api-reference/overview-world-geocoding-service.htm>.
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcgisgeocode versions 0.2.2 dated 2024-09-27 and 0.2.3 dated 2025-04-11
arcgisgeocode-0.2.2/arcgisgeocode/src/Makevars |only arcgisgeocode-0.2.2/arcgisgeocode/src/Makevars.win |only arcgisgeocode-0.2.3/arcgisgeocode/DESCRIPTION | 14 arcgisgeocode-0.2.3/arcgisgeocode/MD5 | 27 arcgisgeocode-0.2.3/arcgisgeocode/NEWS.md | 4 arcgisgeocode-0.2.3/arcgisgeocode/R/extendr-wrappers.R | 1 arcgisgeocode-0.2.3/arcgisgeocode/configure | 2 arcgisgeocode-0.2.3/arcgisgeocode/configure.win | 2 arcgisgeocode-0.2.3/arcgisgeocode/man/arcgisgeocode-package.Rd | 12 arcgisgeocode-0.2.3/arcgisgeocode/man/figures |only arcgisgeocode-0.2.3/arcgisgeocode/src/Makevars.in |only arcgisgeocode-0.2.3/arcgisgeocode/src/Makevars.win.in |only arcgisgeocode-0.2.3/arcgisgeocode/src/arcgisgeocode-win.def |only arcgisgeocode-0.2.3/arcgisgeocode/src/rust/Cargo.lock | 312 ++++++---- arcgisgeocode-0.2.3/arcgisgeocode/src/rust/Cargo.toml | 3 arcgisgeocode-0.2.3/arcgisgeocode/src/rust/vendor.tar.xz |binary arcgisgeocode-0.2.3/arcgisgeocode/tools/config.R |only arcgisgeocode-0.2.3/arcgisgeocode/tools/msrv.R | 4 18 files changed, 222 insertions(+), 159 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with [...truncated...]
Author: Mary Meyer [aut],
Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>
Diff between cgam versions 1.23 dated 2025-02-19 and 1.24 dated 2025-04-11
ChangeLog | 5 DESCRIPTION | 18 - MD5 | 15 NAMESPACE | 16 R/cgam.R | 910 ++++++++++++++++++++++++++++++++++++++++++++++++++++---- R/globals.R |only R/testpar.R |only man/best.fit.Rd | 61 ++- man/cgam.Rd | 17 - man/testpar.Rd |only 10 files changed, 920 insertions(+), 122 deletions(-)
Title: Search Algorithms and Loss Functions for Bayesian Clustering
Description: The SALSO algorithm is an efficient randomized greedy search method to find a point estimate for a random partition based on a loss function and posterior Monte Carlo samples. The algorithm is implemented for many loss functions, including the Binder loss and a generalization of the variation of information loss, both of which allow for unequal weights on the two types of clustering mistakes. Efficient implementations are also provided for Monte Carlo estimation of the posterior expected loss of a given clustering estimate. See Dahl, Johnson, Müller (2022) <doi:10.1080/10618600.2022.2069779>.
Author: David B. Dahl [aut, cre] ,
Devin J. Johnson [aut] ,
Peter Mueller [aut],
Andres Felipe Barrientos [aut],
Garritt Page [aut],
David Dunson [aut],
Alex Crichton [ctb] ,
Brendan Zabarauskas [ctb] ,
David B. Dahl [ctb] ,
David Tolnay [ctb] ,
Jim Turner [c [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.3.51 dated 2025-03-30 and 0.3.53 dated 2025-04-10
DESCRIPTION | 9 MD5 | 22 NEWS | 4 src/rust/Cargo.lock | 81 src/rust/Cargo.toml | 2 src/rust/rbindings/Cargo.lock | 2 src/rust/rbindings/src/lib.rs | 8363 --------------------------------------- src/rust/roxido/Cargo.lock | 23 src/rust/roxido/src/lib.rs | 10 src/rust/roxido_macro/Cargo.lock | 18 src/rust/vendor.tar.gz |binary tools/build_rust_library.R | 36 12 files changed, 104 insertions(+), 8466 deletions(-)
Title: Feature Allocation Neighborhood Greedy Search Algorithm
Description: A neighborhood-based, greedy search algorithm is performed to estimate a feature allocation by minimizing the expected loss based on posterior samples from the feature allocation distribution. The method is described in Dahl, Johnson, and Andros (2023) "Comparison and Bayesian Estimation of Feature Allocations" <doi:10.1080/10618600.2023.2204136>.
Author: David B. Dahl [aut, cre] ,
R. Jacob Andros [aut] ,
Devin J. Johnson [aut] ,
Alex Crichton [ctb] ,
Andrii Dmytrenko [ctb] ,
Brendan Zabarauskas [ctb] ,
David B. Dahl [ctb] ,
David Tolnay [ctb] ,
Jim Turner [ctb] ,
Josh Stone [ctb] ,
Niko Matsakis [ctb [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between fangs versions 0.2.18 dated 2025-03-29 and 0.2.21 dated 2025-04-10
DESCRIPTION | 11 MD5 | 43 NEWS | 5 R/compute_expected_loss.R | 2 R/compute_loss.R | 2 R/fangs.R | 2 man/compute_expected_loss.Rd | 2 man/compute_loss.Rd | 2 man/fangs-package.Rd | 2 man/fangs.Rd | 2 src/rust/Cargo.lock | 78 src/rust/Cargo.toml | 10 src/rust/lapjv-rust/Cargo.lock |only src/rust/lapjv-rust/Cargo.toml | 7 src/rust/lapjv-rust/src/lib.rs | 71 src/rust/rbindings/Cargo.lock | 2 src/rust/rbindings/src/lib.rs | 8363 --------------------------------------- src/rust/roxido/Cargo.lock | 2 src/rust/roxido/src/lib.rs | 10 src/rust/roxido_macro/Cargo.lock | 2 src/rust/src/lib.rs | 2 src/rust/vendor.tar.gz |binary tools/build_rust_library.R | 37 23 files changed, 187 insertions(+), 8470 deletions(-)
Title: Assessing Complex Heterogeneity in Surrogacy
Description: Provides functions to assess complex heterogeneity in the strength of a surrogate marker with respect to multiple baseline covariates, in either a randomized treatment setting or observational setting. For a randomized treatment setting, the functions assess and test for heterogeneity using both a parametric model and a semiparametric two-step model. More details for the randomized setting are available in: Knowlton, R., Tian, L., & Parast, L. (2025). "A General Framework to Assess Complex Heterogeneity in the Strength of a Surrogate Marker," Statistics in Medicine, 44(5), e70001 <doi:10.1002/sim.70001>. For an observational setting, functions in this package assess complex heterogeneity in the strength of a surrogate marker using meta-learners, with options for different base learners. More details for the observational setting will be available in the future in: Knowlton, R., Parast, L. (2025) "Assessing Surrogate Heterogeneity in Real World Data Using Meta-Learners." A tut [...truncated...]
Author: Rebecca Knowlton [aut],
Layla Parast [aut, cre]
Maintainer: Layla Parast <parast@austin.utexas.edu>
Diff between cohetsurr versions 1.1 dated 2025-03-05 and 2.0 dated 2025-04-10
DESCRIPTION | 12 ++++++------ MD5 | 24 +++++++++++++++++------- NAMESPACE | 6 ++++-- R/obs.boot.var.R |only R/obs.estimate.PTE.R |only R/obs.het.surr.R |only data/obs_exampledata_test.RData |only data/obs_exampledata_train.RData |only man/boot.var.Rd | 6 +++--- man/complex.heterogeneity.Rd | 26 ++++++-------------------- man/exampledata.Rd | 2 +- man/obs.boot.var.Rd |only man/obs.estimate.PTE.Rd |only man/obs.het.surr.Rd |only man/obs_exampledata_test.Rd |only man/obs_exampledata_train.Rd |only man/parametric.est.Rd | 6 +++--- man/two.step.est.Rd | 6 +++--- 18 files changed, 43 insertions(+), 45 deletions(-)
Title: Cytokine Profiling Analysis Tool
Description: Provides comprehensive cytokine profiling analysis through quality control using biologically meaningful cutoffs on raw cytokine measurements and by testing for distributional symmetry to recommend appropriate transformations. Offers exploratory data analysis with summary statistics, enhanced boxplots, and barplots, along with univariate and multivariate analytical capabilities for in-depth cytokine profiling such as Principal Component Analysis based on Andrzej Maćkiewicz and Waldemar Ratajczak (1993) <doi:10.1016/0098-3004(93)90090-R>, Sparse Partial Least Squares Discriminant Analysis based on Lê Cao K-A, Boitard S, and Besse P (2011) <doi:10.1186/1471-2105-12-253>, Random Forest based on Breiman, L. (2001) <doi:10.1023/A:1010933404324>, and Extreme Gradient Boosting based on Tianqi Chen and Carlos Guestrin (2016) <doi:10.1145/2939672.2939785>.
Author: Shubh Saraswat [cre, aut, cph]
,
Xiaohua Douglas Zhang [aut]
Maintainer: Shubh Saraswat <shubh.saraswat00@gmail.com>
Diff between CytoProfile versions 0.1.2 dated 2025-04-03 and 0.2.0 dated 2025-04-10
DESCRIPTION | 10 MD5 | 36 +- NEWS.md | 34 ++ R/cyt_bp.R | 8 R/cyt_bp2.R | 10 R/cyt_dualflashplot.R | 6 R/cyt_errbp.R | 448 +++++++++++++++++++----------------- R/cyt_pca.R | 2 R/cyt_skku.R | 18 + R/cyt_splsda.R | 387 +++++++++++++++++-------------- R/cyt_xgb.R | 22 - R/global_variables.R | 4 README.md | 515 ++++++++++-------------------------------- inst/WORDLIST | 5 inst/doc/getting_started.R | 142 +++-------- inst/doc/getting_started.Rmd | 144 +++-------- inst/doc/getting_started.html | 389 ++++++++++++++----------------- man/cyt_errbp.Rd | 141 +++++------ vignettes/getting_started.Rmd | 144 +++-------- 19 files changed, 1051 insertions(+), 1414 deletions(-)
Title: Estimate Functional and Stochastic Parameters of Linear Models
with Correlated Residuals and Missing Data
Description: Implements the Generalized Method of Wavelet Moments with Exogenous Inputs estimator (GMWMX) presented in Voirol, L., Xu, H., Zhang, Y., Insolia, L., Molinari, R. and Guerrier, S. (2024) <doi:10.48550/arXiv.2409.05160>.
The GMWMX estimator allows to estimate functional and stochastic parameters of linear models with correlated residuals in presence of missing data.
The 'gmwmx2' package provides functions to load and plot Global Navigation Satellite System (GNSS) data from the Nevada Geodetic Laboratory and functions to estimate linear model model with correlated residuals in presence of missing data.
Author: Lionel Voirol [aut, cre] ,
Haotian Xu [aut] ,
Yuming Zhang [aut] ,
Luca Insolia [aut] ,
Roberto Molinari [aut] ,
Stephane Guerrier [aut]
Maintainer: Lionel Voirol <lionelvoirol@hotmail.com>
Diff between gmwmx2 versions 0.0.1 dated 2025-03-10 and 0.0.2 dated 2025-04-10
DESCRIPTION | 6 +- MD5 | 26 ++++----- NAMESPACE | 1 NEWS.md | 6 +- R/ngl.R | 78 +++++++++++++++-------------- README.md | 27 ++++++++-- build/vignette.rds |binary inst/doc/estimate_small_network.R | 2 inst/doc/estimate_small_network.Rmd | 2 inst/doc/estimate_small_network.html | 94 ++++++++++++++++++++++++++++++----- inst/doc/fit_model.html | 6 +- inst/doc/load_plot_data_ngl.html | 16 ++--- vignettes/REFERENCES.bib | 2 vignettes/estimate_small_network.Rmd | 2 14 files changed, 181 insertions(+), 87 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Description: Pipeline tools coordinate the pieces of computationally
demanding analysis projects.
The 'targets' package is a 'Make'-like pipeline tool for statistics and
data science in R. The package skips costly runtime for tasks
that are already up to date,
orchestrates the necessary computation with implicit parallel computing,
and abstracts files as R objects. If all the current output matches
the current upstream code and data, then the whole pipeline is up
to date, and the results are more trustworthy than otherwise.
The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
,
Matthew T. Warkentin [ctb],
Mark Edmondson [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between targets versions 1.10.1 dated 2025-01-31 and 1.11.1 dated 2025-04-10
targets-1.10.1/targets/R/class_forecast.R |only targets-1.10.1/targets/R/class_summary.R |only targets-1.10.1/targets/R/class_timestamp_positives.R |only targets-1.10.1/targets/R/class_verbose_positives.R |only targets-1.10.1/targets/R/utils_units.R |only targets-1.10.1/targets/tests/testthat/test-class_summary.R |only targets-1.10.1/targets/tests/testthat/test-class_timestamp_positives.R |only targets-1.10.1/targets/tests/testthat/test-class_verbose_positives.R |only targets-1.10.1/targets/tests/testthat/test-utils_units.R |only targets-1.11.1/targets/DESCRIPTION | 14 targets-1.11.1/targets/MD5 | 409 +++++----- targets-1.11.1/targets/NAMESPACE | 38 targets-1.11.1/targets/NEWS.md | 52 + targets-1.11.1/targets/R/class_active.R | 15 targets-1.11.1/targets/R/class_algorithm.R | 18 targets-1.11.1/targets/R/class_auto.R | 14 targets-1.11.1/targets/R/class_aws.R | 3 targets-1.11.1/targets/R/class_aws_file.R | 6 targets-1.11.1/targets/R/class_balanced.R |only targets-1.11.1/targets/R/class_branch.R | 3 targets-1.11.1/targets/R/class_bud.R | 5 targets-1.11.1/targets/R/class_build.R | 6 targets-1.11.1/targets/R/class_builder.R | 44 - targets-1.11.1/targets/R/class_cloud.R | 2 targets-1.11.1/targets/R/class_clustermq.R | 8 targets-1.11.1/targets/R/class_crew.R | 17 targets-1.11.1/targets/R/class_cue.R | 20 targets-1.11.1/targets/R/class_database.R | 33 targets-1.11.1/targets/R/class_database_aws.R | 75 + targets-1.11.1/targets/R/class_database_gcp.R | 59 + targets-1.11.1/targets/R/class_database_local.R | 12 targets-1.11.1/targets/R/class_file.R | 15 targets-1.11.1/targets/R/class_future.R | 6 targets-1.11.1/targets/R/class_gcp.R | 11 targets-1.11.1/targets/R/class_gcp_file.R | 6 targets-1.11.1/targets/R/class_group.R | 14 targets-1.11.1/targets/R/class_inspection.R | 14 targets-1.11.1/targets/R/class_junction.R | 21 targets-1.11.1/targets/R/class_local.R | 4 targets-1.11.1/targets/R/class_meta.R | 30 targets-1.11.1/targets/R/class_network.R | 4 targets-1.11.1/targets/R/class_options.R | 28 targets-1.11.1/targets/R/class_outdated.R | 16 targets-1.11.1/targets/R/class_parallel.R | 150 ++- targets-1.11.1/targets/R/class_passive.R | 10 targets-1.11.1/targets/R/class_pattern.R | 8 targets-1.11.1/targets/R/class_pipeline.R | 31 targets-1.11.1/targets/R/class_prelocal.R | 4 targets-1.11.1/targets/R/class_progress.R | 28 targets-1.11.1/targets/R/class_queue.R | 3 targets-1.11.1/targets/R/class_record.R | 3 targets-1.11.1/targets/R/class_reference.R | 11 targets-1.11.1/targets/R/class_reporter.R | 56 - targets-1.11.1/targets/R/class_runtime.R | 9 targets-1.11.1/targets/R/class_scheduler.R | 10 targets-1.11.1/targets/R/class_sequential.R | 85 +- targets-1.11.1/targets/R/class_settings.R | 24 targets-1.11.1/targets/R/class_silent.R | 7 targets-1.11.1/targets/R/class_sitrep.R | 18 targets-1.11.1/targets/R/class_stem.R | 7 targets-1.11.1/targets/R/class_store.R | 40 targets-1.11.1/targets/R/class_store_file.R | 2 targets-1.11.1/targets/R/class_store_repository_cas_file.R | 6 targets-1.11.1/targets/R/class_target.R | 33 targets-1.11.1/targets/R/class_terse.R |only targets-1.11.1/targets/R/class_timestamp.R | 100 +- targets-1.11.1/targets/R/class_url.R | 2 targets-1.11.1/targets/R/class_verbose.R | 83 +- targets-1.11.1/targets/R/class_visnetwork.R | 6 targets-1.11.1/targets/R/class_visual.R | 19 targets-1.11.1/targets/R/class_workspace.R | 15 targets-1.11.1/targets/R/rstudio_addin_tar_load.R | 2 targets-1.11.1/targets/R/rstudio_addin_tar_make_bg.R | 2 targets-1.11.1/targets/R/rstudio_addin_tar_read.R | 2 targets-1.11.1/targets/R/tar_active.R | 7 targets-1.11.1/targets/R/tar_config_get.R | 24 targets-1.11.1/targets/R/tar_config_set.R | 82 +- targets-1.11.1/targets/R/tar_cue.R | 2 targets-1.11.1/targets/R/tar_debug_instructions.R | 16 targets-1.11.1/targets/R/tar_destroy.R | 15 targets-1.11.1/targets/R/tar_glimpse.R | 2 targets-1.11.1/targets/R/tar_load.R | 2 targets-1.11.1/targets/R/tar_load_raw.R | 2 targets-1.11.1/targets/R/tar_make.R | 88 +- targets-1.11.1/targets/R/tar_make_clustermq.R | 9 targets-1.11.1/targets/R/tar_make_future.R | 9 targets-1.11.1/targets/R/tar_mermaid.R | 14 targets-1.11.1/targets/R/tar_meta.R | 2 targets-1.11.1/targets/R/tar_network.R | 14 targets-1.11.1/targets/R/tar_option_set.R | 21 targets-1.11.1/targets/R/tar_option_with.R |only targets-1.11.1/targets/R/tar_outdated.R | 63 + targets-1.11.1/targets/R/tar_package.R | 8 targets-1.11.1/targets/R/tar_poll.R | 4 targets-1.11.1/targets/R/tar_progress_summary.R | 6 targets-1.11.1/targets/R/tar_sitrep.R | 9 targets-1.11.1/targets/R/tar_target.R | 72 + targets-1.11.1/targets/R/tar_target_raw.R | 3 targets-1.11.1/targets/R/tar_visnetwork.R | 14 targets-1.11.1/targets/R/tar_watch_server.R | 4 targets-1.11.1/targets/R/tar_workspace.R | 10 targets-1.11.1/targets/R/tar_workspace_download.R |only targets-1.11.1/targets/R/tar_workspaces.R | 7 targets-1.11.1/targets/R/use_targets.R | 4 targets-1.11.1/targets/R/utils_assert.R | 2 targets-1.11.1/targets/R/utils_aws.R | 2 targets-1.11.1/targets/R/utils_callr.R | 79 - targets-1.11.1/targets/R/utils_cli.R | 244 +---- targets-1.11.1/targets/R/utils_condition.R | 14 targets-1.11.1/targets/R/utils_imports.R | 13 targets-1.11.1/targets/R/utils_packages.R | 30 targets-1.11.1/targets/R/utils_rstudio.R | 8 targets-1.11.1/targets/R/utils_time.R | 4 targets-1.11.1/targets/build/partial.rdb |binary targets-1.11.1/targets/build/vignette.rds |binary targets-1.11.1/targets/man/tar_config_get.Rd | 3 targets-1.11.1/targets/man/tar_config_projects.Rd | 3 targets-1.11.1/targets/man/tar_config_set.Rd | 26 targets-1.11.1/targets/man/tar_config_unset.Rd | 3 targets-1.11.1/targets/man/tar_config_yaml.Rd | 3 targets-1.11.1/targets/man/tar_cue.Rd | 2 targets-1.11.1/targets/man/tar_destroy.Rd | 10 targets-1.11.1/targets/man/tar_envvars.Rd | 3 targets-1.11.1/targets/man/tar_glimpse.Rd | 2 targets-1.11.1/targets/man/tar_load.Rd | 2 targets-1.11.1/targets/man/tar_load_globals.Rd | 1 targets-1.11.1/targets/man/tar_make.Rd | 51 - targets-1.11.1/targets/man/tar_make_clustermq.Rd | 51 - 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targets-1.11.1/targets/tests/interactive/test-crew_retries.R | 2 targets-1.11.1/targets/tests/interactive/test-reporter.R | 57 - targets-1.11.1/targets/tests/testthat/_targets |only targets-1.11.1/targets/tests/testthat/_targets.R |only targets-1.11.1/targets/tests/testthat/test-class_auto.R | 23 targets-1.11.1/targets/tests/testthat/test-class_bud.R | 2 targets-1.11.1/targets/tests/testthat/test-class_builder.R | 69 + targets-1.11.1/targets/tests/testthat/test-class_clustermq.R | 2 targets-1.11.1/targets/tests/testthat/test-class_cue.R | 4 targets-1.11.1/targets/tests/testthat/test-class_database.R | 56 + targets-1.11.1/targets/tests/testthat/test-class_database_aws.R | 1 targets-1.11.1/targets/tests/testthat/test-class_database_gcp.R | 1 targets-1.11.1/targets/tests/testthat/test-class_feather.R | 4 targets-1.11.1/targets/tests/testthat/test-class_inspection.R | 8 targets-1.11.1/targets/tests/testthat/test-class_junction.R | 7 targets-1.11.1/targets/tests/testthat/test-class_meta.R | 52 + targets-1.11.1/targets/tests/testthat/test-class_options.R | 48 - targets-1.11.1/targets/tests/testthat/test-class_outdated.R | 6 targets-1.11.1/targets/tests/testthat/test-class_parallel.R | 335 ++------ targets-1.11.1/targets/tests/testthat/test-class_parquet.R | 4 targets-1.11.1/targets/tests/testthat/test-class_pattern.R | 35 targets-1.11.1/targets/tests/testthat/test-class_pipeline.R | 34 targets-1.11.1/targets/tests/testthat/test-class_progress.R | 15 targets-1.11.1/targets/tests/testthat/test-class_record.R | 4 targets-1.11.1/targets/tests/testthat/test-class_reference.R | 18 targets-1.11.1/targets/tests/testthat/test-class_reporter.R | 3 targets-1.11.1/targets/tests/testthat/test-class_runtime.R | 12 targets-1.11.1/targets/tests/testthat/test-class_scheduler.R | 44 - targets-1.11.1/targets/tests/testthat/test-class_sequential.R | 188 +++- targets-1.11.1/targets/tests/testthat/test-class_stem.R | 49 - targets-1.11.1/targets/tests/testthat/test-class_store_file.R | 8 targets-1.11.1/targets/tests/testthat/test-class_target.R | 8 targets-1.11.1/targets/tests/testthat/test-class_terse.R |only targets-1.11.1/targets/tests/testthat/test-class_timestamp.R | 32 targets-1.11.1/targets/tests/testthat/test-class_torch.R | 1 targets-1.11.1/targets/tests/testthat/test-class_verbose.R | 20 targets-1.11.1/targets/tests/testthat/test-tar_config_set.R | 44 - targets-1.11.1/targets/tests/testthat/test-tar_delete.R | 2 targets-1.11.1/targets/tests/testthat/test-tar_make.R | 32 targets-1.11.1/targets/tests/testthat/test-tar_make_future.R | 2 targets-1.11.1/targets/tests/testthat/test-tar_meta.R | 2 targets-1.11.1/targets/tests/testthat/test-tar_option_set.R | 29 targets-1.11.1/targets/tests/testthat/test-tar_option_with.R |only targets-1.11.1/targets/tests/testthat/test-tar_outdated.R | 7 targets-1.11.1/targets/tests/testthat/test-tar_poll.R |only targets-1.11.1/targets/tests/testthat/test-tar_progress_summary.R | 2 targets-1.11.1/targets/tests/testthat/test-tar_prune.R | 2 targets-1.11.1/targets/tests/testthat/test-tar_read.R | 2 targets-1.11.1/targets/tests/testthat/test-tar_repository_cas_local.R | 22 targets-1.11.1/targets/tests/testthat/test-tar_target.R | 23 targets-1.11.1/targets/tests/testthat/test-tar_target_raw.R | 4 targets-1.11.1/targets/tests/testthat/test-tar_visnetwork.R | 6 targets-1.11.1/targets/tests/testthat/test-tar_workspace_download.R |only targets-1.11.1/targets/tests/testthat/test-utils_assert.R | 7 targets-1.11.1/targets/tests/testthat/test-utils_cli.R | 107 -- targets-1.11.1/targets/tests/testthat/test-utils_imports.R | 3 213 files changed, 2727 insertions(+), 2157 deletions(-)
Title: Automatically Runs 23 Individual and 17 Ensembles of Models
Description: Automatically runs 23 individual models and 17 ensembles on numeric data. The package automatically returns complete results on all 40 models,
25 charts, multiple tables. The user simply provides the data, and answers a few questions (for example, how many times would you like to resample the data).
From there the package randomly splits the data into train, test and validation sets, builds models on the training data, makes predictions on the test and validation sets,
measures root mean squared error (RMSE), removes features above a user-set level of Variance Inflation Factor, and has several optional features including scaling
all numeric data, four different ways to handle strings in the data. Perhaps the most significant feature is the package's ability to make predictions
using the 40 pre trained models on totally new (untrained) data if the user selects that feature. This feature alone represents a very effective solution
to the issue of reproducibility of models in data science. [...truncated...]
Author: Russ Conte [aut, cre, cph]
Maintainer: Russ Conte <russconte@mac.com>
Diff between NumericEnsembles versions 0.5.0 dated 2025-04-01 and 0.7.0 dated 2025-04-10
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/NumericEnsembles.R | 7 ++++--- R/data.R | 4 ++-- data/Boston_housing.rda |binary data/New_Boston.rda |binary man/Boston_housing.Rd | 2 +- man/New_Boston.Rd | 2 +- 9 files changed, 23 insertions(+), 18 deletions(-)
More information about NumericEnsembles at CRAN
Permanent link
Title: Process ArcGIS Protocol Buffer FeatureCollections
Description: Fast processing of ArcGIS FeatureCollection protocol buffers in R.
It is designed to work seamlessly with 'httr2' and integrates with 'sf'.
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcpbf versions 0.1.6 dated 2024-10-01 and 0.1.7 dated 2025-04-10
arcpbf-0.1.6/arcpbf/src/Makevars |only arcpbf-0.1.6/arcpbf/src/Makevars.win |only arcpbf-0.1.7/arcpbf/DESCRIPTION | 11 - arcpbf-0.1.7/arcpbf/MD5 | 36 ++- arcpbf-0.1.7/arcpbf/NAMESPACE | 1 arcpbf-0.1.7/arcpbf/NEWS.md | 6 arcpbf-0.1.7/arcpbf/R/extendr-wrappers.R | 41 ++-- arcpbf-0.1.7/arcpbf/R/post-process.R | 3 arcpbf-0.1.7/arcpbf/R/resp-body-pbf.R | 1 arcpbf-0.1.7/arcpbf/configure | 2 arcpbf-0.1.7/arcpbf/configure.win | 2 arcpbf-0.1.7/arcpbf/man/httr2.Rd | 5 arcpbf-0.1.7/arcpbf/man/process_pbf.Rd | 2 arcpbf-0.1.7/arcpbf/src/Makevars.in |only arcpbf-0.1.7/arcpbf/src/Makevars.win.in |only arcpbf-0.1.7/arcpbf/src/rust/Cargo.lock | 216 +++++++++++------------ arcpbf-0.1.7/arcpbf/src/rust/arcpbf/Cargo.toml | 3 arcpbf-0.1.7/arcpbf/src/rust/arcpbf/src/parse.rs | 30 ++- arcpbf-0.1.7/arcpbf/src/rust/src |only arcpbf-0.1.7/arcpbf/src/rust/vendor.tar.xz |binary arcpbf-0.1.7/arcpbf/tools/config.R |only arcpbf-0.1.7/arcpbf/tools/msrv.R | 4 22 files changed, 201 insertions(+), 162 deletions(-)
Title: Evapotranspiration R Recipes
Description: An R-based application for exploratory data analysis of global EvapoTranspiration (ET) datasets.
'evapoRe' enables users to download, validate, visualize, and analyze multi-source ET data across various spatio-temporal scales.
Also, the package offers calculation methods for estimating potential ET (PET), including temperature-based, combined type, and radiation-based approaches described in : Oudin et al., (2005) <doi:10.1016/j.jhydrol.2004.08.026>.
'evapoRe' supports hydrological modeling, climate studies, agricultural research, and other data-driven fields by facilitating access to ET data and offering powerful analysis capabilities.
Users can seamlessly integrate the package into their research applications and explore diverse ET data at different resolutions.
Author: Akbar Rahmati Ziveh [aut, cre]
,
Mijael Rodrigo Vargas Godoy [aut]
,
Vishal Thakur [ctb] ,
Yannis Markonis [aut, ths]
Maintainer: Akbar Rahmati Ziveh <rahmati_ziveh@fzp.czu.cz>
Diff between evapoRe versions 1.0.0 dated 2023-11-29 and 1.0.1 dated 2025-04-10
evapoRe-1.0.0/evapoRe/R/download_zheng.R |only evapoRe-1.0.0/evapoRe/R/muldpm.R |only evapoRe-1.0.0/evapoRe/man/download_zheng.Rd |only evapoRe-1.0.0/evapoRe/man/muldpm.Rd |only evapoRe-1.0.1/evapoRe/DESCRIPTION | 17 evapoRe-1.0.1/evapoRe/MD5 | 191 - evapoRe-1.0.1/evapoRe/NAMESPACE | 90 evapoRe-1.0.1/evapoRe/NEWS.md | 27 evapoRe-1.0.1/evapoRe/R/abtew.R |only evapoRe-1.0.1/evapoRe/R/baier_robertson.R |only evapoRe-1.0.1/evapoRe/R/blaney_criddle.R | 118 evapoRe-1.0.1/evapoRe/R/calc_rn.R |only evapoRe-1.0.1/evapoRe/R/calc_u2.R |only evapoRe-1.0.1/evapoRe/R/core_functions.R |only evapoRe-1.0.1/evapoRe/R/day_length.R | 84 evapoRe-1.0.1/evapoRe/R/detect_exeve.R |only evapoRe-1.0.1/evapoRe/R/download_all.R | 83 evapoRe-1.0.1/evapoRe/R/download_bess.R | 84 evapoRe-1.0.1/evapoRe/R/download_camele.R | 84 evapoRe-1.0.1/evapoRe/R/download_data.R | 185 - evapoRe-1.0.1/evapoRe/R/download_era5.R | 84 evapoRe-1.0.1/evapoRe/R/download_era5_land.R | 84 evapoRe-1.0.1/evapoRe/R/download_etmonitor.R |only evapoRe-1.0.1/evapoRe/R/download_etsynthesis.R |only evapoRe-1.0.1/evapoRe/R/download_fldas.R | 88 evapoRe-1.0.1/evapoRe/R/download_gldas_clsm.R | 106 evapoRe-1.0.1/evapoRe/R/download_gldas_noah.R | 102 evapoRe-1.0.1/evapoRe/R/download_gldas_vic.R | 106 evapoRe-1.0.1/evapoRe/R/download_gleam.R | 104 evapoRe-1.0.1/evapoRe/R/download_jra55.R | 87 evapoRe-1.0.1/evapoRe/R/download_merra2.R | 87 evapoRe-1.0.1/evapoRe/R/download_sith.R |only evapoRe-1.0.1/evapoRe/R/download_t_data.R | 228 - 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Title: Frequency Matrix Approach for Assessing Very Low Frequency
Variants in Sequence Records
Description: Using frequency matrices, very low frequency variants (VLFs) are assessed for amino acid and nucleotide sequences. The VLFs are then compared to see if they occur in only one member of a species, singleton VLFs, or if they occur in multiple members of a species, shared VLFs. The amino acid and nucleotide VLFs are then compared to see if they are concordant with one another. Amino acid VLFs are also assessed to determine if they lead to a change in amino acid residue type, and potential changes to protein structures. Based on Stoeckle and Kerr (2012) <doi:10.1371/journal.pone.0043992> and Phillips et al. (2023) <doi:10.3897/BDJ.11.e96480>.
Author: Taryn B. T. Athey [cre],
Paul D. McNicholas [aut],
Jarrett D. Phillips [ctb]
Maintainer: Taryn B. T. Athey <taryn.athey@gmail.com>
Diff between VLF versions 1.1 dated 2022-08-18 and 1.1-3 dated 2025-04-10
DESCRIPTION | 24 ++++++++++++---- MD5 | 11 ++++--- R/vlfFun.R | 75 ++++++++++++++++++++++++++++++++++++++++++++++++++++ README.md |only man/VLF-package.Rd | 9 ------ man/aminoAcidFun.Rd | 2 - man/vlfFun.Rd | 2 - 7 files changed, 102 insertions(+), 21 deletions(-)
Title: Archetypes for Targets
Description: Function-oriented Make-like declarative pipelines for
Statistics and data science are supported in the 'targets' R package.
As an extension to 'targets', the 'tarchetypes' package provides
convenient user-side functions to make 'targets' easier to use.
By establishing reusable archetypes for common kinds of
targets and pipelines, these functions help express complicated
reproducible pipelines concisely and compactly.
The methods in this package were influenced by the 'targets' R package.
by Will Landau (2018) <doi:10.21105/joss.00550>.
Author: William Michael Landau [aut, cre]
,
Rudolf Siegel [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between tarchetypes versions 0.12.0 dated 2025-01-31 and 0.13.0 dated 2025-04-10
DESCRIPTION | 8 +-- MD5 | 48 +++++++++++----------- NAMESPACE | 2 NEWS.md | 8 +++ R/tar_map2.R | 2 R/tar_map2_count.R | 2 R/tar_map2_count_raw.R | 2 R/tar_map2_raw.R | 75 +++++++++++++++++++++++++++++++---- R/tar_map2_size.R | 2 R/tar_map2_size_raw.R | 2 R/tar_package.R | 6 +- R/tar_quarto.R | 6 +- R/tar_quarto_rep.R | 6 +- R/tar_quarto_rep_raw.R | 18 +++++--- R/tar_skip.R | 3 - R/utils_parallel.R | 10 ++++ man/tar_map2.Rd | 8 +++ man/tar_map2_count.Rd | 8 +++ man/tar_map2_size.Rd | 8 +++ man/tar_quarto.Rd | 6 +- man/tar_quarto_rep.Rd | 6 +- man/tar_skip.Rd | 13 ++++++ tests/testthat/test-tar_map2.R | 60 +++++++++++++++++++++++----- tests/testthat/test-tar_map2_count.R | 22 ++++++---- tests/testthat/test-tar_map2_size.R | 22 ++++++---- 25 files changed, 267 insertions(+), 86 deletions(-)
Title: Smooth Additive Quantile Regression Models
Description: Smooth additive quantile regression models, fitted using
the methods of Fasiolo et al. (2020) <doi:10.1080/01621459.2020.1725521>.
See Fasiolo at al. (2021) <doi:10.18637/jss.v100.i09> for an introduction to the package. Differently from
'quantreg', the smoothing parameters are estimated automatically by marginal
loss minimization, while the regression coefficients are estimated using either
PIRLS or Newton algorithm. The learning rate is determined so that the Bayesian
credible intervals of the estimated effects have approximately the correct
coverage. The main function is qgam() which is similar to gam() in 'mgcv', but
fits non-parametric quantile regression models.
Author: Matteo Fasiolo [aut, cre],
Ben Griffiths [aut],
Simon N. Wood [ctb],
Margaux Zaffran [ctb],
Yannig Goude [ctb],
Raphael Nedellec [ctb]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between qgam versions 1.3.4 dated 2021-11-22 and 2.0.0 dated 2025-04-10
qgam-1.3.4/qgam/R/I_gamlssFit.R |only qgam-1.3.4/qgam/R/I_getVp.R |only qgam-2.0.0/qgam/DESCRIPTION | 15 - qgam-2.0.0/qgam/MD5 | 84 +++--- qgam-2.0.0/qgam/NAMESPACE | 2 qgam-2.0.0/qgam/R/I_biasedCov.R | 29 -- qgam-2.0.0/qgam/R/I_brent.R | 6 qgam-2.0.0/qgam/R/I_getErrParam.R | 14 - qgam-2.0.0/qgam/R/I_init_gauss_fit.R |only qgam-2.0.0/qgam/R/I_invert_psdef_matrix.R |only qgam-2.0.0/qgam/R/I_llkGrads.R | 109 ++------ qgam-2.0.0/qgam/R/I_objFunLearnFast.R | 71 ++--- qgam-2.0.0/qgam/R/I_prepBootObj.R | 6 qgam-2.0.0/qgam/R/I_sandwichLoss.R | 94 +++---- qgam-2.0.0/qgam/R/I_should_we_use_discrete.R |only qgam-2.0.0/qgam/R/I_tuneLearnBootstrapping.R | 30 -- qgam-2.0.0/qgam/R/I_tuneLearnFullFits.R | 92 ++++--- qgam-2.0.0/qgam/R/check_learn.R | 2 qgam-2.0.0/qgam/R/check_learnFast.R | 2 qgam-2.0.0/qgam/R/check_qgam.R | 17 - qgam-2.0.0/qgam/R/elf.R | 118 +++++---- qgam-2.0.0/qgam/R/elflss.R | 2 qgam-2.0.0/qgam/R/mqgam.R | 42 +-- qgam-2.0.0/qgam/R/qgam.R | 61 ++-- qgam-2.0.0/qgam/R/tuneLearn.R | 41 +-- qgam-2.0.0/qgam/R/tuneLearnFast.R | 109 +++----- qgam-2.0.0/qgam/build/partial.rdb |binary qgam-2.0.0/qgam/build/vignette.rds |binary qgam-2.0.0/qgam/inst/doc/qgam.R | 7 qgam-2.0.0/qgam/inst/doc/qgam.Rmd | 18 + qgam-2.0.0/qgam/inst/doc/qgam.html | 170 +++++++------ qgam-2.0.0/qgam/man/check.learn.Rd | 2 qgam-2.0.0/qgam/man/check.learnFast.Rd | 2 qgam-2.0.0/qgam/man/check.qgam.Rd | 2 qgam-2.0.0/qgam/man/elf.Rd | 2 qgam-2.0.0/qgam/man/elflss.Rd | 2 qgam-2.0.0/qgam/man/mqgam.Rd | 5 qgam-2.0.0/qgam/man/qgam.Rd | 5 qgam-2.0.0/qgam/man/tuneLearn.Rd | 5 qgam-2.0.0/qgam/man/tuneLearnFast.Rd | 10 qgam-2.0.0/qgam/tests/testthat/test-calFastTuneLearn.R | 39 ++ qgam-2.0.0/qgam/tests/testthat/test-calFastTuneLearnFast.R | 30 +- qgam-2.0.0/qgam/tests/testthat/test-check_qgam.R | 26 - qgam-2.0.0/qgam/tests/testthat/test-qgam_discrete.R |only qgam-2.0.0/qgam/tests/testthat/test-tuneLearnFast.R | 24 - qgam-2.0.0/qgam/vignettes/qgam.Rmd | 18 + 46 files changed, 688 insertions(+), 625 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis (Balduzzi et al., 2023) <doi:10.18637/jss.v106.i02> and supporting Schwarzer et al. (2015) <doi:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <doi:10.1002/jrsm.1058>;
- additive network meta-analysis for combinations of treatments (Rücker et al., 2020) <doi:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <doi:10.1002/sim.8158>, or penalised logistic regression (Evrenoglou et al., 2022) <doi:10.1002/sim.9562>;
- rankograms and ranking of treatments by the Surface under the cumulative ranking curve (SUCRA) (Salanti et al., 2013) <doi:10.1016/j.jclinepi.2010.03.016>;
- ranking of treatments using P-scores (frequentist analogue of SUCRAs without resampling) according to [...truncated...]
Author: Gerta Ruecker [aut] ,
Ulrike Krahn [aut],
Jochem Koenig [aut] ,
Orestis Efthimiou [aut] ,
Annabel Davies [aut] ,
Theodoros Papakonstantinou [aut]
,
Theodoros Evrenoglou [ctb] ,
Krzysztof Ciomek [ctb] ,
Nana-Adjoa Kwarteng [ctb] ,
Guido Schwarzer [aut, [...truncated...]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between netmeta versions 3.1-1 dated 2025-02-06 and 3.2-0 dated 2025-04-10
DESCRIPTION | 15 +- MD5 | 247 +++++++++++++++++++++-------------------- NAMESPACE | 15 ++ NEWS.md | 42 ++++++ R/Baker2009.R | 23 --- R/Dogliotti2014.R | 15 -- R/Dong2013.R | 15 -- R/Franchini2012.R | 25 ---- R/Gurusamy2011.R | 15 -- R/Linde2015.R | 19 --- R/Linde2016.R | 11 - R/Senn2013.R | 26 ---- R/Stowe2010.R | 18 -- R/Woods2010.R | 22 --- R/as.data.frame.netmeta.R | 13 -- R/createC.R | 25 ---- R/crossnma2netmeta.R | 2 R/dietaryfat.R | 33 ----- R/discomb.R | 123 +++++++++++--------- R/forest.netbind.R | 33 ----- R/forest.netcomb.R | 33 ----- R/forest.netcomparison.R | 30 ---- R/forest.netcomplex.R | 2 R/forest.netmeta.R | 68 ----------- R/forest.netsplit.R | 26 ---- R/forest.subgroup.netmeta.R | 2 R/invmat.R | 9 - R/netbind.R | 7 + R/netcomb.R | 111 ++++++++++++------ R/netcomparison.R | 19 ++- R/netcontrib.R | 15 +- R/netgraph.R | 37 ------ R/netgraph.netimpact.R | 29 ---- R/netimpact.R | 16 ++ R/netleague.R | 10 - R/netmeasures.R | 30 ---- R/netmeta-package.R | 7 - R/netmeta.R | 161 ++++++++++++++++++++++++-- R/netmetabin.R | 47 +------ R/netmetareg-internal.R |only R/netmetareg.R |only R/netposet.R | 50 ++++---- R/netrank.R | 97 +++++++++++----- R/netsplit.R | 35 +++++ R/nma.additive.R | 33 +++-- R/nma.ruecker.R | 2 R/plot.netposet.R | 79 ------------- R/plot.netrank.R | 75 ------------ R/prepare.R | 52 -------- R/print.decomp.design.R | 16 -- R/print.netbind.R | 28 ---- R/print.netcomb.R | 96 ++++++--------- R/print.netimpact.R | 15 -- R/print.netmeta.R | 9 + R/print.rankogram.R | 18 +- R/print.summary.netcomb.R | 18 -- R/print.summary.netmeta.R | 49 -------- R/rankings.R | 21 ++- R/rankogram.R | 13 -- R/rankogram.default.R | 47 +++---- R/rankogram.netmeta.R | 30 ++++ R/ranksampling.R | 3 R/smokingcessation.R | 24 --- R/summary.netcomb.R | 34 ----- R/summary.netmeta.R | 27 ---- R/summary.netmetareg.R |only R/summary.rankogram.R |only R/treats.R | 34 +---- build/vignette.rds |binary inst/doc/netmeta.pdf |binary man/Baker2009.Rd | 22 --- man/Dogliotti2014.Rd | 15 -- man/Dong2013.Rd | 15 -- man/Franchini2012.Rd | 25 ---- man/Gurusamy2011.Rd | 15 -- man/Linde2015.Rd | 19 --- man/Linde2016.Rd | 11 - man/Senn2013.Rd | 26 ---- man/Stowe2010.Rd | 17 -- man/Woods2010.Rd | 22 --- man/as.data.frame.netmeta.Rd | 13 -- man/createC.Rd | 25 ---- man/crossnma2netmeta.Rd | 2 man/dietaryfat.Rd | 33 ----- man/discomb.Rd | 3 man/forest.netbind.Rd | 33 ----- man/forest.netcomb.Rd | 33 ----- man/forest.netcomparison.Rd | 30 ---- man/forest.netcomplex.Rd | 2 man/forest.netmeta.Rd | 68 ----------- man/forest.netsplit.Rd | 26 ---- man/forest.subgroup.netmeta.Rd | 2 man/invmat.Rd | 9 - man/netbind.Rd | 7 + man/netcomb.Rd | 17 ++ man/netcomparison.Rd | 19 ++- man/netcontrib.Rd | 9 - man/netgraph.Rd | 38 ------ man/netgraph.netimpact.Rd | 29 ---- man/netimpact.Rd | 14 ++ man/netleague.Rd | 10 - man/netmeasures.Rd | 30 ---- man/netmeta-package.Rd | 2 man/netmeta.Rd | 120 +++++++++++++++++++ man/netmetabin.Rd | 29 ---- man/netmetareg.Rd |only man/netposet.Rd | 48 +++---- man/netrank.Rd | 103 +++++++++++------ man/netsplit.Rd | 35 +++++ man/plot.netposet.Rd | 79 ------------- man/plot.netrank.Rd | 75 ------------ man/print.decomp.design.Rd | 16 -- man/print.netbind.Rd | 28 ---- man/print.netcomb.Rd | 34 ----- man/print.netimpact.Rd | 15 -- man/print.netmeta.Rd | 11 + man/print.rankogram.Rd | 16 +- man/print.summary.netcomb.Rd | 18 -- man/print.summary.netmeta.Rd | 49 -------- man/rankogram.Rd | 13 -- man/rankogram.default.Rd | 22 --- man/rankogram.netmeta.Rd | 3 man/smokingcessation.Rd | 23 --- man/summary.netcomb.Rd | 34 ----- man/summary.netmeta.Rd | 27 ---- man/summary.netmetareg.Rd |only man/summary.rankogram.Rd |only man/treats.Rd | 34 +---- 128 files changed, 1283 insertions(+), 2491 deletions(-)
Title: Estimation of Extreme Conditional Quantiles and Probabilities
Description: Extreme value theory, nonparametric kernel estimation, tail
conditional probabilities, extreme conditional quantile, adaptive estimation,
quantile regression, survival probabilities.
Author: Gilles Durrieu [aut],
Ion Grama [aut],
Kevin Jaunatre [aut, cre],
Quang-Khoai Pham [aut],
Jean-Marie Tricot [aut]
Maintainer: Kevin Jaunatre <kevin.jaunatre@hotmail.fr>
Diff between extremefit versions 1.0.2 dated 2019-05-04 and 1.0.3 dated 2025-04-10
DESCRIPTION | 33 ++++++++++++++++++++++++++------- MD5 | 37 +++++++++++++++++++------------------ NAMESPACE | 2 +- R/PackageOxygen.R | 12 +++--------- build/vignette.rds |binary inst/doc/extremefit.pdf |binary man/CriticalValue.Rd | 15 ++++++++++++--- man/Pareto-Distribution.Rd | 8 +------- man/Pareto-mix.Rd | 11 +++++++++-- man/bandwidth.CV.Rd | 14 +++++++++++--- man/bootCI.Rd | 19 +++++++++++++++---- man/bootCI.ts.Rd | 23 +++++++++++++++++++---- man/cox.adapt.Rd | 16 ++++++++++++---- man/hill.adapt.Rd | 12 ++++++++++-- man/hill.ts.Rd | 16 +++++++++++++--- man/predict.cox.adapt.Rd | 13 ++++++++++--- man/predict.hill.Rd | 11 +++++++++-- man/predict.hill.adapt.Rd | 3 +-- man/predict.hill.ts.Rd | 3 +-- vignettes/extremefit.Rmd |only 20 files changed, 172 insertions(+), 76 deletions(-)
Title: A Distributed Worker Launcher Framework
Description: In computationally demanding analysis projects,
statisticians and data scientists asynchronously
deploy long-running tasks to distributed systems,
ranging from traditional clusters to cloud services.
The 'NNG'-powered 'mirai' R package by Gao (2023)
<doi:10.5281/zenodo.7912722> is a sleek
and sophisticated scheduler that
efficiently processes these intense workloads.
The 'crew' package extends 'mirai' with a unifying
interface for third-party worker launchers.
Inspiration also comes from packages.
'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>,
'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>,
'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
and 'batchtools' by Lang, Bischel, and Surmann (2017)
<doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre]
,
Daniel Woodie [ctb],
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between crew versions 1.0.0 dated 2025-02-03 and 1.1.0 dated 2025-04-10
DESCRIPTION | 6 - MD5 | 86 ++++++++++--------- NAMESPACE | 4 NEWS.md | 7 + R/crew_async.R | 2 R/crew_client.R | 69 ++++++++++----- R/crew_controller.R | 94 +++++++++++---------- R/crew_controller_local.R | 2 R/crew_controller_sequential.R |only R/crew_launcher.R | 6 - R/crew_launcher_local.R | 6 - R/crew_package.R | 6 - R/utils_mirai.R | 4 R/utils_names.R | 2 R/utils_packages.R | 30 +++--- R/utils_promises.R | 2 build/vignette.rds |binary inst/doc/introduction.Rmd | 8 - inst/doc/introduction.html | 18 ++-- inst/doc/plugins.Rmd | 2 inst/doc/plugins.html | 102 +++++++++++------------ inst/doc/risks.Rmd | 8 - inst/doc/risks.html | 25 ++--- inst/doc/shiny.Rmd | 4 inst/doc/shiny.html | 8 - man/crew-package.Rd | 4 man/crew_async.Rd | 2 man/crew_class_client.Rd | 44 ++++++--- man/crew_class_controller.Rd | 7 + man/crew_class_controller_sequential.Rd |only man/crew_class_launcher.Rd | 6 - man/crew_class_launcher_local.Rd | 6 - man/crew_client.Rd | 8 + man/crew_controller_local.Rd | 8 + man/crew_controller_sequential.Rd |only man/crew_launcher.Rd | 2 man/crew_launcher_local.Rd | 2 tests/local/test-launcher-system2.R | 2 tests/testthat/test-crew_client.R | 1 tests/testthat/test-crew_controller.R | 31 ++++++ tests/testthat/test-crew_controller_sequential.R |only tests/testthat/test-plugins.R | 10 ++ vignettes/introduction.Rmd | 8 - vignettes/plugins.Rmd | 2 vignettes/risks.Rmd | 8 - vignettes/shiny.Rmd | 4 46 files changed, 394 insertions(+), 262 deletions(-)
Title: Identify Relevant Clinical Codes and Evaluate Their Use
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre] ,
Marti Catala [ctb] ,
Xihang Chen [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [ctb] ,
Danielle Newby [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CodelistGenerator versions 3.4.1 dated 2025-03-26 and 3.5.0 dated 2025-04-10
CodelistGenerator-3.4.1/CodelistGenerator/R/data.R |only CodelistGenerator-3.4.1/CodelistGenerator/R/inputValidation.R |only CodelistGenerator-3.4.1/CodelistGenerator/data |only CodelistGenerator-3.4.1/CodelistGenerator/inst/cohorts |only CodelistGenerator-3.4.1/CodelistGenerator/inst/cohorts2 |only CodelistGenerator-3.4.1/CodelistGenerator/inst/concepts |only CodelistGenerator-3.4.1/CodelistGenerator/inst/concepts_for_mock/oa_desc.json |only CodelistGenerator-3.4.1/CodelistGenerator/inst/concepts_for_mock/oa_no_desc.json |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a01_Introduction_to_CodelistGenerator.R |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a01_Introduction_to_CodelistGenerator.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a01_Introduction_to_CodelistGenerator.html |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a02_Candidate_codes_OA.R |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a02_Candidate_codes_OA.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a02_Candidate_codes_OA.html |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a03_Options_for_CodelistGenerator.R |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a03_Options_for_CodelistGenerator.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a03_Options_for_CodelistGenerator.html |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a04_Vocab_based_codelists.R |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a04_Vocab_based_codelists.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/inst/doc/a04_Vocab_based_codelists.html |only CodelistGenerator-3.4.1/CodelistGenerator/inst/introData01.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/introData02.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/introData03.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/introData04.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/introData05.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/introVocab.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/medData01.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/medData02a.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/medData02b.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/medData03.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/medDataConceptClass.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/medDataDoseForms.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/not_all_concept_sets |only CodelistGenerator-3.4.1/CodelistGenerator/inst/optionsData01.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/optionsData02.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/optionsData03.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/optionsData04.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/optionsData05.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/optionsData06.RData |only CodelistGenerator-3.4.1/CodelistGenerator/inst/optionsData07.RData |only CodelistGenerator-3.4.1/CodelistGenerator/man/doseFormToRoute.Rd |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/a01_Introduction_to_CodelistGenerator.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/a02_Candidate_codes_OA.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/a03_Options_for_CodelistGenerator.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/a04_Vocab_based_codelists.Rmd |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig1.png |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig2.png |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig3.png |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig4.png |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig5.png |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig6.png |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig7.png |only CodelistGenerator-3.4.1/CodelistGenerator/vignettes/mock_db_fig8.png |only CodelistGenerator-3.5.0/CodelistGenerator/DESCRIPTION | 18 CodelistGenerator-3.5.0/CodelistGenerator/MD5 | 332 +- CodelistGenerator-3.5.0/CodelistGenerator/NAMESPACE | 17 CodelistGenerator-3.5.0/CodelistGenerator/R/CodelistFromCodelistWithDetails.R | 2 CodelistGenerator-3.5.0/CodelistGenerator/R/buildAchillesTables.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/checks.R | 4 CodelistGenerator-3.5.0/CodelistGenerator/R/codesFromConceptSet.R | 46 CodelistGenerator-3.5.0/CodelistGenerator/R/codesInUse.R | 153 - CodelistGenerator-3.5.0/CodelistGenerator/R/compareCodelists.R | 99 CodelistGenerator-3.5.0/CodelistGenerator/R/documentation_helper.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/drugCodes.R | 324 -- CodelistGenerator-3.5.0/CodelistGenerator/R/getCandidateCodes.R | 17 CodelistGenerator-3.5.0/CodelistGenerator/R/getDoseUnit.R | 21 CodelistGenerator-3.5.0/CodelistGenerator/R/getICD10StandardCodes.R | 228 + CodelistGenerator-3.5.0/CodelistGenerator/R/getMappings.R | 44 CodelistGenerator-3.5.0/CodelistGenerator/R/getRoutes.R | 17 CodelistGenerator-3.5.0/CodelistGenerator/R/helperFunctions.R | 97 CodelistGenerator-3.5.0/CodelistGenerator/R/mockVocabRef.R | 112 CodelistGenerator-3.5.0/CodelistGenerator/R/reexports.R |only CodelistGenerator-3.5.0/CodelistGenerator/R/runSearch.R | 6 CodelistGenerator-3.5.0/CodelistGenerator/R/stratifyByConcept.R | 30 CodelistGenerator-3.5.0/CodelistGenerator/R/stratifyByDoseUnit.R | 36 CodelistGenerator-3.5.0/CodelistGenerator/R/stratifyByRoute.R | 38 CodelistGenerator-3.5.0/CodelistGenerator/R/subsetOnDomain.R | 55 CodelistGenerator-3.5.0/CodelistGenerator/R/subsetOnDoseUnit.R | 45 CodelistGenerator-3.5.0/CodelistGenerator/R/subsetOnRouteCategory.R | 61 CodelistGenerator-3.5.0/CodelistGenerator/R/summariseAchillesCodeUse.R | 40 CodelistGenerator-3.5.0/CodelistGenerator/R/summariseCodeUse.R | 159 - CodelistGenerator-3.5.0/CodelistGenerator/R/summariseOrphanCodes.R | 22 CodelistGenerator-3.5.0/CodelistGenerator/R/summariseUnmappedCodes.R | 24 CodelistGenerator-3.5.0/CodelistGenerator/R/sysdata.rda |binary CodelistGenerator-3.5.0/CodelistGenerator/R/tableAchillesCodeUse.R | 71 CodelistGenerator-3.5.0/CodelistGenerator/R/tableCodeUse.R | 88 CodelistGenerator-3.5.0/CodelistGenerator/R/tableUnmappedCodes.R | 59 CodelistGenerator-3.5.0/CodelistGenerator/R/vocabUtilities.R | 194 - CodelistGenerator-3.5.0/CodelistGenerator/README.md | 91 CodelistGenerator-3.5.0/CodelistGenerator/build/vignette.rds |binary CodelistGenerator-3.5.0/CodelistGenerator/inst/cohorts_for_mock/oa_desc.json | 8 CodelistGenerator-3.5.0/CodelistGenerator/inst/concepts_for_mock/arthritis_desc.json |only CodelistGenerator-3.5.0/CodelistGenerator/inst/concepts_for_mock/arthritis_no_desc.json |only CodelistGenerator-3.5.0/CodelistGenerator/inst/concepts_for_mock/arthritis_with_excluded.json |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a01_GettingOmopCdmVocabularies.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a01_GettingOmopCdmVocabularies.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a01_GettingOmopCdmVocabularies.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a02_ExploreCDMvocabulary.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a02_ExploreCDMvocabulary.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a02_ExploreCDMvocabulary.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a03_GenerateCandidateCodelist.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a03_GenerateCandidateCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a03_GenerateCandidateCodelist.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04_GenerateVocabularyBasedCodelist.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04_GenerateVocabularyBasedCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04_GenerateVocabularyBasedCodelist.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04b_icd_codes.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04b_icd_codes.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a04b_icd_codes.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a05_ExtractCodelistFromJSONfile.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a05_ExtractCodelistFromJSONfile.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a05_ExtractCodelistFromJSONfile.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a06_CreateSubsetsFromCodelist.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a06_CreateSubsetsFromCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a06_CreateSubsetsFromCodelist.html |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a07_RunCodelistDiagnostics.R |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a07_RunCodelistDiagnostics.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/inst/doc/a07_RunCodelistDiagnostics.html |only CodelistGenerator-3.5.0/CodelistGenerator/man/ageGroupDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/availableATC.Rd | 12 CodelistGenerator-3.5.0/CodelistGenerator/man/availableICD10.Rd | 13 CodelistGenerator-3.5.0/CodelistGenerator/man/availableIngredients.Rd | 10 CodelistGenerator-3.5.0/CodelistGenerator/man/buildAchillesTables.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/byConceptDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/bySexDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/byYearDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/cdmDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/codesFromCohort.Rd | 25 CodelistGenerator-3.5.0/CodelistGenerator/man/codesFromConceptSet.Rd | 14 CodelistGenerator-3.5.0/CodelistGenerator/man/codesInUse.Rd | 10 CodelistGenerator-3.5.0/CodelistGenerator/man/compareCodelists.Rd | 10 CodelistGenerator-3.5.0/CodelistGenerator/man/countByDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/domainDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/doseFormDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/doseUnitDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/dot-optionsDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/figures/README-unnamed-chunk-8-1.png |only CodelistGenerator-3.5.0/CodelistGenerator/man/figures/logo.png |binary CodelistGenerator-3.5.0/CodelistGenerator/man/getATCCodes.Rd | 33 CodelistGenerator-3.5.0/CodelistGenerator/man/getCandidateCodes.Rd | 12 CodelistGenerator-3.5.0/CodelistGenerator/man/getConceptClassId.Rd | 13 CodelistGenerator-3.5.0/CodelistGenerator/man/getDescendants.Rd | 16 CodelistGenerator-3.5.0/CodelistGenerator/man/getDomains.Rd | 8 CodelistGenerator-3.5.0/CodelistGenerator/man/getDoseForm.Rd | 8 CodelistGenerator-3.5.0/CodelistGenerator/man/getDoseUnit.Rd | 18 CodelistGenerator-3.5.0/CodelistGenerator/man/getDrugIngredientCodes.Rd | 34 CodelistGenerator-3.5.0/CodelistGenerator/man/getICD10StandardCodes.Rd | 26 CodelistGenerator-3.5.0/CodelistGenerator/man/getMappings.Rd | 13 CodelistGenerator-3.5.0/CodelistGenerator/man/getRelationshipId.Rd | 8 CodelistGenerator-3.5.0/CodelistGenerator/man/getRouteCategories.Rd | 16 CodelistGenerator-3.5.0/CodelistGenerator/man/getVocabVersion.Rd | 8 CodelistGenerator-3.5.0/CodelistGenerator/man/getVocabularies.Rd | 8 CodelistGenerator-3.5.0/CodelistGenerator/man/groupColumnDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/groupColumnStrataDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/headerDoc.Rd |only 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CodelistGenerator-3.5.0/CodelistGenerator/man/standardConceptDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/stratifyByConcept.Rd | 22 CodelistGenerator-3.5.0/CodelistGenerator/man/stratifyByDoseUnit.Rd | 22 CodelistGenerator-3.5.0/CodelistGenerator/man/stratifyByRouteCategory.Rd | 22 CodelistGenerator-3.5.0/CodelistGenerator/man/subsetOnDomain.Rd | 35 CodelistGenerator-3.5.0/CodelistGenerator/man/subsetOnDoseUnit.Rd | 32 CodelistGenerator-3.5.0/CodelistGenerator/man/subsetOnRouteCategory.Rd | 28 CodelistGenerator-3.5.0/CodelistGenerator/man/subsetToCodesInUse.Rd | 14 CodelistGenerator-3.5.0/CodelistGenerator/man/summariseAchillesCodeUse.Rd | 12 CodelistGenerator-3.5.0/CodelistGenerator/man/summariseCodeUse.Rd | 21 CodelistGenerator-3.5.0/CodelistGenerator/man/summariseCohortCodeUse.Rd | 29 CodelistGenerator-3.5.0/CodelistGenerator/man/summariseOrphanCodes.Rd | 12 CodelistGenerator-3.5.0/CodelistGenerator/man/summariseUnmappedCodes.Rd | 27 CodelistGenerator-3.5.0/CodelistGenerator/man/tableAchillesCodeUse.Rd | 6 CodelistGenerator-3.5.0/CodelistGenerator/man/tableCodeUse.Rd | 4 CodelistGenerator-3.5.0/CodelistGenerator/man/tableCohortCodeUse.Rd | 16 CodelistGenerator-3.5.0/CodelistGenerator/man/tableDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/tableOrphanCodes.Rd | 8 CodelistGenerator-3.5.0/CodelistGenerator/man/tableUnmappedCodes.Rd | 42 CodelistGenerator-3.5.0/CodelistGenerator/man/typeBroadDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/typeNarrowDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/typeTableDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/man/xDoc.Rd |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/setup.R |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-buildAchillesTables.R |only CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-codesFrom.R | 227 - CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-codesInUse.R | 15 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-compareCodelists.R | 24 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-dbms.R | 1218 +++---- CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-drugCodes.R | 1525 +++++----- CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-getDoseUnit.R | 8 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-getICD10StandardCodes.R | 188 - CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-getRouteCategories.R | 3 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-stratifyByConcept.R | 48 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-stratifyByDoseUnit.R | 44 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-subsetOnDomain.R | 18 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-subsetOnDoseUnit.R | 13 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-subsetOnRouteCategory.R | 83 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-summariseAchillesCodeUse.R | 7 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-summariseCodeUse.R | 302 - CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-summariseOrphanCodes.R | 2 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-tableCodeUse.R | 20 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-tableUnmappedCodes.R | 116 CodelistGenerator-3.5.0/CodelistGenerator/tests/testthat/test-vocabUtilities.R | 2 CodelistGenerator-3.5.0/CodelistGenerator/vignettes/Figures |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a01_GettingOmopCdmVocabularies.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a02_ExploreCDMvocabulary.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a03_GenerateCandidateCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a04_GenerateVocabularyBasedCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a04b_icd_codes.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a05_ExtractCodelistFromJSONfile.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a06_CreateSubsetsFromCodelist.Rmd |only CodelistGenerator-3.5.0/CodelistGenerator/vignettes/a07_RunCodelistDiagnostics.Rmd |only 222 files changed, 3712 insertions(+), 3389 deletions(-)
More information about CodelistGenerator at CRAN
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Title: Bradley-Terry Models
Description: Specify and fit the Bradley-Terry model, including structured
versions in which the parameters are related to explanatory variables
through a linear predictor and versions with contest-specific effects,
such as a home advantage.
Author: Heather Turner [aut, cre],
David Firth [aut]
Maintainer: Heather Turner <ht@heatherturner.net>
Diff between BradleyTerry2 versions 1.1-2 dated 2020-02-03 and 1.1.3 dated 2025-04-10
BradleyTerry2-1.1-2/BradleyTerry2/data/CEMS.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/chameleons.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/citations.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/icehockey.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/seeds.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/sound.fields.rda |only BradleyTerry2-1.1-2/BradleyTerry2/data/springall.rda |only BradleyTerry2-1.1-2/BradleyTerry2/inst/doc/BradleyTerry.Rnw |only BradleyTerry2-1.1-2/BradleyTerry2/inst/doc/BradleyTerry.pdf |only BradleyTerry2-1.1-2/BradleyTerry2/vignettes/BradleyTerry-concordance.tex |only BradleyTerry2-1.1-2/BradleyTerry2/vignettes/BradleyTerry.Rnw |only BradleyTerry2-1.1-2/BradleyTerry2/vignettes/baseball-qvplot.pdf |only BradleyTerry2-1.1-2/BradleyTerry2/vignettes/residuals.pdf |only BradleyTerry2-1.1.3/BradleyTerry2/DESCRIPTION | 27 - BradleyTerry2-1.1.3/BradleyTerry2/MD5 | 70 ++-- BradleyTerry2-1.1.3/BradleyTerry2/NEWS.md | 12 BradleyTerry2-1.1.3/BradleyTerry2/R/flatlizards.R | 2 BradleyTerry2-1.1.3/BradleyTerry2/R/predict.BTm.R | 2 BradleyTerry2-1.1.3/BradleyTerry2/R/qvcalc.BTabilities.R | 4 BradleyTerry2-1.1.3/BradleyTerry2/README.md | 6 BradleyTerry2-1.1.3/BradleyTerry2/build/partial.rdb |only BradleyTerry2-1.1.3/BradleyTerry2/build/vignette.rds |binary BradleyTerry2-1.1.3/BradleyTerry2/data/CEMS.R |only BradleyTerry2-1.1.3/BradleyTerry2/data/chameleons.R |only BradleyTerry2-1.1.3/BradleyTerry2/data/citations.R |only BradleyTerry2-1.1.3/BradleyTerry2/data/icehockey.R |only BradleyTerry2-1.1.3/BradleyTerry2/data/seeds.R |only BradleyTerry2-1.1.3/BradleyTerry2/data/sound.fields.R |only BradleyTerry2-1.1.3/BradleyTerry2/data/springall.R |only BradleyTerry2-1.1.3/BradleyTerry2/inst/CITATION | 31 - BradleyTerry2-1.1.3/BradleyTerry2/inst/doc/BradleyTerry.R | 170 ++-------- BradleyTerry2-1.1.3/BradleyTerry2/inst/doc/BradleyTerry.Rmd |only BradleyTerry2-1.1.3/BradleyTerry2/inst/doc/BradleyTerry.html |only BradleyTerry2-1.1.3/BradleyTerry2/man/CEMS.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/baseball.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/chameleons.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/citations.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/flatlizards.Rd | 8 BradleyTerry2-1.1.3/BradleyTerry2/man/football.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/icehockey.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/predict.BTm.Rd | 2 BradleyTerry2-1.1.3/BradleyTerry2/man/qvcalc.BTabilities.Rd | 4 BradleyTerry2-1.1.3/BradleyTerry2/man/seeds.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/sound.fields.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/man/springall.Rd | 6 BradleyTerry2-1.1.3/BradleyTerry2/vignettes/BradleyTerry.Rmd |only BradleyTerry2-1.1.3/BradleyTerry2/vignettes/BradleyTerry.bib | 46 +- BradleyTerry2-1.1.3/BradleyTerry2/vignettes/baseball-qvplot.png |only BradleyTerry2-1.1.3/BradleyTerry2/vignettes/residuals.png |only 49 files changed, 188 insertions(+), 250 deletions(-)
Title: ArcGIS Utility Functions
Description: Developer oriented utility functions designed to be used as
the building blocks of R packages that work with ArcGIS Location
Services. It provides functionality for authorization, Esri JSON
construction and parsing, as well as other utilities pertaining to
geometry and Esri type conversions. To support 'ArcGIS Pro' users,
authorization can be done via 'arcgisbinding'. Installation
instructions for 'arcgisbinding' can be found at
<https://developers.arcgis.com/r-bridge/installation/>.
Author: Josiah Parry [aut, cre] ,
Kenneth Vernon [ctb] ,
Martha Bass [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcgisutils versions 0.3.1 dated 2024-09-26 and 0.3.3 dated 2025-04-10
arcgisutils-0.3.1/arcgisutils/src/Makevars |only arcgisutils-0.3.1/arcgisutils/src/Makevars.win |only arcgisutils-0.3.3/arcgisutils/DESCRIPTION | 15 arcgisutils-0.3.3/arcgisutils/MD5 | 31 - arcgisutils-0.3.3/arcgisutils/NEWS.md | 7 arcgisutils-0.3.3/arcgisutils/R/arc-base-req.R | 16 arcgisutils-0.3.3/arcgisutils/R/feature-collection.R | 80 +-- arcgisutils-0.3.3/arcgisutils/R/rbind-results.R | 9 arcgisutils-0.3.3/arcgisutils/configure | 2 arcgisutils-0.3.3/arcgisutils/configure.win | 2 arcgisutils-0.3.3/arcgisutils/man/layer_json.Rd | 8 arcgisutils-0.3.3/arcgisutils/src/Makevars.in |only arcgisutils-0.3.3/arcgisutils/src/Makevars.win.in |only arcgisutils-0.3.3/arcgisutils/src/rust/Cargo.lock | 288 ++++++------ arcgisutils-0.3.3/arcgisutils/src/rust/Cargo.toml | 3 arcgisutils-0.3.3/arcgisutils/src/rust/src/to/attributes.rs | 38 - arcgisutils-0.3.3/arcgisutils/src/rust/vendor.tar.xz |binary arcgisutils-0.3.3/arcgisutils/tools/config.R |only arcgisutils-0.3.3/arcgisutils/tools/msrv.R | 4 19 files changed, 255 insertions(+), 248 deletions(-)
Title: Merge and Download International Large-Scale Assessments (ILSA)
Data
Description: Merges and downloads 'SPSS' data from different International Large-Scale Assessments (ILSA), including: Trends in International Mathematics and Science Study (TIMSS), Progress in International Reading Literacy Study (PIRLS), and others.
Author: Andres Christiansen [aut, cre]
,
Andres Strello [ctb]
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>
Diff between ILSAmerge versions 1.3.6 dated 2025-02-12 and 1.3.8 dated 2025-04-10
DESCRIPTION | 6 - MD5 | 34 +++---- NEWS.md | 13 ++ R/ILSAready.R | 10 +- R/addSchools.R | 2 R/mistoNAs.R | 6 + R/sysdata.rda |binary R/untibble.R | 19 ++- build/vignette.rds |binary inst/doc/Download.R | 14 +- inst/doc/Download.html | 50 +++++----- inst/doc/IdentifyILSAfiles.html | 16 +-- inst/doc/Load.html | 102 ++++++++++----------- inst/doc/Merge.R | 6 - inst/doc/Merge.html | 174 ++++++++++++++++++------------------ inst/doc/Onestep.html | 124 ++++++++++++------------- inst/doc/Rename.html | 28 ++--- inst/extdata/ilsainfo/ILSAlinks.csv | 2 18 files changed, 319 insertions(+), 287 deletions(-)
Title: Density and Abundance from Distance-Sampling Surveys
Description: Distance-sampling (<doi:10.1007/978-3-319-19219-2>)
estimates density and abundance of survey targets (e.g., animals) when
detection probability declines with distance.
Distance-sampling is popular in ecology,
especially when survey targets are observed from aerial platforms (e.g.,
airplane or drone), surface vessels (e.g., boat or truck), or along
walking transects.
Distance-sampling includes line-transect studies that measure observation
distances as the closest approach of the sample route (transect) to the target
(i.e., perpendicular off-transect distance), and point-transect studies that
measure observation distances from stationary observers to
the target (i.e., radial distance).
The routines included here fit smooth (parametric) curves to
histograms of observation distances
and use those functions to compute effective sampling distances, density of
targets in the surveyed area, and abundance
of targets in a surrounding study area. Curve shapes include the
half-normal, haza [...truncated...]
Author: Trent McDonald [cre, aut],
Jason Carlisle [aut],
Aidan McDonald [aut] ,
Ryan Nielson [ctb] ,
Ben Augustine [ctb] ,
James Griswald [ctb] ,
Patrick McKann [ctb] ,
Lacey Jeroue [ctb] ,
Hoffman Abigail [ctb] ,
Kleinsausser Michael [ctb] ,
Joel Reynolds [ [...truncated...]
Maintainer: Trent McDonald <trent@mcdonalddatasciences.com>
Diff between Rdistance versions 4.0.3 dated 2025-03-29 and 4.0.5 dated 2025-04-10
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 24 ++++++++++++++++++++---- R/RdistDf.R | 35 ++++++++++++++++++++++++++++------- R/predDensity.R | 6 +++++- man/RdistDf.Rd | 8 ++++---- 6 files changed, 66 insertions(+), 25 deletions(-)
Title: Search for POIs using ArcGIS 'Places Service'
Description: The ArcGIS 'Places service' is a ready-to-use location
service that can search for businesses and geographic locations around
the world. It allows you to find, locate, and discover detailed
information about each place. Query for places near a point, within a
bounding box, filter based on categories, or provide search text.
'arcgisplaces' integrates with 'sf' for out of the box compatibility
with other spatial libraries. Learn more in the 'Places service' API reference <https://developers.arcgis.com/rest/places/>.
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcgisplaces versions 0.1.1 dated 2025-01-15 and 0.1.2 dated 2025-04-10
DESCRIPTION | 8 MD5 | 19 - configure | 15 - configure.win | 15 - src/Makevars.in | 18 - src/Makevars.win.in | 25 - src/rust/Cargo.lock | 627 +++++++++++++++++++++++++++++++------------------ src/rust/Cargo.toml | 13 - src/rust/vendor.tar.xz |binary tools/config.R |only tools/msrv.R | 4 11 files changed, 440 insertions(+), 304 deletions(-)
Title: Execute 'SQL' Scripts in 'R' Containing Multiple Queries
Description: The nature of working with structured query language ('SQL') scripts
efficiently often requires the creation of temporary tables and there
are few clean and simple 'R' 'SQL' execution approaches that allow
you to complete this kind of work with the 'R' environment. This
package seeks to give 'SQL' implementations in 'R' a little love
by deploying functions that allow you to deploy complex 'SQL'
scripts within a typical 'R' workflow.
Author: Kerns Sam [aut, cre]
Maintainer: Kerns Sam <samwkerns@gmail.com>
Diff between SQLove versions 0.0.4 dated 2023-11-13 and 1.0.1 dated 2025-04-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/dbGetMultiQuery.R | 23 ++++++++++++++++++++--- R/dbSendMultiUpdate.R | 3 +++ inst/doc/SQLove.html | 4 ++-- 6 files changed, 37 insertions(+), 13 deletions(-)
Title: Truncated Exponential Family
Description: Handles truncated members from the exponential family of
probability distributions. Contains functions such as rtruncnorm() and
dtruncpois(), which are truncated versions of rnorm() and dpois() from the
stats package that also offer richer output containing, for example, the
distribution parameters. It also provides functions to retrieve the original
distribution parameters from a truncated sample by maximum-likelihood
estimation.
Author: Rene Holst [aut],
Waldir Leoncio [cre, aut]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between TruncExpFam versions 1.2.0 dated 2024-09-26 and 1.2.1 dated 2025-04-10
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/Sampling_and_ML_estimation.R | 2 +- inst/doc/Sampling_and_ML_estimation.html | 2 +- tests/testthat/test-qtrunc-truncated-a.R | 2 +- 7 files changed, 18 insertions(+), 13 deletions(-)
Title: Pre- And Post-Processing in Bayesian Evolutionary Analyses
Description: Functions are provided for prior specification in divergence time
estimation using fossils as well as other kinds of data. It
provides tools for interacting with the input and output of Bayesian
platforms in evolutionary biology such as 'BEAST2', 'MrBayes', 'RevBayes',
or 'MCMCTree'.
It Implements a simple measure similarity between probability
density functions for comparing prior and
posterior Bayesian densities, as well as code for calculating the
combination of distributions using conflation of Hill (2008). Functions for estimating the
origination time in collections of distributions using the x-intercept (e.g., Draper and Smith, 1998) and
stratigraphic intervals (Marshall 2010) are also available.
Hill, T. 2008. "Conflations of probability distributions". Transactions of the American Mathematical Society, 363:3351-3372. <doi:10.48550/arXiv.0808.1808>,
Draper, N. R. and Smith, H. 1998. "Applied Regression Analysis". 1--706. Wiley Interscience, New York. <DOI:10.1002/978111 [...truncated...]
Author: Gustavo A. Ballen [aut, cre],
Sandra Reinales [aut]
Maintainer: Gustavo A. Ballen <gustavo.a.ballen@gmail.com>
Diff between tbea versions 1.5.0 dated 2024-07-01 and 1.6.1 dated 2025-04-10
DESCRIPTION | 6 +-- MD5 | 19 +++++----- NAMESPACE | 2 + R/conflate.R | 82 ++++++++++++++++++++++++++++++++++++++++++++- README.md | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/intro.html | 13 +++---- inst/doc/whyInitVals.html | 25 +++++++------ man/conflate.Rd | 2 - man/quantile_conflation.Rd |only 11 files changed, 118 insertions(+), 32 deletions(-)
Title: Sample Size Calculation in Reversible Catalytic Models
Description: Sample size and confidence interval calculations in reversible catalytic models, with applications in malaria research. Further details can be found in the paper by Sepúlveda and Drakeley (2015, <doi:10.1186/s12936-015-0661-z>).
Author: Marcia Graca [aut, cre],
Fernanda Diamantino [aut, ths],
Nuno Sepulveda [aut, ctb, ths]
Maintainer: Marcia Graca <marcia_da_graca@hotmail.com>
Diff between RCMsize versions 1.0.0 dated 2024-12-02 and 1.0.1 dated 2025-04-10
DESCRIPTION | 17 ++++++++++------- MD5 | 12 ++++++------ NEWS.md | 16 +++++++++++----- inst/doc/Using_RCMsize_for_Malaria_Research.Rmd | 4 ---- inst/doc/Using_RCMsize_for_Malaria_Research.html | 5 ----- man/RCMsize-package.Rd | 11 ++++++++--- vignettes/Using_RCMsize_for_Malaria_Research.Rmd | 4 ---- 7 files changed, 35 insertions(+), 34 deletions(-)
Title: Personalised Synthetic Controls
Description: Allows the comparison of data cohorts (DC) against a Counter Factual Model (CFM) and measures the difference in terms of an efficacy parameter. Allows the application of Personalised Synthetic Controls.
Author: Richard Jackson [cre, aut, cph]
Maintainer: Richard Jackson <richJ23@liverpool.ac.uk>
Diff between psc versions 1.1.0 dated 2024-12-12 and 1.2.0 dated 2025-04-10
DESCRIPTION | 14 MD5 | 34 - R/dataComb.flexsurvreg.R | 49 +- R/dataComb.glm.R | 53 +- R/plot.psc.flexsurvreg.R | 2 R/pscEst.R | 3 R/pscEst.flexsurvreg.R | 13 R/pscEst.glm.R | 11 R/pscfit.R | 8 README.md | 6 build/vignette.rds |binary inst/doc/psc-vignette.R | 2 inst/doc/psc-vignette.html | 792 ++------------------------------------ man/figures/README-pressure-1.png |binary man/psc-package.Rd | 2 man/pscEst.Rd | 4 man/pscEst.flexsurvreg.Rd | 4 man/pscEst.glm.Rd | 4 18 files changed, 173 insertions(+), 828 deletions(-)
Title: Prior Diagnostics and Sensitivity Analysis
Description: Provides functions for prior and likelihood sensitivity analysis in Bayesian models. Currently it implements methods to determine the sensitivity of the posterior to power-scaling perturbations of the prior and likelihood.
Author: Noa Kallioinen [aut, cre, cph],
Topi Paananen [aut],
Paul-Christian Buerkner [aut],
Aki Vehtari [aut],
Frank Weber [ctb]
Maintainer: Noa Kallioinen <noa.kallioinen@aalto.fi>
Diff between priorsense versions 1.0.4 dated 2024-11-01 and 1.1.0 dated 2025-04-10
priorsense-1.0.4/priorsense/inst/doc/powerscaling.Rmd |only priorsense-1.0.4/priorsense/man/figures/README-dens_plot-1.png |only priorsense-1.0.4/priorsense/man/figures/README-ecdf_plot-1.png |only priorsense-1.0.4/priorsense/man/figures/README-quants_plot-1.png |only priorsense-1.0.4/priorsense/man/measure_divergence.Rd |only priorsense-1.0.4/priorsense/man/scaled_log_ratio.Rd |only priorsense-1.0.4/priorsense/man/weighted_quantities.Rd |only priorsense-1.0.4/priorsense/man/weighted_summary_measures.Rd |only priorsense-1.0.4/priorsense/vignettes/powerscaling.Rmd |only priorsense-1.1.0/priorsense/DESCRIPTION | 26 priorsense-1.1.0/priorsense/MD5 | 111 +- priorsense-1.1.0/priorsense/NAMESPACE | 6 priorsense-1.1.0/priorsense/NEWS.md | 9 priorsense-1.1.0/priorsense/R/additional_divergence_measures.R | 122 +- priorsense-1.1.0/priorsense/R/cjs.R | 48 priorsense-1.1.0/priorsense/R/create_priorsense_data.R | 66 + priorsense-1.1.0/priorsense/R/cumulative_plot.R | 38 priorsense-1.1.0/priorsense/R/example_powerscale_model.R | 1 priorsense-1.1.0/priorsense/R/find_alpha_threshold.R | 28 priorsense-1.1.0/priorsense/R/ggplot_theme.R | 4 priorsense-1.1.0/priorsense/R/helpers.R | 74 - priorsense-1.1.0/priorsense/R/log_prior_draws.R | 14 priorsense-1.1.0/priorsense/R/measure_divergence.R | 1 priorsense-1.1.0/priorsense/R/plots.R | 409 +++++-- priorsense-1.1.0/priorsense/R/powerscale.R | 91 + priorsense-1.1.0/priorsense/R/powerscale_derivative.R | 4 priorsense-1.1.0/priorsense/R/powerscale_gradients.R | 31 priorsense-1.1.0/priorsense/R/powerscale_sensitivity.R | 19 priorsense-1.1.0/priorsense/R/powerscale_sequence.R | 43 priorsense-1.1.0/priorsense/R/print.R | 27 priorsense-1.1.0/priorsense/R/priorsense-package.R | 27 priorsense-1.1.0/priorsense/R/scale_draws.R | 7 priorsense-1.1.0/priorsense/R/scaled_log_ratio.R | 11 priorsense-1.1.0/priorsense/R/srr-stats-standards.R |only priorsense-1.1.0/priorsense/R/summarise_draws.R | 1 priorsense-1.1.0/priorsense/R/weighted_quantities.R | 78 + priorsense-1.1.0/priorsense/R/whiten_draws.R | 6 priorsense-1.1.0/priorsense/README.md | 41 priorsense-1.1.0/priorsense/build/vignette.rds |binary priorsense-1.1.0/priorsense/inst/doc/powerscaling.R | 64 - priorsense-1.1.0/priorsense/inst/doc/powerscaling.html | 546 +++------- priorsense-1.1.0/priorsense/inst/doc/powerscaling.qmd |only priorsense-1.1.0/priorsense/inst/doc/priorsense_with_jags.R |only priorsense-1.1.0/priorsense/inst/doc/priorsense_with_jags.html |only priorsense-1.1.0/priorsense/inst/doc/priorsense_with_jags.qmd |only priorsense-1.1.0/priorsense/inst/logo/logo.R | 19 priorsense-1.1.0/priorsense/man/cjs_dist.Rd | 15 priorsense-1.1.0/priorsense/man/create-priorsense-data.Rd | 19 priorsense-1.1.0/priorsense/man/figures/powerscale-plot_dens-1.png |only priorsense-1.1.0/priorsense/man/figures/powerscale_plot_ecdf-1.png |only priorsense-1.1.0/priorsense/man/figures/powerscale_plot_quantities-1.png |only priorsense-1.1.0/priorsense/man/powerscale-gradients.Rd | 16 priorsense-1.1.0/priorsense/man/powerscale-overview.Rd | 32 priorsense-1.1.0/priorsense/man/powerscale-sensitivity.Rd | 23 priorsense-1.1.0/priorsense/man/powerscale_derivative.Rd | 4 priorsense-1.1.0/priorsense/man/powerscale_plots.Rd | 15 priorsense-1.1.0/priorsense/man/priorsense-package.Rd | 13 priorsense-1.1.0/priorsense/tests/testthat/test_cjs.R | 11 priorsense-1.1.0/priorsense/tests/testthat/test_deriv.R | 2 priorsense-1.1.0/priorsense/tests/testthat/test_div_measures.R |only priorsense-1.1.0/priorsense/tests/testthat/test_plots.R | 25 priorsense-1.1.0/priorsense/tests/testthat/test_powerscale.R | 73 + priorsense-1.1.0/priorsense/tests/testthat/test_print.R |only priorsense-1.1.0/priorsense/tests/testthat/test_rstan.R | 5 priorsense-1.1.0/priorsense/tests/testthat/test_scale_draws.R |only priorsense-1.1.0/priorsense/tests/testthat/test_whiten_draws.R |only priorsense-1.1.0/priorsense/vignettes/powerscaling.qmd |only priorsense-1.1.0/priorsense/vignettes/priorsense_with_jags.qmd |only 68 files changed, 1376 insertions(+), 849 deletions(-)
Title: Interface for 'Google Gemini' API
Description: Provides a comprehensive interface for Google Gemini API,
enabling users to access and utilize Gemini Large Language Model (LLM) functionalities directly from R.
This package facilitates seamless integration with Google Gemini, allowing for advanced language processing,
text generation, and other AI-driven capabilities within the R environment.
For more information, please visit <https://ai.google.dev/docs/gemini_api_overview>.
Author: Jinhwan Kim [aut, cre, cph] ,
Maciej Nasinski [ctb]
Maintainer: Jinhwan Kim <hwanistic@gmail.com>
Diff between gemini.R versions 0.11.0 dated 2025-03-29 and 0.12.0 dated 2025-04-10
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++++-------- NAMESPACE | 4 ++++ NEWS.md | 6 +++++- R/countTokens.R | 4 ++-- R/gemini.R | 6 +++--- R/gemini_search.R |only R/gemini_searchR.R |only R/gen_image.R | 24 +++++++++++++----------- R/setEnv.R | 24 ++++++++++++------------ man/countTokens.Rd | 4 ++-- man/gemini_search.Rd |only man/gemini_searchR.Rd |only 13 files changed, 56 insertions(+), 42 deletions(-)
Title: Plotting for Bayesian Models
Description: Plotting functions for posterior analysis, MCMC diagnostics,
prior and posterior predictive checks, and other visualizations
to support the applied Bayesian workflow advocated in
Gabry, Simpson, Vehtari, Betancourt, and Gelman (2019) <doi:10.1111/rssa.12378>.
The package is designed not only to provide convenient functionality
for users, but also a common set of functions that can be easily used by
developers working on a variety of R packages for Bayesian modeling,
particularly (but not exclusively) packages interfacing with 'Stan'.
Author: Jonah Gabry [aut, cre],
Tristan Mahr [aut],
Paul-Christian Buerkner [ctb],
Martin Modrak [ctb],
Malcolm Barrett [ctb],
Frank Weber [ctb],
Eduardo Coronado Sroka [ctb],
Teemu Sailynoja [ctb],
Aki Vehtari [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between bayesplot versions 1.11.1 dated 2024-02-15 and 1.12.0 dated 2025-04-10
DESCRIPTION | 12 - MD5 | 107 +++++------ NEWS.md | 14 + R/available-module-functions.R | 3 R/mcmc-diagnostics.R | 9 R/mcmc-distributions.R | 2 R/mcmc-overview.R | 2 R/mcmc-scatterplots.R | 2 R/mcmc-traces.R | 17 + R/ppc-discrete.R | 1 R/ppc-distributions.R | 4 R/ppc-errors.R | 2 R/ppc-test-statistics.R | 36 ++- R/ppd-distributions.R | 2 build/vignette.rds |binary inst/doc/graphical-ppcs.R | 6 inst/doc/graphical-ppcs.html | 35 +-- inst/doc/plotting-mcmc-draws.R | 38 ++-- inst/doc/plotting-mcmc-draws.Rmd | 36 +-- inst/doc/plotting-mcmc-draws.html | 60 +++--- inst/doc/visual-mcmc-diagnostics.R | 32 +-- inst/doc/visual-mcmc-diagnostics.Rmd | 38 ++-- inst/doc/visual-mcmc-diagnostics.html | 222 +++++++++++------------- man/MCMC-combos.Rd | 2 man/MCMC-diagnostics.Rd | 2 man/MCMC-distributions.Rd | 2 man/MCMC-intervals.Rd | 2 man/MCMC-overview.Rd | 2 man/MCMC-parcoord.Rd | 2 man/MCMC-recover.Rd | 2 man/MCMC-scatterplots.Rd | 4 man/MCMC-traces.Rd | 2 man/PPC-test-statistics.Rd | 17 + tests/testthat/data-for-mcmc-tests.R | 7 tests/testthat/helper.R |only tests/testthat/test-aesthetics.R | 1 tests/testthat/test-available_ppc.R | 1 tests/testthat/test-mcmc-combo.R | 3 tests/testthat/test-mcmc-diagnostics.R | 17 + tests/testthat/test-mcmc-distributions.R | 6 tests/testthat/test-mcmc-intervals.R | 3 tests/testthat/test-mcmc-nuts.R | 5 tests/testthat/test-mcmc-recover.R | 3 tests/testthat/test-mcmc-scatter-and-parcoord.R | 4 tests/testthat/test-mcmc-traces.R | 18 + tests/testthat/test-ppc-censoring.R | 2 tests/testthat/test-ppc-discrete.R | 11 - tests/testthat/test-ppc-distributions.R | 13 + tests/testthat/test-ppc-errors.R | 19 ++ tests/testthat/test-ppc-intervals.R | 4 tests/testthat/test-ppc-loo.R | 4 tests/testthat/test-ppc-scatterplots.R | 3 tests/testthat/test-ppc-test-statistics.R | 35 +++ vignettes/plotting-mcmc-draws.Rmd | 36 +-- vignettes/visual-mcmc-diagnostics.Rmd | 38 ++-- 55 files changed, 577 insertions(+), 373 deletions(-)
Title: Wrapper for 'SUNDIALS' Solving ODE and Sensitivity Problem
Description: Wrapper for widely used 'SUNDIALS' software (SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers) and more precisely to its 'CVODES' solver. It is aiming to solve ordinary differential equations (ODE) and optionally pending forward sensitivity problem. The wrapper is made 'R' friendly by allowing to pass custom parameters to user's callback functions. Such functions can be both written in 'R' and in 'C++' ('RcppArmadillo' flavor). In case of 'C++', performance is greatly improved so this option is highly advisable when performance matters. If provided, Jacobian matrix can be calculated either in dense or sparse format. In the latter case 'rmumps' package is used to solve corresponding linear systems. Root finding and pending event management are optional and can be specified as 'R' or 'C++' functions too. This makes them a very flexible tool for controlling the ODE system during the time course simulation. 'SUNDIALS' library was published in Hindmarsh et al. (2005) <doi:1 [...truncated...]
Author: Serguei Sokol [cre, aut],
Carol S. Woodward [ctb],
Daniel R. Reynolds [ctb],
Alan C. Hindmarsh [ctb],
David J. Gardner [ctb],
Cody J. Balos [ctb],
Radu Serban [ctb],
Scott D. Cohen [ctb],
Peter N. Brown [ctb],
George Byrne [ctb],
Allan G. Taylor [ctb [...truncated...]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between r2sundials versions 6.5.0-5 dated 2024-07-22 and 7.2.1-3 dated 2025-04-10
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r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_hip_kernels.hip.hpp | 253 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_iterative.c | 730 - r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_iterative_impl.h | 15 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_lapack_defs.h | 136 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_lapack_defs.h.in |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_linearsolver.c | 191 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_logger.c | 459 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_logger_impl.h | 149 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_macros.h |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_math.c | 128 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_matrix.c | 125 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_memory.c | 260 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_nonlinearsolver.c | 172 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_nvector.c | 809 - r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_nvector_senswrapper.c | 344 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_profiler.c | 463 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_reductions.hpp | 33 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_stepper.c |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_stepper_impl.h |only r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_sycl.h | 80 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_utils.h | 78 r2sundials-7.2.1-3/r2sundials/src/lib/sundials/sundials_version.c | 35 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/band/sunlinsol_band.c | 172 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/cusolversp/sunlinsol_cusolversp_batchqr.cu | 168 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/dense/sunlinsol_dense.c | 148 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/lapackband/sunlinsol_lapackband.c | 181 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/lapackdense/sunlinsol_lapackdense.c | 165 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/magmadense/sunlinsol_magmadense.cpp | 283 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/onemkldense/sunlinsol_onemkldense.cpp | 366 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/pcg/sunlinsol_pcg.c | 601 r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/spbcgs/sunlinsol_spbcgs.c | 824 - r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/spfgmr/sunlinsol_spfgmr.c | 751 - r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/spgmr/sunlinsol_spgmr.c | 855 - r2sundials-7.2.1-3/r2sundials/src/lib/sunlinsol/sptfqmr/sunlinsol_sptfqmr.c | 1147 - r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/band/sunmatrix_band.c | 447 r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/cusparse/cusparse_kernels.cuh | 225 r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/cusparse/sunmatrix_cusparse.cu | 904 - r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/dense/sunmatrix_dense.c | 244 r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/magmadense/dense_cuda_kernels.cuh | 127 r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/magmadense/dense_hip_kernels.hip.hpp | 129 r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/magmadense/sunmatrix_magmadense.cpp | 547 r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/onemkldense/sunmatrix_onemkldense.cpp | 450 r2sundials-7.2.1-3/r2sundials/src/lib/sunmatrix/sparse/sunmatrix_sparse.c | 1152 - r2sundials-7.2.1-3/r2sundials/src/lib/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.c | 698 - r2sundials-7.2.1-3/r2sundials/src/lib/sunnonlinsol/newton/sunnonlinsol_newton.c | 391 r2sundials-7.2.1-3/r2sundials/src/r2sundials.cpp | 33 r2sundials-7.2.1-3/r2sundials/src/sunlinsol_rmumps.cpp | 23 r2sundials-7.2.1-3/r2sundials/tests/RUnit.R | 1 218 files changed, 27008 insertions(+), 25161 deletions(-)
Title: 'WebSocket' Client Library
Description: Provides a 'WebSocket' client interface for R.
'WebSocket' is a protocol for low-overhead real-time communication:
<https://en.wikipedia.org/wiki/WebSocket>.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
Alan Dipert [aut],
Barbara Borges [aut],
Posit, PBC [cph],
Peter Thorson [ctb, cph] ,
Rene Nyffenegger [ctb, cph] ,
Micael Hildenborg [ctb, cph] ,
Aladdin Enterprises [cph] ,
Bjoern Hoehrmann [ctb, cph]
Maintainer: Winston Chang <winston@posit.co>
Diff between websocket versions 1.4.2 dated 2024-07-22 and 1.4.4 dated 2025-04-10
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 10 +++++++++- build/vignette.rds |binary cleanup | 1 - inst/doc/overview.R | 50 +++++++++++++++++++++++++------------------------- src/Makevars.in | 2 +- src/Makevars.ucrt | 9 +++++++-- 8 files changed, 52 insertions(+), 40 deletions(-)
Title: Get Executing Script's Path
Description: Determine the path of the executing script. Compatible
with several popular GUIs: 'Rgui', 'RStudio', 'Positron',
'VSCode', 'Jupyter', 'Emacs', and 'Rscript' (shell). Compatible
with several functions and packages: 'source()',
'sys.source()', 'debugSource()' in 'RStudio',
'compiler::loadcmp()', 'utils::Sweave()', 'box::use()',
'knitr::knit()', 'plumber::plumb()', 'shiny::runApp()',
'package:targets', and 'testthat::source_file()'.
Author: Iris Simmons [aut, cre]
Maintainer: Iris Simmons <ikwsimmo@gmail.com>
Diff between this.path versions 2.6.0 dated 2024-12-18 and 2.7.0 dated 2025-04-10
DESCRIPTION | 8 LICENSE | 2 MD5 | 70 ++--- NAMESPACE | 45 +-- NEWS | 23 + R/defunct.R | 10 R/files.R | 30 +- R/make_fix_funs.R | 75 ++++-- R/setsyspath.R | 12 - R/zzz.R | 40 +-- README.md | 16 + build/stage23.rdb |binary build/this.path.pdf |binary inst/NEWS.in.Rd | 26 ++ inst/doc/NEWS.1 | 2 man/basename2.Rd | 10 man/ext.Rd | 18 - man/make_fix_funs.Rd | 14 - man/set.sys.path.Rd | 7 man/this.path-defunct.Rd | 10 src/0.c | 2 src/backports.c | 2 src/backports.h | 44 +++ src/basename2.c | 54 ++-- src/ext.c | 101 ++++---- src/files.c | 44 ++- src/files.h | 14 - src/ns-hooks.c | 14 + src/ns-hooks.h | 3 src/pathjoin.c | 563 ++++++++++++++++++++++++++++++----------------- src/pathsplit.c | 106 +++++--- src/promises.c | 14 - src/setsyspath.c | 11 src/startup.c | 6 src/thispathdefn.h | 93 ++++++- tests/ext-tests.R | 8 36 files changed, 972 insertions(+), 525 deletions(-)
Title: Testing for Shiny Applications
Description: Automated unit testing of Shiny applications through a headless 'Chromium' browser.
Author: Barret Schloerke [cre, aut] ,
Posit Software, PBC [cph, fnd],
Winston Chang [ctb] ,
Gabor Csardi [ctb] ,
Hadley Wickham [ctb] ,
Mango Solutions [cph, ccp]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between shinytest2 versions 0.3.2 dated 2024-04-28 and 0.4.0 dated 2025-04-10
DESCRIPTION | 14 - MD5 | 81 +++--- NAMESPACE | 15 - NEWS.md | 21 + R/app-driver-expect-download.R | 37 +- R/app-driver-expect-js.R | 65 +++-- R/app-driver-expect-screenshot.R | 106 +++++--- R/app-driver-expect-values.R | 145 +++++++---- R/app-driver-initialize.R | 131 +++++++--- R/app-driver-start.R | 11 R/app-driver.R | 310 ++++++++++++++++-------- R/compare-screenshot-threshold.R | 55 ++-- R/expect-snapshot.R | 38 +- R/shinytest2-logs.R | 8 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/in-depth.R | 210 ++++++++-------- inst/doc/in-depth.html | 8 inst/doc/robust.Rmd | 4 inst/doc/robust.html | 10 inst/doc/shinytest2.R | 54 ++-- inst/doc/shinytest2.html | 12 inst/doc/use-application-audit.html | 8 inst/doc/use-ci.html | 4 inst/doc/use-package.R | 78 +++--- inst/doc/use-package.Rmd | 19 + inst/doc/use-package.html | 32 +- inst/doc/using-monkey-testing.html | 16 - inst/doc/z-migration.html | 4 inst/doc/zzz-faq.R | 58 ++-- inst/doc/zzz-faq.html | 4 inst/internal/js/shiny-tracer.js | 8 man/AppDriver.Rd | 120 +++++---- man/compare_screenshot_threshold.Rd | 43 ++- man/figures/logo.svg | 167 ++++-------- tests/testthat/_snaps |only tests/testthat/test-app-expect-file-transform.R |only tests/testthat/test-image-diff.R | 49 +++ tests/testthat/test-migration-transformation.R | 4 vignettes/robust.Rmd | 4 vignettes/use-package.Rmd | 19 + 41 files changed, 1199 insertions(+), 774 deletions(-)
Title: Graphic Devices Based on AGG
Description: Anti-Grain Geometry (AGG) is a high-quality and
high-performance 2D drawing library. The 'ragg' package provides a set
of graphic devices based on AGG to use as alternative to the raster
devices provided through the 'grDevices' package.
Author: Thomas Lin Pedersen [cre, aut]
,
Maxim Shemanarev [aut, cph] ,
Tony Juricic [ctb, cph] ,
Milan Marusinec [ctb, cph] ,
Spencer Garrett [ctb] ,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between ragg versions 1.3.3 dated 2024-09-11 and 1.4.0 dated 2025-04-10
DESCRIPTION | 9 MD5 | 39 +-- NAMESPACE | 1 NEWS.md | 8 R/aaa.R | 8 R/agg_dev.R | 280 ++++++++++++++---------- R/ragg-package.R | 6 README.md | 1 configure | 2 man/agg_record.Rd |only src/AggDevice.h | 435 +++++++++++++++++++------------------- src/AggDeviceRecord.h |only src/AggDeviceTiff.h | 75 ++++-- src/Makevars.win | 31 +- src/agg/include/agg_dda_line.h | 14 - src/agg/include/agg_pixfmt_rgba.h | 30 ++ src/init.cpp | 3 src/init_device.h | 203 ++++++++++------- src/ragg.h | 22 + src/record_dev.cpp |only src/tiff_dev.cpp | 4 tests/testthat/test-tiff.R | 19 + 22 files changed, 681 insertions(+), 509 deletions(-)
Title: Detect Heatwaves and Cold-Spells
Description: The different methods for defining, detecting, and categorising the extreme events
known as heatwaves or cold-spells, as first proposed in Hobday et al. (2016) <doi: 10.1016/j.pocean.2015.12.014>
and Hobday et al. (2018) <https://www.jstor.org/stable/26542662>. The functions in this package work on both air
and water temperature data. These detection algorithms may be used on non-temperature data as well.
Author: Robert W. Schlegel [aut, cre, ctb]
,
Albertus J. Smit [aut, ctb]
Maintainer: Robert W. Schlegel <robwschlegel@gmail.com>
Diff between heatwaveR versions 0.4.6 dated 2021-10-27 and 0.5.4 dated 2025-04-10
heatwaveR-0.4.6/heatwaveR/R/make_whole.R |only heatwaveR-0.4.6/heatwaveR/man/make_whole.Rd |only heatwaveR-0.4.6/heatwaveR/src/Makevars.win |only heatwaveR-0.4.6/heatwaveR/tests/testthat/test-make_whole.R |only heatwaveR-0.5.4/heatwaveR/DESCRIPTION | 18 heatwaveR-0.5.4/heatwaveR/MD5 | 188 +- heatwaveR-0.5.4/heatwaveR/NAMESPACE | 11 heatwaveR-0.5.4/heatwaveR/NEWS.md | 174 + heatwaveR-0.5.4/heatwaveR/R/block_average.R | 117 - heatwaveR-0.5.4/heatwaveR/R/category.R | 273 +- heatwaveR-0.5.4/heatwaveR/R/clim_calc.R | 32 heatwaveR-0.5.4/heatwaveR/R/clim_spread.R | 40 heatwaveR-0.5.4/heatwaveR/R/detect_event.R | 363 ++- heatwaveR-0.5.4/heatwaveR/R/detect_event3.R |only heatwaveR-0.5.4/heatwaveR/R/exceedance.R | 322 +-- heatwaveR-0.5.4/heatwaveR/R/geoms.R | 22 heatwaveR-0.5.4/heatwaveR/R/graph_functions.R | 235 +- heatwaveR-0.5.4/heatwaveR/R/make_whole_fast.R | 82 heatwaveR-0.5.4/heatwaveR/R/na_interp.R | 8 heatwaveR-0.5.4/heatwaveR/R/proto_event.R | 58 heatwaveR-0.5.4/heatwaveR/R/proto_event3.R |only heatwaveR-0.5.4/heatwaveR/R/smooth_percentile.R | 44 heatwaveR-0.5.4/heatwaveR/R/sst_med.R | 5 heatwaveR-0.5.4/heatwaveR/R/sst_nw_atl.R | 5 heatwaveR-0.5.4/heatwaveR/R/sst_wa.R | 5 heatwaveR-0.5.4/heatwaveR/R/ts2clm.R | 262 +- heatwaveR-0.5.4/heatwaveR/R/ts2clm3.R |only heatwaveR-0.5.4/heatwaveR/README.md | 72 heatwaveR-0.5.4/heatwaveR/build/partial.rdb |only heatwaveR-0.5.4/heatwaveR/build/vignette.rds |binary heatwaveR-0.5.4/heatwaveR/data/sst_Med.rda |binary heatwaveR-0.5.4/heatwaveR/data/sst_NW_Atl.rda |binary heatwaveR-0.5.4/heatwaveR/data/sst_WA.rda |binary heatwaveR-0.5.4/heatwaveR/inst/CITATION | 2 heatwaveR-0.5.4/heatwaveR/inst/doc/Download_SST_v2.R |only heatwaveR-0.5.4/heatwaveR/inst/doc/Download_SST_v2.Rmd |only heatwaveR-0.5.4/heatwaveR/inst/doc/Download_SST_v2.html |only heatwaveR-0.5.4/heatwaveR/inst/doc/MHW_metric_trends.R |only heatwaveR-0.5.4/heatwaveR/inst/doc/MHW_metric_trends.Rmd |only heatwaveR-0.5.4/heatwaveR/inst/doc/MHW_metric_trends.html |only heatwaveR-0.5.4/heatwaveR/inst/doc/MHW_to_nc.R | 272 +- heatwaveR-0.5.4/heatwaveR/inst/doc/MHW_to_nc.html | 639 ++++-- heatwaveR-0.5.4/heatwaveR/inst/doc/OISST_preparation.R | 266 +- heatwaveR-0.5.4/heatwaveR/inst/doc/OISST_preparation.Rmd | 130 - heatwaveR-0.5.4/heatwaveR/inst/doc/OISST_preparation.html | 800 ++++++-- heatwaveR-0.5.4/heatwaveR/inst/doc/complex_clims.R | 12 heatwaveR-0.5.4/heatwaveR/inst/doc/complex_clims.Rmd | 12 heatwaveR-0.5.4/heatwaveR/inst/doc/complex_clims.html | 869 ++++++--- heatwaveR-0.5.4/heatwaveR/inst/doc/detection_and_visualisation.R | 222 +- heatwaveR-0.5.4/heatwaveR/inst/doc/detection_and_visualisation.Rmd | 8 heatwaveR-0.5.4/heatwaveR/inst/doc/detection_and_visualisation.html | 937 ++++++---- heatwaveR-0.5.4/heatwaveR/inst/doc/event_categories.R | 29 heatwaveR-0.5.4/heatwaveR/inst/doc/event_categories.Rmd | 35 heatwaveR-0.5.4/heatwaveR/inst/doc/event_categories.html | 818 +++++--- heatwaveR-0.5.4/heatwaveR/inst/doc/exceedance.html | 508 +++-- heatwaveR-0.5.4/heatwaveR/inst/doc/gridded_event_detection.R | 220 +- heatwaveR-0.5.4/heatwaveR/inst/doc/gridded_event_detection.Rmd | 2 heatwaveR-0.5.4/heatwaveR/inst/doc/gridded_event_detection.html | 691 +++++-- heatwaveR-0.5.4/heatwaveR/inst/doc/internal_workflow.R |only heatwaveR-0.5.4/heatwaveR/inst/doc/internal_workflow.Rmd |only heatwaveR-0.5.4/heatwaveR/inst/doc/internal_workflow.html |only heatwaveR-0.5.4/heatwaveR/man/block_average.Rd | 9 heatwaveR-0.5.4/heatwaveR/man/category.Rd | 61 heatwaveR-0.5.4/heatwaveR/man/clim_calc.Rd | 3 heatwaveR-0.5.4/heatwaveR/man/clim_spread.Rd | 5 heatwaveR-0.5.4/heatwaveR/man/detect_event.Rd | 40 heatwaveR-0.5.4/heatwaveR/man/detect_event3.Rd |only heatwaveR-0.5.4/heatwaveR/man/event_line.Rd | 40 heatwaveR-0.5.4/heatwaveR/man/exceedance.Rd | 35 heatwaveR-0.5.4/heatwaveR/man/geom_flame.Rd | 12 heatwaveR-0.5.4/heatwaveR/man/geom_lolli.Rd | 2 heatwaveR-0.5.4/heatwaveR/man/heatwaveR-package.Rd | 2 heatwaveR-0.5.4/heatwaveR/man/lolli_plot.Rd | 21 heatwaveR-0.5.4/heatwaveR/man/make_whole_fast.Rd | 25 heatwaveR-0.5.4/heatwaveR/man/na_interp.Rd | 7 heatwaveR-0.5.4/heatwaveR/man/proto_event.Rd | 1 heatwaveR-0.5.4/heatwaveR/man/proto_event3.Rd |only heatwaveR-0.5.4/heatwaveR/man/smooth_percentile.Rd | 3 heatwaveR-0.5.4/heatwaveR/man/sst_Med.Rd | 7 heatwaveR-0.5.4/heatwaveR/man/sst_NW_Atl.Rd | 7 heatwaveR-0.5.4/heatwaveR/man/sst_WA.Rd | 7 heatwaveR-0.5.4/heatwaveR/man/ts2clm.Rd | 64 heatwaveR-0.5.4/heatwaveR/man/ts2clm3.Rd |only heatwaveR-0.5.4/heatwaveR/src/Makevars | 2 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-block_average.R | 20 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-category.R | 90 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-clim_calc.R | 3 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-clim_spread.R | 4 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-detect_event.R | 110 - heatwaveR-0.5.4/heatwaveR/tests/testthat/test-detect_event3.R |only heatwaveR-0.5.4/heatwaveR/tests/testthat/test-exceedance.R | 78 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-graph_functions.R | 99 - heatwaveR-0.5.4/heatwaveR/tests/testthat/test-make_whole_fast.R | 4 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-na_interp.R | 8 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-proto_event.R | 20 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-proto_event3.R |only heatwaveR-0.5.4/heatwaveR/tests/testthat/test-smooth_percentile.R | 2 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-ts2clm.R | 86 heatwaveR-0.5.4/heatwaveR/tests/testthat/test-ts2clm3.R |only heatwaveR-0.5.4/heatwaveR/vignettes/Download_SST_v2.Rmd |only heatwaveR-0.5.4/heatwaveR/vignettes/MHW_metric_trends.Rmd |only heatwaveR-0.5.4/heatwaveR/vignettes/OISST_preparation.Rmd | 130 - heatwaveR-0.5.4/heatwaveR/vignettes/bibliography.bib | 106 + heatwaveR-0.5.4/heatwaveR/vignettes/complex_clims.Rmd | 12 heatwaveR-0.5.4/heatwaveR/vignettes/detection_and_visualisation.Rmd | 8 heatwaveR-0.5.4/heatwaveR/vignettes/event_categories.Rmd | 35 heatwaveR-0.5.4/heatwaveR/vignettes/gridded_event_detection.Rmd | 2 heatwaveR-0.5.4/heatwaveR/vignettes/internal_workflow.Rmd |only 108 files changed, 6517 insertions(+), 3461 deletions(-)
Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and
unified Future API for sequential and parallel processing of R
expression via futures. The simplest way to evaluate an expression
in parallel is to use `x %<-% { expression }` with `plan(multisession)`.
This package implements sequential, multicore, multisession, and
cluster futures. With these, R expressions can be evaluated on the
local machine, in parallel a set of local machines, or distributed
on a mix of local and remote machines.
Extensions to this package implement additional backends for
processing futures via compute cluster schedulers, etc.
Because of its unified API, there is no need to modify any code in order
switch from sequential on the local machine to, say, distributed
processing on a remote compute cluster.
Another strength of this package is that global variables and functions
are automatically identified and exported as needed, making it
straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.34.0 dated 2024-07-29 and 1.40.0 dated 2025-04-10
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2612 insertions(+), 1793 deletions(-)
Title: A 'ggplot2' Extension for Consistent Axis Alignment
Description: A 'ggplot2' extension offers various tools the creation of complex,
multi-plot visualizations. Built on the familiar grammar of graphics, it
provides intuitive tools to align and organize plots, making it ideal for
complex visualizations. It excels in multi-omics research—such as genomics
and microbiomes—by simplifying the visualization of intricate relationships
between datasets, for example, linking genes to pathways. Whether you need
to stack plots, arrange them around a central figure, or create a circular
layout, 'ggalign' delivers flexibility and accuracy with minimal effort.
Author: Yun Peng [aut, cre] ,
Shixiang Wang [aut] ,
Guangchuang Yu [ths]
Maintainer: Yun Peng <yunyunp96@163.com>
Diff between ggalign versions 1.0.0 dated 2025-03-15 and 1.0.1 dated 2025-04-10
ggalign-1.0.0/ggalign/R/geom-draw.R |only ggalign-1.0.0/ggalign/R/geom-gshape.R |only ggalign-1.0.0/ggalign/R/geom-pie.R |only ggalign-1.0.0/ggalign/R/geom-subrect.R |only ggalign-1.0.0/ggalign/R/geom-tile3d.R |only ggalign-1.0.0/ggalign/R/utils-grid.R |only ggalign-1.0.1/ggalign/DESCRIPTION | 29 - ggalign-1.0.1/ggalign/MD5 | 103 ++--- ggalign-1.0.1/ggalign/NAMESPACE | 7 ggalign-1.0.1/ggalign/NEWS.md | 8 ggalign-1.0.1/ggalign/R/align-.R | 4 ggalign-1.0.1/ggalign/R/alignpatch-.R | 42 +- ggalign-1.0.1/ggalign/R/alignpatch-align_plots.R | 12 ggalign-1.0.1/ggalign/R/alignpatch-alignpatches.R | 199 +++++++--- ggalign-1.0.1/ggalign/R/alignpatch-free-guide.R | 20 - ggalign-1.0.1/ggalign/R/alignpatch-guides.R | 35 + ggalign-1.0.1/ggalign/R/alignpatch-patch.R | 4 ggalign-1.0.1/ggalign/R/fortify-matrix-matrix.R | 3 ggalign-1.0.1/ggalign/R/ggfree.R | 2 ggalign-1.0.1/ggalign/R/ggmark.R | 2 ggalign-1.0.1/ggalign/R/ggplot-coord-circle.R | 46 +- ggalign-1.0.1/ggalign/R/ggplot-facet-sector.R | 24 - ggalign-1.0.1/ggalign/R/ggplot-geom-draw.R |only ggalign-1.0.1/ggalign/R/ggplot-geom-gshape.R |only ggalign-1.0.1/ggalign/R/ggplot-geom-pie.R |only ggalign-1.0.1/ggalign/R/ggplot-geom-subrect.R |only ggalign-1.0.1/ggalign/R/ggplot-geom-tile3d.R |only ggalign-1.0.1/ggalign/R/ggplot-helper.R | 44 +- ggalign-1.0.1/ggalign/R/ggplot-theme.R | 4 ggalign-1.0.1/ggalign/R/ggplot-utils.R | 23 - ggalign-1.0.1/ggalign/R/grid-grob-channel.R |only ggalign-1.0.1/ggalign/R/grid-utils.R |only ggalign-1.0.1/ggalign/R/import-standalone-pkg.R | 92 ++-- ggalign-1.0.1/ggalign/R/layout-align.R | 30 - ggalign-1.0.1/ggalign/R/layout-chain-circle-build.R | 23 - ggalign-1.0.1/ggalign/R/mark.R | 2 ggalign-1.0.1/ggalign/R/raster-magick.R | 39 + ggalign-1.0.1/ggalign/R/scheme-align.R | 6 ggalign-1.0.1/ggalign/R/utils-assert.R | 18 ggalign-1.0.1/ggalign/man/align_plots.Rd | 4 ggalign-1.0.1/ggalign/man/channelGrob.Rd |only ggalign-1.0.1/ggalign/man/coord_circle.Rd | 6 ggalign-1.0.1/ggalign/man/draw_key_gshape.Rd | 2 ggalign-1.0.1/ggalign/man/free.Rd | 6 ggalign-1.0.1/ggalign/man/geom_draw.Rd | 2 ggalign-1.0.1/ggalign/man/geom_gshape.Rd | 2 ggalign-1.0.1/ggalign/man/geom_pie.Rd | 2 ggalign-1.0.1/ggalign/man/geom_rect3d.Rd | 2 ggalign-1.0.1/ggalign/man/geom_subrect.Rd | 2 ggalign-1.0.1/ggalign/man/ggalign-package.Rd | 2 ggalign-1.0.1/ggalign/man/layout_design.Rd | 4 ggalign-1.0.1/ggalign/man/raster_magick.Rd | 35 - ggalign-1.0.1/ggalign/man/reexports.Rd | 2 ggalign-1.0.1/ggalign/man/scale_gshape_manual.Rd | 2 ggalign-1.0.1/ggalign/man/scheme_align.Rd | 4 ggalign-1.0.1/ggalign/tests/testthat/_snaps/alignpatch/collect-inside-guides.svg |only ggalign-1.0.1/ggalign/tests/testthat/_snaps/grid |only ggalign-1.0.1/ggalign/tests/testthat/_snaps/layout-heatmap/heatmap-hmanno-align-action-guides.svg | 4 ggalign-1.0.1/ggalign/tests/testthat/helper-setup.R | 23 - ggalign-1.0.1/ggalign/tests/testthat/test-alignpatch.R | 29 + ggalign-1.0.1/ggalign/tests/testthat/test-grid.R |only 61 files changed, 617 insertions(+), 337 deletions(-)
Title: Tools for Functional Response Analysis
Description: Tools to support sensible statistics for functional response analysis.
Author: Daniel Pritchard [aut, cre],
Daniel Barrios-O'Neill [ctb],
Helene Bovy [ctb],
Rachel Paterson [ctb]
Maintainer: Daniel Pritchard <daniel@pritchard.co>
Diff between frair versions 0.5.100 dated 2017-03-26 and 0.5.203 dated 2025-04-10
DESCRIPTION | 11 ++++++----- MD5 | 38 +++++++++++++++++++------------------- NAMESPACE | 1 + NEWS.md | 28 ++++++++++++++++++++++++---- man/fr_emdII.Rd | 4 ++-- man/fr_flexp.Rd | 7 +++---- man/fr_flexpnr.Rd | 6 +++--- man/fr_hassIII.Rd | 2 +- man/fr_hassIIInr.Rd | 4 ++-- man/fr_hollingsII.Rd | 2 +- man/fr_rogersII.Rd | 4 ++-- man/fr_typeI.Rd | 2 +- man/frair_boot.Rd | 1 + man/frair_boot_methods.Rd | 4 ++-- man/frair_compare.Rd | 3 ++- man/frair_fit.Rd | 2 +- man/frair_fit_methods.Rd | 1 + tests/testthat/test_flexpnr.R | 1 + tests/testthat/test_frair_fit.R | 1 + tests/testthat/test_typeI.R | 11 ++++++----- 20 files changed, 80 insertions(+), 53 deletions(-)
Title: S3 Infrastructure for Regular and Irregular Time Series (Z's
Ordered Observations)
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Author: Achim Zeileis [aut, cre] ,
Gabor Grothendieck [aut],
Jeffrey A. Ryan [aut],
Joshua M. Ulrich [ctb],
Felix Andrews [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between zoo versions 1.8-13 dated 2025-02-22 and 1.8-14 dated 2025-04-10
DESCRIPTION | 10 MD5 | 38 +- NEWS | 610 +++++++++++++++++++++++---------------------- R/ggplot2.zoo.R | 8 build/vignette.rds |binary inst/doc/msft2004.rda |only inst/doc/zoo-design.pdf |binary inst/doc/zoo-faq.pdf |binary inst/doc/zoo-quickref.R | 63 +--- inst/doc/zoo-quickref.Rnw | 72 +---- inst/doc/zoo-quickref.pdf |binary inst/doc/zoo-read.R | 59 ++-- inst/doc/zoo-read.Rnw | 16 + inst/doc/zoo-read.pdf |binary inst/doc/zoo.Rnw | 4 inst/doc/zoo.pdf |binary src/lag.c | 4 vignettes/.install_extras | 1 vignettes/msft2004.rda |only vignettes/zoo-quickref.Rnw | 72 +---- vignettes/zoo-read.Rnw | 16 + vignettes/zoo.Rnw | 4 22 files changed, 496 insertions(+), 481 deletions(-)
Title: Network Analysis for Omics Data
Description: Comprehensive network analysis package.
Calculate correlation network fastly, accelerate lots of analysis by parallel computing.
Support for multi-omics data, search sub-nets fluently.
Handle bigger data, more than 10,000 nodes in each omics.
Offer various layout method for multi-omics network and some interfaces to other software ('Gephi', 'Cytoscape', 'ggplot2'), easy to visualize.
Provide comprehensive topology indexes calculation, including ecological network stability.
Author: Chen Peng [aut, cre]
Maintainer: Chen Peng <pengchen2001@zju.edu.cn>
Diff between MetaNet versions 0.1.2 dated 2024-03-25 and 0.2.5 dated 2025-04-10
MetaNet-0.1.2/MetaNet/R/build.R |only MetaNet-0.1.2/MetaNet/R/calculate.R |only MetaNet-0.1.2/MetaNet/R/modules.R |only MetaNet-0.1.2/MetaNet/R/plot.R |only MetaNet-0.1.2/MetaNet/R/stability.R |only MetaNet-0.1.2/MetaNet/R/topological.R |only MetaNet-0.1.2/MetaNet/man/extract_sub_net.Rd |only MetaNet-0.1.2/MetaNet/man/input_corr.Rd |only MetaNet-0.2.5/MetaNet/DESCRIPTION | 13 - MetaNet-0.2.5/MetaNet/MD5 | 183 +++++++++--------- MetaNet-0.2.5/MetaNet/NAMESPACE | 24 ++ MetaNet-0.2.5/MetaNet/NEWS.md | 41 ++++ MetaNet-0.2.5/MetaNet/R/1.calculate.R |only MetaNet-0.2.5/MetaNet/R/2-1.build.R |only MetaNet-0.2.5/MetaNet/R/2-2.manipulate.R |only MetaNet-0.2.5/MetaNet/R/2-3.RMT.R |only MetaNet-0.2.5/MetaNet/R/3-1.layout.R |only MetaNet-0.2.5/MetaNet/R/3-2.shapes.R |only MetaNet-0.2.5/MetaNet/R/3-3.plot.R |only MetaNet-0.2.5/MetaNet/R/3-4.other_plot.R |only MetaNet-0.2.5/MetaNet/R/5.topological.R |only MetaNet-0.2.5/MetaNet/R/6.modules.R |only MetaNet-0.2.5/MetaNet/R/7.stability.R |only MetaNet-0.2.5/MetaNet/R/MetaNet-package.R | 11 - MetaNet-0.2.5/MetaNet/R/print.R | 59 +++++ MetaNet-0.2.5/MetaNet/R/utils-pipe.R | 34 +++ MetaNet-0.2.5/MetaNet/README.md | 10 MetaNet-0.2.5/MetaNet/data/c_net.rda |binary MetaNet-0.2.5/MetaNet/inst/doc/MetaNet.html | 7 MetaNet-0.2.5/MetaNet/man/Cohesion.Rd | 2 MetaNet-0.2.5/MetaNet/man/RMT_threshold.Rd | 2 MetaNet-0.2.5/MetaNet/man/anno_edge.Rd | 3 MetaNet-0.2.5/MetaNet/man/anno_vertex.Rd | 3 MetaNet-0.2.5/MetaNet/man/as.ggig.Rd | 3 MetaNet-0.2.5/MetaNet/man/as_arc.Rd | 6 MetaNet-0.2.5/MetaNet/man/as_circle_tree.Rd | 4 MetaNet-0.2.5/MetaNet/man/as_coors.Rd |only MetaNet-0.2.5/MetaNet/man/as_line.Rd | 4 MetaNet-0.2.5/MetaNet/man/as_multi_layer.Rd |only MetaNet-0.2.5/MetaNet/man/as_poly_sector.Rd |only MetaNet-0.2.5/MetaNet/man/as_polyarc.Rd | 4 MetaNet-0.2.5/MetaNet/man/as_polycircle.Rd | 6 MetaNet-0.2.5/MetaNet/man/as_polygon.Rd | 4 MetaNet-0.2.5/MetaNet/man/c_net_annotate.Rd | 3 MetaNet-0.2.5/MetaNet/man/c_net_build.Rd | 4 MetaNet-0.2.5/MetaNet/man/c_net_calculate.Rd | 6 MetaNet-0.2.5/MetaNet/man/c_net_filter.Rd | 3 MetaNet-0.2.5/MetaNet/man/c_net_from_edgelist.Rd | 8 MetaNet-0.2.5/MetaNet/man/c_net_layout.Rd | 7 MetaNet-0.2.5/MetaNet/man/c_net_load.Rd |only MetaNet-0.2.5/MetaNet/man/c_net_plot.Rd | 47 +++- MetaNet-0.2.5/MetaNet/man/c_net_save.Rd | 3 MetaNet-0.2.5/MetaNet/man/c_net_set.Rd | 7 MetaNet-0.2.5/MetaNet/man/c_net_stability.Rd | 2 MetaNet-0.2.5/MetaNet/man/c_net_union.Rd | 3 MetaNet-0.2.5/MetaNet/man/c_net_update.Rd | 17 + MetaNet-0.2.5/MetaNet/man/cal_sim.Rd | 12 - MetaNet-0.2.5/MetaNet/man/check_tabs.Rd | 2 MetaNet-0.2.5/MetaNet/man/clean_igraph.Rd | 2 MetaNet-0.2.5/MetaNet/man/clean_multi_edge_metanet.Rd |only MetaNet-0.2.5/MetaNet/man/compare_rand.Rd | 8 MetaNet-0.2.5/MetaNet/man/df2net_tree.Rd | 2 MetaNet-0.2.5/MetaNet/man/extract_sample_net.Rd |only MetaNet-0.2.5/MetaNet/man/fast_cor.Rd | 6 MetaNet-0.2.5/MetaNet/man/filter_n_module.Rd | 2 MetaNet-0.2.5/MetaNet/man/fit_power.Rd | 4 MetaNet-0.2.5/MetaNet/man/g_layout.Rd | 24 -- MetaNet-0.2.5/MetaNet/man/g_layout_nice.Rd |only MetaNet-0.2.5/MetaNet/man/g_layout_poly_sector.Rd |only MetaNet-0.2.5/MetaNet/man/g_layout_polygon.Rd | 23 ++ MetaNet-0.2.5/MetaNet/man/get_community.Rd | 2 MetaNet-0.2.5/MetaNet/man/get_e.Rd | 7 MetaNet-0.2.5/MetaNet/man/get_group_skeleton.Rd | 8 MetaNet-0.2.5/MetaNet/man/get_module.Rd | 2 MetaNet-0.2.5/MetaNet/man/get_module_eigen.Rd | 2 MetaNet-0.2.5/MetaNet/man/get_n.Rd | 7 MetaNet-0.2.5/MetaNet/man/get_v.Rd | 7 MetaNet-0.2.5/MetaNet/man/input_cytoscape.Rd |only MetaNet-0.2.5/MetaNet/man/input_gephi.Rd | 3 MetaNet-0.2.5/MetaNet/man/is_metanet.Rd | 3 MetaNet-0.2.5/MetaNet/man/links_stat.Rd | 35 +-- MetaNet-0.2.5/MetaNet/man/module_detect.Rd | 2 MetaNet-0.2.5/MetaNet/man/module_expression.Rd | 2 MetaNet-0.2.5/MetaNet/man/module_net.Rd | 2 MetaNet-0.2.5/MetaNet/man/multi_net_build.Rd | 2 MetaNet-0.2.5/MetaNet/man/nc.Rd | 4 MetaNet-0.2.5/MetaNet/man/netD3plot.Rd | 3 MetaNet-0.2.5/MetaNet/man/net_par.Rd | 13 - MetaNet-0.2.5/MetaNet/man/olympic_rings_net.Rd | 3 MetaNet-0.2.5/MetaNet/man/p.adjust.table.Rd | 4 MetaNet-0.2.5/MetaNet/man/plot.ggig.Rd | 20 + MetaNet-0.2.5/MetaNet/man/plot.metanet.Rd | 2 MetaNet-0.2.5/MetaNet/man/plot.rmt_res.Rd | 2 MetaNet-0.2.5/MetaNet/man/rand_net.Rd | 8 MetaNet-0.2.5/MetaNet/man/read_corr.Rd |only MetaNet-0.2.5/MetaNet/man/robust_test.Rd | 4 MetaNet-0.2.5/MetaNet/man/robustness.Rd | 2 MetaNet-0.2.5/MetaNet/man/save_corr.Rd |only MetaNet-0.2.5/MetaNet/man/smallworldness.Rd | 4 MetaNet-0.2.5/MetaNet/man/spatstat_layout.Rd |only MetaNet-0.2.5/MetaNet/man/summ_2col.Rd | 2 MetaNet-0.2.5/MetaNet/man/summary.corr.Rd |only MetaNet-0.2.5/MetaNet/man/summary_module.Rd | 2 MetaNet-0.2.5/MetaNet/man/to_module_net.Rd | 6 MetaNet-0.2.5/MetaNet/man/transform_coors.Rd |only MetaNet-0.2.5/MetaNet/man/twocol_edgelist.Rd | 3 MetaNet-0.2.5/MetaNet/man/venn_net.Rd | 3 MetaNet-0.2.5/MetaNet/man/vulnerability.Rd | 2 MetaNet-0.2.5/MetaNet/man/zp_analyse.Rd | 9 109 files changed, 533 insertions(+), 265 deletions(-)
Title: Expanded Replacement and Extension of the 'optim' Function
Description: Provides a replacement and extension of the optim()
function to call to several function minimization codes in R in a single
statement. These methods handle smooth, possibly box constrained functions
of several or many parameters. Note that function 'optimr()' was prepared to
simplify the incorporation of minimization codes going forward. Also implements some
utility codes and some extra solvers, including safeguarded Newton methods.
Many methods previously separate are now included here.
This is the version for CRAN.
Author: John C Nash [aut, cre],
Ravi Varadhan [aut],
Hans W Borchers [ctb],
Gabor Grothendieck [ctb]
Maintainer: John C Nash <profjcnash@gmail.com>
Diff between optimx versions 2024-12.2 dated 2024-12-10 and 2025-4.9 dated 2025-04-10
DESCRIPTION | 8 +- MD5 | 43 ++++++------ NAMESPACE | 2 NEWS | 19 +++++ R/ctrldefault.R | 1 R/kktchk.R | 67 ++++++++++--------- R/opm.R | 8 +- R/optimr.R | 20 ++++- R/optimr2opm.R | 124 +++++++++++++++++++----------------- R/pd_check.R |only build/vignette.rds |binary inst/doc/AddPracmaNM2optimx.pdf |binary inst/doc/ExplainGradMinR.pdf |binary inst/doc/Extend-optimx.pdf |binary inst/doc/Intro-to-optimx.pdf |binary inst/doc/Rvmmin.pdf |binary inst/doc/SNewton.pdf |binary inst/doc/vignette-source/Rvmmin.Rmd | 2 man/kktchk.Rd | 4 - man/opm.Rd | 4 + man/opm2optimr.Rd | 2 man/optimr.Rd | 17 ++++ man/optimr2opm.Rd |only man/pd_check.Rd |only 24 files changed, 192 insertions(+), 129 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 2.21.2 dated 2025-04-02 and 2.21.3 dated 2025-04-10
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Parse, Read, and Edit 'TOML'
Description: A toolkit for working with 'TOML' files in R while preserving
formatting, comments, and structure. 'tomledit' enables serialization of R
objects such as lists, data.frames, numeric, logical, and date vectors.
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between tomledit versions 0.1.0 dated 2025-02-13 and 0.1.1 dated 2025-04-09
DESCRIPTION | 12 +++++--- MD5 | 37 ++++++++++++++------------ NEWS.md |only R/modify.R | 2 - R/toml.R | 4 +- README.md |only configure | 15 ---------- configure.win | 15 ---------- man/tomledit-package.Rd | 4 ++ src/Makevars.in | 14 +++++----- src/Makevars.win.in | 25 ++++++----------- src/rust/Cargo.lock | 67 +++++++++++++++++++++++++++--------------------- src/rust/Cargo.toml | 3 +- src/rust/src/array.rs | 13 +++++++++ src/rust/src/item.rs | 9 +++++- src/rust/src/lib.rs | 7 ++--- src/rust/src/table.rs | 37 ++++++++++++-------------- src/rust/src/values.rs | 5 ++- src/rust/vendor.tar.xz |binary tools/config.R |only tools/msrv.R | 4 +- 21 files changed, 138 insertions(+), 135 deletions(-)
Title: The FPCdpca Criterion on Distributed Principal Component
Analysis
Description: We consider optimal subset selection in the setting that one needs to use only one data subset to represent the whole data set with minimum information loss, and devise a novel intersection-based criterion on selecting optimal subset, called as the FPC criterion, to handle with the optimal sub-estimator in distributed principal component analysis; That is, the FPCdpca. The philosophy of the package is described in Guo G. (2025) <doi:10.1016/j.physa.2024.130308>.
Author: Guangbao Guo [aut, cre] ,
Jiarui Li [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between FPCdpca versions 0.1.0 dated 2024-05-27 and 0.2.0 dated 2025-04-09
DESCRIPTION | 23 +++++++---- MD5 | 38 +++++++++++-------- NAMESPACE | 26 ++++++------- R/Depca.R | 90 +++++++++++++++++++++++---------------------- R/Dpca.R | 40 ++++++++++++++------ R/Drp.R | 6 ++- R/Drpca.R | 6 ++- R/Drsvd.R | 98 ++++++++++++++++++++++++++++---------------------- R/Dsvd.R | 6 ++- R/FPC.R | 4 +- data |only man/Depca.Rd | 78 +++++++++++++++++++++------------------ man/Dpca.Rd | 65 +++++++++++++++++++++------------ man/Drp.Rd | 55 +++++++++++++++------------- man/Drpca.Rd | 53 ++++++++++++++------------- man/Drsvd.Rd | 78 ++++++++++++++++++++------------------- man/Dsvd.Rd | 59 ++++++++++++++---------------- man/FPC.Rd | 49 +++++++++++++------------ man/review.Rd |only man/riboflavin.Rd |only man/riboflavinv100.Rd |only 21 files changed, 434 insertions(+), 340 deletions(-)
Title: Regularized Joint Assignment Forest with Treatment Arm
Clustering
Description: Personalized assignment to one of many treatment arms via regularized and clustered joint assignment forests as described in Ladhania, Spiess, Ungar, and Wu (2023) <doi:10.48550/arXiv.2311.00577>. The algorithm pools information across treatment arms: it considers a regularized forest-based assignment algorithm based on greedy recursive partitioning that shrinks effect estimates across arms; and it incorporates a clustering scheme that combines treatment arms with consistently similar outcomes.
Author: Wenbo Wu [aut, cph] ,
Xinyi Zhang [aut, cre, cph] ,
Jann Spiess [aut, cph] ,
Rahul Ladhania [aut, cph]
Maintainer: Xinyi Zhang <zhang.xinyi@nyu.edu>
Diff between rjaf versions 0.1.2 dated 2025-02-16 and 0.1.3 dated 2025-04-09
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/RcppExports.R | 4 ++-- R/rjaf.R | 41 ++++++++++++++++++++++++----------------- man/rjaf.Rd | 16 +++++++++------- src/RcppExports.cpp | 10 ++++------ src/rjaf.cpp | 14 ++------------ tests/testthat/test-rjaf.R | 4 ++-- 8 files changed, 53 insertions(+), 56 deletions(-)
Title: Lookup Geolocation and Proxy Information using 'IP2Location.io'
API
Description: Query for enriched data such as country, region, city, latitude & longitude, ZIP code, time zone, Autonomous System, Internet Service Provider, domain, net speed, International direct dialing (IDD) code, area code, weather station data, mobile data, elevation, usage type, address type, advertisement category, fraud score, and proxy data with an IP address. You can also query a list of hosted domain names for the IP address too.
This package uses the 'IP2Location.io' API to query this data. To get started with a free API key, sign up here <https://www.ip2location.io/sign-up?ref=1>.
Author: IP2Location.io [aut, cre]
Maintainer: IP2Location.io <support@ip2location.io>
Diff between ip2locationio versions 1.0.0 dated 2024-10-31 and 1.1.0 dated 2025-04-09
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NAMESPACE | 1 + R/IP2Locationio.R | 29 +++++++++++++++++++++++++++++ man/lookupHostedDomain.Rd |only 5 files changed, 38 insertions(+), 7 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ctb],
Paola Sebastiani [ctb],
Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.80 dated 2025-01-30 and 2.0.81 dated 2025-04-09
DESCRIPTION | 8 - MD5 | 14 +-- NEWS | 9 +- inst/doc/epiR_descriptive.html | 16 +-- inst/doc/epiR_measures_of_association.html | 12 +- inst/doc/epiR_sample_size.html | 4 inst/doc/epiR_surveillance.html | 14 +-- man/epi.edr.Rd | 127 +++++++++++++++-------------- 8 files changed, 110 insertions(+), 94 deletions(-)
Title: Visualizing of Distributions of Covariance Matrices
Description: Visualizing of distributions of covariance matrices.
The package implements the methodology described in Tokuda, T., Goodrich, B., Van Mechelen, I., Gelman, A., & Tuerlinckx, F. (2012) <https://sites.stat.columbia.edu/gelman/research/unpublished/Visualization.pdf>.
Author: Tomoki Tokuda [aut],
Ben Goodrich [ctb],
Iven Van Mechelen [ctb],
Andrew Gelman [ctb],
Francis Tuerlinckx [ctb],
Kristof Meers [cre]
Maintainer: Kristof Meers <kristof.meers+cran@kuleuven.be>
Diff between VisCov versions 1.5.0 dated 2024-12-04 and 1.6.0 dated 2025-04-09
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS.md |only R/VisCov.R | 16 +++++++++++++++- man/VisCov.Rd | 2 +- 5 files changed, 24 insertions(+), 9 deletions(-)
Title: Phylogenetic Analysis with Discrete Character Data
Description: Reconstruct phylogenetic trees from discrete data.
Inapplicable character states are handled using the algorithm of Brazeau,
Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy"
library, under equal or implied step weights.
Contains a "shiny" user interface for interactive tree search and exploration
of results, including character visualization, rogue taxon detection,
tree space mapping, and cluster consensus trees (Smith 2022a, b)
<doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>.
Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>,
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>
and custom optimality criteria are implemented.
Author: Martin R. Smith [aut, cre, cph]
,
Martin Brazeau [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeSearch versions 1.5.1 dated 2024-05-23 and 1.6.0 dated 2025-04-09
TreeSearch-1.5.1/TreeSearch/R/mpl_visualise.R |only TreeSearch-1.6.0/TreeSearch/DESCRIPTION | 10 TreeSearch-1.6.0/TreeSearch/MD5 | 174 TreeSearch-1.6.0/TreeSearch/NAMESPACE | 437 TreeSearch-1.6.0/TreeSearch/NEWS.md | 634 TreeSearch-1.6.0/TreeSearch/R/AdditionTree.R | 264 TreeSearch-1.6.0/TreeSearch/R/Bootstrap.R | 10 TreeSearch-1.6.0/TreeSearch/R/Concordance.R | 104 TreeSearch-1.6.0/TreeSearch/R/Consistency.R | 172 TreeSearch-1.6.0/TreeSearch/R/CustomSearch.R | 45 TreeSearch-1.6.0/TreeSearch/R/IWScore.R | 29 TreeSearch-1.6.0/TreeSearch/R/Jackknife.R | 9 TreeSearch-1.6.0/TreeSearch/R/MaximizeParsimony.R | 1937 +- TreeSearch-1.6.0/TreeSearch/R/NNI.R | 22 TreeSearch-1.6.0/TreeSearch/R/PlotCharacter.R | 953 - TreeSearch-1.6.0/TreeSearch/R/PolEscapa.R | 250 TreeSearch-1.6.0/TreeSearch/R/RandomTreeScore.R | 2 TreeSearch-1.6.0/TreeSearch/R/Ratchet.R | 19 TreeSearch-1.6.0/TreeSearch/R/SPR.R | 53 TreeSearch-1.6.0/TreeSearch/R/Sectorial.R | 7 TreeSearch-1.6.0/TreeSearch/R/SuccessiveApproximations.R | 5 TreeSearch-1.6.0/TreeSearch/R/TBR.R | 20 TreeSearch-1.6.0/TreeSearch/R/TaxonInfluence.R | 388 TreeSearch-1.6.0/TreeSearch/R/data.R | 417 TreeSearch-1.6.0/TreeSearch/R/data_manipulation.R | 448 TreeSearch-1.6.0/TreeSearch/R/length_range.R | 592 TreeSearch-1.6.0/TreeSearch/R/mpl_morphy_objects.R | 13 TreeSearch-1.6.0/TreeSearch/R/tree_length.R | 28 TreeSearch-1.6.0/TreeSearch/R/tree_rearrangement.R | 12 TreeSearch-1.6.0/TreeSearch/build/partial.rdb |binary TreeSearch-1.6.0/TreeSearch/build/vignette.rds |binary TreeSearch-1.6.0/TreeSearch/inst/Parsimony/app.R | 7305 +++++----- TreeSearch-1.6.0/TreeSearch/inst/Parsimony/log.lg |only TreeSearch-1.6.0/TreeSearch/inst/Parsimony/www/app.css | 256 TreeSearch-1.6.0/TreeSearch/inst/REFERENCES.bib | 1204 - TreeSearch-1.6.0/TreeSearch/inst/WORDLIST | 498 TreeSearch-1.6.0/TreeSearch/inst/apa-old-doi-prefix.csl | 2306 ++- TreeSearch-1.6.0/TreeSearch/inst/doc/custom.html | 30 TreeSearch-1.6.0/TreeSearch/inst/doc/getting-started.Rmd | 136 TreeSearch-1.6.0/TreeSearch/inst/doc/getting-started.html | 11 TreeSearch-1.6.0/TreeSearch/inst/doc/profile-scores.html | 24 TreeSearch-1.6.0/TreeSearch/inst/doc/profile.R | 4 TreeSearch-1.6.0/TreeSearch/inst/doc/profile.Rmd | 294 TreeSearch-1.6.0/TreeSearch/inst/doc/profile.html | 68 TreeSearch-1.6.0/TreeSearch/inst/doc/tree-search.R | 4 TreeSearch-1.6.0/TreeSearch/inst/doc/tree-search.Rmd | 722 TreeSearch-1.6.0/TreeSearch/inst/doc/tree-search.html | 230 TreeSearch-1.6.0/TreeSearch/inst/doc/tree-space.R | 10 TreeSearch-1.6.0/TreeSearch/inst/doc/tree-space.html | 32 TreeSearch-1.6.0/TreeSearch/man/AdditionTree.Rd | 125 TreeSearch-1.6.0/TreeSearch/man/AllSPR.Rd | 76 TreeSearch-1.6.0/TreeSearch/man/CharacterLength.Rd | 125 TreeSearch-1.6.0/TreeSearch/man/ConcordantInformation.Rd | 115 TreeSearch-1.6.0/TreeSearch/man/Consistency.Rd | 151 TreeSearch-1.6.0/TreeSearch/man/DoubleNNI.Rd | 65 TreeSearch-1.6.0/TreeSearch/man/JackLabels.Rd | 140 TreeSearch-1.6.0/TreeSearch/man/Jackknife.Rd | 192 TreeSearch-1.6.0/TreeSearch/man/LengthAdded.Rd | 161 TreeSearch-1.6.0/TreeSearch/man/MaximizeParsimony.Rd | 624 TreeSearch-1.6.0/TreeSearch/man/MorphyTreeLength.Rd | 172 TreeSearch-1.6.0/TreeSearch/man/NNI.Rd | 239 TreeSearch-1.6.0/TreeSearch/man/PlotCharacter.Rd | 238 TreeSearch-1.6.0/TreeSearch/man/Ratchet.Rd | 444 TreeSearch-1.6.0/TreeSearch/man/RearrangeEdges.Rd | 161 TreeSearch-1.6.0/TreeSearch/man/SPR.Rd | 232 TreeSearch-1.6.0/TreeSearch/man/SiteConcordance.Rd | 189 TreeSearch-1.6.0/TreeSearch/man/StopUnlessBifurcating.Rd | 47 TreeSearch-1.6.0/TreeSearch/man/SuccessiveApproximations.Rd | 143 TreeSearch-1.6.0/TreeSearch/man/TBR.Rd | 224 TreeSearch-1.6.0/TreeSearch/man/TBRWarning.Rd | 84 TreeSearch-1.6.0/TreeSearch/man/TaxonInfluence.Rd | 293 TreeSearch-1.6.0/TreeSearch/man/TreeLength.Rd | 186 TreeSearch-1.6.0/TreeSearch/man/TreeSearch.Rd | 301 TreeSearch-1.6.0/TreeSearch/man/cSPR.Rd | 64 TreeSearch-1.6.0/TreeSearch/man/dot-NonDuplicateRoot.Rd | 94 TreeSearch-1.6.0/TreeSearch/man/inapplicable.datasets.Rd | 325 TreeSearch-1.6.0/TreeSearch/tests/testthat/_snaps/PlotCharacter/plotchar-consensus.svg |only TreeSearch-1.6.0/TreeSearch/tests/testthat/_snaps/PlotCharacter/plotchar-invar-ambig.svg |only TreeSearch-1.6.0/TreeSearch/tests/testthat/_snaps/PlotCharacter/plotchar-invariant.svg |only TreeSearch-1.6.0/TreeSearch/tests/testthat/test-AdditionTree.R | 192 TreeSearch-1.6.0/TreeSearch/tests/testthat/test-Concordance.R | 291 TreeSearch-1.6.0/TreeSearch/tests/testthat/test-Consistency.R | 116 TreeSearch-1.6.0/TreeSearch/tests/testthat/test-CustomSearch.R | 272 TreeSearch-1.6.0/TreeSearch/tests/testthat/test-Jackknife.R | 92 TreeSearch-1.6.0/TreeSearch/tests/testthat/test-PlotCharacter.R | 307 TreeSearch-1.6.0/TreeSearch/tests/testthat/test-SPR.R |only TreeSearch-1.6.0/TreeSearch/tests/testthat/test-pp-random-tree.R | 279 TreeSearch-1.6.0/TreeSearch/tests/testthat/test-zzz-tree-rearrange.R | 540 TreeSearch-1.6.0/TreeSearch/vignettes/getting-started.Rmd | 136 TreeSearch-1.6.0/TreeSearch/vignettes/profile.Rmd | 294 TreeSearch-1.6.0/TreeSearch/vignettes/tree-search.Rmd | 722 91 files changed, 15137 insertions(+), 13502 deletions(-)
Title: Exploratory Graph Analysis – a Framework for Estimating the
Number of Dimensions in Multivariate Data using Network
Psychometrics
Description: Implements the Exploratory Graph Analysis (EGA) framework for dimensionality
and psychometric assessment. EGA estimates the number of dimensions in
psychological data using network estimation methods and community detection
algorithms. A bootstrap method is provided to assess the stability of dimensions
and items. Fit is evaluated using the Entropy Fit family of indices. Unique
Variable Analysis evaluates the extent to which items are locally dependent (or
redundant). Network loadings provide similar information to factor loadings and
can be used to compute network scores. A bootstrap and permutation approach are
available to assess configural and metric invariance. Hierarchical structures
can be detected using Hierarchical EGA. Time series and intensive longitudinal
data can be analyzed using Dynamic EGA, supporting individual, group, and
population level assessments.
Author: Hudson Golino [aut, cre] ,
Alexander Christensen [aut] ,
Robert Moulder [ctb] ,
Luis E. Garrido [ctb] ,
Laura Jamison [ctb] ,
Dingjing Shi [ctb]
Maintainer: Hudson Golino <hfg9s@virginia.edu>
Diff between EGAnet versions 2.2.0 dated 2025-03-07 and 2.3.0 dated 2025-04-09
DESCRIPTION | 8 MD5 | 34 +-- NAMESPACE | 3 NEWS | 11 + R/EGM.R | 486 ++++++++++----------------------------------- R/EGM.compare.R | 74 +++++- R/EGM.optimizations.R |only R/UVA.R | 495 +++++++++++++++++++++++----------------------- R/bootEGA.R | 4 R/community.detection.R | 3 R/helpers.R | 31 ++ R/itemDiagnostics.R |only R/itemStability.R | 236 +++++++++++----------- R/oldsimEGM.R |only R/simEGM.R | 514 ++++++++++-------------------------------------- man/EGM.Rd | 26 -- man/EGM.compare.Rd | 28 ++ man/UVA.Rd | 18 - man/itemDiagnostics.Rd |only man/simEGM.Rd | 26 -- 20 files changed, 755 insertions(+), 1242 deletions(-)
Title: Continuous Cartogram
Description: Procedures for making continuous cartogram. Procedures available are:
flow based cartogram (Gastner & Newman (2004) <doi:10.1073/pnas.0400280101>),
fast flow based cartogram (Gastner, Seguy & More (2018) <doi:10.1073/pnas.1712674115>),
rubber band based cartogram (Dougenik et al. (1985)
<doi:10.1111/j.0033-0124.1985.00075.x>).
Author: Pierre-Andre Cornillon [aut, cre],
Florent Demoraes [aut],
Flow-Based-Cartograms [cph]
Maintainer: Pierre-Andre Cornillon <pierre-andre.cornillon@univ-rennes2.fr>
Diff between cartogramR versions 1.2-0 dated 2024-09-03 and 1.5-0 dated 2025-04-09
cartogramR-1.2-0/cartogramR/src/Makevars |only cartogramR-1.5-0/cartogramR/DESCRIPTION | 35 cartogramR-1.5-0/cartogramR/MD5 | 38 cartogramR-1.5-0/cartogramR/R/cartogramR.R | 130 +- cartogramR-1.5-0/cartogramR/R/cartogramR_options.R | 64 - cartogramR-1.5-0/cartogramR/cleanup |only cartogramR-1.5-0/cartogramR/configure |only cartogramR-1.5-0/cartogramR/inst/cc |only cartogramR-1.5-0/cartogramR/man/cartogramR_options.Rd | 27 cartogramR-1.5-0/cartogramR/src/Makevars.in |only cartogramR-1.5-0/cartogramR/src/Makevars.win | 24 cartogramR-1.5-0/cartogramR/src/cartogram.c | 88 - cartogramR-1.5-0/cartogramR/src/cartogram.h | 2 cartogramR-1.5-0/cartogramR/src/cartogramR.c | 316 ++++- cartogramR-1.5-0/cartogramR/src/checkring.c | 4 cartogramR-1.5-0/cartogramR/src/dcn.c | 972 ++++++++++++------ cartogramR-1.5-0/cartogramR/src/dcn.h | 5 cartogramR-1.5-0/cartogramR/src/diff_integrate.c | 42 cartogramR-1.5-0/cartogramR/src/ffb_integrate.c | 108 +- cartogramR-1.5-0/cartogramR/src/fill_with_density.c | 25 cartogramR-1.5-0/cartogramR/src/init.c | 2 cartogramR-1.5-0/cartogramR/src/iocartogramR.c | 4 cartogramR-1.5-0/cartogramR/src/myomp.h |only 23 files changed, 1313 insertions(+), 573 deletions(-)
Title: Watch the File System for Changes
Description: R binding for 'libfswatch', a file system monitoring library. Watch
files, or directories recursively, for changes in the background. Log
activity, or run an R function every time a change event occurs.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between watcher versions 0.1.2 dated 2025-02-25 and 0.1.3 dated 2025-04-09
DESCRIPTION | 7 ++++--- MD5 | 23 ++++++++++++----------- NEWS.md | 6 ++++++ R/watch.R | 4 ++-- configure | 27 +++++++++++++-------------- configure.ucrt |only configure.win | 43 ++++++++++++++++++++++++++++++------------- man/watcher.Rd | 4 ++-- src/Makevars.ucrt | 2 +- src/Makevars.win | 4 ++-- src/fswatch-5c443d2.tar.gz |binary src/watcher.c | 7 +++++++ tests/testthat/test-watch.R | 16 +++++++++++++++- 13 files changed, 94 insertions(+), 49 deletions(-)
Title: Quick and Essential 'R' Tricks for Better Scripts
Description: The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to improve your scripts. Improve the quality and reproducibility of 'R' scripts.
Author: Obinna Obianom [aut, cre],
Brice Richard [aut]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between quickcode versions 1.0.6 dated 2025-03-02 and 1.0.7 dated 2025-04-09
DESCRIPTION | 6 +- MD5 | 20 +++---- R/OR.R | 1 R/constants.R | 21 +++++++ R/list_shuffle.R | 5 - README.md | 6 +- inst/doc/add_today_date_to_filenames_quickcode.html | 54 ++++++++++---------- inst/doc/nullish_coalescing_operator_r.html | 4 - inst/doc/quickcode_r_introduction.html | 4 - inst/doc/track_function_usage_r.html | 4 - man/const.Rd | 22 ++++++++ 11 files changed, 95 insertions(+), 52 deletions(-)
Title: Multivariate Time Series Data Imputation
Description: This is an EM algorithm based method for imputation of missing values in multivariate normal time series. The imputation algorithm accounts for both spatial and temporal correlation structures. Temporal patterns can be modeled using an ARIMA(p,d,q), optionally with seasonal components, a non-parametric cubic spline or generalized additive models with exogenous covariates. This algorithm is specially tailored for climate data with missing measurements from several monitors along a given region.
Author: Washington Junger [aut, cre],
Antonio Ponce de Leon [ctb]
Maintainer: Washington Junger <wjunger@ims.uerj.br>
Diff between mtsdi versions 0.3.5 dated 2018-01-23 and 0.3.7 dated 2025-04-09
DESCRIPTION | 17 ++++++++++------- MD5 | 14 +++++++------- man/internal.Rd | 1 + man/mkjnw.Rd | 4 ++-- man/mnimput.Rd | 16 ++++++++-------- man/plot.mtsdi.Rd | 4 ++-- man/print.mtsdi.Rd | 2 +- man/print.summary.mtsdi.Rd | 2 +- 8 files changed, 32 insertions(+), 28 deletions(-)
Title: Analysis of Archaeological Mortality Data
Description: A collection of functions for the analysis of archaeological mortality
data (on the topic see e.g. Chamberlain 2006
<https://books.google.de/books?id=nG5FoO_becAC&lpg=PA27&ots=LG0b_xrx6O&dq=life%20table%20archaeology&pg=PA27#v=onepage&q&f=false>).
It takes demographic data in different formats and displays the result in a standard life table
as well as plots the relevant indices (percentage of deaths, survivorship, probability of death,
life expectancy, percentage of population). It also checks for possible biases in the age
structure and applies corrections to life tables.
Author: Nils Mueller-Scheessel [aut, cre, cph]
,
Martin Hinz [aut],
Clemens Schmid [aut],
Christoph Rinne [aut],
Daniel Knitter [aut],
Wolfgang Hamer [aut],
Dirk Seidensticker [aut],
Franziska Faupel [aut],
Carolin Tietze [aut],
Nicole Grunert [aut]
Maintainer: Nils Mueller-Scheessel <nils.mueller-scheessel@ufg.uni-kiel.de>
Diff between mortAAR versions 1.1.7 dated 2025-01-12 and 1.1.8 dated 2025-04-09
mortAAR-1.1.7/mortAAR/inst/doc/mortAAR_vignette-1.R |only mortAAR-1.1.7/mortAAR/inst/doc/mortAAR_vignette-1.Rmd |only mortAAR-1.1.7/mortAAR/inst/doc/mortAAR_vignette-1.html |only mortAAR-1.1.7/mortAAR/inst/doc/mortAAR_vignette_extended.R |only mortAAR-1.1.7/mortAAR/inst/doc/mortAAR_vignette_extended.Rmd |only mortAAR-1.1.7/mortAAR/inst/doc/mortAAR_vignette_extended.html |only mortAAR-1.1.7/mortAAR/inst/doc/mortAAR_vignette_lt_correction.R |only mortAAR-1.1.7/mortAAR/inst/doc/mortAAR_vignette_lt_correction.Rmd |only mortAAR-1.1.7/mortAAR/inst/doc/mortAAR_vignette_lt_correction.html |only mortAAR-1.1.7/mortAAR/inst/doc/mortAAR_vignette_reproduction.R |only mortAAR-1.1.7/mortAAR/inst/doc/mortAAR_vignette_reproduction.Rmd |only mortAAR-1.1.7/mortAAR/inst/doc/mortAAR_vignette_reproduction.html |only mortAAR-1.1.7/mortAAR/vignettes/mortAAR_vignette-1.Rmd |only mortAAR-1.1.7/mortAAR/vignettes/mortAAR_vignette_extended.Rmd |only mortAAR-1.1.7/mortAAR/vignettes/mortAAR_vignette_lt_correction.Rmd |only mortAAR-1.1.7/mortAAR/vignettes/mortAAR_vignette_reproduction.Rmd |only mortAAR-1.1.8/mortAAR/DESCRIPTION | 36 +++---- mortAAR-1.1.8/mortAAR/MD5 | 51 +++++----- mortAAR-1.1.8/mortAAR/NEWS.md | 3 mortAAR-1.1.8/mortAAR/R/halley_band.R | 4 mortAAR-1.1.8/mortAAR/build/partial.rdb |binary mortAAR-1.1.8/mortAAR/build/vignette.rds |binary mortAAR-1.1.8/mortAAR/inst/doc/background.Rmd |only mortAAR-1.1.8/mortAAR/inst/doc/background.html |only mortAAR-1.1.8/mortAAR/inst/doc/example_1.R |only mortAAR-1.1.8/mortAAR/inst/doc/example_1.Rmd |only mortAAR-1.1.8/mortAAR/inst/doc/example_1.html |only mortAAR-1.1.8/mortAAR/inst/doc/example_2.R |only mortAAR-1.1.8/mortAAR/inst/doc/example_2.Rmd |only mortAAR-1.1.8/mortAAR/inst/doc/example_2.html |only mortAAR-1.1.8/mortAAR/inst/doc/lt_correction.R |only mortAAR-1.1.8/mortAAR/inst/doc/lt_correction.Rmd |only mortAAR-1.1.8/mortAAR/inst/doc/lt_correction.html |only mortAAR-1.1.8/mortAAR/inst/doc/mortAAR.R |only mortAAR-1.1.8/mortAAR/inst/doc/mortAAR.Rmd |only mortAAR-1.1.8/mortAAR/inst/doc/mortAAR.html |only mortAAR-1.1.8/mortAAR/inst/doc/reproduction.R |only mortAAR-1.1.8/mortAAR/inst/doc/reproduction.Rmd |only mortAAR-1.1.8/mortAAR/inst/doc/reproduction.html |only mortAAR-1.1.8/mortAAR/man/mortAAR-package.Rd | 5 mortAAR-1.1.8/mortAAR/vignettes/background.Rmd |only mortAAR-1.1.8/mortAAR/vignettes/example_1.Rmd |only mortAAR-1.1.8/mortAAR/vignettes/example_2.Rmd |only mortAAR-1.1.8/mortAAR/vignettes/lt_correction.Rmd |only mortAAR-1.1.8/mortAAR/vignettes/mortAAR.Rmd |only mortAAR-1.1.8/mortAAR/vignettes/reproduction.Rmd |only 46 files changed, 57 insertions(+), 42 deletions(-)
Title: Homomorphic Computations in R
Description: Homomorphic computations in R for privacy-preserving applications. Currently only
the Paillier Scheme is implemented.
Author: Balasubramanian Narasimhan [aut, cre]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between homomorpheR versions 0.2-2 dated 2019-01-23 and 0.3 dated 2025-04-09
homomorpheR-0.2-2/homomorpheR/vignettes/assets/round_robin.pdf |only homomorpheR-0.3/homomorpheR/DESCRIPTION | 17 homomorpheR-0.3/homomorpheR/MD5 | 66 - homomorpheR-0.3/homomorpheR/NEWS.md |only homomorpheR-0.3/homomorpheR/R/homomorpheR.R | 17 homomorpheR-0.3/homomorpheR/R/paillier.R | 371 +++-- homomorpheR-0.3/homomorpheR/README.md | 60 homomorpheR-0.3/homomorpheR/build/vignette.rds |binary homomorpheR-0.3/homomorpheR/inst/doc/DHCox.R | 41 homomorpheR-0.3/homomorpheR/inst/doc/DHCox.Rmd | 8 homomorpheR-0.3/homomorpheR/inst/doc/DHCox.html | 655 +++++++--- homomorpheR-0.3/homomorpheR/inst/doc/DHCoxNCP.R |only homomorpheR-0.3/homomorpheR/inst/doc/DHCoxNCP.Rmd |only homomorpheR-0.3/homomorpheR/inst/doc/DHCoxNCP.html |only homomorpheR-0.3/homomorpheR/inst/doc/QueryNCP.R |only homomorpheR-0.3/homomorpheR/inst/doc/QueryNCP.Rmd |only homomorpheR-0.3/homomorpheR/inst/doc/QueryNCP.html |only homomorpheR-0.3/homomorpheR/inst/doc/homomorphing.R | 30 homomorpheR-0.3/homomorpheR/inst/doc/homomorphing.Rmd | 2 homomorpheR-0.3/homomorpheR/inst/doc/homomorphing.html | 521 +++++-- homomorpheR-0.3/homomorpheR/inst/doc/introduction.R | 12 homomorpheR-0.3/homomorpheR/inst/doc/introduction.Rmd | 12 homomorpheR-0.3/homomorpheR/inst/doc/introduction.html | 524 +++++--- homomorpheR-0.3/homomorpheR/man/PaillierKeyPair.Rd | 85 + homomorpheR-0.3/homomorpheR/man/PaillierPrivateKey.Rd | 100 + homomorpheR-0.3/homomorpheR/man/PaillierPublicKey.Rd | 217 +++ homomorpheR-0.3/homomorpheR/man/homomorpheR.Rd | 21 homomorpheR-0.3/homomorpheR/man/random.bigz.Rd | 1 homomorpheR-0.3/homomorpheR/vignettes/DHCox.Rmd | 8 homomorpheR-0.3/homomorpheR/vignettes/DHCoxNCP.Rmd |only homomorpheR-0.3/homomorpheR/vignettes/QueryNCP.Rmd |only homomorpheR-0.3/homomorpheR/vignettes/assets/mpc.png |only homomorpheR-0.3/homomorpheR/vignettes/assets/mpc2.png |only homomorpheR-0.3/homomorpheR/vignettes/assets/nc-masters-v1.tex |only homomorpheR-0.3/homomorpheR/vignettes/assets/nc-masters1.tex |only homomorpheR-0.3/homomorpheR/vignettes/assets/nc-query-masters-v1.png |only homomorpheR-0.3/homomorpheR/vignettes/assets/nc-query-masters-v1.tex |only homomorpheR-0.3/homomorpheR/vignettes/assets/non_cooperating_masters.png |only homomorpheR-0.3/homomorpheR/vignettes/assets/non_cooperating_masters.tex |only homomorpheR-0.3/homomorpheR/vignettes/assets/non_cooperating_query_masters.png |only homomorpheR-0.3/homomorpheR/vignettes/assets/non_cooperating_query_masters.tex |only homomorpheR-0.3/homomorpheR/vignettes/homomorphing.Rmd | 2 homomorpheR-0.3/homomorpheR/vignettes/homomorphing.bib | 5 homomorpheR-0.3/homomorpheR/vignettes/introduction.Rmd | 12 44 files changed, 1974 insertions(+), 813 deletions(-)
Title: Quantitative Pest Risk Assessment at the Entry Step
Description: Supports risk assessors in performing the entry step of the
quantitative Pest Risk Assessment. It allows the estimation of the
amount of a plant pest entering a risk assessment area (in terms of
founder populations) through the calculation of the imported
commodities that could be potential pathways of pest entry, and the
development of a pathway model. Two 'Shiny' apps based on the
functionalities of the package are included, that simplify the process
of assessing the risk of entry of plant pests. The approach is based
on the work of the European Food Safety Authority (EFSA PLH Panel et
al., 2018) <doi:10.2903/j.efsa.2018.5350>.
Author: Martina Cendoya [aut, cre] ,
Maria Chiara Rosace [aut]
Maintainer: Martina Cendoya <cendoya_marmar@gva.es>
Diff between qPRAentry versions 0.1.0 dated 2024-12-17 and 0.1.1 dated 2025-04-09
DESCRIPTION | 16 +-- MD5 | 20 ++-- NEWS.md | 5 + R/mod_ntrade_redistribution.R | 7 + R/utils.R | 26 +++-- README.md | 33 ++++-- inst/doc/qPRAentry_workflow.R | 45 ++++++--- inst/doc/qPRAentry_workflow.Rmd | 36 ++++++- inst/doc/qPRAentry_workflow.html | 191 +++++++++++++++++++-------------------- man/qPRAentry-package.Rd | 8 + vignettes/qPRAentry_workflow.Rmd | 36 ++++++- 11 files changed, 272 insertions(+), 151 deletions(-)
Title: Operations to Ease Data Analyses Specific to Nigeria
Description: A set of convenience functions as well as geographical/political
data about Nigeria, aimed at simplifying work with data and information that
are specific to the country.
Author: Victor Ordu [aut, cre] ,
Laura DeCicco [ctb],
Emily Riederer [rev],
Margaret Siple [rev],
Cagri Alican [rev]
Maintainer: Victor Ordu <victorordu@outlook.com>
Diff between naijR versions 0.6.1 dated 2024-10-10 and 0.6.2 dated 2025-04-09
DESCRIPTION | 8 +- MD5 | 24 +++---- NEWS.md | 130 +++++++++++++++++++++++++----------------- R/fixreg.R | 20 +++--- R/regions.R | 20 +++++- build/vignette.rds |binary inst/doc/interactive.R | 6 + inst/doc/interactive.html | 31 +++++----- inst/doc/nigeria-maps.R | 4 + inst/doc/nigeria-maps.html | 29 ++++----- man/fix_region.Rd | 16 ++--- man/naijR.Rd | 8 ++ tests/testthat/test-regions.R | 11 ++- 13 files changed, 188 insertions(+), 119 deletions(-)
Title: Interpretable Machine Learning and Statistical Inference with
Accumulated Local Effects (ALE)
Description: Accumulated Local Effects (ALE) were initially developed as a model-agnostic approach for global explanations of the results of black-box machine learning algorithms. ALE has a key advantage over other approaches like partial dependency plots (PDP) and SHapley Additive exPlanations (SHAP): its values represent a clean functional decomposition of the model. As such, ALE values are not affected by the presence or absence of interactions among variables in a mode. Moreover, its computation is relatively rapid. This package reimplements the algorithms for calculating ALE data and develops highly interpretable visualizations for plotting these ALE values. It also extends the original ALE concept to add bootstrap-based confidence intervals and ALE-based statistics that can be used for statistical inference. For more details, see Okoli, Chitu. 2023. “Statistical Inference Using Machine Learning and Classical Techniques Based on Accumulated Local Effects (ALE).” arXiv. <doi:10.48550/arXiv.2 [...truncated...]
Author: Chitu Okoli [aut, cre]
Maintainer: Chitu Okoli <Chitu.Okoli@skema.edu>
Diff between ale versions 0.3.1 dated 2025-03-10 and 0.5.0 dated 2025-04-09
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Title: R Wrapper to Access a Wide Range of Germany's Federal
Statistical System Databases Based on the GENESIS Web Service
RESTful API of the German Federal Statistical Office
(Statistisches Bundesamt/Destatis)
Description: A RESTful API wrapper for accessing the GENESIS database of
the German Federal Statistical Office (Destatis) as well as its Census
Database and the database of Germany's regional statistics. Supports data
search functions, credential management, result caching, and handling
remote background jobs for large datasets.
Author: Yannik Buhl [aut, cre],
Zoran Kovacevic [aut] ,
Dorian Le Jeune [aut],
Long Nguyen [aut] ,
Johannes Ritter [aut]
Maintainer: Yannik Buhl <ybuhl@posteo.de>
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restatis-0.3.0/restatis/tests/testthat/xy_statistic1/api/catalogue/cubes2statistic-86e7c4-c0c2a9-POST.json |only restatis-0.3.0/restatis/tests/testthat/xy_statistic1/api/catalogue/tables2statistic-86e7c4-c0c2a9-POST.json |only restatis-0.3.0/restatis/tests/testthat/xy_statistic1/api/catalogue/variables2statistic-86e7c4-c0c2a9-POST.json |only restatis-0.3.0/restatis/tests/testthat/xy_statistic2/api/catalogue/tables2statistic-86e7c4-c0c2a9-POST.json |only restatis-0.3.0/restatis/tests/testthat/xy_statistic3/api/catalogue/tables2statistic-86e7c4-c0c2a9-POST.json |only restatis-0.3.0/restatis/tests/testthat/xy_variable1/api/catalogue/statistics2variable-86e7c4-1f2606-POST.json |only restatis-0.3.0/restatis/tests/testthat/xy_variable1/api/catalogue/tables2variable-86e7c4-1f2606-POST.json |only restatis-0.3.0/restatis/tests/testthat/xy_variable1/api/catalogue/timeseries2variable-86e7c4-1f2606-POST.json |only restatis-0.3.0/restatis/tests/testthat/xy_variable2/api/catalogue/tables2variable-86e7c4-1f2606-POST.json |only restatis-0.3.0/restatis/tests/testthat/xy_variable3/api/catalogue/tables2variable-86e7c4-1f2606-POST.json |only restatis-0.3.0/restatis/vignettes/additional_parameter.Rmd | 60 restatis-0.3.0/restatis/vignettes/restatis.Rmd | 12 162 files changed, 7288 insertions(+), 7217 deletions(-)
Title: Exploratory Chemometrics for 2D Spectroscopy
Description: A collection of functions for exploratory chemometrics of 2D spectroscopic data sets such as COSY (correlated spectroscopy) and HSQC (heteronuclear single quantum coherence) 2D NMR (nuclear magnetic resonance) spectra. 'ChemoSpec2D' deploys methods aimed primarily at classification of samples and the identification of spectral features which are important in distinguishing samples from each other. Each 2D spectrum (a matrix) is treated as the unit of observation, and thus the physical sample in the spectrometer corresponds to the sample from a statistical perspective. In addition to chemometric tools, a few tools are provided for plotting 2D spectra, but these are not intended to replace the functionality typically available on the spectrometer. 'ChemoSpec2D' takes many of its cues from 'ChemoSpec' and tries to create consistent graphical output and to be very user friendly.
Author: Bryan A. Hanson [aut, cre]
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between ChemoSpec2D versions 0.5.0 dated 2021-10-11 and 0.5.1 dated 2025-04-09
DESCRIPTION | 10 +++--- MD5 | 64 +++++++++++++++++++++-------------------- NAMESPACE | 24 --------------- NEWS.md | 6 +++ R/AlignArraysMBO.R | 1 R/ChemoSpec2D-package.R | 8 +---- R/cleanArgs2D.R | 3 - R/createScale.R | 1 R/drawScale.R | 1 R/evalArrayOverlapMBO.R | 1 R/findExtreme.R | 1 R/findZeros.R | 1 R/getAlignOrder.R | 1 R/getPN.R | 1 R/hats_alignSpectra2D.R | 2 - R/makeArray.R | 24 --------------- R/makeArray2.R |only R/mapColors.R | 1 R/noiseSurface.R | 1 R/onAttach.R | 2 - R/plotEngine.R | 1 R/rescale.R | 1 R/shiftArray.R | 1 R/showHist.R | 1 R/symAroundZero.R | 1 R/unstack.R | 1 build/vignette.rds |binary data/MUD1.RData |binary data/MUD2.RData |binary inst/doc/ChemoSpec2D.pdf |binary inst/tinytest/test_makeArray.R | 5 +-- man/ChemoSpec2D-package.Rd | 8 +++++ man/hats_alignSpectra2D.Rd | 2 - vignettes/pinp.cls |only 34 files changed, 60 insertions(+), 114 deletions(-)
Title: Machine Learning Immunogenicity and Vaccine Response Analysis
Description: Used for analyzing immune responses and predicting vaccine efficacy using machine learning and advanced data processing techniques. 'Immunaut' integrates both unsupervised and supervised learning methods, managing outliers and capturing immune response variability. It performs multiple rounds of predictive model testing to identify robust immunogenicity signatures that can predict vaccine responsiveness. The platform is designed to handle high-dimensional immune data, enabling researchers to uncover immune predictors and refine personalized vaccination strategies across diverse populations.
Author: Ivan Tomic [aut, cre, cph] ,
Adriana Tomic [aut, ctb, cph, fnd]
,
Stephanie Hao [aut]
Maintainer: Ivan Tomic <info@ivantomic.com>
Diff between immunaut versions 1.0.0 dated 2024-10-25 and 1.0.2 dated 2025-04-09
DESCRIPTION | 15 MD5 | 54 +- NAMESPACE | 20 NEWS.md |only R/functions.R | 761 +++++++++++++++++++++++++++--------- R/immunaut.R | 238 ++++++++--- R/immunautLAIV-data.R |only R/utils.R | 191 +++++---- R/zzz.R | 3 README.md | 134 +++--- data/immunautDemo.rda |binary data/immunautLAIV.rda |only man/auto_simon_ml.Rd | 36 + man/calculate_tsne.Rd | 16 man/castAllStringsToNA.Rd | 7 man/cluster_tsne_density.Rd | 12 man/cluster_tsne_hierarchical.Rd | 15 man/cluster_tsne_knn_louvain.Rd | 39 - man/cluster_tsne_mclust.Rd | 14 man/find_optimal_resolution.Rd | 42 - man/generate_demo_data.Rd | 2 man/immunaut.Rd | 98 ++-- man/immunautLAIV.Rd |only man/isNumeric.Rd | 1 man/is_var_empty.Rd | 1 man/pick_best_cluster_modularity.Rd |only man/pick_best_cluster_overall.Rd |only man/pick_best_cluster_silhouette.Rd |only man/pick_best_cluster_simon.Rd |only man/preProcessData.Rd | 21 man/preProcessResample.Rd | 7 man/remove_outliers.Rd | 9 32 files changed, 1147 insertions(+), 589 deletions(-)
Title: Fast and Scalable Single Cell Differential Expression Analysis
using Mixed-Effects Models
Description: A fast and scalable linear mixed-effects model (LMM) estimation algorithm
for analysis of single-cell differential expression. The algorithm uses
summary-level statistics and requires less computer memory to fit the LMM.
Author: Changjiang Xu [aut, cre],
Gary Bader [aut]
Maintainer: Changjiang Xu <changjiang.xu@utoronto.ca>
Diff between FLASHMM versions 1.2.0 dated 2025-03-31 and 1.2.1 dated 2025-04-09
DESCRIPTION | 6 MD5 | 14 +- NEWS.md | 2 README.md | 74 ++++++++--- inst/doc/FLASHMM-vignette.R | 19 +- inst/doc/FLASHMM-vignette.Rmd | 25 ++- inst/doc/FLASHMM-vignette.html | 267 ++++++++++++++++++++--------------------- vignettes/FLASHMM-vignette.Rmd | 25 ++- 8 files changed, 241 insertions(+), 191 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible
outcome to evaluate the effectiveness of a new therapy (the true endpoint) is
difficult to measure. In such a situation, it can be an effective strategy to
replace the true endpoint by a (bio)marker that is easier to measure and that
allows for a prediction of the treatment effect on the true endpoint (a
surrogate endpoint). The package 'Surrogate' allows for an evaluation of the
appropriateness of a candidate surrogate endpoint based on the meta-analytic,
information-theoretic, and causal-inference frameworks. Part of this software
has been developed using funding provided from the European Union's Seventh
Framework Programme for research, technological development and demonstration
(Grant Agreement no 602552), the Special Research Fund (BOF) of Hasselt
University (BOF-number: BOF2OCPO3), GlaxoSmithKline Biologicals, Baekeland
Mandaat (HBC.2022.0145), and Johnson & Johnson Innovative Medicine.
Author: Wim Van Der Elst [cre, aut],
Florian Stijven [aut],
Fenny Ong [aut],
Dries De Witte [aut],
Gokce Deliorman [aut],
Paul Meyvisch [aut],
Alvaro Poveda [aut],
Ariel Alonso [aut],
Hannah Ensor [aut],
Christoper Weir [aut],
Geert Molenberghs [aut]
Maintainer: Wim Van Der Elst <wim.vanderelst@gmail.com>
Diff between Surrogate versions 3.3.3 dated 2025-02-11 and 3.4.0 dated 2025-04-09
DESCRIPTION | 10 ++++++---- MD5 | 14 ++++++++++---- NAMESPACE | 3 +++ NEWS.md | 12 ++++++++++++ R/ICA_alpha_ContCont.R |only R/ICA_t.R |only man/ICA_alpha_ContCont.Rd |only man/ICA_t.Rd |only man/Surrogate-package.Rd | 1 + tests/testthat/test_ICA_alpha_ContCont.R |only tests/testthat/test_ICA_t.R |only 11 files changed, 32 insertions(+), 8 deletions(-)
Title: Download and Import Open Street Map Data Extracts
Description: Match, download, convert and import Open Street Map data extracts
obtained from several providers.
Author: Andrea Gilardi [aut, cre] ,
Robin Lovelace [aut] ,
Barry Rowlingson [ctb] ,
Salva Fernandez [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/395>),
Nicholas Potter [rev] for
rOpenSci, see
<https://github.com/ropensci/soft [...truncated...]
Maintainer: Andrea Gilardi <andrea.gilardi@unimib.it>
Diff between osmextract versions 0.5.2 dated 2024-11-22 and 0.5.3 dated 2025-04-09
DESCRIPTION | 10 MD5 | 52 +- NEWS.md | 332 ++++++------ R/get-network.R | 3 R/get.R | 8 R/match.R | 35 + R/utils.R | 21 build/vignette.rds |binary data/bbbike_zones.rda |binary data/geofabrik_zones.rda |binary data/openstreetmap_fr_zones.rda |binary inst/WORDLIST | 1 inst/doc/osmextract.R | 11 inst/doc/osmextract.Rmd | 28 + inst/doc/osmextract.html | 774 +++++++++++++++--------------- inst/doc/providers.html | 2 inst/doc/providers_comparisons.html | 14 man/figures/README-iow1-1.png |binary man/figures/README-points-lines-iow-1.png |binary man/figures/README-points-lines-iow-2.png |binary man/geofabrik_zones.Rd | 2 man/oe_get.Rd | 8 man/oe_get_network.Rd | 3 man/oe_match.Rd | 17 man/osmextract-package.Rd | 2 tests/testthat/test-match.R | 19 vignettes/osmextract.Rmd | 28 + 27 files changed, 790 insertions(+), 580 deletions(-)
Title: Analyze Data from Electronic Adherence Monitoring Devices
Description: Medication adherence, defined as medication-taking behavior that aligns with the agreed-upon
treatment protocol, is critical for realizing the benefits of prescription medications.
Medication adherence can be assessed using electronic adherence monitoring devices (EAMDs),
pill bottles or boxes that contain a computer chip that records the date and time of each
opening (or “actuation”). Before researchers can use EAMD data, they must apply a series of
decision rules to transform actuation data into adherence data.
The purpose of this R package ('oncmap') is to transform EAMD actuations in the form of a raw .csv file,
information about the patient, regimen, and non-monitored periods into two daily adherence values --
Dose Taken and Correct Dose Taken.
Author: Michal Kouril [aut, cre] ,
Meghan McGrady [aut] ,
Mara Constance [aut] ,
Kevin Hommel [aut]
Maintainer: Michal Kouril <Michal.Kouril@cchmc.org>
Diff between oncmap versions 0.1.5 dated 2025-01-27 and 0.1.7 dated 2025-04-09
DESCRIPTION | 8 ++-- LICENSE | 2 - MD5 | 25 +++++++------- NEWS.md |only R/adherence_preprocess.R | 45 ++++++++++++------------- R/globals.R | 9 ++--- R/process_eamd.R | 36 +++++++++++--------- R/read_input.R | 46 +++++++++++++++++--------- R/report_adherence.R | 36 ++++++++++---------- build/vignette.rds |binary tests/testthat/test-adherence_preprocessing.R | 6 +-- tests/testthat/test-detect.R | 4 +- tests/testthat/test-process_eamd-script.R | 40 +++++++++++++--------- tests/testthat/test-process_eamd.R | 14 +++---- 14 files changed, 150 insertions(+), 121 deletions(-)
Title: Distributed Gaussian Process Calculations
Description: Distributes Gaussian process calculations across nodes
in a distributed memory setting, using Rmpi. The bigGP class
provides high-level methods for maximum likelihood with normal data,
prediction, calculation of uncertainty (i.e., posterior covariance
calculations), and simulation of realizations. In addition, bigGP
provides an API for basic matrix calculations with distributed
covariance matrices, including Cholesky decomposition, back/forwardsolve,
crossproduct, and matrix multiplication.
Author: Christopher Paciorek [aut, cre],
Benjamin Lipshitz [aut],
Prabhat [ctb],
Cari Kaufman [ctb],
Tina Zhuo [ctb],
Rollin Thomas [ctb]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between bigGP versions 0.1.8 dated 2023-04-25 and 0.1.9 dated 2025-04-09
DESCRIPTION | 10 MD5 | 14 NEWS | 6 build/partial.rdb |binary configure | 2957 ++++++++++++++++++++++++++++-------------------------- configure.ac | 18 data/SN2011fe.rda |binary man/bigGP.exit.Rd | 4 8 files changed, 1582 insertions(+), 1427 deletions(-)
Title: Transformation Boosting Machines
Description: Boosting the likelihood of conditional and shift transformation models as introduced in <DOI:10.1007/s11222-019-09870-4>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tbm versions 0.3-6 dated 2024-04-17 and 0.3-7 dated 2025-04-09
DESCRIPTION | 10 ++++---- MD5 | 10 ++++---- build/vignette.rds |binary inst/NEWS.Rd | 7 +++++ inst/doc/tbm_supplement.R | 54 ++++++++++++++++++++++---------------------- inst/doc/tbm_supplement.pdf |binary 6 files changed, 44 insertions(+), 37 deletions(-)
Title: Spectrally Deconfounded Models
Description: Screen for and analyze non-linear sparse direct effects in the presence of unobserved confounding using the spectral deconfounding techniques (Ćevid, Bühlmann, and Meinshausen (2020)<jmlr.org/papers/v21/19-545.html>, Guo, Ćevid, and Bühlmann (2022) <doi:10.1214/21-AOS2152>). These methods have been shown to be a good estimate for the true direct effect if we observe many covariates, e.g., high-dimensional settings, and we have fairly dense confounding. Even if the assumptions are violated, it seems like there is not much to lose, and the deconfounded models will, in general, estimate a function closer to the true one than classical least squares optimization. 'SDModels' provides functions SDAM() for Spectrally Deconfounded Additive Models (Scheidegger, Guo, and Bühlmann (2025) <doi:10.1145/3711116>) and SDForest() for Spectrally Deconfounded Random Forests (Ulmer, Scheidegger, and Bühlmann (2025) <doi:10.48550/arXiv.2502.03969>).
Author: Markus Ulmer [aut, cre, cph] ,
Cyrill Scheidegger [aut]
Maintainer: Markus Ulmer <markus.ulmer@stat.math.ethz.ch>
Diff between SDModels versions 1.0.4 dated 2025-02-19 and 1.0.7 dated 2025-04-09
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 13 +++++++++++++ R/SDTree.R | 5 +++-- R/paths.R | 6 +++++- R/predict.R | 28 +++++++++++++++++++++++++--- README.md | 8 +++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Runtime.R | 26 +++++++++++++------------- inst/doc/Runtime.html | 7 ++++--- man/predict.SDForest.Rd | 5 ++++- tests/testthat/test-anchor.R | 6 ++++++ tests/testthat/test-parallel.R | 16 ++++++++++++---- tests/testthat/test-tree.R | 41 +++++++++++++++++++++++++++++++++++++++++ 15 files changed, 149 insertions(+), 48 deletions(-)
Title: Interface Utilities, Model Templates, Parallel Computing Methods
and Additional Distributions for MCMC Models in JAGS
Description: User-friendly interface utilities for MCMC models via
Just Another Gibbs Sampler (JAGS), facilitating the use of parallel
(or distributed) processors for multiple chains, automated control
of convergence and sample length diagnostics, and evaluation of the
performance of a model using drop-k validation or against simulated
data. Template model specifications can be generated using a standard
lme4-style formula interface to assist users less familiar with the
BUGS syntax. A JAGS extension module provides additional distributions
including the Pareto family of distributions, the DuMouchel prior and
the half-Cauchy prior.
Author: Matthew Denwood [aut, cre],
Martyn Plummer [cph]
Maintainer: Matthew Denwood <md@sund.ku.dk>
Diff between runjags versions 2.2.2-4 dated 2024-03-10 and 2.2.2-5 dated 2025-04-09
DESCRIPTION | 10 +-- MD5 | 18 +++--- R/template_huiwalter.R | 3 - build/vignette.rds |binary configure | 8 +- configure.ac | 6 +- inst/doc/UserGuide.pdf |binary inst/doc/quickjags.R | 24 ++++---- inst/doc/quickjags.html | 130 +++++++++++++++++++++++------------------------- man/runjags-package.Rd | 2 10 files changed, 98 insertions(+), 103 deletions(-)
Title: Radiocarbon Equations
Description: Provides functions for the calibration of radiocarbon dates, as well as options to calculate different radiocarbon realms (C14 age, F14C, pMC, D14C) and estimating the effects of contamination or local reservoir offsets (Reimer and Reimer 2001 <doi:10.1017/S0033822200038339>). The methods follow long-established recommendations such as Stuiver and Polach (1977) <doi:10.1017/S0033822200003672> and Reimer et al. (2004) <doi:10.1017/S0033822200033154>. This package complements the data package 'rintcal'.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rice versions 1.0.0 dated 2025-01-07 and 1.1.1 dated 2025-04-09
rice-1.0.0/rice/R/calc.R |only rice-1.0.0/rice/man/overlap.Rd |only rice-1.1.1/rice/DESCRIPTION | 15 - rice-1.1.1/rice/MD5 | 115 ++++---- rice-1.1.1/rice/NAMESPACE | 8 rice-1.1.1/rice/NEWS.md | 15 + rice-1.1.1/rice/R/calibrate.R | 106 +++++-- rice-1.1.1/rice/R/marine.R | 195 +++++++------- rice-1.1.1/rice/R/plots.R | 177 +++++++----- rice-1.1.1/rice/R/realms.R | 325 ++++++++++++++++++----- rice-1.1.1/rice/R/rice-package.R | 4 rice-1.1.1/rice/R/rice.R | 61 ++++ rice-1.1.1/rice/R/sets.R | 114 +++++++- rice-1.1.1/rice/R/sources.R |only rice-1.1.1/rice/build/partial.rdb |binary rice-1.1.1/rice/build/vignette.rds |binary rice-1.1.1/rice/data/shells.rda |binary rice-1.1.1/rice/inst/doc/rice.R | 32 +- rice-1.1.1/rice/inst/doc/rice.Rmd | 60 +++- rice-1.1.1/rice/inst/doc/rice.html | 473 ++++++++++++++++++---------------- rice-1.1.1/rice/man/BCADtoD14C.Rd | 5 rice-1.1.1/rice/man/BCADtoF14C.Rd | 5 rice-1.1.1/rice/man/BCADtocalBP.Rd | 2 rice-1.1.1/rice/man/BCADtopMC.Rd | 5 rice-1.1.1/rice/man/C14toD14C.Rd | 4 rice-1.1.1/rice/man/C14toF14C.Rd | 6 rice-1.1.1/rice/man/C14tocalBP.Rd | 2 rice-1.1.1/rice/man/C14topMC.Rd | 4 rice-1.1.1/rice/man/D14CtoC14.Rd | 4 rice-1.1.1/rice/man/F14CtoC14.Rd | 4 rice-1.1.1/rice/man/as.bin.Rd | 2 rice-1.1.1/rice/man/as.one.Rd | 2 rice-1.1.1/rice/man/calBPtoBCAD.Rd | 2 rice-1.1.1/rice/man/calBPtoD14C.Rd | 5 rice-1.1.1/rice/man/calBPtoF14C.Rd | 5 rice-1.1.1/rice/man/calBPtopMC.Rd | 5 rice-1.1.1/rice/man/caldist.Rd | 3 rice-1.1.1/rice/man/calib.t.Rd | 3 rice-1.1.1/rice/man/calibrate.Rd | 8 rice-1.1.1/rice/man/clean.Rd | 9 rice-1.1.1/rice/man/contaminate.Rd | 9 rice-1.1.1/rice/man/draw.ccurve.Rd | 3 rice-1.1.1/rice/man/find.shells.Rd | 20 + rice-1.1.1/rice/man/fractions.Rd | 2 rice-1.1.1/rice/man/fromto.Rd |only rice-1.1.1/rice/man/howmanyC14.Rd |only rice-1.1.1/rice/man/hpd.Rd | 8 rice-1.1.1/rice/man/l.calib.Rd | 3 rice-1.1.1/rice/man/map.shells.Rd | 18 + rice-1.1.1/rice/man/muck.Rd | 9 rice-1.1.1/rice/man/older.Rd | 3 rice-1.1.1/rice/man/overlapping.Rd |only rice-1.1.1/rice/man/p.range.Rd | 3 rice-1.1.1/rice/man/push.gamma.Rd | 8 rice-1.1.1/rice/man/push.normal.Rd | 5 rice-1.1.1/rice/man/r.calib.Rd | 3 rice-1.1.1/rice/man/shells.mean.Rd | 2 rice-1.1.1/rice/man/span.Rd |only rice-1.1.1/rice/man/spread.Rd | 4 rice-1.1.1/rice/man/weighted_means.Rd | 2 rice-1.1.1/rice/man/younger.Rd | 3 rice-1.1.1/rice/vignettes/rice.Rmd | 60 +++- 62 files changed, 1300 insertions(+), 650 deletions(-)
Title: Spatial Phylogenetic Analysis
Description: Conduct various analyses on spatial phylogenetic diversity patterns.
Use your data on an evolutionary tree and geographic distributions of the
terminal taxa to compute diversity and endemism metrics, test significance
with null model randomization, analyze community turnover and biotic
regionalization, and perform spatial conservation prioritizations. All
functions support quantitative community data in addition to binary data.
Author: Matthew Kling [aut, cre, cph]
Maintainer: Matthew Kling <mattkling@berkeley.edu>
Diff between phylospatial versions 1.0.0 dated 2025-01-24 and 1.1.0 dated 2025-04-09
DESCRIPTION | 24 +++--- MD5 | 54 +++++++------ NAMESPACE | 1 NEWS.md |only R/phylospatial.R | 7 + R/ps_canape.R | 4 - R/ps_diversity.R | 143 ++++++++++++++++++++++++++++++------- R/ps_ordinate.R | 2 R/ps_rand.R | 26 ++++-- README.md | 18 ++-- inst/doc/alpha-diversity.R | 11 +- inst/doc/alpha-diversity.Rmd | 36 +++++---- inst/doc/alpha-diversity.html | 86 +++++++++++++--------- inst/doc/beta-diversity.R | 2 inst/doc/phylospatial-data.R | 2 inst/doc/phylospatial-data.Rmd | 4 - inst/doc/phylospatial-data.html | 8 +- inst/doc/prioritization.R | 2 man/clade_dist.Rd |only man/phylospatial-package.Rd | 4 - man/ps_canape.Rd | 4 - man/ps_diversity.Rd | 63 ++++++++++------ man/ps_ordinate.Rd | 3 man/ps_rand.Rd | 18 ++-- tests/testthat/test-phylospatial.R | 1 tests/testthat/test-ps_diversity.R | 66 +++++++++++------ tests/testthat/test-ps_rand.R | 1 vignettes/alpha-diversity.Rmd | 36 +++++---- vignettes/phylospatial-data.Rmd | 4 - 29 files changed, 410 insertions(+), 220 deletions(-)
Title: Data Sets from the History of Statistics and Data Visualization
Description: The 'HistData' package provides a collection of small data sets
that are interesting and important in the history of statistics and data
visualization. The goal of the package is to make these available, both for
instructional use and for historical research. Some of these present interesting
challenges for graphics or analysis in R.
Author: Michael Friendly [aut, cre] ,
Stephane Dray [ctb] ,
Hadley Wickham [ctb],
James Hanley [ctb],
Dennis Murphy [ctb],
Peter Li [ctb],
Luiz Droubi [ctb],
James Riley [ctb],
Antoine de Falguerolles [ctb],
Monique Graf [ctb],
Neville Verlander [ctb],
Brian [...truncated...]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between HistData versions 0.9-1 dated 2023-08-09 and 0.9-3 dated 2025-04-09
DESCRIPTION | 30 ++++++++++++-------- MD5 | 52 +++++++++++++++++------------------ NEWS.md | 18 +++++++++++- build/partial.rdb |binary build/vignette.rds |binary data/Armada.RData |binary inst/WORDLIST | 14 +++++++++ inst/doc/Snow_deaths-duplicates.R | 14 ++++----- inst/doc/Snow_deaths-duplicates.Rmd | 2 - inst/doc/Snow_deaths-duplicates.html | 20 ++++++------- man/Arbuthnot.Rd | 2 - man/Armada.Rd | 38 ++++++++++++++++--------- man/Cavendish.Rd | 2 - man/Cholera.Rd | 2 - man/CholeraDeaths1849.Rd | 2 - man/Galton.Rd | 3 +- man/GaltonFamilies.Rd | 2 - man/Guerry.Rd | 2 - man/HistData-package.Rd | 2 - man/Michelson.Rd | 2 - man/Minard.Rd | 22 ++++---------- man/PearsonLee.Rd | 5 ++- man/PolioTrials.Rd | 2 - man/Pollen.Rd | 2 - man/Pyx.Rd | 21 ++++++++++++++ man/Snow.Rd | 13 ++++++-- vignettes/Snow_deaths-duplicates.Rmd | 2 - 27 files changed, 172 insertions(+), 102 deletions(-)
Title: Fit a Penalized Constrained Continuation Ratio Model for
Predicting an Ordinal Response
Description: Penalized methods are useful for fitting over-parameterized models. This package includes functions for restructuring an ordinal
response dataset for fitting continuation ratio models for datasets where the number of covariates exceeds the sample size or when
there is collinearity among the covariates. The 'glmnet' fitting algorithm is used to fit the continuation ratio model after data restructuring.
Author: Kellie J. Archer [aut, cre]
Maintainer: Kellie J. Archer <archer.43@osu.edu>
Diff between glmnetcr versions 1.0.6 dated 2020-07-03 and 1.0.7 dated 2025-04-09
DESCRIPTION | 14 ++++++++------ MD5 | 20 ++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary data/diabetes.rda |binary inst/CITATION | 36 +++++++++++++++--------------------- inst/NEWS.Rd | 5 +++++ inst/doc/glmnetcr.pdf |binary man/diabetes.Rd | 2 +- man/glmnetcr-package.Rd | 2 +- man/glmnetcr.Rd | 2 +- 11 files changed, 41 insertions(+), 40 deletions(-)
Title: An Adaptive Lifting Scheme Algorithm
Description: Adaptive wavelet lifting transforms for signal denoising using optimal local neighbourhood regression, from Nunes et al. (2006) <doi:10.1007/s11222-006-6560-y>.
Author: Matt Nunes [aut, cre],
Marina Knight [aut],
Guy Nason [ctb, ths]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>
Diff between adlift versions 1.4-5 dated 2023-03-22 and 1.4-6 dated 2025-04-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/Amatdual.Rd | 2 +- man/fwtnp.Rd | 2 +- src/adlift.c | 32 ++++++++++++++++++++++++++++---- 5 files changed, 38 insertions(+), 14 deletions(-)
Title: Climate Classification According to Several Indices
Description: Classification of climate according to Koeppen - Geiger, of aridity
indices, of continentality indices, of water balance after Thornthwaite, of
viticultural bioclimatic indices. Drawing climographs: Thornthwaite, Peguy,
Bagnouls-Gaussen.
Author: Emanuele Eccel [aut],
Fabio Zottele [aut, cre],
Emanuele Cordano [aut],
Giambattista Toller [aut],
Fondazione Edmund Mach [cph]
Maintainer: Fabio Zottele <fabio.zottele@fmach.it>
Diff between ClimClass versions 2.1.0 dated 2016-08-04 and 2.1.1 dated 2025-04-09
DESCRIPTION | 19 +- MD5 | 66 ++++----- NEWS.md | 24 ++- R/ClimClass.R | 7 - R/as.datcli.R | 186 +++++++++++++-------------- R/peguy.R | 286 ++++++++++++++++++++---------------------- R/thornthwaite.R | 2 man/ClimClass.Rd | 23 ++- man/ExAtRa.Rd | 7 - man/P.Rd | 5 man/RDI.Rd | 20 +- man/Tm.Rd | 5 man/Tn.Rd | 5 man/Trent_climate.Rd | 1 man/Tx.Rd | 5 man/W_balance.Rd | 5 man/arid.Rd | 16 +- man/arid_ind_tables.Rd | 5 man/as.datcli.Rd | 27 ++- man/bagn_gau.Rd | 23 ++- man/clima_81_10.Rd | 5 man/climate.Rd | 1 man/coeff_rad.Rd | 5 man/contin.Rd | 16 +- man/continental_ind_tables.Rd | 5 man/coord_elev.Rd | 5 man/koeppen_geiger.Rd | 15 +- man/lista_cli.Rd | 5 man/oiv_ind.Rd | 25 ++- man/peguy.Rd | 27 ++- man/plot.thornthwaite.Rd | 24 ++- man/quantiles.Rd | 5 man/thornt_lst.Rd | 5 man/thornthwaite.Rd | 236 +++++++++++++++++----------------- 34 files changed, 606 insertions(+), 510 deletions(-)
Title: Spatial Analysis in Archaeology from Refitting Fragments (GUI)
Description: A 'Shiny' application to access the functionalities and datasets of the 'archeofrag' package for spatial analysis in archaeology from refitting data. Quick and seamless exploration of archaeological refitting datasets, focusing on physical refits only. Features include: built-in documentation and convenient workflow, plot generation and exports, exploration of spatial units merging solutions, simulation of archaeological site formation processes, support for parallel computing, R code generation to re-execute simulations and ensure reproducibility, code generation for the 'openMOLE' model exploration software. A demonstration of the app is available at <https://analytics.huma-num.fr/Sebastien.Plutniak/archeofrag/>.
Author: Sebastien Plutniak [aut, cre]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between archeofrag.gui versions 1.0.0 dated 2025-03-10 and 1.1.0 dated 2025-04-09
DESCRIPTION | 10 - MD5 | 10 - NAMESPACE | 6 NEWS.md | 5 R/app_server.R | 495 +++++++++++++++++++++++++++++++++++++++++++++++++-------- R/app_ui.R | 171 ++++++++++++++----- 6 files changed, 580 insertions(+), 117 deletions(-)
More information about archeofrag.gui at CRAN
Permanent link
Title: Analysis of Differential Behaviour of SPARRA Score Across
Demographic Groups
Description: The SPARRA risk score (Scottish Patients At Risk of admission and Re-Admission) estimates yearly risk of emergency hospital admission using electronic health records on a monthly basis for most of the Scottish population. This package implements a suite of functions used to analyse the behaviour and performance of the score, focusing particularly on differential performance over demographically-defined groups. It includes useful utility functions to plot receiver-operator-characteristic, precision-recall and calibration curves, draw stock human figures, estimate counterfactual quantities without the need to re-compute risk scores, to simulate a semi-realistic dataset. Our manuscript can be found at: <doi:10.1371/journal.pdig.0000675>.
Author: Ioanna Thoma [aut] ,
Catalina Vallejos [ctb] ,
Louis Aslett [ctb] ,
Jill Ireland [ctb] ,
Simon Rogers [ctb] ,
James Liley [cre, aut]
Maintainer: James Liley <james.liley@durham.ac.uk>
Diff between SPARRAfairness versions 0.0.0.2 dated 2024-11-07 and 0.1.0.0 dated 2025-04-09
SPARRAfairness-0.0.0.2/SPARRAfairness/inst/doc/SPARRAfairness_example.html |only SPARRAfairness-0.1.0.0/SPARRAfairness/DESCRIPTION | 10 SPARRAfairness-0.1.0.0/SPARRAfairness/MD5 | 18 SPARRAfairness-0.1.0.0/SPARRAfairness/NEWS.md | 4 SPARRAfairness-0.1.0.0/SPARRAfairness/build/vignette.rds |binary SPARRAfairness-0.1.0.0/SPARRAfairness/data/all_data.RData |binary SPARRAfairness-0.1.0.0/SPARRAfairness/data/decomposition_matrix.RData |binary SPARRAfairness-0.1.0.0/SPARRAfairness/inst/doc/SPARRAfairness_example.Rmd | 6 SPARRAfairness-0.1.0.0/SPARRAfairness/inst/doc/SPARRAfairness_example.pdf |only SPARRAfairness-0.1.0.0/SPARRAfairness/vignettes/SPARRAfairness.bib | 898 ---------- SPARRAfairness-0.1.0.0/SPARRAfairness/vignettes/SPARRAfairness_example.Rmd | 6 11 files changed, 53 insertions(+), 889 deletions(-)
More information about SPARRAfairness at CRAN
Permanent link
Title: Get Spanish Origin-Destination Data
Description: Gain seamless access to origin-destination (OD) data from the
Spanish Ministry of Transport, hosted at
<https://www.transportes.gob.es/ministerio/proyectos-singulares/estudios-de-movilidad-con-big-data/opendata-movilidad>.
This package simplifies the management of these large datasets by
providing tools to download zone boundaries, handle associated
origin-destination data, and process it efficiently with the 'duckdb'
database interface. Local caching minimizes repeated downloads,
streamlining workflows for researchers and analysts. Extensive
documentation is available at
<https://ropenspain.github.io/spanishoddata/index.html>, offering
guides on creating static and dynamic mobility flow visualizations and
transforming large datasets into analysis-ready formats.
Author: Egor Kotov [aut, cre] ,
Robin Lovelace [aut] ,
Eugeni Vidal-Tortosa [ctb]
Maintainer: Egor Kotov <kotov.egor@gmail.com>
Diff between spanishoddata versions 0.1.0 dated 2024-12-18 and 0.1.1 dated 2025-04-09
DESCRIPTION | 12 MD5 | 139 ++++---- NAMESPACE | 2 NEWS.md | 22 + R/available-data.R | 4 R/cite.R |only R/codebook.R | 3 R/connect.R | 13 R/convert.R | 5 R/data-dir.R | 8 R/dev-tools.R | 2 R/disconnect.R | 3 R/download_data.R | 4 R/duckdb-helpers.R | 4 R/get-zones.R | 3 R/get.R | 24 + R/internal-utils.R | 59 +++ R/onload.R |only R/quick-get.R | 139 ++++---- R/spanishoddata-package.R |only README.md | 168 ++++++---- build/vignette.rds |binary inst/CITATION | 69 ++-- inst/doc/convert.html | 83 +--- inst/doc/convert.qmd | 46 +- inst/doc/quick-get.R | 9 inst/doc/quick-get.html | 46 +- inst/doc/quick-get.qmd | 27 - inst/doc/v1-2020-2021-mitma-data-codebook.R | 5 inst/doc/v1-2020-2021-mitma-data-codebook.html | 158 ++++----- inst/doc/v1-2020-2021-mitma-data-codebook.qmd | 41 +- inst/doc/v2-2022-onwards-mitma-data-codebook.html | 146 ++++---- inst/doc/v2-2022-onwards-mitma-data-codebook.qmd | 31 + inst/extdata/sql-queries/v1-od-distritos-clean-csv-view-en.sql | 7 inst/extdata/sql-queries/v1-od-distritos-clean-csv-view-es.sql | 4 inst/extdata/sql-queries/v1-od-municipios-clean-csv-view-en.sql | 2 inst/extdata/sql-queries/v2-od-distritos-clean-csv-view-en.sql | 5 inst/extdata/sql-queries/v2-od-gau-clean-csv-view-en.sql | 2 inst/extdata/sql-queries/v2-od-municipios-clean-csv-view-en.sql | 2 inst/schemaorg.json | 26 + inst/vignette-include/install-package.qmd | 17 - inst/vignette-include/overall-approach.qmd | 2 man/figures/README-desire-lines-1.png |binary man/figures/README-distritos-1.png |binary man/figures/flows_plot_all_districts.png |binary man/figures/flows_plot_barcelona.png |binary man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/figures/zones_barcelona_fua_plot.png |binary man/figures/zones_barcelona_plot.png |only man/spanishoddata-package.Rd |only man/spod_available_data.Rd | 2 man/spod_cite.Rd |only man/spod_codebook.Rd | 2 man/spod_connect.Rd | 4 man/spod_convert.Rd | 2 man/spod_disconnect.Rd | 2 man/spod_download.Rd | 2 man/spod_duckdb_limit_resources.Rd | 2 man/spod_duckdb_od.Rd | 2 man/spod_get.Rd | 4 man/spod_get_data_dir.Rd | 2 man/spod_get_valid_dates.Rd | 4 man/spod_get_zones.Rd | 2 man/spod_graphql_valid_dates.Rd |only man/spod_quick_get_od.Rd | 4 man/spod_set_data_dir.Rd | 2 tests/testthat/test-quick-get.R | 43 -- vignettes/convert.qmd | 46 +- vignettes/media/flows_plot_barcelona.svg |only vignettes/private |only vignettes/quick-get.qmd | 27 - vignettes/references.bib | 30 - vignettes/v1-2020-2021-mitma-data-codebook.qmd | 41 +- vignettes/v2-2022-onwards-mitma-data-codebook.qmd | 31 + 77 files changed, 922 insertions(+), 674 deletions(-)
Title: Radiation and Photovoltaic Systems
Description: Calculation methods of solar radiation and performance of photovoltaic systems from daily and intradaily irradiation data sources.
Author: Oscar Perpinan Lamigueiro [cre, aut]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@upm.es>
Diff between solaR versions 0.46 dated 2021-10-19 and 0.47 dated 2025-04-09
DESCRIPTION | 10 ++-- MD5 | 88 +++++++++++++++++++++---------------------- R/corrFdKt.R | 4 - R/fCompD.R | 8 +-- R/fCompI.R | 6 +- R/fProd.R | 6 +- R/fTemp.R | 4 - R/prodGCPV.R | 2 R/prodPVPS.R | 2 README.md | 13 +----- build/partial.rdb |binary inst/CITATION | 4 - man/G0-class.Rd | 4 - man/Gef-class.Rd | 4 - man/HQCurve.Rd | 4 - man/NmgSFB.Rd | 4 - man/ProdGCPV-class.Rd | 4 - man/ProdPVPS-class.Rd | 4 - man/Shade-class.Rd | 6 +- man/Sol-class.Rd | 4 - man/calcG0.Rd | 4 - man/calcGef.Rd | 4 - man/calcShd.Rd | 4 - man/calcSol.Rd | 4 - man/compareLosses-methods.Rd | 4 - man/fBTd.Rd | 4 - man/fCompD.Rd | 4 - man/fCompI.Rd | 4 - man/fInclin.Rd | 4 - man/fProd.Rd | 4 - man/fPump.Rd | 4 - man/fSolD.Rd | 4 - man/fSolI.Rd | 4 - man/fSombra.Rd | 6 +- man/fTemp.Rd | 4 - man/fTheta.Rd | 4 - man/indexD-methods.Rd | 9 ++++ man/indexI-methods.Rd | 6 ++ man/local2UTC.Rd | 4 - man/optimShd.Rd | 6 +- man/prodGCPV.Rd | 4 - man/prodPVPS.Rd | 4 - man/pumpCoef.Rd | 6 +- man/window-methods.Rd | 2 man/writeSolar.Rd | 8 +-- 45 files changed, 153 insertions(+), 143 deletions(-)
Title: Spatial ARCH and GARCH Models (spGARCH)
Description: A collection of functions to deal with spatial and spatiotemporal autoregressive conditional heteroscedasticity (spatial ARCH and GARCH models) by Otto, Schmid, Garthoff (2018, Spatial Statistics) <doi:10.1016/j.spasta.2018.07.005>: simulation of spatial ARCH-type processes (spARCH, log/exponential-spARCH, complex-spARCH); quasi-maximum-likelihood estimation of the parameters of spARCH models and spatial autoregressive models with spARCH disturbances, diagnostic checks, visualizations.
Author: Philipp Otto [cre, aut]
Maintainer: Philipp Otto <philipp.otto89@gmail.com>
Diff between spGARCH versions 0.2.2 dated 2020-09-02 and 0.2.3 dated 2025-04-09
DESCRIPTION | 16 +- MD5 | 33 ++--- R/RcppExports.R | 94 +++++++-------- R/zzz.R | 56 ++++---- build |only inst/CITATION | 65 +++++----- man/extractAIC.spARCH.Rd | 66 +++++----- man/fitted.spARCH.Rd | 58 ++++----- man/logLik.spARCH.Rd | 62 ++++----- man/plot.spARCH.Rd | 76 ++++++------ man/qml.SARspARCH.Rd | 274 +++++++++++++++++++++---------------------- man/qml.spARCH.Rd | 260 ++++++++++++++++++++--------------------- man/residuals.spARCH.Rd | 58 ++++----- man/spARCHsim.Rd | 238 +++++++++++++++++++------------------- man/spGARCH.Rd | 33 ++--- man/spGARCHsim.Rd | 294 +++++++++++++++++++++++------------------------ man/summary.spARCH.Rd | 134 ++++++++++----------- src/RcppExports.cpp | 5 18 files changed, 921 insertions(+), 901 deletions(-)
Title: Ensemble Empirical Mode Decomposition (EEMD) and Its Complete
Variant (CEEMDAN)
Description: An R interface for libeemd (Luukko, Helske, Räsänen, 2016) <doi:10.1007/s00180-015-0603-9>,
a C library of highly efficient parallelizable functions for performing the ensemble empirical mode decomposition (EEMD),
its complete variant (CEEMDAN), the regular empirical mode decomposition (EMD), and bivariate EMD (BEMD).
Due to the possible portability issues CRAN version no longer supports OpenMP, but you can install OpenMP-supported version
from GitHub: <https://github.com/helske/Rlibeemd/>.
Author: Jouni Helske [aut, cre] ,
Perttu Luukko [aut]
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between Rlibeemd versions 1.4.3 dated 2023-09-05 and 1.4.4 dated 2025-04-09
ChangeLog | 7 +++++ DESCRIPTION | 10 +++---- MD5 | 58 +++++++++++++++++++++++---------------------- R/Rlibeemd-package.R | 2 - R/emd_num_imfs.R | 2 - R/zzz.R | 7 ++--- README.md |only configure | 2 - man/Rlibeemd.Rd | 16 ++++++++++++ src/Makevars.in | 1 src/Makevars.win | 1 src/RcppExports.cpp | 4 +-- src/array.h | 26 +++----------------- src/array_complex.h |only src/bemd.c | 36 ++++++++++++++++++--------- src/bemd.h | 21 +++++++++------- src/bemdR.cpp | 14 +++++++--- src/ceemdan.c | 6 ++-- src/ceemdanR.cpp | 2 - src/eemd.h | 21 +++++++--------- src/eemdR.cpp | 2 - src/eemd_routine.c | 4 +-- src/emd.c | 8 +++--- src/emd.h | 8 +++--- src/emd_num_imfsR.cpp | 4 +-- src/extras.h | 4 --- src/extrema.c | 8 +++--- src/extrema.h | 2 - src/spline.c | 4 +-- src/workspace.h | 22 ++++++++--------- tests/testthat/test-bemd.R | 2 - 31 files changed, 162 insertions(+), 142 deletions(-)
Title: Estimation of Optimal Size for a Holdout Set for Updating a
Predictive Score
Description: Predictive scores must be updated with care, because actions taken on the basis of existing risk scores causes bias in risk estimates from the updated score. A holdout set is a straightforward way to manage this problem: a proportion of the population is 'held-out' from computation of the previous risk score. This package provides tools to estimate a size for this holdout set and associated errors. Comprehensive vignettes are included. Please see: Haidar-Wehbe S, Emerson SR, Aslett LJM, Liley J (2022) <doi:10.48550/arXiv.2202.06374> (to appear in Annals of Applied Statistics) for details of methods.
Author: Sami Haidar-Wehbe [aut],
Sam Emerson [aut] ,
Louis Aslett [aut] ,
James Liley [cre, aut]
Maintainer: James Liley <james.liley@durham.ac.uk>
Diff between OptHoldoutSize versions 0.1.0.0 dated 2022-02-18 and 0.1.0.1 dated 2025-04-09
OptHoldoutSize-0.1.0.0/OptHoldoutSize/inst/doc/ASPRE_example.html |only OptHoldoutSize-0.1.0.0/OptHoldoutSize/inst/doc/comparison_of_algorithms.html |only OptHoldoutSize-0.1.0.0/OptHoldoutSize/inst/doc/simulated_example.html |only OptHoldoutSize-0.1.0.1/OptHoldoutSize/DESCRIPTION | 10 OptHoldoutSize-0.1.0.1/OptHoldoutSize/MD5 | 57 ++-- OptHoldoutSize-0.1.0.1/OptHoldoutSize/NEWS.md | 6 OptHoldoutSize-0.1.0.1/OptHoldoutSize/R/OptHoldoutSize_estimation.R | 2 OptHoldoutSize-0.1.0.1/OptHoldoutSize/build/vignette.rds |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/aspre_emulation.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/aspre_parametric.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/ci_cover_a_yn.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/ci_cover_cost_a_yn.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/ci_cover_cost_e_yn.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/ci_cover_e_yn.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/data_example_simulation.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/data_nextpoint_em.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/data_nextpoint_par.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/ohs_array.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/ohs_resample.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/data/params_aspre.RData |binary OptHoldoutSize-0.1.0.1/OptHoldoutSize/inst/doc/ASPRE_example.Rmd | 4 OptHoldoutSize-0.1.0.1/OptHoldoutSize/inst/doc/ASPRE_example.pdf |only OptHoldoutSize-0.1.0.1/OptHoldoutSize/inst/doc/comparison_of_algorithms.R | 12 - OptHoldoutSize-0.1.0.1/OptHoldoutSize/inst/doc/comparison_of_algorithms.Rmd | 4 OptHoldoutSize-0.1.0.1/OptHoldoutSize/inst/doc/comparison_of_algorithms.pdf |only OptHoldoutSize-0.1.0.1/OptHoldoutSize/inst/doc/simulated_example.Rmd | 4 OptHoldoutSize-0.1.0.1/OptHoldoutSize/inst/doc/simulated_example.pdf |only OptHoldoutSize-0.1.0.1/OptHoldoutSize/man/optimal_holdout_size.Rd | 2 OptHoldoutSize-0.1.0.1/OptHoldoutSize/vignettes/ASPRE_example.Rmd | 4 OptHoldoutSize-0.1.0.1/OptHoldoutSize/vignettes/ASPRE_example.html |only OptHoldoutSize-0.1.0.1/OptHoldoutSize/vignettes/comparison_of_algorithms.Rmd | 4 OptHoldoutSize-0.1.0.1/OptHoldoutSize/vignettes/optimal_holdout_sizing.bib | 117 ---------- OptHoldoutSize-0.1.0.1/OptHoldoutSize/vignettes/simulated_example.Rmd | 4 33 files changed, 66 insertions(+), 164 deletions(-)
More information about OptHoldoutSize at CRAN
Permanent link
Title: Open Perimetry Interface
Description: Implementation of the Open Perimetry Interface (OPI) for simulating and controlling visual field machines using R. The OPI is a standard for interfacing with visual field testing machines (perimeters) first started as an open source project with support of Haag-Streit in 2010. It specifies basic functions that allow many visual field tests to be constructed. As of February 2022 it is fully implemented on the Haag-Streit Octopus 900 and 'CrewT ImoVifa' ('Topcon Tempo') with partial implementations on the Centervue Compass, Kowa AP 7000 and Android phones. It also has a cousin: the R package 'visualFields', which has tools for analysing and manipulating visual field data.
Author: Andrew Turpin [cre, aut, cph] ,
David Lawson [ctb, cph],
Ivan Marin-Franch [ctb, cph],
Matthias Muller [ctb],
Jonathan Denniss [ctb, cph],
Astrid Zeman [ctb],
Giovanni Montesano [ctb]
Maintainer: Andrew Turpin <andrew.turpin@lei.org.au>
Diff between OPI versions 3.0.2 dated 2024-07-09 and 3.0.4 dated 2025-04-09
DESCRIPTION | 10 +-- MD5 | 102 +++++++++++++++++++------------------ NEWS.md | 8 ++ R/Compass.r | 8 ++ R/Display.r | 10 +++ R/ImoVifa.r | 18 +++++- R/MAIA.r |only R/Octopus600.r | 2 R/Octopus900.r | 5 + R/PhoneHMD.r | 10 +++ R/PicoVR.r | 10 +++ R/SimGaussian.r | 1 R/SimHenson.r | 6 +- R/SimHensonRT.r | 16 ++--- R/SimNo.r | 5 + R/SimYes.r | 5 + R/full_threshold.r | 4 + R/opi.r | 23 ++++++-- R/zest.r | 4 - README.md | 4 - man/ZEST.Rd | 4 - man/dot-opi_env.Rd | 2 man/full_threshold.Rd | 4 + man/opiClose.Rd | 1 man/opiClose_for_Display.Rd | 2 man/opiClose_for_ImoVifa.Rd | 2 man/opiClose_for_MAIA.Rd |only man/opiClose_for_PhoneHMD.Rd | 2 man/opiClose_for_PicoVR.Rd | 2 man/opiInitialise.Rd | 1 man/opiInitialise_for_Display.Rd | 2 man/opiInitialise_for_ImoVifa.Rd | 2 man/opiInitialise_for_MAIA.Rd |only man/opiInitialise_for_PhoneHMD.Rd | 2 man/opiInitialise_for_PicoVR.Rd | 2 man/opiPresent.Rd | 1 man/opiPresent_for_Display.Rd | 2 man/opiPresent_for_ImoVifa.Rd | 10 ++- man/opiPresent_for_MAIA.Rd |only man/opiPresent_for_PhoneHMD.Rd | 2 man/opiPresent_for_PicoVR.Rd | 2 man/opiPresent_for_SimHensonRT.Rd | 7 -- man/opiQueryDevice.Rd | 1 man/opiQueryDevice_for_Display.Rd | 2 man/opiQueryDevice_for_ImoVifa.Rd | 2 man/opiQueryDevice_for_MAIA.Rd |only man/opiQueryDevice_for_PhoneHMD.Rd | 2 man/opiQueryDevice_for_PicoVR.Rd | 2 man/opiSetup.Rd | 1 man/opiSetup_for_Display.Rd | 2 man/opiSetup_for_ImoVifa.Rd | 2 man/opiSetup_for_MAIA.Rd |only man/opiSetup_for_PhoneHMD.Rd | 2 man/opiSetup_for_PicoVR.Rd | 2 tests/testthat/test-opiPresent.r | 6 +- 55 files changed, 232 insertions(+), 95 deletions(-)
Title: Generating Funky Heatmaps for Data Frames
Description: Allows generating heatmap-like visualisations for data
frames. Funky heatmaps can be fine-tuned by providing annotations of the
columns and rows, which allows assigning multiple palettes or geometries
or grouping rows and columns together in categories.
Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [aut] ,
Louise Deconinck [ctb] ,
Artuur Couckuyt [ctb] ,
Nick Markov [ctb] ,
Luke Zappia [ctb]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between funkyheatmap versions 0.5.1 dated 2025-01-15 and 0.5.2 dated 2025-04-09
funkyheatmap-0.5.1/funkyheatmap/inst/doc/mtcars.R |only funkyheatmap-0.5.1/funkyheatmap/inst/doc/mtcars.Rmd |only funkyheatmap-0.5.1/funkyheatmap/inst/doc/mtcars.html |only funkyheatmap-0.5.1/funkyheatmap/vignettes/mtcars.Rmd |only funkyheatmap-0.5.2/funkyheatmap/DESCRIPTION | 6 +- funkyheatmap-0.5.2/funkyheatmap/MD5 | 28 ++++++---- funkyheatmap-0.5.2/funkyheatmap/NEWS.md | 6 ++ funkyheatmap-0.5.2/funkyheatmap/README.md | 13 +++- funkyheatmap-0.5.2/funkyheatmap/build/partial.rdb |binary funkyheatmap-0.5.2/funkyheatmap/build/vignette.rds |binary funkyheatmap-0.5.2/funkyheatmap/inst/doc/funkyheatmap.R |only funkyheatmap-0.5.2/funkyheatmap/inst/doc/funkyheatmap.Rmd |only funkyheatmap-0.5.2/funkyheatmap/inst/doc/funkyheatmap.html |only funkyheatmap-0.5.2/funkyheatmap/inst/doc/scIB.html | 10 +++ funkyheatmap-0.5.2/funkyheatmap/vignettes/funkyheatmap.Rmd |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/automatic.png |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/automatic.svg |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/manual.png |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/manual.svg |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/straight.png |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/straight.svg |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/vengine.png |only funkyheatmap-0.5.2/funkyheatmap/vignettes/images/vengine.svg |only 23 files changed, 45 insertions(+), 18 deletions(-)
Title: Find Clinical Trial Sites Under-Reporting Adverse Events
Description: Monitoring of Adverse Event (AE) reporting in clinical trials is
important for patient safety. Sites that are under-reporting AEs can be detected
using Bootstrap-based simulations that simulate overall AE reporting. Based on the
simulation an AE under-reporting probability is assigned to each site in a
given trial (Koneswarakantha 2021 <doi:10.1007/s40264-020-01011-5>).
Author: Bjoern Koneswarakantha [aut, cre, cph]
,
F. Hoffmann-La Roche Ltd [cph]
Maintainer: Bjoern Koneswarakantha <bjoern.koneswarakantha@roche.com>
Diff between simaerep versions 0.6.0 dated 2024-09-30 and 0.7.0 dated 2025-04-09
simaerep-0.6.0/simaerep/R/lint.R |only simaerep-0.7.0/simaerep/DESCRIPTION | 8 simaerep-0.7.0/simaerep/MD5 | 79 +-- simaerep-0.7.0/simaerep/NAMESPACE | 2 simaerep-0.7.0/simaerep/NEWS.md | 9 simaerep-0.7.0/simaerep/R/S3_orivisit.R | 43 + simaerep-0.7.0/simaerep/R/S3_simaerep.R | 184 ++++--- simaerep-0.7.0/simaerep/R/inframe.R | 170 ++++-- simaerep-0.7.0/simaerep/R/simaerep.R | 247 ++++++---- simaerep-0.7.0/simaerep/R/simaerep_plot.R | 224 ++++----- simaerep-0.7.0/simaerep/R/simulate_test_data.R | 154 ++++-- simaerep-0.7.0/simaerep/README.md | 14 simaerep-0.7.0/simaerep/inst/WORDLIST | 3 simaerep-0.7.0/simaerep/man/aggr_duplicated_visits.Rd | 4 simaerep-0.7.0/simaerep/man/check_df_visit.Rd | 4 simaerep-0.7.0/simaerep/man/eval_sites.Rd | 14 simaerep-0.7.0/simaerep/man/exp_implicit_missing_visits.Rd | 4 simaerep-0.7.0/simaerep/man/figures/README-unnamed-chunk-3-1.png |binary simaerep-0.7.0/simaerep/man/figures/README-unnamed-chunk-4-1.png |binary simaerep-0.7.0/simaerep/man/get_site_mean_ae_dev.Rd | 4 simaerep-0.7.0/simaerep/man/orivisit.Rd | 4 simaerep-0.7.0/simaerep/man/p_adjust_bh_inframe.Rd | 2 simaerep-0.7.0/simaerep/man/plot.simaerep.Rd | 5 simaerep-0.7.0/simaerep/man/plot_study.Rd | 8 simaerep-0.7.0/simaerep/man/plot_visit_med75.Rd | 8 simaerep-0.7.0/simaerep/man/sim_inframe.Rd | 4 simaerep-0.7.0/simaerep/man/sim_test_data_events.Rd |only simaerep-0.7.0/simaerep/man/sim_test_data_study.Rd | 11 simaerep-0.7.0/simaerep/man/simaerep.Rd | 11 simaerep-0.7.0/simaerep/man/simaerep_inframe.Rd | 5 simaerep-0.7.0/simaerep/man/site_aggr.Rd | 10 simaerep-0.7.0/simaerep/tests/testthat/_snaps/eval_sites.md | 12 simaerep-0.7.0/simaerep/tests/testthat/test_S3_orivisit.R | 33 + simaerep-0.7.0/simaerep/tests/testthat/test_S3_simaerep.R | 16 simaerep-0.7.0/simaerep/tests/testthat/test_check_df_visit.R | 2 simaerep-0.7.0/simaerep/tests/testthat/test_data.R | 67 ++ simaerep-0.7.0/simaerep/tests/testthat/test_event_names.R |only simaerep-0.7.0/simaerep/tests/testthat/test_get_portf_perf.R | 2 simaerep-0.7.0/simaerep/tests/testthat/test_inframe.R | 6 simaerep-0.7.0/simaerep/tests/testthat/test_plot.R | 84 +++ simaerep-0.7.0/simaerep/tests/testthat/test_sim_sites.R | 64 ++ simaerep-0.7.0/simaerep/tests/testthat/test_sim_studies.R | 14 42 files changed, 1078 insertions(+), 457 deletions(-)
Title: The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages
Description: Individual based simulations of hybridizing populations,
where the accumulation of junctions is tracked. Furthermore,
mathematical equations are provided to verify simulation outcomes.
Both simulations and mathematical equations are based on Janzen
(2018, <doi:10.1101/058107>) and Janzen (2022,
<doi:10.1111/1755-0998.13519>).
Author: Thijs Janzen [aut, cre]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between junctions versions 2.1.1 dated 2025-03-12 and 2.1.3 dated 2025-04-09
DESCRIPTION | 8 - MD5 | 32 ++--- NEWS.md | 137 ++++++++++++------------ README.md | 4 build/vignette.rds |binary inst/doc/Overview_of_the_junctions_package.html | 12 +- inst/doc/junctions_vignette.R | 24 ++-- inst/doc/junctions_vignette.html | 4 inst/doc/phased_and_unphased_data.html | 68 +++++------ man/junctions-package.Rd | 6 + tests/testthat/test-backcrossing.R | 1 tests/testthat/test-estim_time_haploid.R | 2 tests/testthat/test-marker_dist.R | 4 tests/testthat/test-one-chrom.R | 1 tests/testthat/test-phased-error.R | 1 tests/testthat/test-phased.R | 2 tests/testthat/test-unphased.R | 12 -- 17 files changed, 159 insertions(+), 159 deletions(-)
Title: Create Elegant Data Visualisations Using the Grammar of Graphics
Description: A system for 'declaratively' creating graphics, based on "The
Grammar of Graphics". You provide the data, tell 'ggplot2' how to map
variables to aesthetics, what graphical primitives to use, and it
takes care of the details.
Author: Hadley Wickham [aut] ,
Winston Chang [aut] ,
Lionel Henry [aut],
Thomas Lin Pedersen [aut, cre]
,
Kohske Takahashi [aut],
Claus Wilke [aut] ,
Kara Woo [aut] ,
Hiroaki Yutani [aut] ,
Dewey Dunnington [aut] ,
Teun van den Brand [aut] ,
Posit, PBC [cph, [...truncated...]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between ggplot2 versions 3.5.1 dated 2024-04-23 and 3.5.2 dated 2025-04-09
ggplot2-3.5.1/ggplot2/man/is.Coord.Rd |only ggplot2-3.5.1/ggplot2/man/is.facet.Rd |only ggplot2-3.5.1/ggplot2/man/is.ggplot.Rd |only ggplot2-3.5.1/ggplot2/man/is.theme.Rd |only ggplot2-3.5.2/ggplot2/DESCRIPTION | 8 ggplot2-3.5.2/ggplot2/MD5 | 140 ggplot2-3.5.2/ggplot2/NAMESPACE | 18 ggplot2-3.5.2/ggplot2/NEWS.md | 1487 +++++----- ggplot2-3.5.2/ggplot2/R/aes.R | 4 ggplot2-3.5.2/ggplot2/R/coord-.R | 16 ggplot2-3.5.2/ggplot2/R/coord-cartesian-.R | 2 ggplot2-3.5.2/ggplot2/R/facet-.R | 20 ggplot2-3.5.2/ggplot2/R/fortify.R | 2 ggplot2-3.5.2/ggplot2/R/geom-.R | 3 ggplot2-3.5.2/ggplot2/R/geom-defaults.R | 48 ggplot2-3.5.2/ggplot2/R/ggproto.R | 21 ggplot2-3.5.2/ggplot2/R/guide-.R | 10 ggplot2-3.5.2/ggplot2/R/guide-axis.R | 2 ggplot2-3.5.2/ggplot2/R/guide-colorbar.R | 3 ggplot2-3.5.2/ggplot2/R/guide-legend.R | 3 ggplot2-3.5.2/ggplot2/R/guides-.R | 14 ggplot2-3.5.2/ggplot2/R/labels.R | 33 ggplot2-3.5.2/ggplot2/R/layer.R | 7 ggplot2-3.5.2/ggplot2/R/margins.R | 6 ggplot2-3.5.2/ggplot2/R/plot-build.R | 12 ggplot2-3.5.2/ggplot2/R/plot-construction.R | 6 ggplot2-3.5.2/ggplot2/R/plot.R | 15 ggplot2-3.5.2/ggplot2/R/position-.R | 4 ggplot2-3.5.2/ggplot2/R/scale-.R | 4 ggplot2-3.5.2/ggplot2/R/scale-colour.R | 2 ggplot2-3.5.2/ggplot2/R/stat-.R | 4 ggplot2-3.5.2/ggplot2/R/stat-ellipse.R | 2 ggplot2-3.5.2/ggplot2/R/theme-current.R | 4 ggplot2-3.5.2/ggplot2/R/theme-elements.R | 18 ggplot2-3.5.2/ggplot2/R/theme.R | 21 ggplot2-3.5.2/ggplot2/README.md | 12 ggplot2-3.5.2/ggplot2/build/vignette.rds |binary ggplot2-3.5.2/ggplot2/inst/doc/extending-ggplot2.Rmd | 2 ggplot2-3.5.2/ggplot2/inst/doc/extending-ggplot2.html | 160 - ggplot2-3.5.2/ggplot2/inst/doc/ggplot2-in-packages.R | 10 ggplot2-3.5.2/ggplot2/inst/doc/ggplot2-in-packages.html | 4 ggplot2-3.5.2/ggplot2/inst/doc/ggplot2-specs.html | 90 ggplot2-3.5.2/ggplot2/inst/doc/ggplot2.html | 54 ggplot2-3.5.2/ggplot2/man/element.Rd | 6 ggplot2-3.5.2/ggplot2/man/figures/README-example-1.png |binary ggplot2-3.5.2/ggplot2/man/get_geom_defaults.Rd |only ggplot2-3.5.2/ggplot2/man/ggplot2-ggproto.Rd | 4 ggplot2-3.5.2/ggplot2/man/ggplot_gtable.Rd | 4 ggplot2-3.5.2/ggplot2/man/ggproto.Rd | 9 ggplot2-3.5.2/ggplot2/man/guide_colourbar.Rd | 2 ggplot2-3.5.2/ggplot2/man/is_tests.Rd |only ggplot2-3.5.2/ggplot2/man/labs.Rd | 7 ggplot2-3.5.2/ggplot2/man/stat_ellipse.Rd | 2 ggplot2-3.5.2/ggplot2/tests/testthat/Rplots.pdf |binary ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/coord-cartesian.md | 2 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/coord-flip.md | 2 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/coord-map.md | 2 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/coord-transform.md | 2 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/coord_sf.md | 2 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-basic.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-check-overlap.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-negative-rotation.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-positive-rotation.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-text-dodged-into-rows-cols.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-vertical-negative-rotation.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-vertical-rotation.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-zero-breaks.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/_snaps/guides/axis-guides-zero-rotation.svg | 41 ggplot2-3.5.2/ggplot2/tests/testthat/test-function-args.R | 2 ggplot2-3.5.2/ggplot2/tests/testthat/test-ggsave.R | 6 ggplot2-3.5.2/ggplot2/tests/testthat/test-labels.R | 65 ggplot2-3.5.2/ggplot2/tests/testthat/test-theme.R | 12 ggplot2-3.5.2/ggplot2/tests/testthat/test-utilities-checks.R | 29 ggplot2-3.5.2/ggplot2/vignettes/extending-ggplot2.Rmd | 2 74 files changed, 1394 insertions(+), 1406 deletions(-)
Title: Pre-Processing of 'GENEActiv' Data
Description: Analytics to read in and segment raw 'GENEActiv' accelerometer data into epochs and events.
For more details on the 'GENEActiv' device, see <https://activinsights.com/resources/geneactiv-support-1-2/>.
Author: Joss Langford [aut],
Ian Long [aut],
Jia Ying Chua [aut, cre],
Activinsights Ltd [cph]
Maintainer: Jia Ying Chua <jiayingc@activinsights.com>
Diff between GENEAcore versions 1.0.0 dated 2025-04-01 and 1.0.1 dated 2025-04-09
DESCRIPTION | 8 MD5 | 26 R/MPI_calibrate.R | 560 +++++++------- R/MPI_create.R | 1368 +++++++++++++++++------------------ R/MPI_detect.R | 788 ++++++++++---------- R/aggregate_periods.R | 508 ++++++------ R/geneacore.R | 492 ++++++------ R/sample_binfile.R | 316 ++++---- inst/doc/GENEAcore.Rmd | 990 ++++++++++++------------- tests/testthat/test-MPI_calibrate.R | 3 tests/testthat/test-MPI_create.R | 29 tests/testthat/test-sample_binfile.R | 9 tests/testthat/test-step_counter.R | 93 +- vignettes/GENEAcore.Rmd | 990 ++++++++++++------------- 14 files changed, 3092 insertions(+), 3088 deletions(-)
Title: ASCII Formatting for Values and Tables
Description: We provide a framework for rendering complex tables to ASCII,
and a set of formatters for transforming values or sets of values into
ASCII-ready display strings.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [ctb] ,
Joe Zhu [aut, cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between formatters versions 0.5.10 dated 2025-01-08 and 0.5.11 dated 2025-04-09
DESCRIPTION | 23 ++- MD5 | 52 ++++---- NEWS.md | 6 R/format_value.R | 242 +++++++++++++++++++++++++++------------ R/generics.R | 14 +- R/matrix_form.R | 1 R/mpf_exporters.R | 40 ++++-- R/pagination.R | 36 +++-- R/tostring.R | 18 +- build/vignette.rds |binary inst/WORDLIST | 5 inst/doc/formatters.html | 13 +- man/export_as_pdf.Rd | 7 - man/export_as_rtf.Rd | 4 man/export_as_txt.Rd | 7 - man/format_value.Rd | 12 + man/formatters-package.Rd | 6 man/make_row_df.Rd | 10 + man/matrix_form.Rd | 10 + man/mpf_to_rtf.Rd | 5 man/paginate_indices.Rd | 10 + man/propose_column_widths.Rd | 11 + man/round_fmt.Rd | 15 +- man/tostring.Rd | 7 - man/vert_pag_indices.Rd | 7 - tests/testthat/test-formatters.R | 125 ++++++++++++++++++++ tests/testthat/test-pagination.R | 2 27 files changed, 520 insertions(+), 168 deletions(-)
Title: Easy Management of File Names
Description: Create descriptive file names with ease. New file names are
automatically (but optionally) time stamped and placed in date stamped
directories. Streamline your analysis pipeline with input and output file
names that have informative tags and proper file extensions.
Author: David J. H. Shih [aut, cre]
Maintainer: David J. H. Shih <djh.shih@gmail.com>
Diff between filenamer versions 0.2.4 dated 2024-04-04 and 0.3 dated 2025-04-09
DESCRIPTION | 16 +++++++++----- MD5 | 10 ++++----- R/filename.R | 45 +++++++++++++++++++++++++++++++++++------ R/make_path.R | 4 ++- man/as.character.filename.Rd | 6 ++++- tests/testthat/test_filename.R | 7 ++++++ 6 files changed, 69 insertions(+), 19 deletions(-)
Title: Groupwise Statistics, LSmeans, Linear Estimates, Utilities
Description: Utility package containing:
1) Facilities for working with grouped data: 'do' something to data
stratified 'by' some variables.
2) LSmeans (least-squares means), general linear estimates.
3) Restrict functions to a smaller domain.
4) Miscellaneous other utilities.
Author: Ulrich Halekoh [aut, cph],
Soeren Hoejsgaard [aut, cre, cph]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between doBy versions 4.6.25 dated 2025-01-30 and 4.6.26 dated 2025-04-09
DESCRIPTION | 6 MD5 | 54 +++--- NAMESPACE | 12 + NEWS.md | 8 R/DATA_doby.R | 117 +++++++++++-- R/NAMESPACE_doby.R | 5 R/a_handle_dots_and_symbols.R |only R/by_lmBy.R | 68 +++++--- R/by_splitBy.R | 160 ++++++++++++++---- R/by_transformBy.R | 2 R/doby_utilities.R | 1 R/linear_modelling.R |only R/linest_matrix.R | 15 + R/plot_functions.r | 70 ++++++-- data/child_growth.RData |only data/crickets.RData |binary data/shoes.RData |binary data/wine.RData |only inst/doc/doby.html | 355 +++++++++++++++++++++--------------------- inst/doc/linest_lsmeans.pdf |binary inst/doc/section_fun.html | 222 +++++++++++--------------- man/add_int.Rd |only man/add_pred.Rd |only man/add_resid.Rd |only man/by-lmby.Rd | 8 man/by-split.Rd | 45 +++-- man/child_growth.Rd |only man/crickets.Rd | 21 +- man/data-wine.Rd |only man/income.Rd | 26 --- man/plot_lm.Rd | 8 man/reciprocal.Rd |only man/response.Rd |only man/shoes.Rd |only 34 files changed, 725 insertions(+), 478 deletions(-)
Title: A Repository of Bayesian Networks from the Academic Literature
Description: A collection of Bayesian networks (discrete, Gaussian, and conditional linear Gaussian) collated from recent academic literature. The 'bnRep_summary' object provides an overview of the Bayesian networks in the repository and the package documentation includes details about the variables in each network. A Shiny app to explore the repository can be launched with 'bnRep_app()' and is available online at <https://manueleleonelli.shinyapps.io/bnRep>. Reference: 'M. Leonelli' (2025) <doi:10.1016/j.neucom.2025.129502>.
Author: Manuele Leonelli [aut, cre, cph]
Maintainer: Manuele Leonelli <manuele.leonelli@ie.edu>
Diff between bnRep versions 0.0.2 dated 2024-10-01 and 0.0.3 dated 2025-04-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- README.md | 10 ++++++---- inst/CITATION | 9 ++++----- inst/doc/overview.html | 2 +- 5 files changed, 19 insertions(+), 18 deletions(-)
Title: Automated and Early Detection of Seasonal Epidemic Onset and
Burden Levels
Description: A powerful tool for automating the early detection of seasonal epidemic
onsets in time series data. It offers the ability to estimate growth rates
across consecutive time intervals, calculate the sum of cases (SoC) within
those intervals, and estimate seasonal onsets within user defined seasons.
With use of a disease-specific threshold it also offers the possibility to
estimate seasonal onset of epidemics.
Additionally it offers the ability to estimate burden levels for seasons
based on historical data. It is aimed towards epidemiologists,
public health professionals, and researchers seeking to identify and respond
to seasonal epidemics in a timely fashion.
Author: Sofia Myrup Otero [aut] ,
Kasper Schou Telkamp [aut] ,
Lasse Engbo Christiansen [aut, cre]
,
Rasmus Skytte Randloev [rev] ,
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Lasse Engbo Christiansen <lsec@ssi.dk>
Diff between aedseo versions 0.1.2 dated 2023-11-27 and 0.3.0 dated 2025-04-09
aedseo-0.1.2/aedseo/R/aedseo.R |only aedseo-0.1.2/aedseo/R/tsd.R |only aedseo-0.1.2/aedseo/R/utils-pipe.R |only aedseo-0.1.2/aedseo/build/partial.rdb |only aedseo-0.1.2/aedseo/inst/doc/aedseo_introduction.R |only aedseo-0.1.2/aedseo/inst/doc/aedseo_introduction.Rmd |only aedseo-0.1.2/aedseo/inst/doc/aedseo_introduction.html |only aedseo-0.1.2/aedseo/man/pipe.Rd |only aedseo-0.1.2/aedseo/man/predict.aedseo.Rd |only aedseo-0.1.2/aedseo/man/summary.aedseo.Rd |only aedseo-0.1.2/aedseo/tests/testthat/test-aedseo.R |only aedseo-0.1.2/aedseo/tests/testthat/test-tsd.R |only aedseo-0.1.2/aedseo/vignettes/aedseo_introduction.Rmd |only aedseo-0.3.0/aedseo/DESCRIPTION | 46 aedseo-0.3.0/aedseo/MD5 | 125 +- aedseo-0.3.0/aedseo/NAMESPACE | 28 aedseo-0.3.0/aedseo/NEWS.md | 64 + aedseo-0.3.0/aedseo/R/0_documentation.R |only aedseo-0.3.0/aedseo/R/1_utils.R |only aedseo-0.3.0/aedseo/R/aedseo-package.R | 18 aedseo-0.3.0/aedseo/R/autoplot.R | 587 ++++++++-- aedseo-0.3.0/aedseo/R/combined_seasonal_output.R |only aedseo-0.3.0/aedseo/R/consecutive_growth_warnings.R |only aedseo-0.3.0/aedseo/R/epi_calendar.R | 46 aedseo-0.3.0/aedseo/R/fit_growth_rate.R | 20 aedseo-0.3.0/aedseo/R/fit_percentiles.R |only aedseo-0.3.0/aedseo/R/generate_seasonal_data.R |only aedseo-0.3.0/aedseo/R/historical_summary.R |only aedseo-0.3.0/aedseo/R/plot.R | 89 - aedseo-0.3.0/aedseo/R/predict.R | 88 - aedseo-0.3.0/aedseo/R/seasonal_burden_levels.R |only aedseo-0.3.0/aedseo/R/seasonal_onset.R |only aedseo-0.3.0/aedseo/R/summary.R | 286 +++- aedseo-0.3.0/aedseo/R/to_time_series.R |only aedseo-0.3.0/aedseo/README.md | 61 - aedseo-0.3.0/aedseo/build/vignette.rds |binary aedseo-0.3.0/aedseo/inst/doc/aedseo.R |only aedseo-0.3.0/aedseo/inst/doc/aedseo.Rmd |only aedseo-0.3.0/aedseo/inst/doc/aedseo.html |only aedseo-0.3.0/aedseo/inst/doc/burden_levels.R |only aedseo-0.3.0/aedseo/inst/doc/burden_levels.Rmd |only aedseo-0.3.0/aedseo/inst/doc/burden_levels.html |only aedseo-0.3.0/aedseo/inst/doc/generate_seasonal_wave.R |only aedseo-0.3.0/aedseo/inst/doc/generate_seasonal_wave.Rmd |only aedseo-0.3.0/aedseo/inst/doc/generate_seasonal_wave.html |only aedseo-0.3.0/aedseo/inst/doc/seasonal_onset.R |only aedseo-0.3.0/aedseo/inst/doc/seasonal_onset.Rmd |only aedseo-0.3.0/aedseo/inst/doc/seasonal_onset.html |only aedseo-0.3.0/aedseo/man/aedseo-package.Rd | 7 aedseo-0.3.0/aedseo/man/aedseo.Rd | 81 - aedseo-0.3.0/aedseo/man/autoplot.Rd | 206 ++- aedseo-0.3.0/aedseo/man/combined_seasonal_output.Rd |only aedseo-0.3.0/aedseo/man/consecutive_growth_warnings.Rd |only aedseo-0.3.0/aedseo/man/epi_calendar.Rd | 27 aedseo-0.3.0/aedseo/man/figures/lifecycle-archived.svg | 42 aedseo-0.3.0/aedseo/man/figures/lifecycle-defunct.svg | 42 aedseo-0.3.0/aedseo/man/figures/lifecycle-deprecated.svg | 42 aedseo-0.3.0/aedseo/man/figures/lifecycle-experimental.svg | 42 aedseo-0.3.0/aedseo/man/figures/lifecycle-maturing.svg | 42 aedseo-0.3.0/aedseo/man/figures/lifecycle-questioning.svg | 42 aedseo-0.3.0/aedseo/man/figures/lifecycle-soft-deprecated.svg | 42 aedseo-0.3.0/aedseo/man/figures/lifecycle-stable.svg | 58 aedseo-0.3.0/aedseo/man/figures/lifecycle-superseded.svg | 42 aedseo-0.3.0/aedseo/man/fit_growth_rate.Rd | 21 aedseo-0.3.0/aedseo/man/fit_percentiles.Rd |only aedseo-0.3.0/aedseo/man/generate_seasonal_data.Rd |only aedseo-0.3.0/aedseo/man/historical_summary.Rd |only aedseo-0.3.0/aedseo/man/plot.Rd | 79 - aedseo-0.3.0/aedseo/man/predict.tsd_onset.Rd |only aedseo-0.3.0/aedseo/man/seasonal_burden_levels.Rd |only aedseo-0.3.0/aedseo/man/seasonal_onset.Rd |only aedseo-0.3.0/aedseo/man/summary.tsd_burden_levels.Rd |only aedseo-0.3.0/aedseo/man/summary.tsd_onset.Rd |only aedseo-0.3.0/aedseo/man/to_time_series.Rd |only aedseo-0.3.0/aedseo/man/tsd.Rd | 59 - aedseo-0.3.0/aedseo/tests/testthat.R | 24 aedseo-0.3.0/aedseo/tests/testthat/helper-setup.R |only aedseo-0.3.0/aedseo/tests/testthat/test-combined_seasonal_output.R |only aedseo-0.3.0/aedseo/tests/testthat/test-consecutive_growth_warnings.R |only aedseo-0.3.0/aedseo/tests/testthat/test-epi_calendar.R | 50 aedseo-0.3.0/aedseo/tests/testthat/test-fit_growth_rate.R | 8 aedseo-0.3.0/aedseo/tests/testthat/test-fit_percentiles.R |only aedseo-0.3.0/aedseo/tests/testthat/test-generate_seasonal_data.R |only aedseo-0.3.0/aedseo/tests/testthat/test-historical_summary.R |only aedseo-0.3.0/aedseo/tests/testthat/test-predict.R | 195 ++- aedseo-0.3.0/aedseo/tests/testthat/test-seasonal_burden_levels.R |only aedseo-0.3.0/aedseo/tests/testthat/test-seasonal_onset.R |only aedseo-0.3.0/aedseo/tests/testthat/test-summary.R | 101 + aedseo-0.3.0/aedseo/tests/testthat/test-to_time_series.R |only aedseo-0.3.0/aedseo/vignettes/aedseo.Rmd |only aedseo-0.3.0/aedseo/vignettes/burden_levels.Rmd |only aedseo-0.3.0/aedseo/vignettes/generate_seasonal_wave.Rmd |only aedseo-0.3.0/aedseo/vignettes/seasonal_onset.Rmd |only 93 files changed, 1749 insertions(+), 961 deletions(-)
Title: Computing Graph Structures on WikiPathways
Description: Converts pathways from 'WikiPathways' GPML format or
'KEGG' KGML format into 'igraph' objects. Includes tools to find all
cycles in the resulting graphs and determine which ones involve
negative feedback (inhibition).
Author: Kevin R. Coombes [aut, cre],
Polina Bombina [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between WayFindR versions 0.1.2 dated 2024-04-10 and 0.3.1 dated 2025-04-09
WayFindR-0.1.2/WayFindR/inst/doc/WayFindR_graphs.R |only WayFindR-0.1.2/WayFindR/inst/doc/WayFindR_graphs.Rmd |only WayFindR-0.1.2/WayFindR/inst/doc/WayFindR_graphs.html |only WayFindR-0.1.2/WayFindR/vignettes/WayFindR_graphs.Rmd |only WayFindR-0.3.1/WayFindR/DESCRIPTION | 25 +- WayFindR-0.3.1/WayFindR/MD5 | 49 +++-- WayFindR-0.3.1/WayFindR/NAMESPACE | 25 ++ WayFindR-0.3.1/WayFindR/R/05-toIgraph.R | 2 WayFindR-0.3.1/WayFindR/R/09-ellipse.R |only WayFindR-0.3.1/WayFindR/R/10-keggUtil.R |only WayFindR-0.3.1/WayFindR/R/11-graphNEL.R |only WayFindR-0.3.1/WayFindR/R/12-kgml.R |only WayFindR-0.3.1/WayFindR/R/sysdata.rda |binary WayFindR-0.3.1/WayFindR/R/zzz.R |only WayFindR-0.3.1/WayFindR/build/vignette.rds |binary WayFindR-0.3.1/WayFindR/data/edgeColors.rda |binary WayFindR-0.3.1/WayFindR/data/edgeTypes.rda |binary WayFindR-0.3.1/WayFindR/data/nodeColors.rda |binary WayFindR-0.3.1/WayFindR/data/nodeShapes.rda |binary WayFindR-0.3.1/WayFindR/inst/doc/WayFindR_getStarted.html | 121 +++++++------- WayFindR-0.3.1/WayFindR/inst/doc/WayFindR_metrics.R |only WayFindR-0.3.1/WayFindR/inst/doc/WayFindR_metrics.Rmd |only WayFindR-0.3.1/WayFindR/inst/doc/WayFindR_metrics.html |only WayFindR-0.3.1/WayFindR/inst/doc/WayFindR_plots.R |only WayFindR-0.3.1/WayFindR/inst/doc/WayFindR_plots.Rmd |only WayFindR-0.3.1/WayFindR/inst/doc/WayFindR_plots.html |only WayFindR-0.3.1/WayFindR/inst/pathways/kegg_hsa00510.xml |only WayFindR-0.3.1/WayFindR/inst/profile |only WayFindR-0.3.1/WayFindR/man/02-util.Rd | 4 WayFindR-0.3.1/WayFindR/man/03-main.Rd | 80 +++++---- WayFindR-0.3.1/WayFindR/man/10-kgml-util.Rd |only WayFindR-0.3.1/WayFindR/man/11-coerce.Rd |only WayFindR-0.3.1/WayFindR/tests/06-testShapes.R |only WayFindR-0.3.1/WayFindR/tests/10-testKeggUtil.R |only WayFindR-0.3.1/WayFindR/tests/11-testkgml.R |only WayFindR-0.3.1/WayFindR/vignettes/WayFindR_metrics.Rmd |only WayFindR-0.3.1/WayFindR/vignettes/WayFindR_plots.Rmd |only 37 files changed, 182 insertions(+), 124 deletions(-)
Title: ToxCast Data Analysis Pipeline
Description: The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.
Author: Richard S Judson [ctb, ths] ,
Dayne L Filer [aut],
Jason Brown [ctb] ,
Sarah E Davidson-Fritz [ctb] ,
Madison Feshuk [cre] ,
Carter Thunes [ctb],
Ashley Ko [ctb],
Kelly Carstens [ctb] ,
Todd Zurlinden [ctb] ,
Lori Kolaczkowski [ctb],
Kurt Dunham [ctb [...truncated...]
Maintainer: Madison Feshuk <feshuk.madison@epa.gov>
Diff between tcpl versions 3.2.0 dated 2024-10-09 and 3.2.1 dated 2025-04-09
DESCRIPTION | 18 MD5 | 10 NEWS.md | 4 build/vignette.rds |binary inst/doc/Introduction_Appendices.html | 2813 +++++++++++++++++----------------- tests/testthat/_snaps/tcplDefine.md | 350 ++-- 6 files changed, 1610 insertions(+), 1585 deletions(-)
Title: Quantile-Frequency Analysis (QFA) of Time Series
Description: Quantile-frequency analysis (QFA) of time series based on trigonometric quantile regression.
Spline quantile regression (SQR) for regression coefficient estimation.
References:
[1] Li, T.-H. (2012) "Quantile periodograms," Journal of the American Statistical
Association, 107, 765–776, <doi:10.1080/01621459.2012.682815>.
[2] Li, T.-H. (2014) Time Series with Mixed Spectra, CRC Press, <doi:10.1201/b15154>
[3] Li, T.-H. (2022) "Quantile Fourier transform, quantile series, and nonparametric
estimation of quantile spectra," <doi:10.48550/arXiv.2211.05844>.
[4] Li, T.-H. (2024) "Quantile crossing spectrum and spline autoregression
estimation," <doi:10.48550/arXiv.2412.02513>.
[5] Li, T.-H. (2024) "Spline autoregression method for estimation of quantile spectrum,"
<doi:10.48550/arXiv.2412.17163>.
[6] Li, T.-H., and Megiddo, N. (2025) "Spline quantile regression,"
<doi:10.48550/arXiv.2501.03883>.
Author: Ta-Hsin Li [cre, aut]
Maintainer: Ta-Hsin Li <thl024@outlook.com>
Diff between qfa versions 4.0 dated 2025-01-08 and 4.1 dated 2025-04-09
qfa-4.0/qfa/R/qfa4.0.R |only qfa-4.1/qfa/DESCRIPTION | 16 ++++---- qfa-4.1/qfa/MD5 | 66 ++++++++++++++++++------------------ qfa-4.1/qfa/R/qfa4.1.R |only qfa-4.1/qfa/man/per.Rd | 2 - qfa-4.1/qfa/man/qacf.Rd | 2 - qfa-4.1/qfa/man/qcser.Rd | 2 - qfa-4.1/qfa/man/qdft.Rd | 2 - qfa-4.1/qfa/man/qdft2qacf.Rd | 2 - qfa-4.1/qfa/man/qdft2qper.Rd | 2 - qfa-4.1/qfa/man/qdft2qser.Rd | 2 - qfa-4.1/qfa/man/qfa.plot.Rd | 2 - qfa-4.1/qfa/man/qkl.divergence.Rd | 2 - qfa-4.1/qfa/man/qper.Rd | 2 - qfa-4.1/qfa/man/qper2.Rd | 2 - qfa-4.1/qfa/man/qser.Rd | 2 - qfa-4.1/qfa/man/qser2ar.Rd | 2 - qfa-4.1/qfa/man/qser2qacf.Rd | 2 - qfa-4.1/qfa/man/qser2sar.Rd | 2 - qfa-4.1/qfa/man/qspec.ar.Rd | 2 - qfa-4.1/qfa/man/qspec.lw.Rd | 2 - qfa-4.1/qfa/man/qspec.sar.Rd | 2 - qfa-4.1/qfa/man/qspec2qcoh.Rd | 2 - qfa-4.1/qfa/man/sar.eq.bootstrap.Rd | 2 - qfa-4.1/qfa/man/sar.eq.test.Rd | 2 - qfa-4.1/qfa/man/sar.gc.bootstrap.Rd | 2 - qfa-4.1/qfa/man/sar.gc.coef.Rd | 2 - qfa-4.1/qfa/man/sar.gc.test.Rd | 2 - qfa-4.1/qfa/man/sqdft.Rd | 8 ++-- qfa-4.1/qfa/man/sqdft.fit.Rd | 6 +-- qfa-4.1/qfa/man/sqr.Rd | 6 +-- qfa-4.1/qfa/man/sqr.fit.Rd | 4 +- qfa-4.1/qfa/man/sqr.fit.optim.Rd | 2 - qfa-4.1/qfa/man/tqr.fit.Rd | 2 - qfa-4.1/qfa/man/tsqr.fit.Rd | 2 - 35 files changed, 81 insertions(+), 79 deletions(-)
Title: Variable Selection in Partial Least Squares
Description: Interfaces and methods for variable selection in Partial Least
Squares. The methods include filter methods, wrapper methods and embedded
methods. Both regression and classification is supported.
Author: Kristian Hovde Liland [aut, cre]
,
Tahir Mehmood [ctb],
Solve Saeboe [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between plsVarSel versions 0.9.12 dated 2024-05-22 and 0.9.13 dated 2025-04-09
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS | 4 ++++ R/REP.R | 2 ++ R/T2.R | 7 ++++++- R/filters.R | 2 +- R/stpls.R | 7 +++++-- man/VIP.Rd | 2 +- man/rep_pls.Rd | 2 ++ man/stpls.Rd | 7 +++++-- 10 files changed, 40 insertions(+), 21 deletions(-)
Title: Photosynthetic Gas Exchange Analysis
Description: Read, process, fit, and analyze photosynthetic gas exchange
measurements. Documentation is provided by several vignettes; also see
Lochocki, Salesse-Smith, & McGrath (2025) <doi:10.1111/pce.15501>.
Author: Edward B. Lochocki [cre, aut] ,
Coralie E. Salesse-Smith [aut]
,
Justin M. McGrath [aut] ,
PhotoGEA authors [cph]
Maintainer: Edward B. Lochocki <eloch@illinois.edu>
Diff between PhotoGEA versions 1.3.1 dated 2025-04-08 and 1.3.2 dated 2025-04-09
DESCRIPTION | 8 ++-- MD5 | 23 +++++++------ NAMESPACE | 3 + NEWS.md | 8 +++- R/check_response_curve_data.R | 19 ++++++----- R/exdf.R | 50 ++++++++++++++++++++---------- README.md | 4 ++ inst/doc/PhotoGEA.html | 2 - man/read_cr3000.Rd | 2 - man/read_licor_6800_Excel.Rd | 4 +- man/read_licor_6800_plaintext.Rd | 2 - tests/testthat/test-factorize_id_column.R | 15 +++++++-- tests/testthat/test-rbind.exdf.R |only 13 files changed, 91 insertions(+), 49 deletions(-)
Title: A Nondecimated Lifting Transform for Signal Denoising
Description: Uses a modified lifting algorithm on which it builds the
nondecimated lifting transform. It has applications in wavelet
shrinkage.
Author: Marina Knight [aut],
Matt Nunes [aut, cre]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>
Diff between nlt versions 2.2-1 dated 2018-07-10 and 2.2-2 dated 2025-04-09
DESCRIPTION | 12 +++++++----- MD5 | 6 +++--- man/fwtnpperm.Rd | 4 ++-- man/transmatdualperm.Rd | 6 +++--- 4 files changed, 15 insertions(+), 13 deletions(-)
Title: Named Capture to Data Tables
Description: User-friendly functions for extracting a data
table (row for each match, column for each group)
from non-tabular text data using regular expressions,
and for melting columns that match a regular expression.
Patterns are defined using a readable syntax
that makes it easy to build complex patterns
in terms of simpler, re-usable sub-patterns.
Named R arguments are translated to column names
in the output; capture groups without names are used
internally in order to provide a standard interface
to three regular expression 'C' libraries
('PCRE', 'RE2', 'ICU').
Output can also include numeric columns via
user-specified type conversion functions.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between nc versions 2025.1.21 dated 2025-01-21 and 2025.3.24 dated 2025-04-09
DESCRIPTION | 6 MD5 | 28 NAMESPACE | 1 NEWS | 4 R/alevels.R |only build/vignette.rds |binary inst/doc/v0-overview.html | 372 +++--- inst/doc/v1-capture-first.html | 1278 +++++++++++---------- inst/doc/v2-capture-all.html | 878 +++++++------- inst/doc/v3-capture-melt.html | 956 ++++++++------- inst/doc/v4-comparisons.html | 1942 ++++++++++++++++---------------- inst/doc/v5-helpers.html | 382 +++--- inst/doc/v6-engines.html | 317 +++-- inst/doc/v7-capture-glob.html | 957 ++++++++------- man/alevels.Rd |only tests/testthat/test-CRAN-alternatives.R | 26 16 files changed, 3791 insertions(+), 3356 deletions(-)
Title: Resampling Algorithms for 'mlr3' Framework
Description: A supervised learning algorithm inputs a train set,
and outputs a prediction function, which can be used on a test set.
If each data point belongs to a subset
(such as geographic region, year, etc), then
how do we know if subsets are similar enough so that
we can get accurate predictions on one subset,
after training on Other subsets?
And how do we know if training on All subsets would improve
prediction accuracy, relative to training on the Same subset?
SOAK, Same/Other/All K-fold cross-validation, <doi:10.48550/arXiv.2410.08643>
can be used to answer these question, by fixing a test subset,
training models on Same/Other/All subsets, and then
comparing test error rates (Same versus Other and Same versus All).
Also provides code for estimating how many train samples
are required to get accurate predictions on a test set.
Author: Toby Hocking [aut, cre] ,
Michel Lang [ctb] ,
Bernd Bischl [ctb] ,
Jakob Richter [ctb] ,
Patrick Schratz [ctb] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [ctb],
Florian Pfisterer [ctb] ,
Raphael Sonabend [ctb] , [...truncated...]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between mlr3resampling versions 2024.9.6 dated 2024-09-11 and 2025.3.30 dated 2025-04-09
DESCRIPTION | 40 MD5 | 52 NAMESPACE | 11 NEWS | 178 R/ResamplingBase.R | 166 R/ResamplingSameOtherCV.R | 244 R/ResamplingSameOtherSizesCV.R | 357 R/ResamplingVariableSizeTrainCV.R | 190 R/pvalue.R |only R/score.R | 50 R/zzz.R | 37 build/vignette.rds |binary inst/doc/Newer_resamplers.R | 1069 - inst/doc/Newer_resamplers.Rmd | 1671 +- inst/doc/Newer_resamplers.html | 3717 ++-- inst/doc/Older_resamplers.R | 1944 +- inst/doc/Older_resamplers.Rmd | 2888 +-- inst/doc/Older_resamplers.html |26117 ++++++++++++++++++----------------- man/AZtrees.Rd | 120 man/ResamplingSameOtherCV.Rd | 355 man/ResamplingSameOtherSizesCV.Rd | 422 man/ResamplingVariableSizeTrainCV.Rd | 310 man/pvalue.Rd |only man/score.Rd | 139 tests/testthat.R | 4 tests/testthat/test-CRAN.R | 888 - vignettes/Newer_resamplers.Rmd | 1671 +- vignettes/Older_resamplers.Rmd | 2888 +-- 28 files changed, 23573 insertions(+), 21955 deletions(-)
More information about mlr3resampling at CRAN
Permanent link
Title: Wrapper for 'minimap2'
Description: Wrapper for 'Minimap2'. 'Minimap2' is a very valuable long read aligner for the Pacbio and Oxford Nanopore Technologies sequencing platforms. 'minimapR' is an R wrapper for 'minimap2' which was developed by Heng Li <me@liheng.org>.
*SPECIAL NOTES
1. Examples can only be run from 'GitHub' installation.
2. 'conda' or 'mamba' must be used to install 'minimapR' on your system.
3. For Windows users, 'minimap2' and 'samtools' can be installed via MSYS2, instructions are provided when 'minimap2_installation()' is run.
Li, Heng (2018) <doi:10.1093/bioinformatics/bty191> "Minimap2: pairwise alignment for nucleotide sequences".
Author: Jake Reed [aut, cre] ,
Pradyun Pulipaka [ctb]
Maintainer: Jake Reed <hreed.ga@gmail.com>
Diff between minimapR versions 0.0.1.1 dated 2025-03-30 and 0.0.1.3 dated 2025-04-09
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- R/minimapR-helper.R | 16 ++++++++++++++-- inst/doc/minimapR.html | 22 +++++++++++----------- 4 files changed, 33 insertions(+), 20 deletions(-)
Title: Continuous Confidence Interval Plots using t-Distribution
Description: Provides an extension to 'ggplot2'
(Wickham, 2016, <doi:10.1007/978-3-319-24277-4>) for creating two types of
continuous confidence interval plots (Violin CI and Gradient CI plots),
typically for the sample mean. These plots contain multiple user-defined
confidence areas with varying colours, defined by the underlying
t-distribution used to compute standard confidence intervals for the mean of
the normal distribution when the variance is unknown. Two types of plots are
available, a gradient plot with rectangular areas, and a violin plot where
the shape (horizontal width) is defined by the probability density function
of the t-distribution. These visualizations are studied in
(Helske, Helske, Cooper, Ynnerman, and Besancon, 2021)
<doi:10.1109/TVCG.2021.3073466>.
Author: Jouni Helske [aut, cre]
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between ggstudent versions 0.1.1-1 dated 2020-05-11 and 0.1.2 dated 2025-04-09
DESCRIPTION | 30 ++++++++++++++---------- MD5 | 12 ++++----- R/statStudent.R | 17 ++++++++----- README.md | 15 ++++++++---- man/GeomStudent.Rd | 4 ++- man/StatStudent.Rd | 4 ++- man/geom_student.Rd | 64 ++++++++++++++++++++-------------------------------- 7 files changed, 75 insertions(+), 71 deletions(-)
Title: Rename and Encode Data Frames Using External Crosswalk Files
Description: A pair of functions for renaming and encoding data frames
using external crosswalk files. It is especially useful when
constructing master data sets from multiple smaller data
sets that do not name or encode variables consistently
across files. Based on similar commands in 'Stata'.
Author: Benjamin Skinner [aut, cre]
Maintainer: Benjamin Skinner <ben@btskinner.io>
Diff between crosswalkr versions 0.2.6 dated 2020-01-08 and 0.3.0 dated 2025-04-09
DESCRIPTION | 26 +- MD5 | 33 +-- NEWS.md | 4 R/crosswalkr.R | 5 R/data.R | 22 ++ build/vignette.rds |binary data/sttercrosswalk.rda |only inst/doc/collapse.R | 2 inst/doc/collapse.Rmd | 2 inst/doc/collapse.html | 230 +++++++++++++----------- inst/doc/crosswalkr.R | 6 inst/doc/crosswalkr.html | 375 +++++++++++++++++++++++----------------- inst/extdata/sttercrosswalk.rda |only man/crosswalkr.Rd | 14 + man/encodefrom.Rd | 4 man/renamefrom.Rd | 4 man/stcrosswalk.Rd | 6 man/sttercrosswalk.Rd |only vignettes/collapse.Rmd | 2 19 files changed, 431 insertions(+), 304 deletions(-)
Title: Complex-Valued Wavelet Lifting Estimators of the Hurst Exponent
for Irregularly Sampled Time Series
Description: Implementation of Hurst exponent estimators based on complex-valued lifting wavelet energy from Knight, M. I and Nunes, M. A. (2018) <doi:10.1007/s11222-018-9820-8>.
Author: Matt Nunes [aut, cre],
Marina Knight [aut]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>
Diff between CliftLRD versions 0.1-1 dated 2018-07-18 and 0.1-2 dated 2025-04-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/CliftLRD-package.Rd | 2 +- man/liftHurstC.Rd | 8 ++++---- man/liftHurstCC.Rd | 8 ++++---- man/meanC.Rd | 2 +- 6 files changed, 19 insertions(+), 19 deletions(-)
Title: Asymptotic Timing
Description: Computing and visualizing comparative
asymptotic timings of different algorithms and code versions.
Also includes functionality for comparing empirical timings with
expected references such as linear or quadratic,
<https://en.wikipedia.org/wiki/Asymptotic_computational_complexity>
Also includes functionality for measuring asymptotic memory and other
quantities.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between atime versions 2025.1.21 dated 2025-01-21 and 2025.4.1 dated 2025-04-09
DESCRIPTION | 6 MD5 | 22 +- NEWS | 4 R/predict.R | 13 + build/vignette.rds |binary inst/doc/Custom_Plots.html | 200 +++++++++++--------------- inst/doc/Custom_References.html | 278 ++++++++++++++++-------------------- inst/doc/Custom_Units.html | 213 ++++++++++++--------------- inst/doc/cum_median.html | 210 +++++++++++---------------- inst/doc/regex.html | 238 +++++++++++++------------------ inst/doc/sparse.html | 306 +++++++++++++++++++--------------------- tests/testthat/test-CRAN.R | 5 12 files changed, 677 insertions(+), 818 deletions(-)
Title: Conduct Simulation Studies with a Minimal Amount of Source Code
Description: Tool for statistical simulations that have two components.
One component generates the data and the other one
analyzes the data. The main aims of the package are the reduction
of the administrative source code (mainly loops and management code for the
results) and a simple applicability of the package that allows the user to
quickly learn how to work with it. Parallel computing is
also supported. Finally, convenient functions are provided to summarize the
simulation results.
Author: Marsel Scheer [aut, cre]
Maintainer: Marsel Scheer <scheer@freescience.de>
Diff between simTool versions 1.1.7 dated 2020-09-22 and 1.1.8 dated 2025-04-09
DESCRIPTION | 13 MD5 | 24 - NEWS.md |only R/expand_tibble.R | 2 R/extract_fun_and_parameter.R | 11 R/print.eval_tibbles.R | 1 README.md |only build/vignette.rds |binary inst/doc/simTool.R | 350 +++++++-------- inst/doc/simTool.Rmd | 8 inst/doc/simTool.html | 923 +++++++++++++++++++++++++----------------- man/expand_tibble.Rd | 2 man/print.eval_tibbles.Rd | 1 vignettes/simTool.Rmd | 8 14 files changed, 781 insertions(+), 562 deletions(-)
Title: Model-Free Covariate Selection
Description: Model-free selection of covariates under unconfoundedness for situations where the parameter of interest is an average causal effect. This package is based on model-free backward elimination algorithms proposed in de Luna, Waernbaum and Richardson (2011). Marginal co-ordinate hypothesis testing is used in situations where all covariates are continuous while kernel-based smoothing appropriate for mixed data is used otherwise.
Author: Jenny Haeggstroem [aut, cre],
Emma Persson [aut],
Sandy Weisberg [aut]
Maintainer: Jenny Haeggstroem <jenny.haggstrom@umu.se>
Diff between CovSel versions 1.2.1 dated 2015-11-09 and 1.2.2 dated 2025-04-09
DESCRIPTION | 21 +++++++++++++++------ MD5 | 12 ++++++++---- NAMESPACE | 9 +++++++-- R/dr.R |only R/psave.R |only R/psir.R |only R/zzz.R |only man/cov.sel.Rd | 2 +- man/lalonde.Rd | 2 +- 9 files changed, 32 insertions(+), 14 deletions(-)
Title: A Method to Download Department of Education College Scorecard
Data
Description: A method to download Department of Education College
Scorecard data using the public API
<https://collegescorecard.ed.gov/data/data-documentation/>. It is based on
the 'dplyr' model of piped commands to select and filter data in a
single chained function call. An API key from the U.S. Department of
Education is required.
Author: Benjamin Skinner [aut, cre]
Maintainer: Benjamin Skinner <ben@btskinner.io>
Diff between rscorecard versions 0.30.0 dated 2024-10-23 and 0.31.0 dated 2025-04-09
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 10 +++++++--- R/sysdata.rda |binary man/rscorecard.Rd | 2 +- tests/testthat/test-get.R | 6 +++--- 6 files changed, 21 insertions(+), 17 deletions(-)
Title: Model Infectious Disease Parameters from Serosurveys
Description: An easy-to-use and efficient tool to estimate infectious diseases parameters using serological data. Implemented models include SIR models (basic_sir_model(), static_sir_model(), mseir_model(), sir_subpops_model()), parametric models (polynomial_model(), fp_model()), nonparametric models (lp_model()), semiparametric models (penalized_splines_model()), hierarchical models (hierarchical_bayesian_model()).
The package is based on the book "Modeling Infectious Disease Parameters Based on Serological and Social Contact Data: A Modern Statistical Perspective" (Hens, Niel & Shkedy, Ziv & Aerts, Marc & Faes, Christel & Damme, Pierre & Beutels, Philippe., 2013) <doi:10.1007/978-1-4614-4072-7>.
Author: Anh Phan Truong Quynh [aut, cre],
Nguyen Pham Nguyen The [aut],
Long Bui Thanh [aut],
Tuyen Huynh [aut],
Thinh Ong [aut] ,
Marc Choisy [aut]
Maintainer: Anh Phan Truong Quynh <anhptq@oucru.org>
Diff between serosv versions 1.0.1 dated 2024-10-18 and 1.1.0 dated 2025-04-09
DESCRIPTION | 21 +- MD5 | 142 ++++++++++-------- NAMESPACE | 14 + NEWS.md | 5 R/compare_models.R |only R/correct_prevalence.R |only R/fractional_polynomial_models.R | 40 ++--- R/hierarchical_bayesian_model.R | 27 +-- R/mixture_model.R | 2 R/nonparametric.R | 28 +-- R/plots.R | 15 + R/polynomial_models.R | 66 ++------ R/semiparametric_models.R | 29 +-- R/stanmodels.R | 3 R/utils.R | 49 ++++++ R/weibull_model.R | 30 +-- README.md | 57 ++++++- build/vignette.rds |binary inst/doc/data_transformation.Rmd | 2 inst/doc/data_transformation.html | 2 inst/doc/hierarchical_model.R | 4 inst/doc/hierarchical_model.Rmd | 4 inst/doc/hierarchical_model.html | 136 +++++++++-------- inst/doc/imperfect_test.R |only inst/doc/imperfect_test.Rmd |only inst/doc/imperfect_test.html |only inst/doc/linelisting_vs_aggregated.R |only inst/doc/linelisting_vs_aggregated.Rmd |only inst/doc/linelisting_vs_aggregated.html |only inst/doc/model_selection.R |only inst/doc/model_selection.Rmd |only inst/doc/model_selection.html |only inst/doc/nonparametric_model.R | 8 - inst/doc/nonparametric_model.Rmd | 8 - inst/doc/nonparametric_model.html | 10 - inst/doc/parametric_model.R | 40 +---- inst/doc/parametric_model.Rmd | 44 +---- inst/doc/parametric_model.html | 165 +++------------------ inst/doc/semiparametric_model.R | 11 - inst/doc/semiparametric_model.Rmd | 15 + inst/doc/semiparametric_model.html | 75 ++++----- inst/doc/visualizing_model.R | 10 - inst/doc/visualizing_model.Rmd | 10 - inst/doc/visualizing_model.html | 42 ++--- inst/stan/fra_2.stan | 4 inst/stan/fra_3.stan | 4 inst/stan/log_logistic.stan | 4 inst/stan/prevalence_correction.stan |only man/compare_models.Rd |only man/correct_prevalence.Rd |only man/farrington_model.Rd | 19 -- man/figures/README-unnamed-chunk-48-1.png |only man/figures/README-unnamed-chunk-49-1.png |only man/figures/README-unnamed-chunk-49-2.png |only man/find_best_fp_powers.Rd | 10 - man/fp_model.Rd | 12 - man/hierarchical_bayesian_model.Rd | 15 - man/lp_model.Rd | 21 -- man/penalized_spline_model.Rd | 16 -- man/polynomial_model.Rd | 28 --- man/transform_data.Rd | 4 man/weibull_model.Rd | 17 -- src/RcppExports.cpp | 2 src/stanExports_fra_2.h | 8 - src/stanExports_fra_3.h | 8 - src/stanExports_log_logistic.h | 8 - src/stanExports_prevalence_correction.cc |only src/stanExports_prevalence_correction.h |only tests/testthat/test-fractional-polynomial-models.R | 6 tests/testthat/test-hierarchical_bayesian_model.R | 6 tests/testthat/test-nonparametric.R | 6 tests/testthat/test-penalized_spline_model.R | 23 +- tests/testthat/test-polynomial-models.R | 27 +-- tests/testthat/test-weibull-model.R | 8 - vignettes/data_transformation.Rmd | 2 vignettes/hierarchical_model.Rmd | 4 vignettes/imperfect_test.Rmd |only vignettes/linelisting_vs_aggregated.Rmd |only vignettes/model_selection.Rmd |only vignettes/nonparametric_model.Rmd | 8 - vignettes/parametric_model.Rmd | 44 +---- vignettes/semiparametric_model.Rmd | 15 + vignettes/visualizing_model.Rmd | 10 - 83 files changed, 640 insertions(+), 813 deletions(-)
Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of R documentation objects,
including functions reprompt() and ereprompt() for updating 'Rd'
documentation for functions, methods and classes; 'Rd' macros for
citations and import of references from 'bibtex' files for use in
'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and
inserting snippets of 'R' code and the results of its evaluation or
creating graphics on the fly; and many functions for manipulation of
references and Rd files.
Author: Georgi N. Boshnakov [aut, cre]
,
Duncan Murdoch [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between Rdpack versions 2.6.3 dated 2025-03-16 and 2.6.4 dated 2025-04-08
DESCRIPTION | 6 MD5 | 20 NEWS.md | 7 build/partial.rdb |binary inst/doc/Inserting_bibtex_references.pdf |binary inst/doc/Inserting_figures_and_evaluated_examples.pdf |binary tests/testthat/StructureClasses.Rd | 362 +++++++++--------- tests/testthat/as.character.f_usage.Rd | 124 +++--- tests/testthat/myshow-methods.Rd | 40 - tests/testthat/show.Rd | 162 ++++---- tests/testthat/test-reprompt.R | 37 + 11 files changed, 386 insertions(+), 372 deletions(-)
Title: Bindings to 'Tree-Sitter'
Description: Provides bindings to 'Tree-sitter', an incremental parsing
system for programming tools. 'Tree-sitter' builds concrete syntax
trees for source files of any language, and can efficiently update
those syntax trees as the source file is edited. It also includes a
robust error recovery system that provides useful parse results even
in the presence of syntax errors.
Author: Davis Vaughan [aut, cre],
Posit Software, PBC [cph, fnd],
Tree-sitter authors [cph]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between treesitter versions 0.1.0 dated 2024-06-24 and 0.2.0 dated 2025-04-08
DESCRIPTION | 11 MD5 | 60 ++-- NAMESPACE | 1 NEWS.md | 14 + R/query.R | 344 +++++++++++++++++++++++- README.md | 6 man/query-accessors.Rd | 17 - man/query-matches-and-captures.Rd | 269 +++++++++++++++++++ man/query.Rd | 47 ++- src/decl/query-decl.h | 2 src/decl/query-matches-decl.h | 17 + src/init.c | 4 src/node.c | 6 src/query-matches.c | 163 +++++++++-- src/query.c | 12 src/rlang/env.h | 4 src/rlang/fn.h | 5 src/rlang/rlang.c | 2 src/tree-sitter/lib/include/tree_sitter/api.h | 19 + src/tree-sitter/lib/src/clock.h | 2 src/tree-sitter/lib/src/lexer.c | 13 src/tree-sitter/lib/src/parser.c | 14 - src/tree-sitter/lib/src/parser.h | 1 src/tree-sitter/lib/src/query.c | 33 +- src/tree-sitter/lib/src/wasm_store.c | 21 - src/utils.c | 33 +- src/utils.h | 7 tests/testthat/_snaps/print.md | 51 ++- tests/testthat/_snaps/query.md | 8 tests/testthat/test-print.R | 13 tests/testthat/test-query.R | 364 +++++++++++++++++++++++++- 31 files changed, 1384 insertions(+), 179 deletions(-)
Title: Sample Size Calculation for RNA-Seq Experimental Design
Description: We propose a procedure for sample size calculation while
controlling false discovery rate for RNA-seq experimental design. Our
procedure depends on the Voom method proposed for RNA-seq data analysis
by Law et al. (2014) <DOI:10.1186/gb-2014-15-2-r29> and the sample size
calculation method proposed for microarray experiments by Liu and Hwang
(2007) <DOI:10.1093/bioinformatics/btl664>. We develop a set of functions
that calculates appropriate sample sizes for two-sample t-test for RNA-seq
experiments with fixed or varied set of parameters. The outputs also contain a
plot of power versus sample size, a table of power at different sample sizes,
and a table of critical test values at different sample sizes.
To install this package, please use
'source("http://bioconductor.org/biocLite.R"); biocLite("ssizeRNA")'.
For R version 3.5 or greater, please use
'if(!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")}; BiocManager::install("ssizeRNA")'.
Author: Ran Bi [aut, cre],
Peng Liu [aut],
Tim Triche [ctb]
Maintainer: Ran Bi <biranpier@gmail.com>
Diff between ssizeRNA versions 1.3.2 dated 2019-08-20 and 1.3.3 dated 2025-04-08
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- R/ssize.twoSampVaryDelta.R | 6 +++--- build/partial.rdb |only inst/doc/ssizeRNA.pdf |binary man/hammer.eset.Rd | 2 +- man/ssize.twoSampVaryDelta.Rd | 6 +++--- 7 files changed, 17 insertions(+), 16 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions II
Description: A collection of fast statistical and utility functions for data analysis. Functions for regression, maximum likelihood, column-wise statistics and many more have been included. C++ has been utilized to speed up the functions. References: Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>.
Author: Manos Papadakis [aut, cre, cph],
Michail Tsagris [aut],
Stefanos Fafalios [aut],
Marios Dimitriadis [aut],
Manos Lasithiotakis [aut],
Nikolaos Kontemeniotis [ctb]
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast2 versions 0.1.5.2 dated 2024-03-10 and 0.1.5.3 dated 2025-04-08
Rfast2-0.1.5.2/Rfast2/R/lm.parboot.R |only Rfast2-0.1.5.2/Rfast2/man/lm.parboot.Rd |only Rfast2-0.1.5.2/Rfast2/man/negbin.regs.Rd |only Rfast2-0.1.5.2/Rfast2/man/perm.ttest2.Rd |only Rfast2-0.1.5.2/Rfast2/man/propjs.reg.Rd |only Rfast2-0.1.5.3/Rfast2/DESCRIPTION | 26 - Rfast2-0.1.5.3/Rfast2/MD5 | 241 +++++---- Rfast2-0.1.5.3/Rfast2/NAMESPACE | 4 Rfast2-0.1.5.3/Rfast2/NEWS.md | 22 Rfast2-0.1.5.3/Rfast2/R/bessel.R |only Rfast2-0.1.5.3/Rfast2/R/eqdist.etest.R |only Rfast2-0.1.5.3/Rfast2/R/frechet.nn.R |only Rfast2-0.1.5.3/Rfast2/R/kernel.R |only Rfast2-0.1.5.3/Rfast2/R/lm.boot.R |only Rfast2-0.1.5.3/Rfast2/R/means_tests.R | 78 ++- Rfast2-0.1.5.3/Rfast2/R/naive.bayes.classifiers.R | 2 Rfast2-0.1.5.3/Rfast2/R/normal.etest.R | 2 Rfast2-0.1.5.3/Rfast2/R/pca_and_pcr.R | 7 Rfast2-0.1.5.3/Rfast2/R/random_generators.R | 2 Rfast2-0.1.5.3/Rfast2/R/rbeta1.R | 2 Rfast2-0.1.5.3/Rfast2/R/reg.mle.lda.R | 4 Rfast2-0.1.5.3/Rfast2/R/silhouette.R |only Rfast2-0.1.5.3/Rfast2/build/partial.rdb |binary Rfast2-0.1.5.3/Rfast2/inst/include/Rfast2/helpers.hpp | 232 ++++++--- Rfast2-0.1.5.3/Rfast2/inst/include/Rfast2/matrix.hpp | 1 Rfast2-0.1.5.3/Rfast2/inst/include/Rfast2/templates.h | 19 Rfast2-0.1.5.3/Rfast2/inst/include/Rfast2/templates_rfast2.h | 55 ++ Rfast2-0.1.5.3/Rfast2/inst/include/Rfast2/vector.hpp | 28 - Rfast2-0.1.5.3/Rfast2/man/Rfast2-package.Rd | 3 Rfast2-0.1.5.3/Rfast2/man/Runif.Rd | 31 - Rfast2-0.1.5.3/Rfast2/man/add.term.Rd | 15 Rfast2-0.1.5.3/Rfast2/man/batch.logistic.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/bessel.Rd |only Rfast2-0.1.5.3/Rfast2/man/bic.regs.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/big.knn.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/bigknn.cv.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/boot.james.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/boot.student2.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/boot.ttest1.Rd | 17 Rfast2-0.1.5.3/Rfast2/man/censpois.mle.Rd | 7 Rfast2-0.1.5.3/Rfast2/man/circ.cor1.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/collognorm.mle.Rd | 9 Rfast2-0.1.5.3/Rfast2/man/cor_test.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/covdist.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/covlikel.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/depth.mahala.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/el.cor.test.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/empirical.entropy.Rd | 3 Rfast2-0.1.5.3/Rfast2/man/eqdist.etest.Rd |only Rfast2-0.1.5.3/Rfast2/man/fedhc.skel.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/fp.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/frechet.nn.Rd |only Rfast2-0.1.5.3/Rfast2/man/gammapois.mle.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/gammaregs.Rd | 3 Rfast2-0.1.5.3/Rfast2/man/halfcauchy.mle.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/hcf.circaov.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/het.lmfit.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/hp.reg.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/is.skew.symmetric.Rd | 6 Rfast2-0.1.5.3/Rfast2/man/kernel.Rd |only Rfast2-0.1.5.3/Rfast2/man/lm.boot.Rd |only Rfast2-0.1.5.3/Rfast2/man/lm.bsreg.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/logiquant.regs.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/macros/system.Rd | 3 Rfast2-0.1.5.3/Rfast2/man/mci.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/mmhc.skel.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/mmpc.Rd | 10 Rfast2-0.1.5.3/Rfast2/man/moranI.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/multinomreg.cv.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/multivm.mle.Rd | 1 Rfast2-0.1.5.3/Rfast2/man/nb.cv.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/negbin.reg.Rd | 41 + Rfast2-0.1.5.3/Rfast2/man/normal.etest.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/omp2.Rd | 3 Rfast2-0.1.5.3/Rfast2/man/pc.sel.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/pca.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/pcr.Rd | 6 Rfast2-0.1.5.3/Rfast2/man/perm.ttest.Rd |only Rfast2-0.1.5.3/Rfast2/man/prophelling.reg.Rd |only Rfast2-0.1.5.3/Rfast2/man/propols.reg.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/purka.mle.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/regmlelda.cv.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/score.zipregs.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/silhouette.Rd |only Rfast2-0.1.5.3/Rfast2/man/sp.logiregs.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/tobit.reg.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/weib.regs.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/weibullnb.pred.Rd | 4 Rfast2-0.1.5.3/Rfast2/man/welch.tests.Rd | 2 Rfast2-0.1.5.3/Rfast2/man/wild.boot.Rd | 9 Rfast2-0.1.5.3/Rfast2/src/Eval.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/Makevars | 4 Rfast2-0.1.5.3/Rfast2/src/Makevars.win | 4 Rfast2-0.1.5.3/Rfast2/src/Random.cpp | 256 ++++++++-- Rfast2-0.1.5.3/Rfast2/src/Random.h | 248 ++++++++-- Rfast2-0.1.5.3/Rfast2/src/add_term.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/calc_qpois_regs.h | 1 Rfast2-0.1.5.3/Rfast2/src/censweib_reg.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/col_row_utilities.cpp | 3 Rfast2-0.1.5.3/Rfast2/src/colbeta_mle.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/colcauchy_mle.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/colspml_mle.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/cts.h | 1 Rfast2-0.1.5.3/Rfast2/src/fbed_reg.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/fedhc_skeleton.cpp | 15 Rfast2-0.1.5.3/Rfast2/src/frechet_nn.cpp |only Rfast2-0.1.5.3/Rfast2/src/gamma_reg.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/gamma_regs.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/init.c | 22 Rfast2-0.1.5.3/Rfast2/src/is_symmetric.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/kernel.cpp |only Rfast2-0.1.5.3/Rfast2/src/mmhc_skeleton.cpp | 11 Rfast2-0.1.5.3/Rfast2/src/mmp_c.cpp | 2 Rfast2-0.1.5.3/Rfast2/src/mmp_c.h | 1 Rfast2-0.1.5.3/Rfast2/src/mmpc2.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/mn.cpp | 5 Rfast2-0.1.5.3/Rfast2/src/mn.h | 3 Rfast2-0.1.5.3/Rfast2/src/multinom_reg.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/negbin_reg.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/negbin_regs.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/reg_lib2.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/reg_lib2.h | 1 Rfast2-0.1.5.3/Rfast2/src/reg_lib_helper.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/reg_lib_helper.h | 1 Rfast2-0.1.5.3/Rfast2/src/sf.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/skel_helper.cpp | 13 Rfast2-0.1.5.3/Rfast2/src/skel_helper.h | 11 Rfast2-0.1.5.3/Rfast2/src/univariate_mle.cpp | 11 Rfast2-0.1.5.3/Rfast2/src/utilities.cpp | 267 ++++++----- Rfast2-0.1.5.3/Rfast2/src/weib_regs.cpp | 1 Rfast2-0.1.5.3/Rfast2/src/welch_tests.cpp | 21 Rfast2-0.1.5.3/Rfast2/src/wild_boot.cpp | 9 132 files changed, 1308 insertions(+), 632 deletions(-)