Title: Optimal Convex M-Estimation for Linear Regression via Antitonic
Score Matching
Description: Performs linear regression with respect to a data-driven convex loss function that is chosen to minimize the asymptotic covariance of the resulting M-estimator. The convex loss function is estimated in 5 steps: (1) form an initial OLS (ordinary least squares) or LAD (least absolute deviation) estimate of the regression coefficients; (2) use the resulting residuals to obtain a kernel estimator of the error density; (3) estimate the score function of the errors by differentiating the logarithm of the kernel density estimate; (4) compute the L2 projection of the estimated score function onto the set of decreasing functions; (5) take a negative antiderivative of the projected score function estimate. Newton's method (with Hessian modification) is then used to minimize the convex empirical risk function. Further details of the method are given in Feng et al. (2024) <doi:10.48550/arXiv.2403.16688>.
Author: Yu-Chun Kao [aut],
Oliver Y. Feng [aut],
Lucy Xia [aut],
Yang Feng [aut],
Min Xu [aut, cre],
Richard J. Samworth [aut]
Maintainer: Min Xu <min.cut@gmail.com>
Diff between asm versions 0.2.0 dated 2024-05-10 and 0.2.1 dated 2025-01-28
DESCRIPTION | 16 +++++++++++----- MD5 | 6 ++++-- R/asm.R | 29 +++++++++++++++++++++++++++++ tests |only 4 files changed, 44 insertions(+), 7 deletions(-)
Title: Joint Feature Screening via Sparse MLE
Description: Feature screening is a powerful tool in processing ultrahigh dimensional data. It attempts to screen out most irrelevant features in preparation for a more elaborate analysis. Xu and Chen (2014)<doi:10.1080/01621459.2013.879531> proposed an effective screening method SMLE, which naturally incorporates the joint effects among features in the screening process. This package provides an efficient implementation of SMLE-screening for high-dimensional linear, logistic, and Poisson models. The package also provides a function for conducting accurate post-screening feature selection based on an iterative hard-thresholding procedure and a user-specified selection criterion.
Author: Qianxiang Zang [aut, cre],
Chen Xu [aut],
Kelly Burkett [aut]
Maintainer: Qianxiang Zang <SMLEmaintainer@gmail.com>
Diff between SMLE versions 2.1-1 dated 2024-02-12 and 2.2-2 dated 2025-01-28
DESCRIPTION | 24 ++++++++++++---- MD5 | 21 +++++++++++--- R/ICselect.R | 80 ++++++++++++++++++++++++++++---------------------------- R/SMLE.R | 5 +-- R/SMLE_fit.R | 2 + R/smle_select.R | 54 ++++++++++++++++++++----------------- build |only inst/doc |only tests |only vignettes |only 10 files changed, 107 insertions(+), 79 deletions(-)
Title: 'ggplot2' Pattern Geoms
Description: Provides 'ggplot2' geoms filled with various patterns. Includes a patterned version of every 'ggplot2' geom that has a region that can be filled with a pattern. Provides a suite of 'ggplot2' aesthetics and scales for controlling pattern appearances. Supports over a dozen builtin patterns (every pattern implemented by 'gridpattern') as well as allowing custom user-defined patterns.
Author: Mike FC [aut],
Trevor L. Davis [aut, cre] ,
ggplot2 authors [aut]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between ggpattern versions 1.1.3 dated 2024-12-13 and 1.1.4 dated 2025-01-28
DESCRIPTION | 6 MD5 | 32 +- NEWS.md | 7 R/scale-pattern-alpha.R | 2 R/scale-pattern-linetype.R | 2 R/scale-pattern-size.R | 2 inst/doc/developing-patterns.R | 4 inst/doc/developing-patterns.html | 93 +++----- inst/doc/patterns-noise.R | 53 ++-- inst/doc/patterns-noise.Rmd | 59 +++-- inst/doc/patterns-noise.html | 377 ++++++++++++++++------------------ inst/doc/patterns-points.html | 193 ++++++++--------- inst/doc/patterns-stripes.html | 219 +++++++++---------- man/scale_pattern_alpha_continuous.Rd | 2 man/scale_pattern_linetype.Rd | 2 man/scale_pattern_size_continuous.Rd | 2 vignettes/patterns-noise.Rmd | 59 +++-- 17 files changed, 545 insertions(+), 569 deletions(-)
Title: Data from the 'Access to Opportunities Project (AOP)'
Description: Download data from the 'Access to Opportunities Project (AOP)'. The
'aopdata' package brings annual estimates of access to employment,
health, education and social assistance services by transport mode,
as well as data on the spatial distribution of population, jobs,
health care, schools and social assistance facilities at a fine
spatial resolution for all cities included in the project. More
info on the 'AOP' website <https://www.ipea.gov.br/acessooportunidades/en/>.
Author: Rafael H. M. Pereira [aut, cre]
,
Daniel Herszenhut [aut] ,
Marcus Saraiva [aut] ,
Carlos Kaue Vieira Braga [aut]
,
Diego Bogado Tomasiello [ctb],
Joao Bazzo [ctb],
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between aopdata versions 1.1.0 dated 2024-08-27 and 1.1.1 dated 2025-01-28
DESCRIPTION | 6 MD5 | 55 - NEWS.md | 10 R/download_metadata.R | 20 R/read_access.R | 4 R/read_grid.R | 2 R/read_landuse.R | 4 R/read_population.R | 3 R/utils.R | 8 README.md | 311 +++++----- build/vignette.rds |binary inst/doc/access_inequality.html | 14 inst/doc/access_maps.html | 11 inst/doc/data_dic_en.html | 4 inst/doc/data_dic_pt.html | 4 inst/doc/intro_to_aopdata.R | 56 - inst/doc/intro_to_aopdata.Rmd | 56 - inst/doc/intro_to_aopdata.html | 64 +- inst/doc/landuse_maps.html | 8 inst/doc/population_maps.html | 8 man/check_connection.Rd | 2 man/download_metadata.Rd | 6 tests/tests_rafa/test_rafa.R | 1012 +++++++++++++++++----------------- tests/testthat/test_read_access.R | 45 + tests/testthat/test_read_grid.R | 26 tests/testthat/test_read_landuse.R | 45 + tests/testthat/test_read_population.R | 35 + tests/testthat/test_utils.R |only vignettes/intro_to_aopdata.Rmd | 56 - 29 files changed, 1039 insertions(+), 836 deletions(-)
Title: Functional Data Analysis using Splines and Orthogonal Spline
Bases
Description: Splines are efficiently represented through their Taylor expansion at the knots. The representation accounts for the support sets and is thus suitable for sparse functional data. Two cases of boundary conditions are considered: zero-boundary or periodic-boundary for all derivatives except the last. The periodical splines are represented graphically using polar coordinates. The B-splines and orthogonal bases of splines that reside on small total support are implemented. The orthogonal bases are referred to as 'splinets' and are utilized for functional data analysis. Random spline generator is implemented as well as all fundamental algebraic and calculus operations on splines. The optimal, in the least square sense, functional fit by 'splinets' to data consisting of sampled values of functions as well as splines build over another set of knots is obtained and used for functional data analysis. The S4-version of the object oriented R is used. <doi:10.48550/arXiv.2102.00733>, < [...truncated...]
Author: Rani Basna [aut],
Xijia Liu [aut],
Hiba Nassar [aut],
Krzysztof Podgorski [aut, cre, cph]
Maintainer: Krzysztof Podgorski <Krzysztof.Podgorski@stat.lu.se>
Diff between Splinets versions 1.5.0 dated 2023-03-06 and 1.5.1 dated 2025-01-28
DESCRIPTION | 28 - MD5 | 87 ++-- R/AuxFun.R | 44 +- R/Examples/ExDintegra.R | 4 R/Examples/ExEvspline.R | 2 R/Examples/ExExsupp.R | 2 R/Examples/ExGramian.R | 6 R/Examples/ExIntegra.R | 6 R/Examples/ExIsSplinets.R | 10 R/Examples/ExLincomb.R | 6 R/Examples/ExProject.R | 8 R/Examples/ExRspline.R | 2 R/Examples/ExSplinetsObject.R | 9 R/Examples/ExSym2one.R | 2 R/Examples/ExWind.R | 6 R/class_Splinets.R | 12 R/fun_construct.R | 10 R/fun_deriva.R | 6 R/fun_evspline.R | 2 R/fun_gramian.R | 6 R/fun_integra.R | 6 R/fun_lincomb.R | 2 R/fun_project.R | 800 +++++++++++++++++++++--------------------- R/fun_refine.R | 2 R/fun_rspline.R | 2 R/fun_seq2dyad.R | 2 R/fun_splinet.R | 14 R/meth_is_spline.R | 6 man/Splinets-class.Rd | 15 man/construct.Rd | 8 man/deriva.Rd | 2 man/dintegra.Rd | 4 man/evspline.Rd | 2 man/exsupp.Rd | 2 man/figures |only man/gramian.Rd | 8 man/integra.Rd | 8 man/is.splinets.Rd | 12 man/lincomb.Rd | 6 man/project.Rd | 18 man/rspline.Rd | 4 man/seq2dyad.Rd | 2 man/splinet.Rd | 10 man/sym2one.Rd | 2 man/wind.Rd | 6 45 files changed, 605 insertions(+), 596 deletions(-)
Title: Tools for Environmental Analyses, Ecotoxicology and Various R
Functions
Description: Contains miscellaneous functions useful for managing 'NetCDF' files (see <https://en.wikipedia.org/wiki/NetCDF>), get moon phase and time for sun rise and fall, tide level, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between HelpersMG versions 6.3 dated 2024-11-19 and 6.4 dated 2025-01-28
DESCRIPTION | 8 ++--- MD5 | 30 ++++++++++---------- NAMESPACE | 2 - NEWS | 13 ++++++++ R/HelpersMG-package.R | 4 +- R/MHalgoGen.R | 14 ++++----- R/as.parameters.R | 9 +++--- R/flexit.R | 68 ++++++++++++++++++++++++++++++++++------------ R/plot.mcmcComposite.R | 52 +++++++++++++++++++++++++---------- R/sysdata.rda |binary inst/shiny/cutter/ui.R | 2 - man/HelpersMG-package.Rd | 4 +- man/MHalgoGen.Rd | 10 ++---- man/as.parameters.Rd | 8 +++-- man/flexit.Rd | 9 ++++-- man/plot.mcmcComposite.Rd | 10 +++++- 16 files changed, 160 insertions(+), 83 deletions(-)
Title: Fast Agent-Based Epi Models
Description: A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.
Author: George Vega Yon [aut] ,
Derek Meyer [aut] ,
Andrew Pulsipher [aut, cre] ,
Susan Holmes [rev] ,
Abinash Satapathy [rev] ,
Carinogurjao [rev],
Centers for Disease Control and Prevention [fnd]
Maintainer: Andrew Pulsipher <pulsipher.a@gmail.com>
Diff between epiworldR versions 0.6.0.0 dated 2025-01-16 and 0.6.1.0 dated 2025-01-28
DESCRIPTION | 7 +++-- MD5 | 18 ++++++------- NEWS.md | 11 +++++--- inst/CITATION | 2 - inst/doc/getting-started.html | 8 +++--- inst/doc/likelihood-free-mcmc.html | 10 +++---- inst/doc/mixing.html | 6 ++-- inst/doc/run-multiple.html | 4 +-- inst/include/epiworld/epiworld.hpp | 2 - inst/include/epiworld/math/lfmcmc/lfmcmc-meat-print.hpp | 21 ++++++++++++++-- 10 files changed, 55 insertions(+), 34 deletions(-)
Title: Create Satisficing 'Excel', 'HTML', 'LaTeX', and 'RTF' Tables
using a Simple Formula
Description: Create "good enough" tables with a single formula. 'tablespan' tables
can be exported to 'Excel', 'HTML', 'LaTeX', and 'RTF' by leveraging
the packages 'openxlsx' and 'gt'. See <https://jhorzek.github.io/tablespan/> for
an introduction.
Author: Jannik H. Orzek [aut, cre, cph]
Maintainer: Jannik H. Orzek <jannik.orzek@mailbox.org>
Diff between tablespan versions 0.1.7 dated 2024-12-06 and 0.2.1 dated 2025-01-28
DESCRIPTION | 9 MD5 | 46 + NAMESPACE | 4 R/as_excel.R | 233 +++++--- R/tab_styles.R | 264 ++++++++-- R/tablespan.R | 17 README.md | 32 + man/cell_style.Rd | 4 man/figures/tablespan_example_cars_color.png |only man/style_color.Rd |only man/tablespan.Rd | 2 man/tbl_styles.Rd | 79 ++ tests/testthat/test-Merge-Cells.R |only tests/testthat/test-data_frame.R |only tests/testthat/test-excel-cars.R | 131 ++++ tests/testthat/xlsx_files/cars.xlsx |binary tests/testthat/xlsx_files/cars_893485.xlsx |only tests/testthat/xlsx_files/cars_987349.xlsx |only tests/testthat/xlsx_files/cars_additional_spanners.xlsx |binary tests/testthat/xlsx_files/cars_additional_spanners_left_right.xlsx |binary tests/testthat/xlsx_files/cars_cell_styles.xlsx |binary tests/testthat/xlsx_files/cars_complex_merge.xlsx |only tests/testthat/xlsx_files/cars_data_styles.xlsx |binary tests/testthat/xlsx_files/cars_missing_rownames.xlsx |only tests/testthat/xlsx_files/cars_no_row_names.xlsx |binary tests/testthat/xlsx_files/cars_no_titles.xlsx |binary tests/testthat/xlsx_files/cars_no_titles_no_footnote.xlsx |binary tests/testthat/xlsx_files/cars_offset.xlsx |binary 28 files changed, 631 insertions(+), 190 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of discrete response data using
unidimensional and multidimensional item analysis models under the Item
Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>).
Exploratory and confirmatory item factor analysis models
are estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier models are available for modeling item testlets using
dimension reduction EM algorithms, while multiple group analyses and
mixed effects designs are included for detecting differential item, bundle,
and test functioning, and for modeling item and person covariates.
Finally, latent class models such as the DINA, DINO, multidimensional latent class,
mixture IRT models, and zero-inflated response models are supported, as well
as a wide family of probabilistic unfolding models.
Author: Phil Chalmers [aut, cre] ,
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb],
Lennart Schneider [ctb],
David King [ctb],
Chen-Wei Liu [ctb],
Ogreden Oguzhan [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.43 dated 2024-11-14 and 1.44.0 dated 2025-01-28
mirt-1.43/mirt/tests/testthat/test-14-GGUM.R |only mirt-1.44.0/mirt/DESCRIPTION | 11 mirt-1.44.0/mirt/MD5 | 74 ++-- mirt-1.44.0/mirt/NAMESPACE | 1 mirt-1.44.0/mirt/NEWS.md | 33 ++ mirt-1.44.0/mirt/R/02a-general_methods.R | 3 mirt-1.44.0/mirt/R/02b-item_methods.R | 261 +++++++++++++++- mirt-1.44.0/mirt/R/03-estimation.R | 41 -- mirt-1.44.0/mirt/R/06-LoadPars.R | 45 ++ mirt-1.44.0/mirt/R/DIF.R | 9 mirt-1.44.0/mirt/R/DeltaMethod.R |only mirt-1.44.0/mirt/R/EMstep.group.R | 10 mirt-1.44.0/mirt/R/M2.R | 20 - mirt-1.44.0/mirt/R/RCI.R | 10 mirt-1.44.0/mirt/R/SingleGroup-methods.R | 232 ++++++-------- mirt-1.44.0/mirt/R/extract.mirt.R | 6 mirt-1.44.0/mirt/R/itemfit.R | 3 mirt-1.44.0/mirt/R/mirt-package.R | 70 ++++ mirt-1.44.0/mirt/R/mirt.R | 112 +++++- mirt-1.44.0/mirt/R/mirt.model.R | 5 mirt-1.44.0/mirt/R/personfit.R | 2 mirt-1.44.0/mirt/R/reverse.score.R | 5 mirt-1.44.0/mirt/R/simdata.R | 32 + mirt-1.44.0/mirt/R/utils.R | 60 +++ mirt-1.44.0/mirt/build/partial.rdb |binary mirt-1.44.0/mirt/build/vignette.rds |binary mirt-1.44.0/mirt/data/Attitude.RData |only mirt-1.44.0/mirt/man/Attitude.Rd |only mirt-1.44.0/mirt/man/DeltaMethod.Rd |only mirt-1.44.0/mirt/man/RCI.Rd | 10 mirt-1.44.0/mirt/man/extract.mirt.Rd | 4 mirt-1.44.0/mirt/man/mirt.Rd | 112 +++++- mirt-1.44.0/mirt/man/mirt.model.Rd | 5 mirt-1.44.0/mirt/man/personfit.Rd | 2 mirt-1.44.0/mirt/man/reverse.score.Rd | 3 mirt-1.44.0/mirt/man/simdata.Rd | 22 + mirt-1.44.0/mirt/man/summary-method.Rd | 7 mirt-1.44.0/mirt/tests/testthat/test-01-mirtOne.R | 2 mirt-1.44.0/mirt/tests/testthat/test-04-multipleGroup.R | 2 mirt-1.44.0/mirt/tests/testthat/test-14-unfolding.R |only mirt-1.44.0/mirt/tests/testthat/test-15-IRTpars.R | 2 41 files changed, 932 insertions(+), 284 deletions(-)
Title: Data Model for 'teal' Applications
Description: Provides a 'teal_data' class as a unified data model for
'teal' applications focusing on reproducibility and relational data.
Author: Dawid Kaledkowski [aut, cre] ,
Aleksander Chlebowski [aut] ,
Marcin Kosinski [aut],
Andre Verissimo [aut] ,
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Nikolas Burkoff [aut],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Junlue Zhao [aut],
Chendi Liao [re [...truncated...]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.data versions 0.6.0 dated 2024-04-30 and 0.7.0 dated 2025-01-28
teal.data-0.6.0/teal.data/R/teal_data-datanames.R |only teal.data-0.6.0/teal.data/R/teal_data.R |only teal.data-0.6.0/teal.data/R/utils-get_code_dependency.R |only teal.data-0.6.0/teal.data/man/TealData.Rd |only teal.data-0.6.0/teal.data/man/get_code_dependency.Rd |only teal.data-0.6.0/teal.data/man/new_teal_data.Rd |only teal.data-0.6.0/teal.data/tests/testthat/test-datanames.R |only teal.data-0.6.0/teal.data/tests/testthat/test-get_code.R |only teal.data-0.6.0/teal.data/vignettes/delayed-data-loading.R |only teal.data-0.6.0/teal.data/vignettes/delayed-data-loading.html |only teal.data-0.6.0/teal.data/vignettes/delayed-data-objects.R |only teal.data-0.6.0/teal.data/vignettes/delayed-data-objects.html |only teal.data-0.6.0/teal.data/vignettes/preprocessing-delayed-data.R |only teal.data-0.6.0/teal.data/vignettes/preprocessing-delayed-data.html |only teal.data-0.6.0/teal.data/vignettes/reproducibility.html |only teal.data-0.6.0/teal.data/vignettes/teal.data-with-python.R |only teal.data-0.6.0/teal.data/vignettes/teal.data-with-python.html |only teal.data-0.6.0/teal.data/vignettes/testing-delayed-data.R |only teal.data-0.6.0/teal.data/vignettes/testing-delayed-data.html |only teal.data-0.7.0/teal.data/DESCRIPTION | 24 teal.data-0.7.0/teal.data/MD5 | 116 +-- teal.data-0.7.0/teal.data/NAMESPACE | 56 - teal.data-0.7.0/teal.data/NEWS.md | 24 teal.data-0.7.0/teal.data/R/cdisc_data.R | 5 teal.data-0.7.0/teal.data/R/deprecated.R | 362 ---------- teal.data-0.7.0/teal.data/R/join_keys-extract.R | 6 teal.data-0.7.0/teal.data/R/teal_data-class.R | 136 ++- teal.data-0.7.0/teal.data/R/teal_data-constructor.R |only teal.data-0.7.0/teal.data/R/teal_data-extract.R |only teal.data-0.7.0/teal.data/R/teal_data-get_code.R | 70 - teal.data-0.7.0/teal.data/R/teal_data-names.R |only teal.data-0.7.0/teal.data/R/teal_data-show.R | 3 teal.data-0.7.0/teal.data/R/verify.R | 16 teal.data-0.7.0/teal.data/R/zzz.R | 2 teal.data-0.7.0/teal.data/README.md | 15 teal.data-0.7.0/teal.data/build/vignette.rds |binary teal.data-0.7.0/teal.data/data/rADAE.rda |binary teal.data-0.7.0/teal.data/data/rADCM.rda |binary teal.data-0.7.0/teal.data/data/rADEX.rda |binary teal.data-0.7.0/teal.data/data/rADLB.rda |binary teal.data-0.7.0/teal.data/data/rADRS.rda |binary teal.data-0.7.0/teal.data/data/rADSL.rda |binary teal.data-0.7.0/teal.data/data/rADTR.rda |binary teal.data-0.7.0/teal.data/data/rADTTE.rda |binary teal.data-0.7.0/teal.data/data/rADVS.rda |binary teal.data-0.7.0/teal.data/inst/doc/join-keys.R | 4 teal.data-0.7.0/teal.data/inst/doc/join-keys.Rmd | 4 teal.data-0.7.0/teal.data/inst/doc/join-keys.html | 235 +++--- teal.data-0.7.0/teal.data/inst/doc/teal-data-reproducibility.R | 7 teal.data-0.7.0/teal.data/inst/doc/teal-data-reproducibility.Rmd | 9 teal.data-0.7.0/teal.data/inst/doc/teal-data-reproducibility.html | 115 +-- teal.data-0.7.0/teal.data/inst/doc/teal-data.R | 27 teal.data-0.7.0/teal.data/inst/doc/teal-data.Rmd | 57 + teal.data-0.7.0/teal.data/inst/doc/teal-data.html | 162 ++-- teal.data-0.7.0/teal.data/man/cdisc_data.Rd | 8 teal.data-0.7.0/teal.data/man/col_labels.Rd | 10 teal.data-0.7.0/teal.data/man/datanames.Rd | 34 teal.data-0.7.0/teal.data/man/get_code.Rd | 40 - teal.data-0.7.0/teal.data/man/join_keys.Rd | 6 teal.data-0.7.0/teal.data/man/names.teal_data.Rd |only teal.data-0.7.0/teal.data/man/teal_data-class.Rd | 41 - teal.data-0.7.0/teal.data/man/teal_data.Rd | 56 + teal.data-0.7.0/teal.data/man/verify.Rd | 6 teal.data-0.7.0/teal.data/tests/testthat/test-cdisc_join_keys.R | 2 teal.data-0.7.0/teal.data/tests/testthat/test-deprecated.R |only teal.data-0.7.0/teal.data/tests/testthat/test-extract.R |only teal.data-0.7.0/teal.data/tests/testthat/test-teal_data.R | 59 - teal.data-0.7.0/teal.data/tests/testthat/test-test_data-names.R |only teal.data-0.7.0/teal.data/tests/testthat/test-verify.R | 4 teal.data-0.7.0/teal.data/vignettes/join-keys.Rmd | 4 teal.data-0.7.0/teal.data/vignettes/teal-data-reproducibility.Rmd | 9 teal.data-0.7.0/teal.data/vignettes/teal-data.Rmd | 57 + 72 files changed, 797 insertions(+), 994 deletions(-)
Title: Penalized Data Sharpening for Local Polynomial Regression
Description: Functions and data sets for data sharpening.
Nonparametric regressions are computed subject to smoothness
and other kinds of penalties.
Author: W.J. Braun [aut],
D. Wang [aut, cre],
X.J. Hu [aut, ctb]
Maintainer: D. Wang <wdy@student.ubc.ca>
Diff between sharpPen versions 1.9 dated 2023-10-19 and 2.0 dated 2025-01-28
DESCRIPTION | 6 +++--- MD5 | 6 ++++-- R/dpilc_PTW.R |only man/dpilc.Rd | 4 ++-- man/dpilc_PTW.Rd |only 5 files changed, 9 insertions(+), 7 deletions(-)
Title: Hidden Markov Models
Description: Contains functions for the analysis of Discrete Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated Poisson Process. It includes functions for simulation, parameter estimation, and the Viterbi algorithm. See the topic "HiddenMarkov" for an introduction to the package, and "Change Log" for a list of recent changes. The algorithms are based of those of Walter Zucchini.
Author: David Harte [aut, cre]
Maintainer: David Harte <d.s.harte@gmail.com>
Diff between HiddenMarkov versions 1.8-13 dated 2021-04-27 and 1.8-14 dated 2025-01-28
DESCRIPTION | 16 ++++++++++------ MD5 | 12 ++++++------ R/Viterbi.R | 5 +++-- build/partial.rdb |binary inst/CITATION | 16 ++++++---------- man/Changes.Rd | 2 ++ man/HiddenMarkov-dthmm-deprecated.Rd | 4 +--- 7 files changed, 28 insertions(+), 27 deletions(-)
Title: Mediterranean Landscape Simulation
Description: Simulate forest hydrology, forest function and dynamics over landscapes [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>]. Parallelization is allowed in several simulation functions and simulations may be conducted including spatial processes such as lateral water transfer and seed dispersal.
Author: Miquel De Caceres [aut, cre],
Aitor Ameztegui [aut] ,
Maria Gonzalez [aut] ,
Nuria Aquilue [aut],
Daniel Caviedes-Voullieme [aut],
Mario Morales-Hernandez [aut],
Mario Beltran [ctb],
Rodrigo Balaguer-Romano [ctb] ,
Roberto Molowny-Horas [ctb]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between medfateland versions 2.4.7 dated 2024-10-20 and 2.5.1 dated 2025-01-28
DESCRIPTION | 10 MD5 | 28 - R/RcppExports.R | 64 +-- R/add_forests.R | 6 R/model_land.R | 385 ++++++++---------- R/parse_forestable.R | 2 R/sysdata.rda |binary data/defaultPrescriptionsBySpecies.rda |binary man/spwb_land.Rd | 9 man/spwb_land_day.Rd | 4 src/RcppExports.cpp | 243 +++++++---- src/serghei.cpp |only src/serghei.h |only src/spwbland.cpp | 672 ++++++--------------------------- src/spwbland.h | 52 +- src/tetis.cpp |only src/tetis.h |only 17 files changed, 549 insertions(+), 926 deletions(-)
Title: Cluster Gauss-Newton Method
Description: Find multiple solutions of a nonlinear least squares problem. Cluster Gauss-Newton method does not assume uniqueness of the solution of the nonlinear least squares problem and compute multiple minimizers. Please cite the following paper when this software is used in your research: Aoki et al. (2020) <doi:10.1007/s11081-020-09571-2>. Cluster Gauss–Newton method. Optimization and Engineering, 1-31. Please cite the following paper when profile likelihood plot is drawn with this software and used in your research: Aoki and Sugiyama (2024) <doi:10.1002/psp4.13055>. Cluster Gauss-Newton method for a quick approximation of profile likelihood: With application to physiologically-based pharmacokinetic models. CPT Pharmacometrics Syst Pharmacol.13(1):54-67.
Author: Yasunori Aoki [aut, cre]
Maintainer: Yasunori Aoki <yaoki@uwaterloo.ca>
Diff between CGNM versions 0.9.0 dated 2024-06-12 and 0.9.1 dated 2025-01-28
CGNM-0.9.0/CGNM/inst/shinyCGNM/CGNM_shiny_save-example1.rds |only CGNM-0.9.1/CGNM/DESCRIPTION | 14 CGNM-0.9.1/CGNM/MD5 | 27 CGNM-0.9.1/CGNM/NAMESPACE | 4 CGNM-0.9.1/CGNM/R/Cluster_Gauss_Newton_method.R | 290 + CGNM-0.9.1/CGNM/R/PostProcess.R | 250 - CGNM-0.9.1/CGNM/R/shinyCGNM_related.R |only CGNM-0.9.1/CGNM/build/vignette.rds |binary CGNM-0.9.1/CGNM/inst/doc/CGNM-vignette.html | 353 +- CGNM-0.9.1/CGNM/inst/shinyCGNM/CodeGenerationRelatedFunctions.R |only CGNM-0.9.1/CGNM/inst/shinyCGNM/pitavastatin_rifampicin_CGNM_shiny_example.rds |only CGNM-0.9.1/CGNM/inst/shinyCGNM/server.R | 1534 +++++++--- CGNM-0.9.1/CGNM/inst/shinyCGNM/ui.R | 47 CGNM-0.9.1/CGNM/man/Cluster_Gauss_Newton_EBE_method.Rd |only CGNM-0.9.1/CGNM/man/make_ShinyCGNM_doseData.Rd |only CGNM-0.9.1/CGNM/man/make_ShinyCGNM_observationData.Rd |only CGNM-0.9.1/CGNM/man/plot_simulationMatrixWithCI.Rd | 7 CGNM-0.9.1/CGNM/man/plot_simulationWithCI.Rd | 7 18 files changed, 1871 insertions(+), 662 deletions(-)
Title: Characterise Tables of an OMOP Common Data Model Instance
Description: Summarises key information in data mapped to the Observational
Medical Outcomes Partnership (OMOP) common data model. Assess suitability to
perform specific epidemiological studies and explore the different domains
to obtain feasibility counts and trends.
Author: Marta Alcalde-Herraiz [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut] ,
Cecilia Campanile [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut]
Maintainer: Cecilia Campanile <cecilia.campanile@ndorms.ox.ac.uk>
Diff between OmopSketch versions 0.2.1 dated 2025-01-16 and 0.2.2 dated 2025-01-28
DESCRIPTION | 8 MD5 | 66 ++--- R/documentationHelper.R |only R/summariseClinicalRecords.R | 3 R/summariseConceptCounts.R | 3 R/summariseConceptIdCounts.R | 9 R/summariseConceptSetCounts.R | 3 R/summariseInObservation.R | 11 R/summariseInternal.R | 6 R/summariseMissingData.R | 3 R/summariseObservationPeriod.R | 3 R/summariseRecordCount.R | 3 R/tableConceptIdCounts.R | 4 R/tableOmopSnapshot.R | 2 inst/doc/A-summarise_clinical_tables_records.html | 207 +++++++--------- inst/doc/B-summarise_concept_set_counts.html | 12 inst/doc/C-summarise_observation_period.R | 28 -- inst/doc/C-summarise_observation_period.Rmd | 35 -- inst/doc/C-summarise_observation_period.html | 270 ++++++++++------------ man/dateRange-startDate.Rd |only man/mockOmopSketch.Rd | 4 man/summariseClinicalRecords.Rd | 5 man/summariseConceptCounts.Rd | 5 man/summariseConceptIdCounts.Rd | 5 man/summariseConceptSetCounts.Rd | 5 man/summariseInObservation.Rd | 5 man/summariseMissingData.Rd | 5 man/summariseObservationPeriod.Rd | 5 man/summariseOmopSnapshot.Rd | 2 man/summariseRecordCount.Rd | 5 man/tableOmopSnapshot.Rd | 2 tests/testthat/test-restrictStudyPeriod.R | 8 tests/testthat/test-summariseConceptIdCounts.R | 2 tests/testthat/test-summariseConceptSetCounts.R | 22 - vignettes/C-summarise_observation_period.Rmd | 35 -- 35 files changed, 357 insertions(+), 434 deletions(-)
Title: The Gaussian Covariate Method for Variable Selection
Description: The standard linear regression theory whether frequentist or Bayesian is based on an 'assumed (revealed?) truth' (John Tukey) attitude to models. This is reflected in the language of statistical inference which involves a concept of truth, for example confidence intervals, hypothesis testing and consistency. The motivation behind this package was to remove the word true from the theory and practice of linear regression and to replace it by approximation. The approximations considered are the least squares approximations. An approximation is called valid if it contains no irrelevant covariates. This is operationalized using the concept of a Gaussian P-value which is the probability that pure Gaussian noise is better in term of least squares than the covariate. The precise definition given in the paper, it is intuitive and requires only four simple equations. Its overwhelming advantage compared with a standard F P-value is that is is exact and valid whatever the data. In contrast F P [...truncated...]
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <pldavies44@cantab.net>
Diff between gausscov versions 1.1.3 dated 2024-05-21 and 1.1.4 dated 2025-01-28
gausscov-1.1.3/gausscov/R/f2st.R |only gausscov-1.1.3/gausscov/data/abcq.rda |only gausscov-1.1.3/gausscov/man/abcql.Rd |only gausscov-1.1.3/gausscov/man/f2st.Rd |only gausscov-1.1.4/gausscov/DESCRIPTION | 10 ++++---- gausscov-1.1.4/gausscov/MD5 | 30 ++++++++++--------------- gausscov-1.1.4/gausscov/R/f1st.R | 29 ++++++++++++------------ gausscov-1.1.4/gausscov/R/f3st.R | 12 +++++----- gausscov-1.1.4/gausscov/R/f3sti.R | 36 +++++++++++++++++++++--------- gausscov-1.1.4/gausscov/R/fgr1st.R | 24 ++++++++++++-------- gausscov-1.1.4/gausscov/R/flag.R | 6 ++--- gausscov-1.1.4/gausscov/data/leukemia.rda |binary gausscov-1.1.4/gausscov/data/vardata.rda |binary gausscov-1.1.4/gausscov/man/f3st.Rd | 8 ++++-- gausscov-1.1.4/gausscov/man/f3sti.Rd | 10 +++++--- gausscov-1.1.4/gausscov/man/flag.Rd | 6 ++--- gausscov-1.1.4/gausscov/man/vardata.Rd | 2 - gausscov-1.1.4/gausscov/src/gaucov.f | 9 +++---- 18 files changed, 102 insertions(+), 80 deletions(-)
Title: Efficient Model Functions for Bagging
Description: Tree- and rule-based models can be bagged
(<doi:10.1007/BF00058655>) using this package and their predictions
equations are stored in an efficient format to reduce the model
objects size and speed.
Author: Max Kuhn [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between baguette versions 1.0.2 dated 2024-02-13 and 1.1.0 dated 2025-01-28
baguette-1.0.2/baguette/R/aaa.R |only baguette-1.0.2/baguette/R/aaa_validate.R |only baguette-1.0.2/baguette/R/reexports.R |only baguette-1.1.0/baguette/DESCRIPTION | 27 - baguette-1.1.0/baguette/MD5 | 66 +-- baguette-1.1.0/baguette/NEWS.md | 4 baguette-1.1.0/baguette/R/C5.0.R | 6 baguette-1.1.0/baguette/R/bag_mars_data.R | 2 baguette-1.1.0/baguette/R/bag_nnet_data.R | 2 baguette-1.1.0/baguette/R/bag_tree_data.R | 2 baguette-1.1.0/baguette/R/bagger.R | 66 +-- baguette-1.1.0/baguette/R/baguette-package.R |only baguette-1.1.0/baguette/R/bridge.R | 28 - baguette-1.1.0/baguette/R/cart.R | 6 baguette-1.1.0/baguette/R/constructor.R | 7 baguette-1.1.0/baguette/R/cost_models.R | 17 baguette-1.1.0/baguette/R/import-standalone-obj-type.R |only baguette-1.1.0/baguette/R/import-standalone-types-check.R |only baguette-1.1.0/baguette/R/mars.R | 6 baguette-1.1.0/baguette/R/misc.R | 19 baguette-1.1.0/baguette/R/nnet.R | 6 baguette-1.1.0/baguette/R/out-of-bag.R | 2 baguette-1.1.0/baguette/R/validate.R |only baguette-1.1.0/baguette/R/zzz.R |only baguette-1.1.0/baguette/README.md | 8 baguette-1.1.0/baguette/build/partial.rdb |binary baguette-1.1.0/baguette/man/bagger.Rd | 63 +-- baguette-1.1.0/baguette/man/baguette-package.Rd | 15 baguette-1.1.0/baguette/man/reexports.Rd | 2 baguette-1.1.0/baguette/tests/testthat/_snaps/validation.md | 230 +++++++++++- baguette-1.1.0/baguette/tests/testthat/helper-baguette.R | 13 baguette-1.1.0/baguette/tests/testthat/test-C5.R | 1 baguette-1.1.0/baguette/tests/testthat/test-bag_mars.R |only baguette-1.1.0/baguette/tests/testthat/test-bag_mlp.R |only baguette-1.1.0/baguette/tests/testthat/test-cart.R | 4 baguette-1.1.0/baguette/tests/testthat/test-interfaces.R | 2 baguette-1.1.0/baguette/tests/testthat/test-mars.R | 4 baguette-1.1.0/baguette/tests/testthat/test-nnet.R | 2 baguette-1.1.0/baguette/tests/testthat/test-validation.R | 205 ++++++---- 39 files changed, 561 insertions(+), 254 deletions(-)
Title: Relative Survival
Description: Contains functions for analysing relative survival data, including nonparametric estimators of net (marginal relative) survival, relative survival ratio, crude mortality, methods for fitting and checking additive and multiplicative regression models, transformation approach, methods for dealing with population mortality tables. Work has been described in Pohar Perme, Pavlic (2018) <doi:10.18637/jss.v087.i08>.
Author: Maja Pohar Perme [aut],
Damjan Manevski [aut, cre]
Maintainer: Damjan Manevski <damjan.manevski@mf.uni-lj.si>
Diff between relsurv versions 2.3-1 dated 2025-01-20 and 2.3-2 dated 2025-01-28
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/Rcode.r | 16 ++++++++++++++++ inst/news.Rd | 6 ++++++ 4 files changed, 30 insertions(+), 8 deletions(-)
Title: Statistical Transformations for Post-Processing Climate Model
Output
Description: Empirical adjustment of the distribution of variables originating from (regional) climate model simulations using quantile mapping.
Author: Lukas Gudmundsson [aut, cre]
Maintainer: Lukas Gudmundsson <lukas.gudmundsson@env.ethz.ch>
Diff between qmap versions 1.0-5 dated 2025-01-27 and 1.0-6 dated 2025-01-28
ChangeLog | 30 ++++++++++++++++++------------ DESCRIPTION | 14 ++++++++------ MD5 | 28 ++++++++++++++-------------- inst/CITATION | 2 +- man/berngamma.Rd | 16 ++++++++-------- man/bernlnorm.Rd | 2 +- man/bernweibull.Rd | 2 +- man/fitqmap.Rd | 2 +- man/fitqmapdist.Rd | 8 ++++---- man/fitqmapptf.Rd | 6 +++--- man/fitqmapquant.Rd | 4 ++-- man/fitqmaprquant.Rd | 2 +- man/fitqmapssplin.Rd | 2 +- man/obsprecip.Rd | 4 ++-- man/qmap-package.Rd | 2 +- 15 files changed, 66 insertions(+), 58 deletions(-)
More information about Certara.Xpose.NLME at CRAN
Permanent link
Title: Animated Interactive Grammar of Graphics
Description: Functions are provided for defining animated,
interactive data visualizations in R code, and rendering
on a web page. The 2018 Journal of Computational and
Graphical Statistics paper,
<doi:10.1080/10618600.2018.1513367>
describes the concepts implemented.
Author: Toby Hocking [aut, cre] ,
Biplab Sutradhar [ctb] ,
Hadley Wickham [aut] ,
Winston Chang [aut] ,
RStudio [cph] ,
Nicholas Lewin-Koh [aut] ,
Martin Maechler [aut] ,
Randall Prium [aut] ,
Susan VanderPlas [aut] ,
Carson Sievert [aut] ,
Kevin Ferris [aut [...truncated...]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between animint2 versions 2025.1.21 dated 2025-01-21 and 2025.1.28 dated 2025-01-28
animint2-2025.1.21/animint2/tests/testthat/test-renderer1-knit-print.R |only animint2-2025.1.28/animint2/DESCRIPTION | 6 - animint2-2025.1.28/animint2/MD5 | 51 +++++---- animint2-2025.1.28/animint2/NEWS.md | 25 ++++ animint2-2025.1.28/animint2/R/geom-abline.r | 39 ++----- animint2-2025.1.28/animint2/R/geom-text.r | 2 animint2-2025.1.28/animint2/R/z_animint.R | 3 animint2-2025.1.28/animint2/R/z_animintHelpers.R | 29 +++-- animint2-2025.1.28/animint2/R/z_knitr.R | 4 animint2-2025.1.28/animint2/R/z_pages.R | 12 +- animint2-2025.1.28/animint2/R/z_print.R | 22 ++++ animint2-2025.1.28/animint2/build/partial.rdb |binary animint2-2025.1.28/animint2/inst/htmljs/animint.js | 42 +++++++- animint2-2025.1.28/animint2/inst/htmljs/index.html | 7 - animint2-2025.1.28/animint2/inst/htmljs/vendor/driver.css |only animint2-2025.1.28/animint2/inst/htmljs/vendor/driver.js.iife.js |only animint2-2025.1.28/animint2/man/animint.Rd | 22 ++++ animint2-2025.1.28/animint2/man/animint2pages.Rd | 3 animint2-2025.1.28/animint2/man/checkExtraParams.Rd | 4 animint2-2025.1.28/animint2/tests/testthat/helper-functions.R | 27 +++++ animint2-2025.1.28/animint2/tests/testthat/pids.txt | 2 animint2-2025.1.28/animint2/tests/testthat/test-compiler-save-separate-chunks.R | 15 -- animint2-2025.1.28/animint2/tests/testthat/test-renderer-driverjs.R |only animint2-2025.1.28/animint2/tests/testthat/test-renderer1-WorldBank-NA.R | 8 - animint2-2025.1.28/animint2/tests/testthat/test-renderer1-geom-abline.R | 52 +++++++++- animint2-2025.1.28/animint2/tests/testthat/test-renderer1-theme-text-size.R | 12 ++ animint2-2025.1.28/animint2/tests/testthat/test-renderer2-param-off.R | 2 animint2-2025.1.28/animint2/tests/testthat/test-renderer3-knit-print.R |only animint2-2025.1.28/animint2/tests/testthat/test-renderer3-prostateLasso.R | 12 +- 29 files changed, 297 insertions(+), 104 deletions(-)
Title: Multi-Cohort Selection Bias Correction using IPW and AIPW
Methods
Description: Comprehensive toolkit for addressing selection
bias in binary disease models across diverse non-probability samples, each
with unique selection mechanisms. It utilizes Inverse Probability Weighting
(IPW) and Augmented Inverse Probability Weighting (AIPW) methods to reduce
selection bias effectively in multiple non-probability cohorts by integrating
data from either individual-level or summary-level external sources. The
package also provides a variety of variance estimation techniques. Please
refer to Kundu et al. <doi:10.48550/arXiv.2412.00228>.
Author: Ritoban Kundu [aut],
Michael Kleinsasser [cre]
Maintainer: Michael Kleinsasser <biostat-cran-manager@umich.edu>
Diff between EHRmuse versions 0.0.2.0 dated 2025-01-20 and 0.0.2.1 dated 2025-01-28
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/AIPW_var_approx.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Discontinuous Hamiltonian Monte Carlo with Varying Trajectory
Length
Description: Hamiltonian Monte Carlo for both continuous and discontinuous
posterior distributions with customisable trajectory length
termination criterion. See Nishimura et al. (2020) <doi:10.1093/biomet/asz083> for
the original Discontinuous Hamiltonian Monte Carlo,
Hoffman et al. (2014) <doi:10.48550/arXiv.1111.4246> and Betancourt (2016)
<doi:10.48550/arXiv.1601.00225> for the definition of possible Hamiltonian
Monte Carlo termination criteria.
Author: Paolo Manildo [aut, cre]
Maintainer: Paolo Manildo <paolo.manildo@phd.unipd.it>
Diff between XDNUTS versions 1.5.5 dated 2024-12-22 and 1.5.6 dated 2025-01-28
DESCRIPTION | 12 +-- MD5 | 24 +++--- R/RcppExports.R | 9 +- R/interface.R | 106 +++++++++++++++++++++++------- build/partial.rdb |binary inst/doc/Tutorial_for_main_functions.html | 36 +++++----- man/main_function.Rd | 1 man/set_parameters.Rd | 6 + man/xdnuts.Rd | 7 + man/xdtransform.Rd | 11 +-- src/RcppExports.cpp | 9 +- src/dnuts.cpp | 7 + src/epsilon_adapt.cpp | 6 - 13 files changed, 162 insertions(+), 72 deletions(-)
Title: Worldwide or Coordinates-Based Heat Maps
Description: Easily plot heat maps of the world, based on continuous or categorical data. Country labels can also be added to the map.
Author: Luigi Annicchiarico [cre, aut]
Maintainer: Luigi Annicchiarico <luigi.annic@gmail.com>
Diff between WorldMapR versions 1.0.1 dated 2024-11-25 and 1.1.0 dated 2025-01-28
DESCRIPTION | 6 +-- MD5 | 30 +++++++++-------- NAMESPACE | 1 NEWS.md | 11 ++++++ R/countrycoord_data.R |only R/geometries_data.R | 5 ++ R/worldplot.R | 67 ++++++++++++--------------------------- R/worldplotCat.R | 67 ++++++++++++--------------------------- README.md | 6 +-- inst/doc/WorldMapR_Vignette.Rmd | 2 - inst/doc/WorldMapR_Vignette.html | 16 +++------ man/countrycoord_data.Rd |only man/worldplot.Rd | 9 +++++ man/worldplotCat.Rd | 9 +++++ tests/testthat/test1.R | 4 +- tests/testthat/testCat2.R | 13 ++++++- vignettes/WorldMapR_Vignette.Rmd | 2 - 17 files changed, 120 insertions(+), 128 deletions(-)
Title: Search and Retrieve Data from Eurostat Database
Description: Eurostat is the statistical office of the European Union and provides high quality statistics for Europe.
Large set of the data is disseminated through the Eurostat database (<https://ec.europa.eu/eurostat/web/main/data/database>).
The tools are using the REST API with the Statistical Data and Metadata eXchange (SDMX) Web Services
(<https://wikis.ec.europa.eu/pages/viewpage.action?pageId=44165555>) to search and download data from
the Eurostat database using the SDMX standard.
Author: Matyas Meszaros [aut, cre],
Sebastian Weinand [ctb]
Maintainer: Matyas Meszaros <matyas.meszaros@ec.europa.eu>
Diff between restatapi versions 0.24.1 dated 2025-01-26 and 0.24.2 dated 2025-01-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ inst/tinytest/test_restatapi.R | 8 ++++---- 4 files changed, 15 insertions(+), 10 deletions(-)
Title: Meta-Analysis Package for R
Description: A comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit equal-, fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat, bubble, and GOSH plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta [...truncated...]
Author: Wolfgang Viechtbauer [aut, cre]
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>
Diff between metafor versions 4.6-0 dated 2024-03-28 and 4.8-0 dated 2025-01-28
DESCRIPTION | 23 MD5 | 692 +++++---- NAMESPACE | 7 NEWS.md | 62 R/AIC.rma.r | 4 R/BIC.rma.r | 4 R/addpoly.default.r | 541 +++++-- R/addpoly.predict.rma.r | 19 R/addpoly.rma.r | 32 R/aggregate.escalc.r | 28 R/anova.rma.r | 121 + R/baujat.rma.r | 31 R/blsplit.r | 4 R/blup.rma.uni.r | 22 R/coef.deltamethod.r |only R/confint.rma.ls.r | 20 R/confint.rma.mh.r | 2 R/confint.rma.mv.r | 26 R/confint.rma.peto.r | 2 R/confint.rma.uni.r | 27 R/confint.rma.uni.selmodel.r | 22 R/conv.2x2.r | 7 R/conv.delta.r | 11 R/conv.fivenum.r | 12 R/conv.wald.r | 5 R/cooks.distance.rma.mv.r | 23 R/cumul.rma.mh.r | 181 +- R/cumul.rma.peto.r | 167 +- R/cumul.rma.uni.r | 180 +- R/deltamethod.r |only R/dfbetas.rma.mv.r | 23 R/dfround.r | 11 R/emmprep.r | 7 R/escalc.r | 705 ++++++++-- R/fitstats.rma.r | 5 R/fitted.rma.r | 3 R/forest.cumul.rma.r | 111 - R/forest.default.r | 121 + R/forest.rma.r | 489 +++++- R/formatters.r | 49 R/fsn.r | 27 R/funnel.default.r | 23 R/funnel.rma.r | 20 R/gosh.rma.r | 48 R/hatvalues.rma.mv.r | 4 R/hatvalues.rma.uni.r | 3 R/hc.rma.uni.r | 16 R/influence.rma.uni.r | 17 R/labbe.rma.r | 290 ++-- R/leave1out.rma.mh.r | 129 + R/leave1out.rma.peto.r | 121 + R/leave1out.rma.uni.r | 123 + R/llplot.r | 31 R/matreg.r | 2 R/methods.list.rma.r | 5 R/misc.func.hidden.escalc.r | 6 R/misc.func.hidden.fsn.r | 14 R/misc.func.hidden.funnel.r | 5 R/misc.func.hidden.glmm.r | 2 R/misc.func.hidden.mv.r | 186 +- R/misc.func.hidden.profile.r | 46 R/misc.func.hidden.r | 110 + R/misc.func.hidden.selmodel.r | 78 - R/misc.func.hidden.uni.r | 4 R/nobs.rma.r | 14 R/pairmat.r |only R/permutest.rma.ls.r | 51 R/permutest.rma.uni.r | 34 R/plot.cumul.rma.r | 6 R/plot.gosh.rma.r | 7 R/plot.infl.rma.uni.r | 136 + R/plot.permutest.rma.uni.r | 61 R/plot.profile.rma.r | 24 R/plot.rma.mh.r | 9 R/plot.rma.mv.r |only R/plot.rma.peto.r | 9 R/plot.rma.uni.r | 13 R/plot.vif.rma.r | 72 - R/predict.rma.ls.r | 120 + R/predict.rma.r | 242 ++- R/print.anova.rma.r | 12 R/print.deltamethod.r |only R/print.gosh.rma.r | 6 R/print.list.anova.rma.r | 7 R/print.list.rma.r | 4 R/print.matreg.r | 3 R/print.rma.uni.r | 6 R/profile.rma.ls.r | 48 R/profile.rma.mv.r | 54 R/profile.rma.uni.r | 32 R/profile.rma.uni.selmodel.r | 42 R/qqnorm.rma.mh.r | 20 R/qqnorm.rma.peto.r | 20 R/qqnorm.rma.uni.r | 85 - R/radial.rma.r | 39 R/ranef.rma.mv.r | 46 R/ranef.rma.uni.r | 8 R/ranktest.r | 7 R/rcalc.r | 2 R/regplot.rma.r | 66 R/regtest.r | 11 R/replmiss.r | 7 R/reporter.rma.uni.r | 26 R/residuals.rma.r | 3 R/rma.glmm.r | 164 +- R/rma.mh.r | 30 R/rma.mv.r | 379 +++-- R/rma.peto.r | 22 R/rma.uni.r | 327 +++- R/robust.rma.mv.r | 7 R/robust.rma.uni.r | 7 R/rstandard.rma.mh.r | 3 R/rstandard.rma.mv.r | 5 R/rstandard.rma.peto.r | 3 R/rstandard.rma.uni.r | 3 R/rstudent.rma.mh.r | 11 R/rstudent.rma.mv.r | 29 R/rstudent.rma.peto.r | 11 R/se.r |only R/selmodel.rma.uni.r | 185 +- R/simulate.rma.r | 3 R/summary.escalc.r | 5 R/tes.r | 9 R/to.long.r | 34 R/to.table.r | 34 R/transf.r | 223 ++- R/trimfill.rma.uni.r | 5 R/vcalc.r | 86 - R/vcov.deltamethod.r |only R/vif.rma.r | 1 R/weights.rma.mh.r | 3 R/weights.rma.mv.r | 3 R/weights.rma.peto.r | 3 R/weights.rma.uni.r | 3 R/zzz.r | 2 README.md | 8 build/metafor.pdf |binary build/stage23.rdb |binary build/vignette.rds |binary inst/doc/diagram.pdf |binary man/addpoly.Rd | 8 man/addpoly.default.Rd | 25 man/addpoly.predict.rma.Rd | 28 man/addpoly.rma.Rd | 59 man/aggregate.escalc.Rd | 8 man/anova.rma.Rd | 28 man/baujat.Rd | 2 man/bldiag.Rd | 2 man/blsplit.Rd | 4 man/blup.Rd | 2 man/coef.permutest.rma.uni.Rd | 2 man/coef.rma.Rd | 2 man/confint.rma.Rd | 6 man/contrmat.Rd | 2 man/conv.2x2.Rd | 6 man/conv.delta.Rd | 8 man/conv.fivenum.Rd | 8 man/conv.wald.Rd | 10 man/cumul.Rd | 52 man/deltamethod.Rd |only man/dfround.Rd | 4 man/emmprep.Rd | 2 man/escalc.Rd | 138 + man/figures/ex_bubble_plot.png |binary man/figures/ex_forest_plot.png |binary man/figures/ex_funnel_plot.png |binary man/figures/forest-arrangement.pdf |binary man/figures/forest-arrangement.png |binary man/figures/plots-dark.pdf |binary man/figures/plots-dark.png |binary man/figures/plots-light.pdf |binary man/figures/plots-light.png |binary man/fitstats.Rd | 2 man/fitted.rma.Rd | 2 man/forest.Rd | 4 man/forest.cumul.rma.Rd | 38 man/forest.default.Rd | 65 man/forest.rma.Rd | 200 +- man/formatters.Rd | 18 man/formula.rma.Rd | 2 man/fsn.Rd | 8 man/funnel.Rd | 14 man/gosh.Rd | 4 man/hc.Rd | 2 man/influence.rma.mv.Rd | 12 man/influence.rma.uni.Rd | 16 man/labbe.Rd | 40 man/leave1out.Rd | 20 man/llplot.Rd | 6 man/matreg.Rd | 26 man/metafor-package.Rd | 19 man/metafor.news.Rd | 4 man/methods.anova.rma.Rd | 2 man/methods.confint.rma.Rd | 4 man/methods.deltamethod.Rd |only man/methods.escalc.Rd | 2 man/methods.list.rma.Rd | 2 man/methods.matreg.Rd | 2 man/methods.vif.rma.Rd | 2 man/mfopt.Rd | 4 man/misc-models.Rd | 6 man/misc-options.Rd | 6 man/misc-recs.Rd | 4 man/model.matrix.rma.Rd | 2 man/pairmat.Rd |only man/permutest.Rd | 28 man/plot.cumul.rma.Rd | 6 man/plot.gosh.rma.Rd | 2 man/plot.infl.rma.uni.Rd | 16 man/plot.permutest.rma.uni.Rd | 9 man/plot.rma.Rd | 9 man/plot.rma.uni.selmodel.Rd | 4 man/plot.vif.rma.Rd | 7 man/predict.rma.Rd | 47 man/print.anova.rma.Rd | 2 man/print.confint.rma.Rd | 2 man/print.deltamethod.Rd |only man/print.escalc.Rd | 8 man/print.fsn.Rd | 2 man/print.gosh.rma.Rd | 2 man/print.hc.rma.uni.Rd | 2 man/print.list.rma.Rd | 2 man/print.matreg.Rd | 2 man/print.permutest.rma.uni.Rd | 2 man/print.ranktest.rma.Rd | 2 man/print.regtest.rma.Rd | 2 man/print.rma.Rd | 6 man/profile.rma.Rd | 9 man/qqnorm.rma.Rd | 31 man/radial.Rd | 6 man/ranef.Rd | 2 man/ranktest.Rd | 2 man/rcalc.Rd | 6 man/regplot.Rd | 76 - man/regtest.Rd | 6 man/replmiss.Rd | 2 man/reporter.Rd | 2 man/residuals.rma.Rd | 12 man/rma.glmm.Rd | 31 man/rma.mh.Rd | 12 man/rma.mv.Rd | 46 man/rma.peto.Rd | 12 man/rma.uni.Rd | 48 man/robust.Rd | 4 man/se.Rd |only man/selmodel.Rd | 83 - man/simulate.rma.Rd | 4 man/tes.Rd | 8 man/to.long.Rd | 4 man/to.table.Rd | 2 man/to.wide.Rd | 2 man/transf.Rd | 42 man/trimfill.Rd | 6 man/update.rma.Rd | 2 man/vcalc.Rd | 30 man/vcov.rma.Rd | 4 man/vec2mat.Rd | 2 man/vif.Rd | 39 man/weights.rma.Rd | 4 tests/testthat/settings.r | 2 tests/testthat/test_analysis_example_berkey1995.r | 10 tests/testthat/test_analysis_example_berkey1998.r | 24 tests/testthat/test_analysis_example_dersimonian2007.r | 6 tests/testthat/test_analysis_example_gleser2009.r | 16 tests/testthat/test_analysis_example_henmi2010.r | 4 tests/testthat/test_analysis_example_ishak2007.r | 20 tests/testthat/test_analysis_example_jackson2014.r | 2 tests/testthat/test_analysis_example_konstantopoulos2011.r | 51 tests/testthat/test_analysis_example_law2016.r | 2 tests/testthat/test_analysis_example_lipsey2001.r | 4 tests/testthat/test_analysis_example_miller1978.r | 30 tests/testthat/test_analysis_example_morris2008.r | 4 tests/testthat/test_analysis_example_normand1999.r | 4 tests/testthat/test_analysis_example_raudenbush1985.r | 18 tests/testthat/test_analysis_example_raudenbush2009.r | 4 tests/testthat/test_analysis_example_rothman2008.r | 20 tests/testthat/test_analysis_example_stijnen2010.r | 30 tests/testthat/test_analysis_example_vanhouwelingen1993.r | 26 tests/testthat/test_analysis_example_vanhouwelingen2002.r | 53 tests/testthat/test_analysis_example_viechtbauer2005.r | 4 tests/testthat/test_analysis_example_viechtbauer2007a.r | 4 tests/testthat/test_analysis_example_viechtbauer2007b.r | 30 tests/testthat/test_analysis_example_yusuf1985.r | 26 tests/testthat/test_misc_aggregate.r | 2 tests/testthat/test_misc_anova.r | 2 tests/testthat/test_misc_calc_q.r | 2 tests/testthat/test_misc_coef_se.r |only tests/testthat/test_misc_confint.r | 2 tests/testthat/test_misc_cumul.r |only tests/testthat/test_misc_dfround.r | 2 tests/testthat/test_misc_diagnostics_rma.mv.r | 2 tests/testthat/test_misc_emmprep.r | 2 tests/testthat/test_misc_escalc.r | 46 tests/testthat/test_misc_fitstats.r | 4 tests/testthat/test_misc_formula.r | 2 tests/testthat/test_misc_fsn.r | 2 tests/testthat/test_misc_funnel.r | 56 tests/testthat/test_misc_handling_nas.r | 2 tests/testthat/test_misc_handling_of_edge_cases_due_to_zeros.r | 2 tests/testthat/test_misc_influence.r | 8 tests/testthat/test_misc_list_rma.r | 2 tests/testthat/test_misc_matreg.r | 4 tests/testthat/test_misc_metan_vs_rma.mh_with_dat.bcg.r | 2 tests/testthat/test_misc_metan_vs_rma.peto_with_dat.bcg.r | 2 tests/testthat/test_misc_metan_vs_rma.uni_with_dat.bcg.r | 2 tests/testthat/test_misc_pdfs.r | 2 tests/testthat/test_misc_permutest.r | 26 tests/testthat/test_misc_plot_rma.r | 50 tests/testthat/test_misc_predict.r | 100 + tests/testthat/test_misc_pub_bias.r | 2 tests/testthat/test_misc_replmiss.r | 2 tests/testthat/test_misc_reporter.r | 2 tests/testthat/test_misc_residuals.r | 6 tests/testthat/test_misc_rma_error_handling.r | 2 tests/testthat/test_misc_rma_glmm.r | 10 tests/testthat/test_misc_rma_handling_nas.r | 2 tests/testthat/test_misc_rma_ls.r | 38 tests/testthat/test_misc_rma_mv.r | 21 tests/testthat/test_misc_rma_uni.r | 2 tests/testthat/test_misc_rma_uni_ls.r | 12 tests/testthat/test_misc_rma_vs_direct_computation.r | 2 tests/testthat/test_misc_rma_vs_lm.r | 8 tests/testthat/test_misc_robust.r | 6 tests/testthat/test_misc_selmodel.r | 44 tests/testthat/test_misc_setlab.r | 2 tests/testthat/test_misc_tes.r | 2 tests/testthat/test_misc_to_long_table_wide.r | 2 tests/testthat/test_misc_transf.r | 2 tests/testthat/test_misc_update.r | 2 tests/testthat/test_misc_vcalc.r | 12 tests/testthat/test_misc_vcov.r | 2 tests/testthat/test_misc_vec2mat.r | 2 tests/testthat/test_misc_vif.r | 2 tests/testthat/test_misc_weights.r | 2 tests/testthat/test_plots_baujat_plot.r | 36 tests/testthat/test_plots_caterpillar_plot.r | 55 tests/testthat/test_plots_contour-enhanced_funnel_plot.r | 31 tests/testthat/test_plots_cumulative_forest_plot.r | 11 tests/testthat/test_plots_forest_plot_with_predstyle.r |only tests/testthat/test_plots_forest_plot_with_subgroups.r | 27 tests/testthat/test_plots_funnel_plot_variations.r | 29 tests/testthat/test_plots_funnel_plot_with_trim_and_fill.r | 30 tests/testthat/test_plots_gosh.r | 40 tests/testthat/test_plots_labbe_plot.r | 60 tests/testthat/test_plots_llplot.r | 23 tests/testthat/test_plots_meta-analytic_scatterplot.r | 31 tests/testthat/test_plots_normal_qq_plots.r | 14 tests/testthat/test_plots_plot_of_cumulative_results.r | 29 tests/testthat/test_plots_plot_of_influence_diagnostics.r | 37 tests/testthat/test_plots_radial_plot.r | 25 tests/testthat/test_plots_regplot.r | 33 tests/testthat/test_tips_model_selection_with_glmulti_and_mumin.r |only tests/testthat/test_tips_multiple_imputation_with_mice.r |only tests/testthat/test_tips_regression_with_rma.r | 7 tests/testthat/test_tips_rma_vs_lm_and_lme.r | 15 tests/testthat/test_tips_testing_factors_lincoms.r |only 356 files changed, 7543 insertions(+), 3613 deletions(-)
Title: Mediterranean Forest Simulation
Description: Simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Author: Miquel De Caceres [aut, cre, cph]
,
Nicolas Martin-StPaul [aut] ,
Victor Granda [aut] ,
Antoine Cabon [aut] ,
Jordi Martinez-Vilalta [ctb] ,
Maurizio Mencuccini [ctb] ,
Julien Ruffault [ctb] ,
Francois Pimont [ctb] ,
Herve Cochard [ctb] ,
Aitor Amezt [...truncated...]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between medfate versions 4.7.0 dated 2024-10-18 and 4.8.0 dated 2025-01-28
DESCRIPTION | 13 MD5 | 99 +- R/RcppExports.R | 329 +++++--- R/defaultControl.R | 4 R/evaluation.R | 128 ++- R/plot.spwb_day.R | 7 R/summary.forest.R | 4 build/partial.rdb |binary inst/include/medfate_RcppExports.h | 166 +++- man/communication.Rd |only man/defaultControl.Rd | 1 man/evaluation.Rd | 4 man/plot.spwb_day.Rd | 7 man/spwb_day.Rd | 15 src/RcppExports.cpp | 377 +++++++-- src/aspwb.cpp | 64 + src/aspwb.h | 8 src/carbon.cpp | 28 src/communication_structures.cpp | 1285 +++++++++++++++++++++++++--------- src/communication_structures.h | 66 + src/firebehaviour.cpp | 1 src/forestutils.cpp | 28 src/forestutils.h | 1 src/fuelstructure.cpp | 1 src/growth.cpp | 640 +++++++++------- src/hydrology.cpp | 403 ++++++---- src/hydrology.h | 2 src/incgamma.cpp | 47 - src/inner_sperry.cpp | 22 src/inner_sperry.h | 2 src/inner_sureau.cpp | 19 src/inner_sureau.h | 2 src/lightextinction_advanced.cpp | 26 src/lightextinction_basic.cpp | 7 src/lightextinction_basic.h | 5 src/modelInput.cpp | 51 - src/numerical_solving.cpp | 19 src/numerical_solving.h | 3 src/soil.cpp | 2 src/soil_thermodynamics.cpp | 21 src/spwb.cpp | 1141 ++---------------------------- src/spwb.h | 24 src/spwb_day.cpp |only src/spwb_day.h |only src/transpiration.h | 4 src/transpiration_advanced.cpp | 219 +++-- src/transpiration_basic.cpp | 87 +- src/windKatul.cpp | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test_growth.R | 86 ++ tests/testthat/test_post_processing.R | 14 tests/testthat/test_spwb.R | 76 ++ 52 files changed, 3129 insertions(+), 2433 deletions(-)
Title: Artificial Intelligence for Education
Description: In social and educational settings, the use of Artificial
Intelligence (AI) is a challenging task. Relevant data is often only
available in handwritten forms, or the use of data is restricted by
privacy policies. This often leads to small data sets. Furthermore, in
the educational and social sciences, data is often unbalanced in terms
of frequencies. To support educators as well as educational and social
researchers in using the potentials of AI for their work, this package
provides a unified interface for neural nets in 'PyTorch' to deal with
natural language problems. In addition, the package ships with a shiny
app, providing a graphical user interface. This allows the usage of
AI for people without skills in writing python/R scripts. The tools
integrate existing mathematical and statistical methods for dealing
with small data sets via pseudo-labeling (e.g. Cascante-Bonilla et al.
(2020) <doi:10.48550/arXiv.2001.06001>) and imbalanced data via the
creation of synthetic cases [...truncated...]
Author: Berding Florian [aut, cre] ,
Tykhonova Yuliia [aut] ,
Pargmann Julia [ctb] ,
Leube Anna [ctb] ,
Riebenbauer Elisabeth [ctb] ,
Rebmann Karin [ctb],
Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Diff between aifeducation versions 1.0.0 dated 2024-12-20 and 1.0.1 dated 2025-01-28
DESCRIPTION | 6 +-- MD5 | 28 ++++++++--------- NEWS.md | 4 ++ R/TEClassifierProtoNet.R | 4 +- R/TEClassifierRegular.R | 5 ++- R/dotAIFEBaseTransformer.R | 5 ++- R/install_and_config.R | 2 - R/onLoad.R | 2 - README.md | 2 - man/install_py_modules.Rd | 2 - tests/testthat/test-01_LargeDataSetForTexts.R | 1 tests/testthat/test-02_LargeDataSetForTextEmbeddings.R | 1 tests/testthat/test-03_EmbeddedText.R | 1 tests/testthat/test-04_DataManager.R | 1 tests/testthat/test-07_TextEmbeddingModels.R | 2 - 15 files changed, 41 insertions(+), 25 deletions(-)
Title: Structured Messages and Options
Description: Provides a structured framework for consistent user
communication and configuration management for package developers.
Author: Aksel Thomsen [aut, cre],
Mathias Lerbech Jeppesen [aut],
Cervan Girard [aut],
Kristian Troejelsgaard [aut],
Lovemore Gakava [aut],
Steffen Falgreen Larsen [aut],
Vladimir Obucina [aut],
Novo Nordisk A/S [cph]
Maintainer: Aksel Thomsen <oath@novonordisk.com>
Diff between zephyr versions 0.1.0 dated 2025-01-17 and 0.1.1 dated 2025-01-28
DESCRIPTION | 6 +- MD5 | 16 +++---- NEWS.md | 7 +++ R/options.R | 4 - R/utils.R | 5 +- R/zzz.R | 2 inst/WORDLIST | 1 tests/testthat/_snaps/options.md | 88 +++++++++++++++++++++++++++++++++++++-- tests/testthat/test-options.R | 73 +++++++++++++++++++++++++++++++- 9 files changed, 183 insertions(+), 19 deletions(-)
Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre, cph],
Matt Dennis [ctb],
Antoine Bichat [ctb] ,
Daniel Fahey [ctb],
Johann R. Kleinbub [ctb],
Panagiotis Moulos [ctb],
Swechhya Bista [ctb],
Colin Fay [ctb]
Maintainer: Andrew B. Collier <andrew.b.collier@gmail.com>
Diff between emayili versions 0.9.1 dated 2024-06-24 and 0.9.2 dated 2025-01-28
DESCRIPTION | 8 +-- MD5 | 14 ++--- R/emayili.R | 1 R/envelope.R | 2 R/header-mail.R | 2 README.md | 20 ++++--- inst/WORDLIST | 149 ++++++++++++++++++++++++++++---------------------------- man/id.Rd | 2 8 files changed, 103 insertions(+), 95 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]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CodelistGenerator versions 3.3.1 dated 2024-11-26 and 3.3.2 dated 2025-01-28
DESCRIPTION | 22 +- MD5 | 94 ++++----- R/getMappings.R | 2 R/runSearch.R | 1 R/summariseAchillesCodeUse.R | 6 R/summariseCodeUse.R | 32 +-- R/tableAchillesCodeUse.R | 4 R/tableCodeUse.R | 26 +- R/tableUnmappedCodes.R | 3 README.md | 19 + inst/doc/a01_Introduction_to_CodelistGenerator.R | 112 +++++----- inst/doc/a01_Introduction_to_CodelistGenerator.Rmd | 4 inst/doc/a01_Introduction_to_CodelistGenerator.html | 4 inst/doc/a02_Candidate_codes_OA.R | 206 ++++++++++---------- inst/doc/a02_Candidate_codes_OA.Rmd | 4 inst/doc/a02_Candidate_codes_OA.html | 4 inst/doc/a04_Vocab_based_codelists.R | 10 inst/doc/a04_Vocab_based_codelists.Rmd | 10 inst/doc/a04_Vocab_based_codelists.html | 2 man/getMappings.Rd | 2 man/summariseAchillesCodeUse.Rd | 2 man/summariseCodeUse.Rd | 10 man/summariseCohortCodeUse.Rd | 10 man/tableCodeUse.Rd | 8 man/tableCohortCodeUse.Rd | 8 tests/testthat/test-codesFrom.R | 6 tests/testthat/test-codesInUse.R | 12 - tests/testthat/test-compareCodelists.R | 4 tests/testthat/test-dbms.R | 36 +-- tests/testthat/test-drugCodes.R | 8 tests/testthat/test-findUnmappedCodes.R | 4 tests/testthat/test-getCandidateCodes.R | 8 tests/testthat/test-getICD10StandardCodes.R | 4 tests/testthat/test-getMappings.R | 2 tests/testthat/test-mockVocabRef.R | 2 tests/testthat/test-stratifyByRouteCategory.R | 2 tests/testthat/test-subsetOnDomain.R | 2 tests/testthat/test-subsetOnRouteCategory.R | 2 tests/testthat/test-summariseAchillesCodeUse.R | 4 tests/testthat/test-summariseCodeUse.R | 64 ++++-- tests/testthat/test-summariseOrphanCodes.R | 2 tests/testthat/test-synthea_sql_server.R | 6 tests/testthat/test-tableAchillesCodeUse.R | 4 tests/testthat/test-tableCodeUse.R | 32 +-- tests/testthat/test-vocabUtilities.R | 2 vignettes/a01_Introduction_to_CodelistGenerator.Rmd | 4 vignettes/a02_Candidate_codes_OA.Rmd | 4 vignettes/a04_Vocab_based_codelists.Rmd | 10 48 files changed, 438 insertions(+), 391 deletions(-)
More information about CodelistGenerator at CRAN
Permanent link
Title: Data and Methods Around Reference Values in Pediatrics
Description: Calculation of standard deviation scores and percentiles adduced from different
standards (WHO, UK, Germany, Italy, China, etc). Also, references for laboratory values in
children and adults are available, e.g., serum lipids, iron-related blood parameters, IGF, liver enzymes. See package documentation for full list.
Author: Mandy Vogel [aut, cre]
Maintainer: Mandy Vogel <mandy.vogel@googlemail.com>
Diff between childsds versions 0.8.0 dated 2022-02-10 and 0.9.8 dated 2025-01-28
DESCRIPTION | 15 +- MD5 | 190 ++++++++++++++++++---------- NAMESPACE | 7 + NEWS.md | 35 +++++ R/createlms.R | 131 +++++++++++++++++-- R/data.R | 233 +++++++++++++++++++++++++++++++++-- R/misc.R | 192 ++++++++++++++++++++++++++++ R/refsclass.r | 18 +- R/sdsvals.r | 272 ++++++++++++++++++++++++++++++++++++++++- data/aga_15.ref.rda |binary data/belgium.ref.rda |binary data/bone.ref.rda |binary data/bp_wuehl_age.ref.rda |binary data/bp_wuehl_height.ref.rda |binary data/cdc.ref.rda |binary data/cn.ref.rda |binary data/cole_lobstein.ref.rda |only data/colombia_sf.ref.rda |binary data/doyon_age.ref.rda |binary data/doyon_height.ref.rda |binary data/duran_bf.ref.rda |binary data/ethiop.ref.rda |binary data/fredriks05.ref.rda |binary data/ghouili_anthro.ref.rda |only data/gomez_bmitmi.ref.rda |only data/international_lab.ref.rda |binary data/iron.ref.rda |binary data/italian.ref.rda |binary data/japan_lab.ref.rda |binary data/japanese.ref.rda |binary data/kiggs.ref.rda |binary data/kiggs_bp.ref.rda |binary data/kiggs_lightness.ref.rda |only data/kirk_bf.ref.rda |only data/kro.ref.rda |binary data/kro.ref15.rda |only data/leptin.ref.rda |only data/liao_igf1.ref.rda |only data/life_ap.ref.rda |only data/life_cbc.ref.rda |only data/life_circ.ref.rda |binary data/life_ck.ref.rda |only data/life_cysc.ref.rda |binary data/life_fibroscan.ref.rda |binary data/life_folb12.ref.rda |only data/life_hba1c.ref.rda |only data/life_heart.ref.rda |binary data/life_igf.ref.rda |binary data/life_liver.ref.rda |binary data/life_oxyandrogene.ref.rda |only data/life_shbg.ref.rda |only data/life_steroide.ref.rda |only data/life_stfr.ref.rda |only data/life_thyr.ref.rda |binary data/life_vegf.ref.rda |only data/life_vit.ref.rda |only data/linden_heart.ref.rda |only data/lipids.ref.rda |binary data/metabolom.ref.rda |binary data/momo.ref.rda |binary data/motor.ref.rda |binary data/nl3.ref.rda |binary data/nl4.ref.rda |binary data/ofenheimer_bf.ref.rda |only data/portug.ref.rda |binary data/preterm.ref.rda |binary data/ripka_bf.ref.rda |only data/saudi.ref.rda |binary data/schafmeyer_leg.ref.rda |only data/turkish.ref.rda |binary data/uk1990.ref.rda |binary data/ukwho.ref.rda |binary data/us.ref.rda |binary data/valencia_nc.ref.rda |only data/who.ref.rda |binary data/who2007.ref.rda |binary data/zong13.ref.rda |binary man/bone.ref.Rd | 2 man/calc_percent_excess.Rd |only man/cole_lobstein.ref.Rd |only man/do_iterations.Rd | 9 + man/dummy.refs.Rd |only man/fit_gamlss1.Rd | 2 man/fit_gamlss_2d.Rd |only man/fit_vgam.Rd | 2 man/ghouili_anthro.ref.Rd |only man/gomez_bmitmi.ref.Rd |only man/kawel_boehm.ref.Rd | 2 man/kiggs_lightness.ref.Rd |only man/kirk_bf.ref.Rd |only man/kro.ref.Rd | 4 man/kro.ref15.Rd |only man/leptin.ref.Rd |only man/liao_igf1.ref.Rd |only man/life_ap.ref.Rd |only man/life_cbc.ref.Rd |only man/life_ck.ref.Rd |only man/life_fibroscan.ref.Rd | 2 man/life_folb12.ref.Rd |only man/life_hba1c.ref.Rd |only man/life_heart.ref.Rd | 8 + man/life_igf.ref.Rd | 2 man/life_oxyandrogene.ref.Rd |only man/life_shbg.ref.Rd |only man/life_steroide.ref.Rd |only man/life_stfr.ref.Rd |only man/life_vegf.ref.Rd |only man/life_vit.ref.Rd |only man/linden_heart.ref.Rd |only man/lipids.ref.Rd | 2 man/make_percentile_tab2d.Rd |only man/ofenheimer_bf.ref.Rd |only man/one_iteration.Rd | 9 + man/prepare_data.Rd | 3 man/ripka_bf.ref.Rd |only man/schafmeyer_leg.ref.Rd |only man/sds2d.Rd |only man/sds_2d.Rd | 2 man/sds_pub.Rd |only man/sds_pub2d.Rd |only man/valencia_nc.ref.Rd |only man/who.ref.Rd | 4 man/who2007.ref.Rd | 4 man/wormplot2d_gg.Rd |only 124 files changed, 1021 insertions(+), 129 deletions(-)
Title: Visualising Multiple Pairwise Variable Correlations and Other
Scores
Description: We provide a tidy data structure and visualisations for multiple or grouped variable correlations,
general association measures scagnostics and other pairwise scores suitable for numerical, ordinal and nominal variables.
Supported measures include distance correlation, maximal information, ace correlation, Kendall's tau, and polychoric correlation.
Author: Amit Chinwan [aut],
Catherine Hurley [aut, cre]
Maintainer: Catherine Hurley <catherine.hurley@mu.ie>
Diff between bullseye versions 0.1.1 dated 2025-01-21 and 0.1.2 dated 2025-01-28
DESCRIPTION | 7 ++++--- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ R/pair_methods.R | 4 +++- inst/doc/integrating.html | 4 ++-- inst/doc/vis_pairwise.html | 24 ++++++++++++------------ tests/testthat/test-pair_methods.R | 12 ++++++------ 7 files changed, 40 insertions(+), 30 deletions(-)
Title: Landscape Meteorology Tools
Description: Functions to estimate weather variables at any position of a landscape [De Caceres et al. (2018) <doi:10.1016/j.envsoft.2018.08.003>].
Author: Miquel De Caceres [aut, cre] ,
Victor Granda [aut] ,
Nicolas Martin [aut] ,
Antoine Cabon [aut]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between meteoland versions 2.2.2 dated 2024-10-17 and 2.2.3 dated 2025-01-28
DESCRIPTION | 10 +-- MD5 | 30 +++++------ NEWS.md | 3 + R/tidy_interpolation.R | 2 R/tidy_reshape_meteo.R | 77 +++++++++++++++++++++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/reshaping-meteo.R | 18 +++--- inst/doc/reshaping-meteo.Rmd | 2 inst/doc/reshaping-meteo.html | 64 ++++++++++++------------ inst/doc/tidy-meteoland.R | 2 man/complete_meteo.Rd | 8 ++- man/meteospain2meteoland.Rd | 8 ++- man/worldmet2meteoland.Rd | 8 ++- tests/testthat/test-01_reshape_framework.R | 10 +-- vignettes/reshaping-meteo.Rmd | 2 16 files changed, 164 insertions(+), 80 deletions(-)
Title: A Fast Permutation-Based Split-Half Reliability Algorithm
Description: Accurately estimates the reliability of cognitive tasks using a fast and flexible permutation-based split-half reliability algorithm that supports stratified splitting while maintaining equal split sizes. See Kahveci, Bathke, and Blechert (2022) <doi:10.31234/osf.io/ta59r> for details.
Author: Sercan Kahveci [aut, cre]
Maintainer: Sercan Kahveci <sercan.kahveci@plus.ac.at>
Diff between rapidsplithalf versions 0.3 dated 2024-08-16 and 0.4 dated 2025-01-28
DESCRIPTION | 13 +++----- MD5 | 52 +++++++++++++++++----------------- NAMESPACE | 1 R/RcppExports.R | 31 +++++++++++++++++++- R/cormean.R | 21 +++++++------ R/rapidsplit.R | 30 +++++++++++++++---- R/spearmanbrown.R | 1 R/zzz.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/rapidsplithalf.Rmd | 2 - inst/doc/rapidsplithalf.html | 16 +++++----- man/colAggregators.Rd | 3 + man/corByColumns.Rd | 26 ++++++++++++++++- man/cormean.Rd | 5 ++- man/correlation-tools.Rd | 3 + man/figures/README-iatrel-1.png |binary man/figures/README-plotter-1.png |binary man/figures/README-plotter2-1.png |binary man/maskAggregators.Rd | 3 + man/rapidsplit.Rd | 24 +++++++++++++-- man/rapidsplithalf.Rd | 3 + man/spearmanBrown.Rd | 3 + src/RcppExports.cpp | 13 ++++++++ src/corByColumns.cpp | 58 +++++++++++++++++++++++++++++++++++++- src/matrixAggregators.cpp | 2 + vignettes/rapidsplithalf.Rmd | 2 - 27 files changed, 247 insertions(+), 66 deletions(-)
More information about rapidsplithalf at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-27 1.1.0
2024-11-03 1.0.2