Title: Robust Bayesian Longitudinal Regularized Semiparametric Mixed
Models
Description: Our recently developed fully robust Bayesian semiparametric mixed-effect model for high-dimensional longitudinal studies with heterogeneous observations can be implemented through this package. This model can distinguish between time-varying interactions and constant-effect-only cases to avoid model misspecifications. Facilitated by spike-and-slab priors, this model leads to superior performance in estimation, identification and statistical inference. In particular, robust Bayesian inferences in terms of valid Bayesian credible intervals on both parametric and nonparametric effects can be validated on finite samples. The Markov chain Monte Carlo algorithms of the proposed and alternative models are efficiently implemented in 'C++'.
Author: Kun Fan [aut, cre],
Cen Wu [aut]
Maintainer: Kun Fan <kfan@ksu.edu>
Diff between Blend versions 0.1.0 dated 2024-11-25 and 0.1.1 dated 2025-01-20
DESCRIPTION | 12 +++++----- MD5 | 12 +++++----- R/Blend-package.R | 7 ++---- R/Blend.R | 11 ++++----- README.md | 59 ++++++++++++++++++++++++++++++++++++++++++++++++++- man/Blend-package.Rd | 7 ++---- man/Blend.Rd | 9 ++----- 7 files changed, 84 insertions(+), 33 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-08 2.0.0
Title: NASCAR Race Data
Description: A collection of NASCAR race, driver, owner and manufacturer data across the three major NASCAR divisions: NASCAR Cup Series, NASCAR Xfinity Series, and NASCAR Craftsman Truck Series. The curated data begins with the 1949 season and extends through the end of the 2024 season. Explore race, season, or career performance for drivers, teams, and manufacturers throughout NASCAR's history. Data was sourced with permission from DriverAverages.com.
Author: Kyle Grealis [aut, cre] ,
Gabriel Odom [ctb]
Maintainer: Kyle Grealis <kylegrealis@icloud.com>
Diff between nascaR.data versions 1.0.0 dated 2024-07-09 and 2.1.0 dated 2025-01-20
nascaR.data-1.0.0/nascaR.data/R/cup_driver_career.R |only nascaR.data-1.0.0/nascaR.data/R/cup_driver_season.R |only nascaR.data-1.0.0/nascaR.data/R/cup_mfg_overall.R |only nascaR.data-1.0.0/nascaR.data/R/cup_mfg_season.R |only nascaR.data-1.0.0/nascaR.data/R/cup_owner_career.R |only nascaR.data-1.0.0/nascaR.data/R/cup_owner_season.R |only nascaR.data-1.0.0/nascaR.data/R/cup_race_data.R |only nascaR.data-1.0.0/nascaR.data/R/truck_driver_career.R |only nascaR.data-1.0.0/nascaR.data/R/truck_driver_season.R |only nascaR.data-1.0.0/nascaR.data/R/truck_mfg_overall.R |only nascaR.data-1.0.0/nascaR.data/R/truck_mfg_season.R |only nascaR.data-1.0.0/nascaR.data/R/truck_owner_career.R |only nascaR.data-1.0.0/nascaR.data/R/truck_owner_season.R |only nascaR.data-1.0.0/nascaR.data/R/truck_race_data.R |only nascaR.data-1.0.0/nascaR.data/R/xfinity_driver_career.R |only nascaR.data-1.0.0/nascaR.data/R/xfinity_driver_season.R |only nascaR.data-1.0.0/nascaR.data/R/xfinity_mfg_overall.R |only nascaR.data-1.0.0/nascaR.data/R/xfinity_mfg_season.R |only nascaR.data-1.0.0/nascaR.data/R/xfinity_owner_career.R |only nascaR.data-1.0.0/nascaR.data/R/xfinity_owner_season.R |only nascaR.data-1.0.0/nascaR.data/R/xfinity_race_data.R |only nascaR.data-1.0.0/nascaR.data/build |only nascaR.data-1.0.0/nascaR.data/data/cup_driver_career.rda |only nascaR.data-1.0.0/nascaR.data/data/cup_driver_season.rda |only nascaR.data-1.0.0/nascaR.data/data/cup_mfg_overall.rda |only nascaR.data-1.0.0/nascaR.data/data/cup_mfg_season.rda |only nascaR.data-1.0.0/nascaR.data/data/cup_owner_career.rda |only nascaR.data-1.0.0/nascaR.data/data/cup_owner_season.rda |only nascaR.data-1.0.0/nascaR.data/data/cup_race_data.rda |only nascaR.data-1.0.0/nascaR.data/data/truck_driver_career.rda |only nascaR.data-1.0.0/nascaR.data/data/truck_driver_season.rda |only nascaR.data-1.0.0/nascaR.data/data/truck_mfg_overall.rda |only nascaR.data-1.0.0/nascaR.data/data/truck_mfg_season.rda |only nascaR.data-1.0.0/nascaR.data/data/truck_owner_career.rda |only nascaR.data-1.0.0/nascaR.data/data/truck_owner_season.rda |only nascaR.data-1.0.0/nascaR.data/data/truck_race_data.rda |only nascaR.data-1.0.0/nascaR.data/data/xfinity_driver_career.rda |only nascaR.data-1.0.0/nascaR.data/data/xfinity_driver_season.rda |only nascaR.data-1.0.0/nascaR.data/data/xfinity_mfg_overall.rda |only nascaR.data-1.0.0/nascaR.data/data/xfinity_mfg_season.rda |only nascaR.data-1.0.0/nascaR.data/data/xfinity_owner_career.rda |only nascaR.data-1.0.0/nascaR.data/data/xfinity_owner_season.rda |only nascaR.data-1.0.0/nascaR.data/data/xfinity_race_data.rda |only nascaR.data-1.0.0/nascaR.data/inst/WORDLIST |only nascaR.data-1.0.0/nascaR.data/inst/doc |only nascaR.data-1.0.0/nascaR.data/man/cup_driver_career.Rd |only nascaR.data-1.0.0/nascaR.data/man/cup_driver_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/cup_mfg_overall.Rd |only nascaR.data-1.0.0/nascaR.data/man/cup_mfg_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/cup_owner_career.Rd |only nascaR.data-1.0.0/nascaR.data/man/cup_owner_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/cup_race_data.Rd |only nascaR.data-1.0.0/nascaR.data/man/truck_driver_career.Rd |only nascaR.data-1.0.0/nascaR.data/man/truck_driver_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/truck_mfg_overall.Rd |only nascaR.data-1.0.0/nascaR.data/man/truck_mfg_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/truck_owner_career.Rd |only nascaR.data-1.0.0/nascaR.data/man/truck_owner_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/truck_race_data.Rd |only nascaR.data-1.0.0/nascaR.data/man/xfinity_driver_career.Rd |only nascaR.data-1.0.0/nascaR.data/man/xfinity_driver_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/xfinity_mfg_overall.Rd |only nascaR.data-1.0.0/nascaR.data/man/xfinity_mfg_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/xfinity_owner_career.Rd |only nascaR.data-1.0.0/nascaR.data/man/xfinity_owner_season.Rd |only nascaR.data-1.0.0/nascaR.data/man/xfinity_race_data.Rd |only nascaR.data-1.0.0/nascaR.data/vignettes |only nascaR.data-2.1.0/nascaR.data/DESCRIPTION | 22 - nascaR.data-2.1.0/nascaR.data/MD5 | 111 +----- nascaR.data-2.1.0/nascaR.data/NAMESPACE | 33 + nascaR.data-2.1.0/nascaR.data/NEWS.md | 27 + nascaR.data-2.1.0/nascaR.data/R/data.R |only nascaR.data-2.1.0/nascaR.data/R/get_driver.R |only nascaR.data-2.1.0/nascaR.data/R/get_manufacturer.R |only nascaR.data-2.1.0/nascaR.data/R/get_team.R |only nascaR.data-2.1.0/nascaR.data/R/nascaR.data-package.R |only nascaR.data-2.1.0/nascaR.data/R/utils.R |only nascaR.data-2.1.0/nascaR.data/README.md | 195 ++++++----- nascaR.data-2.1.0/nascaR.data/data/cup_series.rda |only nascaR.data-2.1.0/nascaR.data/data/truck_series.rda |only nascaR.data-2.1.0/nascaR.data/data/xfinity_series.rda |only nascaR.data-2.1.0/nascaR.data/inst/extdata |only nascaR.data-2.1.0/nascaR.data/inst/images/hex-logo.png |only nascaR.data-2.1.0/nascaR.data/inst/updates |only nascaR.data-2.1.0/nascaR.data/man/cup_series.Rd |only nascaR.data-2.1.0/nascaR.data/man/figures/logo.svg |only nascaR.data-2.1.0/nascaR.data/man/get_driver_info.Rd |only nascaR.data-2.1.0/nascaR.data/man/get_manufacturer_info.Rd |only nascaR.data-2.1.0/nascaR.data/man/get_team_info.Rd |only nascaR.data-2.1.0/nascaR.data/man/nascaR.data-package.Rd |only nascaR.data-2.1.0/nascaR.data/man/selected_series_data.Rd |only nascaR.data-2.1.0/nascaR.data/man/truck_series.Rd |only nascaR.data-2.1.0/nascaR.data/man/xfinity_series.Rd |only 93 files changed, 215 insertions(+), 173 deletions(-)
Title: Multiple Imputation of Covariates by Substantive Model
Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by
Substantive Model Compatible Fully Conditional Specification.
This is a modification of the popular FCS/chained equations
multiple imputation approach, and allows imputation of missing
covariate values from models which are compatible with the user
specified substantive model.
Author: Jonathan Bartlett [aut, cre],
Ruth Keogh [aut],
Edouard F. Bonneville [aut],
Claus Thorn Ekstroem [ctb]
Maintainer: Jonathan Bartlett <jonathan.bartlett1@lshtm.ac.uk>
Diff between smcfcs versions 1.9.1 dated 2024-12-04 and 1.9.2 dated 2025-01-20
DESCRIPTION | 6 - MD5 | 10 +- R/smcfcs.r | 24 +++--- inst/doc/smcfcs-vignette.html | 4 - inst/doc/smcfcs_coverror-vignette.html | 4 - tests/testthat/test_dtsam.r | 117 +++++++++++++++++++++++++++++++++ 6 files changed, 140 insertions(+), 25 deletions(-)
Title: Empirical Testing of Surrogate Paradox Assumptions
Description: Provides functions to nonparametrically assess assumptions necessary to prevent the surrogate paradox through hypothesis tests of stochastic dominance, monotonicity of regression functions, and non-negative residual treatment effects. More details are available in Hsiao et al 2025 (under review). A tutorial for this package can be found at <https://laylaparast.com/home/SurrogateParadoxTest.html>.
Author: Emily Hsiao [aut, cre]
Maintainer: Emily Hsiao <ehsiao@utexas.edu>
Diff between SurrogateParadoxTest versions 1.0 dated 2024-12-08 and 2.0 dated 2025-01-20
SurrogateParadoxTest-1.0/SurrogateParadoxTest/R/test-script-2024-09-18.R |only SurrogateParadoxTest-2.0/SurrogateParadoxTest/DESCRIPTION | 18 +++++----- SurrogateParadoxTest-2.0/SurrogateParadoxTest/MD5 | 10 ++--- SurrogateParadoxTest-2.0/SurrogateParadoxTest/NAMESPACE | 2 - SurrogateParadoxTest-2.0/SurrogateParadoxTest/R/test-script-2025-01-20.r |only SurrogateParadoxTest-2.0/SurrogateParadoxTest/man/monotonicity_test.Rd | 5 -- SurrogateParadoxTest-2.0/SurrogateParadoxTest/man/test_assumptions.Rd | 16 +++++--- 7 files changed, 25 insertions(+), 26 deletions(-)
More information about SurrogateParadoxTest at CRAN
Permanent link
Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra.
Differences with other sparse matrix packages are:
(1) we only support (essentially) one sparse matrix format,
(2) based on transparent and simple structure(s),
(3) tailored for MCMC calculations within G(M)RF.
(4) and it is fast and scalable (with the extension package spam64).
Documentation about 'spam' is provided by vignettes included in this package, see also Furrer and Sain (2010) <doi:10.18637/jss.v036.i10>; see 'citation("spam")' for details.
Author: Reinhard Furrer [aut, cre] ,
Florian Gerber [aut] ,
Roman Flury [aut] ,
Daniel Gerber [ctb],
Kaspar Moesinger [ctb],
Annina Cincera [ctb],
Youcef Saad [ctb] ,
Esmond G. Ng [ctb] ,
Barry W. Peyton [ctb] ,
Joseph W.H. Liu [ctb] ,
Alan D. George [ctb] , [...truncated...]
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between spam versions 2.11-0 dated 2024-10-03 and 2.11-1 dated 2025-01-20
spam-2.11-0/spam/tests/Examples |only spam-2.11-1/spam/DESCRIPTION | 8 ++-- spam-2.11-1/spam/MD5 | 27 ++++++-------- spam-2.11-1/spam/NEWS.md | 12 +++++- spam-2.11-1/spam/inst/CITATION | 6 +-- spam-2.11-1/spam/inst/doc/spam.pdf |binary spam-2.11-1/spam/tests/demo_cholesky.Rout.save | 4 +- spam-2.11-1/spam/tests/demo_jss10-example1.Rout.save | 4 +- spam-2.11-1/spam/tests/demo_jss10-figures-table.Rout.save | 4 +- spam-2.11-1/spam/tests/demo_jss15-BYM.Rout.save | 4 +- spam-2.11-1/spam/tests/demo_jss15-Leroux.Rout.save | 4 +- spam-2.11-1/spam/tests/demo_spam.Rout.save | 4 +- spam-2.11-1/spam/tests/demo_timing.Rout.save | 4 +- spam-2.11-1/spam/tests/jss_areal_counts.Rout.save | 4 +- spam-2.11-1/spam/tests/testthat.Rout.save | 4 +- 15 files changed, 49 insertions(+), 40 deletions(-)
Title: Multiblock Data Fusion in Statistics and Machine Learning
Description: Functions and datasets to support Smilde, Næs and Liland (2021, ISBN: 978-1-119-60096-1)
"Multiblock Data Fusion in Statistics and Machine Learning - Applications in the Natural and Life Sciences".
This implements and imports a large collection of methods for multiblock data analysis with common interfaces, result- and plotting
functions, several real data sets and six vignettes covering a range different applications.
Author: Kristian Hovde Liland [aut, cre]
,
Solve Saeboe [ctb],
Stefan Schrunner [rev]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between multiblock versions 0.8.8.2 dated 2024-09-16 and 0.8.9.0 dated 2025-01-20
multiblock-0.8.8.2/multiblock/R/asca.R |only multiblock-0.8.8.2/multiblock/R/asca_plots.R |only multiblock-0.8.8.2/multiblock/R/asca_results.R |only multiblock-0.8.8.2/multiblock/man/asca.Rd |only multiblock-0.8.8.2/multiblock/man/asca_plots.Rd |only multiblock-0.8.8.2/multiblock/man/asca_results.Rd |only multiblock-0.8.9.0/multiblock/DESCRIPTION | 12 multiblock-0.8.9.0/multiblock/MD5 | 36 -- multiblock-0.8.9.0/multiblock/NAMESPACE | 20 - multiblock-0.8.9.0/multiblock/NEWS | 4 multiblock-0.8.9.0/multiblock/R/direct_export.R | 24 + multiblock-0.8.9.0/multiblock/R/lpls_results.R | 1 multiblock-0.8.9.0/multiblock/README.md | 2 multiblock-0.8.9.0/multiblock/build/vignette.rds |binary multiblock-0.8.9.0/multiblock/inst/doc/vignette_A_data.html | 2 multiblock-0.8.9.0/multiblock/inst/doc/vignette_B_basic.html | 6 multiblock-0.8.9.0/multiblock/inst/doc/vignette_C_unsupervised.html | 8 multiblock-0.8.9.0/multiblock/inst/doc/vignette_D_asca.html | 8 multiblock-0.8.9.0/multiblock/inst/doc/vignette_E_supervised.html | 168 +++++----- multiblock-0.8.9.0/multiblock/inst/doc/vignette_F_complex.html | 4 multiblock-0.8.9.0/multiblock/man/reexports.Rd | 10 multiblock-0.8.9.0/multiblock/src/crossprods.cpp | 8 22 files changed, 170 insertions(+), 143 deletions(-)
Title: Simple Handling of Labelled Data
Description: Simple handling of survey data. Smart handling of meta-information like e.g. variable-labels value-labels and scale-levels. Easy access and validation of meta-information. Useage of value labels and values respectively for subsetting and recoding data.
Author: Christof Lewerenz [aut, cre]
Maintainer: Christof Lewerenz <christof.lewerenz@gmx.net>
Diff between ilabelled versions 1.0.0 dated 2024-08-21 and 1.0.1 dated 2025-01-20
ilabelled-1.0.0/ilabelled/R/sample_data.R |only ilabelled-1.0.1/ilabelled/DESCRIPTION | 6 ilabelled-1.0.1/ilabelled/MD5 | 51 ++--- ilabelled-1.0.1/ilabelled/R/coerce.R | 6 ilabelled-1.0.1/ilabelled/R/copy.R | 52 +---- ilabelled-1.0.1/ilabelled/R/helper.R | 24 ++ ilabelled-1.0.1/ilabelled/R/label.R | 12 - ilabelled-1.0.1/ilabelled/R/labelled.R | 29 +- ilabelled-1.0.1/ilabelled/R/labels.R | 130 +++---------- ilabelled-1.0.1/ilabelled/R/missing.R | 5 ilabelled-1.0.1/ilabelled/R/recode.R | 2 ilabelled-1.0.1/ilabelled/R/scale.R | 11 - ilabelled-1.0.1/ilabelled/R/zzz.R | 12 - ilabelled-1.0.1/ilabelled/build/vignette.rds |binary ilabelled-1.0.1/ilabelled/inst/doc/class-coercion.html | 2 ilabelled-1.0.1/ilabelled/inst/doc/class-declaration.html | 2 ilabelled-1.0.1/ilabelled/inst/doc/indexation.html | 2 ilabelled-1.0.1/ilabelled/inst/doc/meta-information.html | 2 ilabelled-1.0.1/ilabelled/man/dot-eval_dots_arg.Rd |only ilabelled-1.0.1/ilabelled/man/dot-valid_labels.Rd | 2 ilabelled-1.0.1/ilabelled/man/i_copy.Rd | 8 ilabelled-1.0.1/ilabelled/man/i_labels.Rd | 2 ilabelled-1.0.1/ilabelled/tests/testthat/test-annotation.R | 7 ilabelled-1.0.1/ilabelled/tests/testthat/test-copy.R | 12 - ilabelled-1.0.1/ilabelled/tests/testthat/test-eval_dots.R |only ilabelled-1.0.1/ilabelled/tests/testthat/test-labels.R | 39 +++ ilabelled-1.0.1/ilabelled/tests/testthat/test-scale.R | 11 - ilabelled-1.0.1/ilabelled/tests/testthat/test-subset.R | 7 28 files changed, 200 insertions(+), 236 deletions(-)
Title: Simple Presentation of Estimated Exponential Semi-Variograms
Description: User friendly interface based on the R package 'gstat' to fit
exponential parametric models to empirical semi-variograms in order to
model the spatial correlation structure of health data. Geo-located
health outcomes of survey participants may be used to model spatial
effects on health in an ego-centred approach. The package contains a
range of functions to help explore the spatial structure of the data
as well as visualize the fit of exponential models for various
metaparameter combinations with respect to the number of lag intervals
and maximal distance. Furthermore, the outcome of interest can be
adjusted for covariates by fitting a linear regression in a
preliminary step before the semi-variogram fitting process.
Author: Julia Dyck [aut, cre],
Odile Sauzet [aut],
Jan-Ole Koslik [aut]
Maintainer: Julia Dyck <j.dyck@uni-bielefeld.de>
Diff between EgoCor versions 1.2.0 dated 2024-03-28 and 1.3.0 dated 2025-01-20
DESCRIPTION | 11 ++++++----- MD5 | 30 ++++++++++++++++++++---------- R/coords.plot.function.R | 21 ++++++++++++++++++--- R/distance.info.function.R | 11 ++++++++--- R/vario.mod.function.gstat.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Intro_to_EgoCor.R | 4 ++-- inst/doc/Intro_to_EgoCor.html | 24 +++++++++++------------- man/coords.plot.Rd | 7 ++++++- man/distance.info.Rd | 6 ++++-- tests |only 12 files changed, 77 insertions(+), 41 deletions(-)
Title: A Class for Working with Time Series Data Based on 'data.table'
and 'R6' with Largely Optional Reference Semantics
Description: Basic time series functionalities such as listing of missing
values, application of arbitrary aggregation as well as rolling (asymmetric)
window functions and automatic detection of periodicity. As it is mainly
based on 'data.table', it is fast and (in combination with the 'R6' package)
offers reference semantics. In addition to its native R6 interface, it
provides an S3 interface for those who prefer the latter. Finally yet
importantly, its functional approach allows for incorporating
functionalities from many other packages.
Author: Gerold Hepp [aut, cre]
Maintainer: Gerold Hepp <gisler@hepp.cc>
Diff between DTSg versions 1.1.3 dated 2023-09-27 and 2.0.0 dated 2025-01-20
DTSg-1.1.3/DTSg/R/deprecated.R |only DTSg-1.1.3/DTSg/inst/tinytest/test_deprecated.R |only DTSg-2.0.0/DTSg/DESCRIPTION | 14 DTSg-2.0.0/DTSg/MD5 | 60 DTSg-2.0.0/DTSg/NAMESPACE | 17 DTSg-2.0.0/DTSg/NEWS.md | 122 - DTSg-2.0.0/DTSg/R/ClassDTSg.R | 296 +-- DTSg-2.0.0/DTSg/R/Swrappers.R | 29 DTSg-2.0.0/DTSg/R/TALFs.R | 504 ++---- DTSg-2.0.0/DTSg/R/aaa.R | 17 DTSg-2.0.0/DTSg/R/assertives.R | 68 DTSg-2.0.0/DTSg/R/utils.R | 11 DTSg-2.0.0/DTSg/README.md | 2 DTSg-2.0.0/DTSg/build/vignette.rds |binary DTSg-2.0.0/DTSg/inst/doc/a_basicUsage.R | 32 DTSg-2.0.0/DTSg/inst/doc/a_basicUsage.html | 1275 +++++++++------- DTSg-2.0.0/DTSg/inst/doc/b_advancedUsage.R | 34 DTSg-2.0.0/DTSg/inst/doc/b_advancedUsage.Rmd | 18 DTSg-2.0.0/DTSg/inst/doc/b_advancedUsage.html | 969 +++++++----- DTSg-2.0.0/DTSg/inst/tinytest/data.R | 8 DTSg-2.0.0/DTSg/inst/tinytest/test_DTSg.R | 98 + DTSg-2.0.0/DTSg/inst/tinytest/test_S3WrapperGenerator.R | 11 DTSg-2.0.0/DTSg/inst/tinytest/test_TALFs.R | 10 DTSg-2.0.0/DTSg/inst/tinytest/test_assertives.R | 52 DTSg-2.0.0/DTSg/inst/tinytest/test_utils.R | 4 DTSg-2.0.0/DTSg/man/DTSg.Rd | 25 DTSg-2.0.0/DTSg/man/TALFs.Rd | 61 DTSg-2.0.0/DTSg/man/aggregate.DTSg.Rd | 18 DTSg-2.0.0/DTSg/man/colapply.DTSg.Rd | 15 DTSg-2.0.0/DTSg/man/interpolateLinear.Rd | 6 DTSg-2.0.0/DTSg/man/subset.DTSg.Rd | 15 DTSg-2.0.0/DTSg/vignettes/b_advancedUsage.Rmd | 18 32 files changed, 2029 insertions(+), 1780 deletions(-)
Title: Estimate Quantitative Genetics Parameters from Generalised
Linear Mixed Models
Description: Compute various quantitative genetics parameters from a Generalised Linear Mixed Model (GLMM) estimates. Especially, it yields the observed phenotypic mean, phenotypic variance and additive genetic variance.
Author: Pierre de Villemereuil [aut, cre]
Maintainer: Pierre de Villemereuil <pierre.de-villemereuil@mnhn.fr>
Diff between QGglmm versions 0.7.4 dated 2020-01-07 and 0.8.0 dated 2025-01-20
DESCRIPTION | 16 +- MD5 | 44 +++---- NEWS.md | 11 + R/source.R | 151 +++++++++++++++--------- R/source.icc.R | 193 ++++++++++++++++++++----------- R/source.mv.R | 278 +++++++++++++++++++++++++++++++--------------- R/source.ordinal.R | 16 +- README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/QGglmmHowTo.Rnw | 2 inst/doc/QGglmmHowTo.pdf |binary man/QGicc.Rd | 14 -- man/QGlink.funcs.Rd | 28 +++- man/QGmvicc.Rd | 26 +--- man/QGmvmean.Rd | 7 - man/QGmvparams.Rd | 24 +-- man/QGmvpred.Rd | 12 - man/QGmvpsi.Rd | 7 - man/QGparams.Rd | 17 -- man/QGpred.Rd | 10 - man/QGvcov.Rd | 8 - vignettes/QGglmmHowTo.Rnw | 2 23 files changed, 525 insertions(+), 345 deletions(-)
Title: Fast Creation of Dummy (Binary) Columns and Rows from
Categorical Variables
Description: Creates dummy columns from columns that have categorical variables (character or factor types). You can also specify which columns to make dummies out of, or which columns to ignore. Also creates dummy rows from character, factor, and Date columns. This package provides a significant speed increase from creating dummy variables through model.matrix().
Author: Jacob Kaplan [aut, cre] ,
Benjamin Schlegel [ctb]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between fastDummies versions 1.7.4 dated 2024-08-16 and 1.7.5 dated 2025-01-20
DESCRIPTION | 8 - MD5 | 20 +-- NEWS.md | 7 + R/dummy_cols.R | 188 +++++++++++++++++++++-------------- R/dummy_rows.R | 35 ++++-- build/vignette.rds |binary inst/doc/making-dummy-rows.html | 6 - inst/doc/making-dummy-variables.html | 6 - man/dummy_cols.Rd | 20 ++- man/dummy_columns.Rd | 20 ++- tests/testthat/test-columns.R | 17 ++- 11 files changed, 205 insertions(+), 122 deletions(-)
Title: Causal Inference and Prediction in Cohort-Based Analyses
Description: Numerous functions for cohort-based analyses, either for prediction or causal inference. For causal inference, it includes Inverse Probability Weighting and G-computation for marginal estimation of an exposure effect when confounders are expected. We deal with binary outcomes, times-to-events, competing events, and multi-state data. For multistate data, semi-Markov model with interval censoring may be considered, and we propose the possibility to consider the excess of mortality related to the disease compared to reference lifetime tables. For predictive studies, we propose a set of functions to estimate time-dependent receiver operating characteristic (ROC) curves with the possible consideration of right-censoring times-to-events or the presence of confounders. Finally, several functions are available to assess time-dependent ROC curves or survival curves from aggregated data.
Author: Yohann Foucher [aut, cre] ,
Florent Le Borgne [aut],
Arthur Chatton [aut]
Maintainer: Yohann Foucher <Yohann.Foucher@univ-poitiers.fr>
Diff between RISCA versions 1.0.5 dated 2024-03-22 and 1.0.6 dated 2025-01-20
DESCRIPTION | 12 MD5 | 46 NAMESPACE | 2 R/markov.3states.rsadd.R | 1390 ++++++++++++++------------- R/markov.4states.rsadd.R | 1914 ++++++++++++++++++++------------------ R/semi.markov.3states.rsadd.R | 1394 ++++++++++++++------------- R/semi.markov.4states.rsadd.R | 1944 ++++++++++++++++++++------------------- data/dataCSL.rda |binary data/dataDIVAT1.rda |binary data/dataDIVAT2.rda |binary data/dataDIVAT3.rda |binary data/dataDIVAT4.rda |binary data/dataDIVAT5.rda |binary data/dataFTR.rda |binary data/dataHepatology.rda |binary data/dataKTFS.rda |binary data/dataKi67.rda |binary data/dataOFSEP.rda |binary data/dataSTR.rda |binary data/fr.ratetable.rda |binary man/markov.3states.rsadd.Rd | 2 man/markov.4states.rsadd.Rd | 2 man/roc.net.Rd | 2 man/semi.markov.3states.rsadd.Rd | 6 24 files changed, 3536 insertions(+), 3178 deletions(-)
Title: Markdown Parser and Renderer for R Graphics
Description: Provides the mean to parse and render markdown text with grid along
with facilities to define the styling of the text.
Author: Thomas Lin Pedersen [aut, cre]
,
Martin Mitas [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between marquee versions 0.1.0 dated 2024-05-28 and 1.0.0 dated 2025-01-20
DESCRIPTION | 14 - MD5 | 89 ++++----- NAMESPACE | 18 + NEWS.md | 17 + R/backports.R | 7 R/classic_style.R | 14 - R/cpp11.R | 4 R/element_marquee.R | 109 +++++++++-- R/geom_marquee.R | 26 +- R/grob.R | 271 +++++++++++++++++++++------- R/guide_marquee.R |only R/images.R | 2 R/ink.R |only R/style.R | 49 ++++- R/style_helpers.R | 14 + R/style_set.R | 74 ++++--- README.md | 19 + build/vignette.rds |binary inst/doc/marquee.R | 93 ++++----- inst/doc/marquee.Rmd | 97 ++++------ inst/doc/marquee.html | 94 ++++----- inst/doc/marquee_style.html | 4 inst/doc/marquee_syntax.Rmd | 2 inst/doc/marquee_syntax.html | 13 - man/GuideMarquee.Rd |only man/classic_style.Rd | 22 +- man/element_marquee.Rd | 7 man/figures/README-unnamed-chunk-2-1.png |binary man/geom_marquee.Rd | 2 man/guide_marquee.Rd |only man/ink.Rd |only man/marquee_glue.Rd | 5 man/marquee_grob.Rd | 44 +++- man/marquefy_theme.Rd |only man/style.Rd | 27 ++ man/style_set.Rd | 13 - src/cpp11.cpp | 8 src/marquee.cpp | 6 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/grob.md | 16 - tests/testthat/_snaps/grob/marquee_grob.png |binary tests/testthat/_snaps/parse/parsed.csv | 122 ++++++------ tests/testthat/test-element_marquee.R | 4 tests/testthat/test-geom_marquee.R | 2 tests/testthat/test-grob.R | 4 tests/testthat/test-guide_marquee.R |only tests/testthat/test-style_set.R | 9 vignettes/marquee.Rmd | 97 ++++------ vignettes/marquee_syntax.Rmd | 2 49 files changed, 904 insertions(+), 516 deletions(-)
More information about AMISforInfectiousDiseases at CRAN
Permanent link
More information about admiralmetabolic at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-19 0.3.4
2022-01-04 0.3
2021-12-11 0.2.4
2021-02-23 0.2.3
2020-05-25 0.2.2
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 2.2-9 dated 2022-12-22 and 2.3-1 dated 2025-01-20
relsurv-2.2-9/relsurv/src/init.c |only relsurv-2.3-1/relsurv/DESCRIPTION | 20 relsurv-2.3-1/relsurv/MD5 | 88 +- relsurv-2.3-1/relsurv/NAMESPACE | 26 relsurv-2.3-1/relsurv/R/Rcode.r | 839 ++++++++++++++++++------ relsurv-2.3-1/relsurv/R/RcppExports.R |only relsurv-2.3-1/relsurv/R/cmprel.r | 122 +-- relsurv-2.3-1/relsurv/R/dLambdaP.R |only relsurv-2.3-1/relsurv/R/popsurv.R |only relsurv-2.3-1/relsurv/R/predict.aalen.relsurv.R |only relsurv-2.3-1/relsurv/R/predict.rsadd.R |only relsurv-2.3-1/relsurv/R/ratetable_add_vals.R |only relsurv-2.3-1/relsurv/R/rformulate.r | 4 relsurv-2.3-1/relsurv/R/rformulate2.r |only relsurv-2.3-1/relsurv/R/rsaalen.R |only relsurv-2.3-1/relsurv/R/rsdiff.r | 64 - relsurv-2.3-1/relsurv/R/rssurvrsadd.r | 21 relsurv-2.3-1/relsurv/R/survaalen.R |only relsurv-2.3-1/relsurv/R/years.R | 22 relsurv-2.3-1/relsurv/R/zzz.R | 2 relsurv-2.3-1/relsurv/data/colrec.rda |binary relsurv-2.3-1/relsurv/data/ebmt1wide.rda |only relsurv-2.3-1/relsurv/data/rdata.rda |binary relsurv-2.3-1/relsurv/data/slopop.rda |binary relsurv-2.3-1/relsurv/inst/CITATION | 16 relsurv-2.3-1/relsurv/inst/news.Rd | 16 relsurv-2.3-1/relsurv/man/cmp.rel.Rd | 4 relsurv-2.3-1/relsurv/man/ebmt1wide.Rd |only relsurv-2.3-1/relsurv/man/epa.Rd | 132 +-- relsurv-2.3-1/relsurv/man/expprep2.Rd | 94 +- relsurv-2.3-1/relsurv/man/invtime.Rd | 133 ++- relsurv-2.3-1/relsurv/man/joinrate.Rd | 94 +- relsurv-2.3-1/relsurv/man/nessie.Rd | 131 +-- relsurv-2.3-1/relsurv/man/plot.rs.zph.Rd | 2 relsurv-2.3-1/relsurv/man/popsurv.Rd |only relsurv-2.3-1/relsurv/man/predict.rsadd.Rd |only relsurv-2.3-1/relsurv/man/rs.diff.Rd | 4 relsurv-2.3-1/relsurv/man/rs.surv.Rd | 303 ++++---- relsurv-2.3-1/relsurv/man/rs.surv.rsadd.Rd | 2 relsurv-2.3-1/relsurv/man/rs.zph.Rd | 2 relsurv-2.3-1/relsurv/man/rsaalen.Rd |only relsurv-2.3-1/relsurv/man/rsadd.Rd | 294 ++++---- relsurv-2.3-1/relsurv/man/rsmul.Rd | 202 +++-- relsurv-2.3-1/relsurv/man/rstrans.Rd | 204 +++-- relsurv-2.3-1/relsurv/man/summary.cmp.rel.Rd | 91 +- relsurv-2.3-1/relsurv/man/survaalen.Rd |only relsurv-2.3-1/relsurv/man/survsplit.Rd | 89 +- relsurv-2.3-1/relsurv/man/transrate.Rd | 99 +- relsurv-2.3-1/relsurv/man/transrate.hld.Rd | 2 relsurv-2.3-1/relsurv/man/transrate.hmd.Rd | 2 relsurv-2.3-1/relsurv/man/years.Rd | 2 relsurv-2.3-1/relsurv/src/Makevars |only relsurv-2.3-1/relsurv/src/Makevars.win |only relsurv-2.3-1/relsurv/src/RcppExports.cpp |only relsurv-2.3-1/relsurv/src/aalen_beta.cpp |only 55 files changed, 1890 insertions(+), 1236 deletions(-)
Title: Accelerated Stability Kinetic Modelling
Description: Estimate the Šesták–Berggren kinetic model (degradation model) from experimental data. A
A closed-form (analytic) solution to the degradation model is implemented as a non-linear fit,
allowing for the extrapolation of the degradation of a drug product - both in time and
temperature. Parametric bootstrap, with kinetic parameters drawn from the multivariate
t-distribution, and analytical formulae (the delta method) are available options to calculate
the confidence and prediction intervals.
The results (modelling, extrapolations and statistical intervals) can be visualised
with multiple plots. The examples illustrate the accelerated stability modelling in drugs and
vaccines development.
Author: Bernard G Franq [aut, cph],
Ben Wells [cre],
Alex Ball [ctb],
Daniel Williams [ctb]
Maintainer: Ben Wells <wellsbenjy@gmail.com>
Diff between AccelStab versions 2.1.0 dated 2025-01-08 and 2.1.1 dated 2025-01-20
DESCRIPTION | 16 +++++++++------- MD5 | 4 ++-- NEWS.md | 5 +++++ 3 files changed, 16 insertions(+), 9 deletions(-)
Title: Tree-Structured Modelling of Varying Coefficients
Description: Fitting tree-structured varying coefficient models (Berger et al. (2019), <doi:10.1007/s11222-018-9804-8>). Simultaneous detection of covariates with varying coefficients and effect modifiers that induce varying coefficients if they are present.
Author: Moritz Berger [aut, cre]
Maintainer: Moritz Berger <moritz.berger@imbie.uni-bonn.de>
Diff between TSVC versions 1.5.3 dated 2023-10-17 and 1.7.2 dated 2025-01-20
DESCRIPTION | 17 +++-- MD5 | 25 ++++---- NAMESPACE | 12 ++++ R/TSVC.R | 13 ++++ R/TSVC.default.R | 8 ++ R/confint.TSVC.R |only R/effmodTree.R | 150 ++++++++++++++++++++++++++++++++++++++++------------ R/functions.R | 144 ++++++++++++++++++++++++++++++++++++++++++++++++- R/plot.TSVC.R | 56 ++++++++++++++++--- R/predict.TSVC.R | 3 - R/ptree.R | 50 +++++++++++++---- man/TSVC.Rd | 17 +++++ man/confint.Rd |only man/confint.TSVC.Rd |only man/plot.TSVC.Rd | 36 ++++++++++++ 15 files changed, 451 insertions(+), 80 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007) (temporarily unavailable)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via 'modsem' it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8. [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre]
,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.5 dated 2024-12-16 and 1.0.6 dated 2025-01-20
modsem-1.0.5/modsem/src/LMS.h |only modsem-1.0.5/modsem/src/QML.h |only modsem-1.0.5/modsem/src/equationsLMS.cpp |only modsem-1.0.5/modsem/src/equationsQML.cpp |only modsem-1.0.6/modsem/DESCRIPTION | 13 modsem-1.0.6/modsem/MD5 | 49 +- modsem-1.0.6/modsem/NAMESPACE | 3 modsem-1.0.6/modsem/R/RcppExports.R | 4 modsem-1.0.6/modsem/R/model_da.R | 11 modsem-1.0.6/modsem/R/plot_interaction.R | 345 +++++++++++----- modsem-1.0.6/modsem/R/simple_slopes.R |only modsem-1.0.6/modsem/build/vignette.rds |binary modsem-1.0.6/modsem/inst/doc/plot_interactions.R | 33 + modsem-1.0.6/modsem/inst/doc/plot_interactions.Rmd | 42 + modsem-1.0.6/modsem/inst/doc/plot_interactions.html | 79 ++- modsem-1.0.6/modsem/inst/doc/simple_slopes.R |only modsem-1.0.6/modsem/inst/doc/simple_slopes.Rmd |only modsem-1.0.6/modsem/inst/doc/simple_slopes.html |only modsem-1.0.6/modsem/man/modsem-package.Rd | 2 modsem-1.0.6/modsem/man/plot_interaction.Rd | 122 ++++- modsem-1.0.6/modsem/man/plot_surface.Rd |only modsem-1.0.6/modsem/man/simple_slopes.Rd |only modsem-1.0.6/modsem/src/RcppExports.cpp | 13 modsem-1.0.6/modsem/src/calc_se_simple_slopes.cpp |only modsem-1.0.6/modsem/src/equations_lms.cpp |only modsem-1.0.6/modsem/src/equations_qml.cpp |only modsem-1.0.6/modsem/src/lms.h |only modsem-1.0.6/modsem/src/qml.h |only modsem-1.0.6/modsem/tests/testthat/test_lms.R | 1 modsem-1.0.6/modsem/tests/testthat/test_qml.R | 2 modsem-1.0.6/modsem/tests/testthat/test_sam.R | 11 modsem-1.0.6/modsem/tests/testthat/test_simple_slopes.R |only modsem-1.0.6/modsem/vignettes/plot_interactions.Rmd | 42 + modsem-1.0.6/modsem/vignettes/simple_slopes.Rmd |only 34 files changed, 557 insertions(+), 215 deletions(-)
Title: Tidy Flowchart Generator
Description: Creates participant flow diagrams directly from a dataframe. Representing the flow of participants through each stage of a study, especially in clinical trials, is essential to assess the generalisability and validity of the results. This package provides a set of functions that can be combined with a pipe operator to create all kinds of flowcharts from a data frame in an easy way.
Author: Pau Satorra [aut, cre] ,
Joao Carmezim [aut] ,
Natalia Pallares [aut] ,
Cristian Tebe [aut] ,
Kenneth Taylor [ctb]
Maintainer: Pau Satorra <psatorra@igtp.cat>
Diff between flowchart versions 0.6.0 dated 2024-11-08 and 0.7.0 dated 2025-01-20
DESCRIPTION | 6 MD5 | 37 +- NEWS.md | 10 R/as_fc.R | 46 ++ R/fc_draw.R | 28 - R/fc_filter.R | 163 ++++++++- R/fc_split.R | 89 ++++- R/fc_stack.R | 2 R/utils.R | 97 +++++ README.md | 2 inst/doc/flowchart.R | 42 ++ inst/doc/flowchart.Rmd | 351 +++----------------- inst/doc/flowchart.html | 742 ++++++++------------------------------------ man/as_fc.Rd | 4 man/fc_filter.Rd | 10 man/fc_split.Rd | 6 man/update_y.Rd | 2 man/update_y_stack.Rd | 2 man/update_y_stack_unite.Rd |only vignettes/flowchart.Rmd | 351 +++----------------- 20 files changed, 714 insertions(+), 1276 deletions(-)
Title: Client for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@data-intuitive.com>
Diff between laminr versions 0.3.1 dated 2025-01-08 and 0.4.0 dated 2025-01-20
DESCRIPTION | 6 ++-- MD5 | 16 ++++++------- R/Artifact.R | 3 -- R/Instance.R | 45 +++++++++++++------------------------ R/Registry.R | 4 +-- R/install.R | 2 - tests/testthat/test-instance_api.R | 4 +-- vignettes/laminr.Rmd | 8 ------ vignettes/setup.Rmd | 43 +++++++++++++++++++++++++---------- 9 files changed, 66 insertions(+), 65 deletions(-)
Title: Diagnostic Index Expectation Maximisation in R
Description: Likelihood-based genome polarisation finds which alleles of genomic markers
belong to which side of the barrier.
Co-estimates which individuals belong to either side of the barrier and barrier strength.
Uses expectation maximisation in likelihood framework. The method is described in
Baird et al. (2023) <doi:10.1111/2041-210X.14010>.
Author: Natalia Martinkova [aut, cre] ,
Stuart Baird [aut]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Diff between diemr versions 1.4.2 dated 2024-12-02 and 1.4.3 dated 2025-01-20
DESCRIPTION | 6 MD5 | 44 - NEWS.md | 10 R/diem.r | 15 R/importPolarized.r | 2 R/plotPolarized.r | 2 R/smoothPolarizedGenotypes.r | 7 R/vcf2diem.r | 51 + build/vignette.rds |binary inst/doc/Importing-data-for-genome-polarisation.R | 82 +- inst/doc/Importing-data-for-genome-polarisation.html | 4 inst/doc/Understanding-genome-polarisation-output-files.R | 14 inst/doc/Understanding-genome-polarisation-output-files.html | 4 inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.R | 288 +++++----- inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.html | 4 inst/extdata/myotis.vcf |binary man/CheckDiemFormat.Rd | 3 man/diem.Rd | 11 man/importPolarized.Rd | 3 man/smoothPolarizedGenotypes.Rd | 7 man/vcf2diem.Rd | 16 tests/testthat/_snaps/vcf2diem.md | 23 tests/testthat/test_vcf2diem.r | 45 + 23 files changed, 380 insertions(+), 261 deletions(-)
Title: Harmonise and Integrate Heterogeneous Areal Data
Description: Many relevant applications in the environmental and socioeconomic
sciences use areal data, such as biodiversity checklists, agricultural statistics,
or socioeconomic surveys. For applications that surpass the spatial, temporal or
thematic scope of any single data source, data must be integrated from several
heterogeneous sources. Inconsistent concepts, definitions, or messy data tables
make this a tedious and error-prone process. 'arealDB' tackles those problems and
helps the user to integrate a harmonised databases of areal data. Read the paper
at Ehrmann, Seppelt & Meyer (2020) <doi:10.1016/j.envsoft.2020.104799>.
Author: Steffen Ehrmann [aut, cre] ,
Arne Ruemmler [aut, ctb] ,
Felipe Melges [ctb] ,
Carsten Meyer [aut]
Maintainer: Steffen Ehrmann <steffen.ehrmann@posteo.de>
Diff between arealDB versions 0.6.3 dated 2023-07-03 and 0.9.4 dated 2025-01-20
arealDB-0.6.3/arealDB/R/makeExampleDB.R |only arealDB-0.6.3/arealDB/R/matchOntology.R |only arealDB-0.6.3/arealDB/R/start_arealDB.R |only arealDB-0.6.3/arealDB/R/updateTable.R |only arealDB-0.6.3/arealDB/inst/test_datasets/match_gadm.csv |only arealDB-0.6.3/arealDB/inst/test_datasets/match_madeUp.csv |only arealDB-0.6.3/arealDB/inst/test_datasets/territories.rds |only arealDB-0.6.3/arealDB/man/getColTypes.Rd |only arealDB-0.6.3/arealDB/man/makeExampleDB.Rd |only arealDB-0.6.3/arealDB/man/matchOntology.Rd |only arealDB-0.6.3/arealDB/man/start_arealDB.Rd |only arealDB-0.6.3/arealDB/man/testCompressed.Rd |only arealDB-0.6.3/arealDB/man/updateTable.Rd |only arealDB-0.6.3/arealDB/tests/testthat/test_01_makeExampleDB.R |only arealDB-0.6.3/arealDB/tests/testthat/test_02_start_arealDB.R |only arealDB-0.6.3/arealDB/tests/testthat/test_03_regDataseries.R |only arealDB-0.6.3/arealDB/tests/testthat/test_04_regGeometry.R |only arealDB-0.6.3/arealDB/tests/testthat/test_05_regTable.R |only arealDB-0.6.3/arealDB/tests/testthat/test_06_normGeometry.R |only arealDB-0.6.3/arealDB/tests/testthat/test_07_normTable.R |only arealDB-0.6.3/arealDB/tests/testthat/test_matchOntology.R |only arealDB-0.6.3/arealDB/tests/testthat/test_testCompressed.R |only arealDB-0.9.4/arealDB/DESCRIPTION | 20 arealDB-0.9.4/arealDB/MD5 | 114 - arealDB-0.9.4/arealDB/NAMESPACE | 42 arealDB-0.9.4/arealDB/NEWS.md | 45 arealDB-0.9.4/arealDB/R/adb_archive.R |only arealDB-0.9.4/arealDB/R/adb_backup.R |only arealDB-0.9.4/arealDB/R/adb_diagnose.R |only arealDB-0.9.4/arealDB/R/adb_example.R |only arealDB-0.9.4/arealDB/R/adb_init.R |only arealDB-0.9.4/arealDB/R/adb_inventory.R |only arealDB-0.9.4/arealDB/R/adb_metadata.R |only arealDB-0.9.4/arealDB/R/adb_ontology.R |only arealDB-0.9.4/arealDB/R/adb_querry.R |only arealDB-0.9.4/arealDB/R/adb_reset.R |only arealDB-0.9.4/arealDB/R/adb_restore.R |only arealDB-0.9.4/arealDB/R/adb_schemas.R |only arealDB-0.9.4/arealDB/R/adb_translations.R |only arealDB-0.9.4/arealDB/R/data.R |only arealDB-0.9.4/arealDB/R/helpers.R | 1005 +++++++++- arealDB-0.9.4/arealDB/R/normGeometry.R | 933 ++++----- arealDB-0.9.4/arealDB/R/normTable.R | 212 -- arealDB-0.9.4/arealDB/R/regDataseries.R | 91 arealDB-0.9.4/arealDB/R/regGeometry.R | 281 +- arealDB-0.9.4/arealDB/R/regTable.R | 356 +-- arealDB-0.9.4/arealDB/R/zzz.R | 84 arealDB-0.9.4/arealDB/README.md | 52 arealDB-0.9.4/arealDB/data |only arealDB-0.9.4/arealDB/inst/doc/arealDB.R | 2 arealDB-0.9.4/arealDB/inst/doc/arealDB.Rmd | 180 - arealDB-0.9.4/arealDB/inst/doc/arealDB.html | 323 +-- arealDB-0.9.4/arealDB/inst/test_datasets/match_gadm.rds |only arealDB-0.9.4/arealDB/inst/test_datasets/match_madeUp.rds |only arealDB-0.9.4/arealDB/man/adb_archive.Rd |only arealDB-0.9.4/arealDB/man/adb_backup.Rd |only arealDB-0.9.4/arealDB/man/adb_diagnose.Rd |only arealDB-0.9.4/arealDB/man/adb_example.Rd |only arealDB-0.9.4/arealDB/man/adb_init.Rd |only arealDB-0.9.4/arealDB/man/adb_inventory.Rd |only arealDB-0.9.4/arealDB/man/adb_metadata.Rd |only arealDB-0.9.4/arealDB/man/adb_ontology.Rd |only arealDB-0.9.4/arealDB/man/adb_querry.Rd |only arealDB-0.9.4/arealDB/man/adb_reset.Rd |only arealDB-0.9.4/arealDB/man/adb_restore.Rd |only arealDB-0.9.4/arealDB/man/adb_schemas.Rd |only arealDB-0.9.4/arealDB/man/adb_translations.Rd |only arealDB-0.9.4/arealDB/man/dot-editMatches.Rd |only arealDB-0.9.4/arealDB/man/dot-getColTypes.Rd |only arealDB-0.9.4/arealDB/man/dot-matchOntology.Rd |only arealDB-0.9.4/arealDB/man/dot-updateOntology.Rd |only arealDB-0.9.4/arealDB/man/normGeometry.Rd | 132 - arealDB-0.9.4/arealDB/man/normTable.Rd | 63 arealDB-0.9.4/arealDB/man/regDataseries.Rd | 38 arealDB-0.9.4/arealDB/man/regGeometry.Rd | 92 arealDB-0.9.4/arealDB/man/regTable.Rd | 121 - arealDB-0.9.4/arealDB/man/territories.Rd |only arealDB-0.9.4/arealDB/tests/testthat/test_01_adb_init.R |only arealDB-0.9.4/arealDB/tests/testthat/test_02_regDataseries.R |only arealDB-0.9.4/arealDB/tests/testthat/test_02_regGeometry.R |only arealDB-0.9.4/arealDB/tests/testthat/test_02_regTable.R |only arealDB-0.9.4/arealDB/tests/testthat/test_03_normGeometry.R |only arealDB-0.9.4/arealDB/tests/testthat/test_03_normTable.R |only arealDB-0.9.4/arealDB/tests/testthat/test_04_adb_backup.R |only arealDB-0.9.4/arealDB/tests/testthat/test_05_adb_data.R |only arealDB-0.9.4/arealDB/tests/testthat/test_05_adb_metadata.R |only arealDB-0.9.4/arealDB/tests/testthat/test_06_adb_inventory.R |only arealDB-0.9.4/arealDB/tests/testthat/test_06_adb_ontology.R |only arealDB-0.9.4/arealDB/tests/testthat/test_06_adb_schemas.R |only arealDB-0.9.4/arealDB/tests/testthat/test_06_adb_translations.R |only arealDB-0.9.4/arealDB/tests/testthat/test_07_matchOntology.R |only arealDB-0.9.4/arealDB/tests/testthat/test_99_adb_exampleDB.R |only arealDB-0.9.4/arealDB/tests/testthat/test_getColTypes.R | 42 arealDB-0.9.4/arealDB/vignettes/arealDB.Rmd | 180 - 94 files changed, 2697 insertions(+), 1711 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics
Description: A collection of functions to create spatial weights matrix
objects from polygon 'contiguities', from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial 'autocorrelation',
including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord'
(1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel'
general cross product statistic, Empirical Bayes estimates and
'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992)
<doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured
join count statistics, 'APLE' ('Li 'et al.' )
<doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I', 'Gearys C'
('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and
'Getis/Ord' G ('Ord' and 'Getis' 1995)
< [...truncated...]
Author: Roger Bivand [cre, aut] ,
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assuncao [ctb],
Anil Bera [ctb],
Olaf Berke [ctb],
F. Guillaume Blanchet [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Steph [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 1.3-9 dated 2025-01-16 and 1.3-10 dated 2025-01-20
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NEWS.md | 12 ++++++++++-- R/skater.R | 2 +- inst/doc/CO69.html | 6 +++--- inst/doc/nb_sf.html | 26 +++++++++++++------------- inst/doc/sids.html | 4 ++-- inst/doc/subgraphs.html | 6 +++--- man/globalG.test.Rd | 1 - man/knearneigh.Rd | 12 +++++++++--- man/moran.test.Rd | 1 - man/read.gwt2nb.Rd | 25 +++++++++++++++++++++++-- man/set.spChkOption.Rd | 4 ---- man/skater.Rd | 25 +++++++++++++------------ src/dfs_ncomp.c | 2 +- src/nbdists.c | 2 +- 16 files changed, 98 insertions(+), 68 deletions(-)
Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of elements
into groups (i.e., anticlusters) with the goal of maximizing
between-group similarity or within-group heterogeneity. The
anticlustering approach thereby reverses the logic of cluster analysis
that strives for high within-group homogeneity and clear separation
between groups. Computationally, anticlustering is accomplished by
maximizing instead of minimizing a clustering objective function, such
as the intra-cluster variance (used in k-means clustering) or the sum
of pairwise distances within clusters. The main function
anticlustering() gives access to optimal and heuristic anticlustering
methods described in Papenberg and Klau (2021;
<doi:10.1037/met0000301>), Brusco et al. (2020;
<doi:10.1111/bmsp.12186>), and Papenberg (2024;
<doi:10.1111/bmsp.12315>). The optimal algorithms require that an
integer linear programming solver is installed. This package will install
'lpSolve' (<https://cran.r-project.org/p [...truncated...]
Author: Martin Papenberg [aut, cre] ,
Meik Michalke [ctb] ,
Gunnar W. Klau [ths],
Juliane V. Nagel [ctb] ,
Martin Breuer [ctb] ,
Marie L. Schaper [ctb] ,
Max Diekhoff [ctb] ,
Hannah Hengelbrock [ctb]
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>
Diff between anticlust versions 0.8.9 dated 2025-01-17 and 0.8.9-1 dated 2025-01-20
DESCRIPTION | 6 - LICENSE | 2 MD5 | 12 +-- inst/doc/Speeding_up_anticlustering.html | 22 ++--- inst/tinytest/test-three-phase-search-dynamic-population-size.R | 38 +++++++--- src/three-phase-dispersion.c | 5 - src/three_phase_search_dynamic_population_size.c | 2 7 files changed, 52 insertions(+), 35 deletions(-)
Title: Spatial Analysis on Network
Description: Perform spatial analysis on network.
Implement several methods for spatial analysis on network: Network Kernel Density estimation,
building of spatial matrices based on network distance ('listw' objects from 'spdep' package), K functions estimation
for point pattern analysis on network, k nearest neighbours on network, reachable area calculation, and graph generation
References: Okabe et al (2019) <doi:10.1080/13658810802475491>;
Okabe et al (2012, ISBN:978-0470770818);Baddeley et al (2015, ISBN:9781482210200).
Author: Jeremy Gelb [aut, cre] ,
Philippe Apparicio [ctb]
Maintainer: Jeremy Gelb <jeremy.gelb@ucs.inrs.ca>
Diff between spNetwork versions 0.4.4.4 dated 2025-01-14 and 0.4.4.5 dated 2025-01-20
DESCRIPTION | 6 - MD5 | 38 +++--- README.md | 11 + build/partial.rdb |binary inst/doc/KNetworkFunctions.html | 4 inst/doc/NKDE.html | 4 inst/doc/NetworkBuilding.html | 4 inst/doc/SpatialWeightMatrices.html | 4 inst/doc/TNKDE.html | 4 man/cross_kfunctions.mc.Rd | 208 +++++++++++++++++------------------ man/ess_kernel.Rd | 64 +++++----- man/figures/unnamed-chunk-8-1.png |binary man/kfunc_cpp2.Rd | 68 +++++------ man/kgfunc_time_counting.Rd | 118 +++++++++---------- man/pair_dists.Rd | 40 +++--- man/rev_matrix.Rd | 38 +++--- man/split_by_grid.mc.Rd | 124 ++++++++++---------- src/k_and_g_func.cpp | 8 + src/k_and_g_func_time.cpp | 130 +++++++++++++-------- tests/testthat/test_k_functions_sf.R | 6 + 20 files changed, 465 insertions(+), 414 deletions(-)
Title: Support for Metrological Applications
Description: Provides classes and calculation and plotting functions
for metrology applications, including measurement uncertainty estimation
and inter-laboratory metrology comparison studies.
Author: Stephen L R Ellison. [aut],
Stephen L R Ellison [cre]
Maintainer: Stephen L R Ellison <s.ellison@lgcgroup.com>
Diff between metRology versions 0.9-28-1 dated 2018-09-10 and 0.9-29-2 dated 2025-01-20
DESCRIPTION | 26 ++++--- MD5 | 150 +++++++++++++++++++++++----------------------- NAMESPACE | 8 ++ R/MSD-class.r | 16 +++- R/M_estimates.r | 6 + R/blockplot.r | 80 +++++++++++++++++++++--- R/boot.pairwise.r |only R/bootMSD.R | 17 ++++- R/contribs.R | 8 +- R/drop1.R | 19 +++-- R/ilab.R | 3 R/msd.R | 4 - R/pdchisq.r |only R/sysdata.rda |binary R/uncert.R | 45 ++++++++++--- R/uncertMC.R | 26 +++---- R/uncertMC_class.R | 24 ++++--- R/uncert_class.R | 14 ++-- build/partial.rdb |binary data/GUM.H.1.rda |binary data/Pb.rda |binary data/RMstudy.rda |binary data/apricot.rda |binary data/chromium.rda |binary data/potassium.rda |binary man/Extract.ilab.Rd | 2 man/GUM.H.1.Rd | 1 man/GUM.Rd | 2 man/LCS.Rd | 2 man/M-estimates.Rd | 2 man/Pb.Rd | 2 man/algA.Rd | 2 man/algS.Rd | 2 man/barplot.mandel.kh.Rd | 2 man/bkp.Rd | 52 +++++++++++---- man/bootMSD.Rd | 33 +++++----- man/bootMSD_class.Rd | 34 +++++----- man/bootMtrPairs_class.Rd |only man/bootMtrPairwise.Rd |only man/boxplot.mandel.kh.Rd | 2 man/buildCor.Rd | 2 man/contribs.Rd | 4 - man/cov.dellipse.Rd | 26 +++---- man/cplot.Rd | 2 man/dmandelh.Rd | 2 man/dmandelk.Rd | 2 man/drop1.uncert.Rd | 2 man/dsl.Rd | 2 man/dt.scaled.Rd | 2 man/dtri.Rd | 2 man/duewer.plot.Rd | 2 man/gplot.Rd | 2 man/ilab.Rd | 2 man/kplot.Rd | 2 man/loc_est.Rd | 2 man/mandel.h.Rd | 2 man/mandel.k.Rd | 2 man/mandel.kh.Rd | 2 man/metRology-package.Rd | 33 +++++++++- man/methods.ilab.Rd | 2 man/mpaule.Rd | 2 man/msd.Rd | 8 ++ man/msd_class.Rd | 13 ++- man/pdchisq.Rd |only man/pdchisq_class.Rd |only man/plot.mandel.kh.Rd | 2 man/plot.uncert.Rd | 4 - man/plot.uncertMC.Rd | 8 +- man/pmsd.Rd | 2 man/pmsd.xnorm.Rd | 2 man/rbind.ilab.Rd | 27 +++----- man/reml_loc.Rd | 2 man/uncertMC.Rd | 4 - man/uncertMC_class.Rd | 2 man/uncert_class.Rd | 2 man/uncertainty.Rd | 23 +++---- man/update.uncert.Rd | 2 man/w.s.Rd | 4 - man/xs.plot.Rd | 6 - 79 files changed, 495 insertions(+), 299 deletions(-)
Title: Knowledge Space Theory Input/Output
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstIO' package
provides basic functionalities to read and write KST data from/to
files to be used together with the 'kst', 'kstMatrix', 'CDSS', 'pks', or
'DAKS' packages.
Author: Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstIO versions 0.4-0 dated 2023-01-26 and 0.4-1 dated 2025-01-20
Changelog | 4 ++++ DESCRIPTION | 12 ++++++------ MD5 | 34 +++++++++++++++++----------------- R/write_surmiserelation.R | 1 + build/vignette.rds |binary inst/doc/kstIO.pdf |binary man/kstIO-package.Rd | 4 ++-- man/read_kbase.Rd | 4 ++-- man/read_kdata.Rd | 4 ++-- man/read_kfamset.Rd | 4 ++-- man/read_kspace.Rd | 4 ++-- man/read_kstructure.Rd | 4 ++-- man/read_surmiserelation.Rd | 4 ++-- man/write_kbase.Rd | 4 ++-- man/write_kdata.Rd | 4 ++-- man/write_kspace.Rd | 4 ++-- man/write_kstructure.Rd | 4 ++-- man/write_surmiserelation.Rd | 4 ++-- 18 files changed, 52 insertions(+), 47 deletions(-)
Title: Extended Changes-in-Changes
Description: Extends the Changes-in-Changes model a la Athey and Imbens
(2006) <doi:10.1111/j.1468-0262.2006.00668.x> to multiple cohorts and
time periods, which generalizes difference-in-differences estimation
techniques to the entire distribution. Computes quantile treatment
effects for every possible two-by-two combination in ecic(). Then,
aggregating all bootstrap runs adds the standard errors in
summary_ecic(). Results can be plotted with plot_ecic() aggregated
over all cohort-group combinations or in an event-study style for
either individual periods or individual quantiles.
Author: Frederic Kluser [aut, cre, cph]
Maintainer: Frederic Kluser <frederic.kluser@unibe.ch>
Diff between ecic versions 0.0.3 dated 2023-02-21 and 0.0.4 dated 2025-01-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/ecic.R | 6 ++++-- build/partial.rdb |binary 5 files changed, 17 insertions(+), 10 deletions(-)
Title: Wrapper for the 'AT' Protocol Behind 'Bluesky'
Description: Wraps the 'AT' Protocol (Authenticated Transfer Protocol) behind
'Bluesky' <https://bsky.social>. Functions can be used for, among others,
retrieving posts and followers from the network or posting content.
Author: Johannes B. Gruber [aut, cre] ,
Benjamin Guinaudeau [aut, ctb]
,
Fabio Votta [aut, ctb]
Maintainer: Johannes B. Gruber <JohannesB.Gruber@gmail.com>
Diff between atrrr versions 0.0.5 dated 2025-01-19 and 0.1.0 dated 2025-01-20
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/auth.r | 1 + R/feed.r | 15 +++++++++++---- README.md | 2 -- 6 files changed, 25 insertions(+), 14 deletions(-)
Title: Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text
Shaping
Description: Provides access to the text shaping functionality in the
'HarfBuzz' library and the bidirectional algorithm in the 'Fribidi'
library. 'textshaping' is a low-level utility package mainly for
graphic devices that expands upon the font tool-set provided by the
'systemfonts' package.
Author: Thomas Lin Pedersen [cre, aut]
,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between textshaping versions 0.4.1 dated 2024-12-06 and 1.0.0 dated 2025-01-20
DESCRIPTION | 11 MD5 | 49 + NAMESPACE | 3 NEWS.md | 16 R/cpp11.R | 4 R/lorem_text.R |only R/shape_text.R | 166 +++++- README.md | 4 configure | 34 - inst/lorem |only man/lorem_text.Rd |only man/plot_shape.Rd |only man/shape_text.Rd | 34 - src/Makevars.win | 25 src/cpp11.cpp | 8 src/string_bidi.cpp | 11 src/string_bidi.h | 2 src/string_metrics.cpp | 38 - src/string_metrics.h | 3 src/string_shape.cpp | 1271 +++++++++++++++++++++++++++++++------------------ src/string_shape.h | 333 +++++++++++- tests |only 22 files changed, 1395 insertions(+), 617 deletions(-)
Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font
handling varies between systems it is difficult to correctly locate
installed fonts across different operating systems. The 'systemfonts'
package provides bindings to the native libraries on Windows, macOS
and Linux for finding font files that can then be used further by e.g.
graphic devices. The main use is intended to be from compiled code but
'systemfonts' also provides access from R.
Author: Thomas Lin Pedersen [aut, cre]
,
Jeroen Ooms [aut] ,
Devon Govett [aut] ,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between systemfonts versions 1.2.0 dated 2025-01-16 and 1.2.1 dated 2025-01-20
DESCRIPTION | 11 +++++------ MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ R/register_font.R | 2 +- R/web_fonts.R | 28 ++++++++++++++++++++-------- man/web-fonts.Rd | 6 +++++- src/FontDescriptor.h | 17 +++++++++++++++-- 7 files changed, 60 insertions(+), 24 deletions(-)
Title: Interface to the 'HDF5' Binary Data Format
Description: 'HDF5' is a data model, library and file format for storing
and managing large amounts of data. This package provides a nearly
feature complete, object oriented wrapper for the 'HDF5' API
<https://support.hdfgroup.org/documentation/hdf5/latest/_r_m.html> using R6 classes.
Additionally, functionality is added so that 'HDF5' objects behave very
similar to their corresponding R counterparts.
Author: Holger Hoefling [aut, cre],
Mario Annau [aut],
Novartis Institute for BioMedical Research [cph]
Maintainer: Holger Hoefling <hhoeflin@gmail.com>
Diff between hdf5r versions 1.3.11 dated 2024-07-07 and 1.3.12 dated 2025-01-20
DESCRIPTION | 8 +- MD5 | 90 ++++++++++++------------ NEWS.md | 20 +++++ R/Common_functions.R | 126 ++++++++++++++++----------------- R/R6Classes.R | 2 R/R6Classes_H5A.R | 14 +-- R/R6Classes_H5D.R | 28 +++---- R/R6Classes_H5File.R | 10 +- R/R6Classes_H5P.R | 142 +++++++++++++++++++------------------- R/R6Classes_H5R.R | 4 - R/R6Classes_H5S.R | 48 ++++++------ R/R6Classes_H5T.R | 74 +++++++++---------- R/adapt_during_onLoad.R | 6 - R/high_level_UI.R | 4 - inst/doc/hdf5r.Rmd | 2 inst/doc/hdf5r.html | 6 - man/H5A-class.Rd | 18 ++-- man/H5D-class.Rd | 68 +++++++++--------- man/H5File-class.Rd | 126 ++++++++++++++++----------------- man/H5Group-class.Rd | 116 +++++++++++++++---------------- man/H5P-class.Rd | 8 +- man/H5P_ATTRIBUTE_CREATE-class.Rd | 4 - man/H5P_CLASS-class.Rd | 2 man/H5P_DATASET_ACCESS-class.Rd | 4 - man/H5P_DATASET_CREATE-class.Rd | 50 ++++++------- man/H5P_DATASET_XFER-class.Rd | 14 +-- man/H5P_FILE_ACCESS-class.Rd | 4 - man/H5P_FILE_CREATE-class.Rd | 20 ++--- man/H5P_LINK_ACCESS-class.Rd | 12 +-- man/H5P_LINK_CREATE-class.Rd | 8 +- man/H5P_OBJECT_COPY-class.Rd | 4 - man/H5P_OBJECT_CREATE-class.Rd | 12 +-- man/H5R_DATASET_REGION-class.Rd | 2 man/H5R_OBJECT-class.Rd | 2 man/H5RefClass-class.Rd | 12 +-- man/H5S-class.Rd | 50 ++++++------- man/H5S_H5D_subset_assign.Rd | 4 - man/H5T-class.Rd | 72 +++++++++---------- man/H5T_ARRAY-class.Rd | 6 - man/H5T_COMPOUND-class.Rd | 2 man/H5T_FLOAT-class.Rd | 16 ++-- man/H5T_INTEGER-class.Rd | 4 - man/H5T_STRING-class.Rd | 10 +- man/H5T_VLEN-class.Rd | 2 src/H5ls.c | 43 +++++------ vignettes/hdf5r.Rmd | 2 46 files changed, 650 insertions(+), 631 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects and adjusted predictions from statistical
models and returns the result as tidy data frames. These data frames are
ready to use with the 'ggplot2'-package. Effects and predictions can be
calculated for many different models. Interaction terms, splines and
polynomial terms are also supported. The main functions are ggpredict(),
ggemmeans() and ggeffect(). There is a generic plot()-method to plot the
results using 'ggplot2'.
Author: Daniel Luedecke [aut, cre] ,
Frederik Aust [ctb] ,
Sam Crawley [ctb] ,
Mattan S. Ben-Shachar [ctb] ,
Sean C. Anderson [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between ggeffects versions 2.0.0 dated 2024-11-27 and 2.1.0 dated 2025-01-20
ggeffects-2.0.0/ggeffects/tests/testthat/_snaps |only ggeffects-2.1.0/ggeffects/DESCRIPTION | 20 - ggeffects-2.1.0/ggeffects/LICENSE | 4 ggeffects-2.1.0/ggeffects/MD5 | 164 ++-------- ggeffects-2.1.0/ggeffects/NEWS.md | 15 ggeffects-2.1.0/ggeffects/R/format.R | 7 ggeffects-2.1.0/ggeffects/R/get_predictions_logitr.R | 3 ggeffects-2.1.0/ggeffects/R/ggaverage.R | 3 ggeffects-2.1.0/ggeffects/R/ggeffect.R | 19 - ggeffects-2.1.0/ggeffects/R/ggemmeans.R | 3 ggeffects-2.1.0/ggeffects/R/ggpredict.R | 9 ggeffects-2.1.0/ggeffects/R/moderator_pattern.R | 54 +-- ggeffects-2.1.0/ggeffects/R/plot.R | 67 ++-- ggeffects-2.1.0/ggeffects/R/post_processing_predictions.R | 9 ggeffects-2.1.0/ggeffects/R/predict_response.R | 7 ggeffects-2.1.0/ggeffects/R/sanitize_type_arg.R | 93 +++-- ggeffects-2.1.0/ggeffects/R/standard_error_predictions.R | 14 ggeffects-2.1.0/ggeffects/R/test_predictions.R | 97 ++++- ggeffects-2.1.0/ggeffects/R/tp_label_hypothesis_formula.R |only ggeffects-2.1.0/ggeffects/R/utils.R | 18 - ggeffects-2.1.0/ggeffects/R/utils_get_data_grid.R | 12 ggeffects-2.1.0/ggeffects/R/utils_get_representative_values.R | 6 ggeffects-2.1.0/ggeffects/R/vcov.R | 24 - ggeffects-2.1.0/ggeffects/man/ggpredict.Rd | 11 ggeffects-2.1.0/ggeffects/man/install_latest.Rd | 80 ++-- ggeffects-2.1.0/ggeffects/man/plot.Rd | 4 ggeffects-2.1.0/ggeffects/man/predict_response.Rd | 4 ggeffects-2.1.0/ggeffects/man/test_predictions.Rd | 58 ++- ggeffects-2.1.0/ggeffects/man/values_at.Rd | 43 +- ggeffects-2.1.0/ggeffects/tests/testthat/test-avg_predictions.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-backtransform_response.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-ci_backticks-names.R | 2 ggeffects-2.1.0/ggeffects/tests/testthat/test-condition.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-emmeans-weights.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-focal_only_random.R | 2 ggeffects-2.1.0/ggeffects/tests/testthat/test-gee.R | 2 ggeffects-2.1.0/ggeffects/tests/testthat/test-ggaverage.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-ggeffect.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-glm.R | 2 ggeffects-2.1.0/ggeffects/tests/testthat/test-johnson_neyman.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-logitr.R |only ggeffects-2.1.0/ggeffects/tests/testthat/test-plot-from-vignettes.R | 52 ++- ggeffects-2.1.0/ggeffects/tests/testthat/test-plot-show_data.R | 1 ggeffects-2.1.0/ggeffects/tests/testthat/test-plot-survival.R |only ggeffects-2.1.0/ggeffects/tests/testthat/test-plot.R | 20 + ggeffects-2.1.0/ggeffects/tests/testthat/test-print.R | 20 + ggeffects-2.1.0/ggeffects/tests/testthat/test-test_predictions-formula.R |only ggeffects-2.1.0/ggeffects/tests/testthat/test-test_predictions.R | 2 48 files changed, 544 insertions(+), 414 deletions(-)
Title: Use 'nlmixr2' to Interact with Open Source and Commercial
Software
Description: Run other estimation and simulation software via the 'nlmixr2' (Fidler et al (2019)
<doi:10.1002/psp4.12445>) interface including 'PKNCA', 'NONMEM' and 'Monolix'. While not required, you can
get/install the 'lixoftConnectors' package in the 'Monolix' installation, as
described at the following url
<https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When
'lixoftConnectors' is available, 'Monolix' can be run directly instead of setting up
command line usage.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [aut] ,
Theodoros Papathanasiou [ctb],
Nook Fulloption [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between babelmixr2 versions 0.1.5 dated 2024-11-06 and 0.1.6 dated 2025-01-20
babelmixr2-0.1.5/babelmixr2/tests/testthat/_snaps |only babelmixr2-0.1.6/babelmixr2/DESCRIPTION | 8 +- babelmixr2-0.1.6/babelmixr2/MD5 | 32 +++----- babelmixr2-0.1.6/babelmixr2/NEWS.md | 11 +++ babelmixr2-0.1.6/babelmixr2/R/RcppExports.R | 4 + babelmixr2-0.1.6/babelmixr2/R/monolixNlmixr2est.R | 1 babelmixr2-0.1.6/babelmixr2/R/nonmem.R | 4 - babelmixr2-0.1.6/babelmixr2/R/nonmemNlmixr2est.R | 1 babelmixr2-0.1.6/babelmixr2/R/poped.R | 16 ++++ babelmixr2-0.1.6/babelmixr2/R/zzz.R | 1 babelmixr2-0.1.6/babelmixr2/inst/tools/workaround.R | 24 +++--- babelmixr2-0.1.6/babelmixr2/src/Makevars.in | 6 - babelmixr2-0.1.6/babelmixr2/src/RcppExports.cpp | 10 ++ babelmixr2-0.1.6/babelmixr2/src/init.c | 3 babelmixr2-0.1.6/babelmixr2/src/poped.cpp | 52 ++++++++++++++ babelmixr2-0.1.6/babelmixr2/tests/testthat/test-nonmem.R | 54 +++++++++++++++ 16 files changed, 191 insertions(+), 36 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.5.5 dated 2024-12-20 and 1.5.5.1 dated 2025-01-20
DESCRIPTION | 8 MD5 | 20 - R/GPModel.R | 2 configure.ac | 2 src/include/GPBoost/cov_fcts.h | 358 +++++++++++++++++------- src/include/GPBoost/likelihoods.h | 120 ++++---- src/include/GPBoost/optim_utils.h | 4 src/include/GPBoost/re_model_template.h | 24 - src/include/GPBoost/utils.h | 74 ++++ tests/testthat/test_GPModel_gaussian_process.R | 24 + tests/testthat/test_GPModel_non_Gaussian_data.R | 104 ++++-- 11 files changed, 530 insertions(+), 210 deletions(-)