Title: Score Matching Estimation by Automatic Differentiation
Description: Hyvärinen's score matching (Hyvärinen, 2005) <https://jmlr.org/papers/v6/hyvarinen05a.html> is a useful estimation technique when the normalising constant for a probability distribution is difficult to compute. This package implements score matching estimators using automatic differentiation in the 'CppAD' library <https://github.com/coin-or/CppAD> and is designed for quickly implementing score matching estimators for new models. Also available is general robustification (Windham, 1995) <https://www.jstor.org/stable/2346159>. Already in the package are estimators for directional distributions (Mardia, Kent and Laha, 2016) <doi:10.48550/arXiv.1604.08470> and the flexible Polynomially-Tilted Pairwise Interaction model for compositional data. The latter estimators perform well when there are zeros in the compositions (Scealy and Wood, 2023) <doi:10.1080/01621459.2021.2016422>, even many zeros (Scealy, Hingee, Kent, and Wood, 2024) <doi:10.1007/s11222-024-1 [...truncated...]
Author: Kassel Liam Hingee [aut, cre] ,
Janice Scealy [aut] ,
Bradley M. Bell [cph]
Maintainer: Kassel Liam Hingee <kassel.hingee@anu.edu.au>
Diff between scorematchingad versions 0.0.64 dated 2024-06-27 and 0.0.67 dated 2024-07-24
scorematchingad-0.0.64/scorematchingad/inst/include/cppad |only scorematchingad-0.0.64/scorematchingad/src/Makevars |only scorematchingad-0.0.67/scorematchingad/DESCRIPTION | 10 scorematchingad-0.0.67/scorematchingad/MD5 | 1654 +++++++--- scorematchingad-0.0.67/scorematchingad/NEWS.md | 12 scorematchingad-0.0.67/scorematchingad/R/Windham.R | 2 scorematchingad-0.0.67/scorematchingad/R/buildsmdtape.R | 2 scorematchingad-0.0.67/scorematchingad/R/inlineCxxPlugin.R | 2 scorematchingad-0.0.67/scorematchingad/R/ppi_cW.R | 2 scorematchingad-0.0.67/scorematchingad/R/ppi_robust.R | 2 scorematchingad-0.0.67/scorematchingad/R/rppi.R | 4 scorematchingad-0.0.67/scorematchingad/R/vMF_robust.R | 4 scorematchingad-0.0.67/scorematchingad/README.md |only scorematchingad-0.0.67/scorematchingad/build/partial.rdb |binary scorematchingad-0.0.67/scorematchingad/cleanup |only scorematchingad-0.0.67/scorematchingad/configure |only scorematchingad-0.0.67/scorematchingad/configure.ac |only scorematchingad-0.0.67/scorematchingad/configure.win |only scorematchingad-0.0.67/scorematchingad/inst/cppad |only scorematchingad-0.0.67/scorematchingad/inst/include/CppAD_LICENSE | 2 scorematchingad-0.0.67/scorematchingad/inst/include/scorematchingad.h | 71 scorematchingad-0.0.67/scorematchingad/inst/include/scorematchingad_forward.h |only scorematchingad-0.0.67/scorematchingad/inst/include/utils/wrapas.hpp | 2 scorematchingad-0.0.67/scorematchingad/man/ADFun.Rd | 2 scorematchingad-0.0.67/scorematchingad/man/buildsmdtape.Rd | 2 scorematchingad-0.0.67/scorematchingad/man/scorematchingad-package.Rd | 8 scorematchingad-0.0.67/scorematchingad/src/approxwrap.h | 2 scorematchingad-0.0.67/scorematchingad/src/cppad_interface.h | 4 scorematchingad-0.0.67/scorematchingad/src/exposemanifold.cpp | 4 scorematchingad-0.0.67/scorematchingad/src/exposemanifold.h | 2 scorematchingad-0.0.67/scorematchingad/src/tapebdryweight.h | 2 scorematchingad-0.0.67/scorematchingad/src/tapell.h | 2 scorematchingad-0.0.67/scorematchingad/src/tapesmd.h | 3 33 files changed, 1317 insertions(+), 483 deletions(-)
More information about scorematchingad at CRAN
Permanent link
Title: Statistical Functions for the
Maxwell-Boltzmann-Bose-Einstein-Fermi-Dirac (MBBEFD) Family of
Distributions
Description: Provides probability mass, distribution, quantile, random variate
generation, and method-of-moments parameter fitting for the MBBEFD family of
distributions used in insurance modeling as described in Bernegger (1997)
<doi:10.2143/AST.27.1.563208> without any external dependencies.
Author: Avraham Adler [aut, cre, cph]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between MBBEFDLite versions 0.0.3 dated 2024-06-20 and 0.0.4 dated 2024-07-24
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- build/partial.rdb |binary inst/CITATION | 2 +- inst/NEWS.Rd | 14 ++++++++++++++ inst/tinytest/test_package_metadata.R | 2 +- man/ecmb.Rd | 11 ++++++----- src/dmb.c | 5 +++-- src/ecmb.c | 2 +- 9 files changed, 37 insertions(+), 21 deletions(-)
Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an efficient implementation
of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.
This package is its R interface. The package includes efficient linear
model solver and tree learning algorithms. The package can automatically
do parallel computation on a single machine which could be more than 10
times faster than existing gradient boosting packages. It supports
various objective functions, including regression, classification and ranking.
The package is made to be extensible, so that users are also allowed to define
their own objectives easily.
Author: Tianqi Chen [aut],
Tong He [aut],
Michael Benesty [aut],
Vadim Khotilovich [aut],
Yuan Tang [aut] ,
Hyunsu Cho [aut],
Kailong Chen [aut],
Rory Mitchell [aut],
Ignacio Cano [aut],
Tianyi Zhou [aut],
Mu Li [aut],
Junyuan Xie [aut],
Min Lin [aut],
Yifen [...truncated...]
Maintainer: Jiaming Yuan <jm.yuan@outlook.com>
Diff between xgboost versions 1.7.7.1 dated 2024-01-25 and 1.7.8.1 dated 2024-07-24
DESCRIPTION | 8 - MD5 | 34 +++---- build/vignette.rds |binary configure | 18 ++-- configure.ac | 2 inst/doc/discoverYourData.Rmd | 2 inst/doc/discoverYourData.html | 57 ++++++------ inst/doc/xgboost.Rnw | 10 +- inst/doc/xgboost.pdf |binary inst/doc/xgboostPresentation.Rmd | 6 - inst/doc/xgboostPresentation.html | 21 ++-- inst/doc/xgboostfromJSON.html | 4 src/include/xgboost/parameter.h | 2 src/xgboost_R.cc | 169 ++++++++++++++++++-------------------- src/xgboost_R.h | 3 vignettes/discoverYourData.Rmd | 2 vignettes/xgboost.Rnw | 10 +- vignettes/xgboostPresentation.Rmd | 6 - 18 files changed, 178 insertions(+), 176 deletions(-)
Title: ROC Surface Analysis Under the Three-Class Problems
Description: Receiver Operating Characteristic (ROC) analysis is performed assuming samples are from the proposed distributions. In addition, the volume under the ROC surface and true positive fractions values are evaluated by ROC surface analysis.
Author: Ertan Akgenc [cre, aut, cph]
,
Coskun Kus [aut, ctb]
Maintainer: Ertan Akgenc <statistician.ertan@gmail.com>
Diff between ROCsurf versions 0.1.0 dated 2024-07-21 and 0.1.1 dated 2024-07-24
DESCRIPTION | 6 ++-- MD5 | 4 +- tests/testthat/testfunction.R | 60 +++++++++++++++++++++--------------------- 3 files changed, 35 insertions(+), 35 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-19 1.9
2023-08-27 1.8
2023-07-07 1.7
2023-04-07 1.6
2023-01-30 1.5
2023-01-15 1.4
2022-10-23 1.3
2022-09-12 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-03 2.0.2.3.1
2023-09-05 2.0.2.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-17 1.1.3
2023-04-27 1.1.2
2023-03-21 1.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-27 1.2
2024-01-10 1.1
2022-12-07 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-12 2.0
2023-01-26 1.6
2022-07-21 1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-09 0.9
2024-04-06 0.8
2024-03-03 0.7
2023-12-03 0.6
2023-10-19 0.5
2023-10-01 0.4
2023-09-02 0.3
2023-08-08 0.2
2023-07-18 0.1
Title: Bayesian Cure Rate Modeling for Time-to-Event Data
Description: A fully Bayesian approach in order to estimate a general family of cure rate models under the presence of covariates, see Papastamoulis and Milienos (2023) <doi:10.48550/arXiv.2310.06926>. The promotion time can be modelled (a) parametrically using typical distributional assumptions for time to event data (including the Weibull, Exponential, Gompertz, log-Logistic distributions), or (b) semiparametrically using finite mixtures of Gamma distributions. Posterior inference is carried out by constructing a Metropolis-coupled Markov chain Monte Carlo (MCMC) sampler, which combines Gibbs sampling for the latent cure indicators and Metropolis-Hastings steps with Langevin diffusion dynamics for parameter updates. The main MCMC algorithm is embedded within a parallel tempering scheme by considering heated versions of the target posterior distribution.
Author: Panagiotis Papastamoulis [aut, cre]
,
Fotios Milienos [aut]
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Diff between bayesCureRateModel versions 1.0 dated 2024-06-27 and 1.1 dated 2024-07-24
DESCRIPTION | 10 - MD5 | 16 +- NAMESPACE | 1 R/bayesian_cure_rate_model.R | 221 ++++++++++++++++++++++++++++++-------- build/partial.rdb |binary man/bayesCureRateModel-package.Rd | 3 man/cure_rate_MC3.Rd | 7 - man/plot.bayesCureModel.Rd | 10 + man/summary.bayesCureModel.Rd | 1 9 files changed, 203 insertions(+), 66 deletions(-)
More information about bayesCureRateModel at CRAN
Permanent link
Title: Analyzing the Behaviour of Wind Generated by Tropical Storms and
Cyclones
Description: Set of functions to quantify and map the
behaviour of winds generated by tropical storms and cyclones in space
and time. It includes functions to compute and analyze fields such as the maximum sustained wind field, power dissipation index and duration of exposure to winds above a given threshold. It also includes functions to map the trajectories as well as characteristics of the storms.
Author: Baptiste Delaporte [aut],
Thomas Ibanez [aut] ,
Gunnar Keppel [aut] ,
Swen Jullien [aut] ,
Christophe Menkes [aut] ,
Thomas Arsouze [aut, cre]
Maintainer: Thomas Arsouze <thomas.arsouze@cirad.fr>
Diff between StormR versions 0.1.1 dated 2023-11-24 and 0.2.1 dated 2024-07-24
StormR-0.1.1/StormR/man/getSSHS-methods.Rd |only StormR-0.2.1/StormR/DESCRIPTION | 12 StormR-0.2.1/StormR/MD5 | 90 StormR-0.2.1/StormR/NAMESPACE | 3 StormR-0.2.1/StormR/NEWS.md | 13 StormR-0.2.1/StormR/R/defStormsDataset.R | 571 - StormR-0.2.1/StormR/R/defStormsList.R | 194 StormR-0.2.1/StormR/R/plotBehaviour.R | 224 StormR-0.2.1/StormR/R/plotStorms.R | 245 StormR-0.2.1/StormR/R/plotTemporal.R |only StormR-0.2.1/StormR/R/spatialBehaviour.R | 206 StormR-0.2.1/StormR/R/sysdata.rda |binary StormR-0.2.1/StormR/R/temporalBehaviour.R | 50 StormR-0.2.1/StormR/README.md | 31 StormR-0.2.1/StormR/build/vignette.rds |binary StormR-0.2.1/StormR/inst/doc/Behaviour.html | 7 StormR-0.2.1/StormR/inst/doc/ExtractStorms.R | 38 StormR-0.2.1/StormR/inst/doc/ExtractStorms.Rmd | 70 StormR-0.2.1/StormR/inst/doc/ExtractStorms.html | 5324 +++++++++++- StormR-0.2.1/StormR/inst/doc/Models.html | 27 StormR-0.2.1/StormR/inst/doc/SpatialBehaviour.R | 5 StormR-0.2.1/StormR/inst/doc/SpatialBehaviour.Rmd | 13 StormR-0.2.1/StormR/inst/doc/SpatialBehaviour.html | 5269 +++++++++++ StormR-0.2.1/StormR/inst/doc/TemporalBehaviour.R | 24 StormR-0.2.1/StormR/inst/doc/TemporalBehaviour.Rmd | 26 StormR-0.2.1/StormR/inst/doc/TemporalBehaviour.html | 72 StormR-0.2.1/StormR/inst/extdata/test_dataset.csv |only StormR-0.2.1/StormR/man/defStormsDataset.Rd | 35 StormR-0.2.1/StormR/man/defStormsList.Rd | 15 StormR-0.2.1/StormR/man/getScale-methods.Rd |only StormR-0.2.1/StormR/man/plotBehaviour.Rd | 12 StormR-0.2.1/StormR/man/plotStorms.Rd | 30 StormR-0.2.1/StormR/man/plotTemporal.Rd |only StormR-0.2.1/StormR/man/spatialBehaviour.Rd | 15 StormR-0.2.1/StormR/man/storm-class.Rd | 7 StormR-0.2.1/StormR/man/stormsDataset-class.Rd | 13 StormR-0.2.1/StormR/man/stormsList-class.Rd | 6 StormR-0.2.1/StormR/man/temporalBehaviour.Rd | 17 StormR-0.2.1/StormR/tests/testthat/test-plotBehaviour.R | 909 +- StormR-0.2.1/StormR/tests/testthat/test-plotStorms.R | 1013 +- StormR-0.2.1/StormR/tests/testthat/test-plotTemporal.R |only StormR-0.2.1/StormR/tests/testthat/test-spatialBehaviour.R | 423 StormR-0.2.1/StormR/tests/testthat/test-stormsDataset.R | 2019 ++-- StormR-0.2.1/StormR/tests/testthat/test-stormsList.R | 884 + StormR-0.2.1/StormR/tests/testthat/test-temporalBehaviour.R | 109 StormR-0.2.1/StormR/tests/testthat/test-writeRast.R | 2 StormR-0.2.1/StormR/vignettes/ExtractStorms.Rmd | 70 StormR-0.2.1/StormR/vignettes/SpatialBehaviour.Rmd | 13 StormR-0.2.1/StormR/vignettes/TemporalBehaviour.Rmd | 26 49 files changed, 15203 insertions(+), 2929 deletions(-)
Title: Quickly Create Elegant Regression Results Tables and Plots when
Modelling
Description: Generate regression results tables and plots in final
format for publication. Explore models and export directly to PDF
and 'Word' using 'RMarkdown'.
Author: Ewen Harrison [aut, cre],
Tom Drake [aut],
Riinu Pius [aut]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>
Diff between finalfit versions 1.0.7 dated 2023-11-16 and 1.0.8 dated 2024-07-24
DESCRIPTION | 8 +- MD5 | 55 +++++++------- NAMESPACE | 5 + NEWS.md | 13 +++ R/coefficient_plot.R | 29 +++++-- R/ff_label.R | 2 R/ff_newdata.R | 105 ++++++++++++++++++++++++++- R/ff_plot.R | 2 R/finalfit.R | 2 R/finalfit_internal_functions.R | 2 R/or_plot.R | 31 +++++--- README.md | 2 inst/doc/all_plots_examples.html | 10 +- inst/doc/all_tables_examples.R | 6 - inst/doc/all_tables_examples.Rmd | 6 - inst/doc/all_tables_examples.html | 94 ++++++++++++------------ inst/doc/bootstrap.R | 6 + inst/doc/bootstrap.Rmd | 16 +++- inst/doc/bootstrap.html | 147 +++++++++++++++++++++++--------------- inst/doc/survival.html | 8 +- man/coefficient_plot.Rd | 5 + man/ff_expand.Rd |only man/ff_mode.Rd |only man/ff_plot.Rd | 2 man/finalfit.Rd | 2 man/or_plot.Rd | 5 + man/summary_df.Rd |only tests/testthat/Rplots.pdf |binary vignettes/all_tables_examples.Rmd | 6 - vignettes/bootstrap.Rmd | 16 +++- 30 files changed, 403 insertions(+), 182 deletions(-)
Title: Analysis of fMRI Experiments
Description: Contains R-functions to perform an fMRI analysis as described in
Polzehl and Tabelow (2019) <DOI:10.1007/978-3-030-29184-6>,
Tabelow et al. (2006) <DOI:10.1016/j.neuroimage.2006.06.029>,
Polzehl et al. (2010) <DOI:10.1016/j.neuroimage.2010.04.241>,
Tabelow and Polzehl (2011) <DOI:10.18637/jss.v044.i11>.
Author: Karsten Tabelow [aut, cre],
Joerg Polzehl [aut],
Brandon Whitcher [ctb],
Dames Sibylle [ctb]
Maintainer: Karsten Tabelow <tabelow@wias-berlin.de>
Diff between fmri versions 1.9.12 dated 2023-09-06 and 1.9.12.1 dated 2024-07-24
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/aws.r | 2 +- man/fmri.lmePar.Rd | 12 ++++++------ man/fmri.metaPar.Rd | 8 ++++---- 5 files changed, 19 insertions(+), 19 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior
distributions and Bayesian models. It includes point-estimates such as
Maximum A Posteriori (MAP), measures of dispersion (Highest Density
Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and
indices used for null-hypothesis testing (such as ROPE percentage, pd
and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Michael D. Wilson [aut] ,
Brenton M. Wiernik [aut] ,
Paul-Christian Buerkner [rev],
Tristan Mahr [rev] ,
Henrik Singmann [ctb] ,
Quentin F. Gr [...truncated...]
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between bayestestR versions 0.13.2 dated 2024-02-12 and 0.14.0 dated 2024-07-24
DESCRIPTION | 30 ++++---- MD5 | 80 +++++++++++----------- NEWS.md | 29 +++++++- R/area_under_curve.R | 6 - R/bayesfactor_models.R | 36 ++++----- R/bayesfactor_parameters.R | 55 +++++++-------- R/check_prior.R | 42 ++++++----- R/contr.equalprior.R | 12 --- R/convert_bayesian_to_frequentist.R | 94 ++++++++++++++++---------- R/describe_posterior.R | 2 R/diagnostic_posterior.R | 14 +-- R/effective_sample.R | 14 ++- R/equivalence_test.R | 29 ++++---- R/estimate_density.R | 83 ++++++++++++---------- R/mediation.R | 7 - R/rope_range.R | 13 +++ R/sexit.R | 73 +++++++++++--------- R/si.R | 4 - R/simulate_data.R | 44 ++++++------ R/simulate_simpson.R | 6 - R/utils.R | 8 +- R/utils_bayesfactor.R | 8 +- R/weighted_posteriors.R | 12 +-- inst/WORDLIST | 12 --- man/bayesfactor_parameters.Rd | 6 + man/bayesfactor_restricted.Rd | 6 + man/check_prior.Rd | 38 +++++----- man/effective_sample.Rd | 7 + man/equivalence_test.Rd | 8 +- man/estimate_density.Rd | 18 ++-- man/mediation.Rd | 1 man/sexit.Rd | 41 ++++++----- man/si.Rd | 6 + man/simulate_correlation.Rd | 2 man/weighted_posteriors.Rd | 4 - tests/testthat/test-bayesian_as_frequentist.R | 77 +++++++++++++++++++-- tests/testthat/test-blavaan.R | 11 --- tests/testthat/test-check_prior.R | 4 - tests/testthat/test-describe_posterior.R | 20 +++-- tests/testthat/test-estimate_density.R | 18 ++-- tests/testthat/test-simulate_data.R | 2 41 files changed, 571 insertions(+), 411 deletions(-)
Title: Spatiotemporal Point Patterns Simulation
Description: Generates artificial point patterns marked by their
spatial and temporal signatures. The resulting point cloud
may exhibit inherent interactions between both signatures.
The simulation integrates microsimulation
(Holm, E., (2017)<doi:10.1002/9781118786352.wbieg0320>)
and agent-based models (Bonabeau, E., (2002)<doi:10.1073/pnas.082080899>),
beginning with the configuration of movement characteristics for
the specified agents (referred to as 'walkers') and their interactions
within the simulation environment. These interactions
(Quaglietta, L. and Porto, M., (2019)<doi:10.1186/s40462-019-0154-8>)
result in specific spatiotemporal patterns that can be visualized,
analyzed, and used for various analytical purposes.
Given the growing scarcity of detailed spatiotemporal data
across many domains, this package provides an alternative data source
for applications in social and life sciences.
Author: Monsuru Adepeju [cre, aut]
Maintainer: Monsuru Adepeju <monsuur2010@yahoo.com>
Diff between stppSim versions 1.3.2 dated 2023-10-29 and 1.3.4 dated 2024-07-24
DESCRIPTION | 34 +++++++++++++++++----------------- MD5 | 14 +++++++------- NEWS.md | 8 ++++++++ R/make_grids.R | 8 ++++---- inst/doc/stppSim-vignette.Rmd | 2 +- inst/doc/stppSim-vignette.html | 4 ++-- man/make_grids.Rd | 6 +++--- vignettes/stppSim-vignette.Rmd | 2 +- 8 files changed, 43 insertions(+), 35 deletions(-)
Title: Conversion of R Regression Output to LaTeX or HTML Tables
Description: Converts coefficients, standard errors, significance stars, and goodness-of-fit statistics of statistical models into LaTeX tables or HTML tables/MS Word documents or to nicely formatted screen output for the R console for easy model comparison. A list of several models can be combined in a single table. The output is highly customizable. New model types can be easily implemented. Details can be found in Leifeld (2013), JStatSoft <doi:10.18637/jss.v055.i08>.)
Author: Philip Leifeld [aut, cre],
Claudia Zucca [ctb]
Maintainer: Philip Leifeld <philip.leifeld@manchester.ac.uk>
Diff between texreg versions 1.39.3 dated 2023-11-09 and 1.39.4 dated 2024-07-24
texreg-1.39.3/texreg/man/extract-Zelig-method.Rd |only texreg-1.39.3/texreg/man/extract-maBina-method.Rd |only texreg-1.39.3/texreg/man/extract-mnlogit-method.Rd |only texreg-1.39.4/texreg/DESCRIPTION | 34 - texreg-1.39.4/texreg/MD5 | 22 texreg-1.39.4/texreg/NAMESPACE | 1 texreg-1.39.4/texreg/R/extract.R | 585 +++--------------- texreg-1.39.4/texreg/R/texreg.R | 4 texreg-1.39.4/texreg/build/partial.rdb |binary texreg-1.39.4/texreg/build/vignette.rds |binary texreg-1.39.4/texreg/inst/doc/texreg.pdf |binary texreg-1.39.4/texreg/man/extract-remstimate-method.Rd |only texreg-1.39.4/texreg/man/texreg-package.Rd | 2 texreg-1.39.4/texreg/tests/testthat/test-extract.R | 89 ++ 14 files changed, 219 insertions(+), 518 deletions(-)
Title: How to Add Two R Tables
Description: Methods to "add" two R tables; also an alternative
interpretation of named vectors as generalized R tables, so that
c(a=1,b=2,c=3) + c(b=3,a=-1) will return c(b=5,c=3). Uses
'disordR' discipline (Hankin, 2022,
<doi:10.48550/arXiv.2210.03856>). Extraction and replacement
methods are provided. The underlying mathematical structure is
the Free Abelian group, hence the name. To cite in publications
please use Hankin (2023) <doi:10.48550/arXiv.2307.13184>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between frab versions 0.0-5 dated 2024-06-21 and 0.0-6 dated 2024-07-24
frab-0.0-5/frab/inst/frab.bib |only frab-0.0-5/frab/inst/frab_arxiv.Rnw |only frab-0.0-5/frab/inst/read.me |only frab-0.0-6/frab/DESCRIPTION | 8 +++--- frab-0.0-6/frab/MD5 | 15 +++++------- frab-0.0-6/frab/NAMESPACE | 1 frab-0.0-6/frab/NEWS.md | 5 ++++ frab-0.0-6/frab/R/frab.R | 3 +- frab-0.0-6/frab/build/partial.rdb |binary frab-0.0-6/frab/vignettes/frab.bib | 43 ++++++++++++++++++++++++++++++++++++ 10 files changed, 60 insertions(+), 15 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 1.0.0 dated 2024-06-28 and 1.0.1 dated 2024-07-24
DESCRIPTION | 8 - MD5 | 26 +-- NEWS.md | 4 R/OptimInstanceAsyncMultiCrit.R | 6 R/OptimInstanceAsyncSingleCrit.R | 4 R/OptimInstanceBatchMultiCrit.R | 4 R/OptimInstanceBatchSingleCrit.R | 4 R/Optimizer.R | 6 R/OptimizerBatchFocusSearch.R | 2 inst/doc/bbotk.html | 240 ++++++++++++++++++------------------ man/OptimInstanceAsyncMultiCrit.Rd | 5 man/OptimInstanceAsyncSingleCrit.Rd | 5 man/OptimInstanceBatchMultiCrit.Rd | 5 man/OptimInstanceBatchSingleCrit.Rd | 5 14 files changed, 176 insertions(+), 148 deletions(-)
Title: Create Visualisations for BART Models
Description: Investigating and visualising Bayesian Additive Regression Tree (BART) (Chipman, H. A., George, E. I., & McCulloch, R. E. 2010) <doi:10.1214/09-AOAS285> model fits. We construct conventional plots to analyze a model’s performance and stability as well as create new tree-based plots to analyze variable importance, interaction, and tree structure. We employ Value Suppressing Uncertainty Palettes (VSUP) to construct heatmaps that display variable importance and interactions jointly using colour scale to represent posterior uncertainty. Our visualisations are designed to work with the most popular BART R packages available, namely 'BART' Rodney Sparapani and Charles Spanbauer and Robert McCulloch 2021 <doi:10.18637/jss.v097.i01>, 'dbarts' (Vincent Dorie 2023) <https://CRAN.R-project.org/package=dbarts>, and 'bartMachine' (Adam Kapelner and Justin Bleich 2016) <doi:10.18637/jss.v070.i04>.
Author: Alan Inglis [aut, cre],
Andrew Parnell [aut],
Catherine Hurley [aut],
Claus Wilke [ctb]
Maintainer: Alan Inglis <alan.inglis@mu.ie>
Diff between bartMan versions 0.1.0 dated 2024-04-15 and 0.1.1 dated 2024-07-24
DESCRIPTION | 6 - MD5 | 18 +-- NAMESPACE | 2 R/bartDiag.R | 6 + R/mdsBart.R | 4 R/vimpBart.R | 3 R/viviBartMatrix.R | 252 ++++++++++++++++++++++++++++--------------------- R/viviBartPlot.R | 11 ++ README.md | 8 + man/bivariate_scale.Rd | 9 - 10 files changed, 190 insertions(+), 129 deletions(-)
Title: Logit Models w/Preference & WTP Space Utility Parameterizations
Description: Fast estimation of multinomial (MNL) and mixed logit (MXL) models in R. Models can be estimated using "Preference" space or "Willingness-to-pay" (WTP) space utility parameterizations. Weighted models can also be estimated. An option is available to run a parallelized multistart optimization loop with random starting points in each iteration, which is useful for non-convex problems like MXL models or models with WTP space utility parameterizations. The main optimization loop uses the 'nloptr' package to minimize the negative log-likelihood function. Additional functions are available for computing and comparing WTP from both preference space and WTP space models and for predicting expected choices and choice probabilities for sets of alternatives based on an estimated model. Mixed logit models can include uncorrelated or correlated heterogeneity covariances and are estimated using maximum simulated likelihood based on the algorithms in Train (2009) <doi:10.1017/CBO9780511805271>. [...truncated...]
Author: John Helveston [aut, cre, cph]
,
Connor Forsythe [ctb]
Maintainer: John Helveston <john.helveston@gmail.com>
Diff between logitr versions 1.1.1 dated 2023-09-29 and 1.1.2 dated 2024-07-24
DESCRIPTION | 12 MD5 | 32 +- NEWS.md | 4 R/data.R | 8 README.md | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/basic_usage.html | 62 ++-- inst/doc/data_formatting.html | 4 inst/doc/interactions.html | 22 - inst/doc/mnl_models.html | 72 ++--- inst/doc/mnl_models_weighted.html | 116 ++++----- inst/doc/mxl_models.html | 18 - inst/doc/summarizing_results.html | 478 +++++++++++++++++++------------------- man/apolloModeChoiceData.Rd | 2 man/electricity.Rd | 2 man/runtimes.Rd | 4 17 files changed, 430 insertions(+), 407 deletions(-)
Title: Analysis and Visualisation of Ecological Communities
Description: Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Author: Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
Maintainer: Lawrence Hudson <quicklizard@googlemail.com>
Diff between cheddar versions 0.1-638 dated 2022-09-01 and 0.1-639 dated 2024-07-24
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ inst/CITATION | 32 +++++++++++++++++--------------- inst/doc/CheddarQuickstart.pdf |binary inst/doc/Collections.pdf |binary inst/doc/Community.pdf |binary inst/doc/ImportExport.pdf |binary inst/doc/PlotsAndStats.pdf |binary man/LoadCollection.Rd | 2 +- man/ShortestPaths.Rd | 3 ++- man/TL84.Rd | 2 +- man/YthanEstuary.Rd | 5 +++-- man/cheddar.Rd | 4 ++-- 13 files changed, 42 insertions(+), 38 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that
the user is probably willing to make: 'import()' and 'export()' determine
the data format from the file extension, reasonable defaults are used for
data import and export, web-based import is natively supported (including
from SSL/HTTPS), compressed files can be read directly, and fast import
packages are used where appropriate. An additional convenience function,
'convert()', provides a simple method for converting between file types.
Author: Jason Becker [aut],
Chung-hong Chan [aut, cre] ,
David Schoch [aut] ,
Geoffrey CH Chan [ctb],
Thomas J. Leeper [aut] ,
Christopher Gandrud [ctb],
Andrew MacDonald [ctb],
Ista Zahn [ctb],
Stanislaus Stadlmann [ctb],
Ruaridh Williamson [ctb],
Patrick K [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between rio versions 1.1.1 dated 2024-06-05 and 1.2.0 dated 2024-07-24
DESCRIPTION | 16 +++--- MD5 | 58 ++++++++++++------------ NEWS.md | 12 ++++- R/compression.R | 25 +++++----- R/export.R | 4 - R/export_methods.R | 10 ++-- R/extensions.R | 2 R/gather_attrs.R | 4 - R/import.R | 3 - R/import_list.R | 3 - R/import_methods.R | 18 +++---- R/onLoad.R | 2 R/remote_to_local.R | 6 +- R/standardize_attributes.R | 4 - R/sysdata.rda |binary R/utils.R | 5 +- README.md | 93 +++++++++++++++++++-------------------- build/vignette.rds |binary inst/doc/labelled.html | 22 ++++----- inst/doc/remap.R | 5 -- inst/doc/rio.R | 2 inst/doc/rio.html | 64 +++++++++++++++----------- man/export.Rd | 2 man/import.Rd | 2 man/rio.Rd | 1 tests/testthat/test_check_file.R | 4 + tests/testthat/test_compress.R | 21 ++++++++ tests/testthat/test_format_csv.R | 10 ++++ vignettes/remap.Rmd | 2 vignettes/rio.Rmd | 2 30 files changed, 227 insertions(+), 175 deletions(-)
Title: Parameter Space Partitioning MCMC for Global Model Evaluation
Description: Implements an n-dimensional parameter space partitioning algorithm for evaluating the global behaviour of formal computational models as described by Pitt, Kim, Navarro and Myung (2006) <doi:10.1037/0033-295X.113.1.57>.
Author: Lenard Dome [aut, cre],
Andy Wills [aut]
Maintainer: Lenard Dome <lenarddome@gmail.com>
Diff between psp versions 1.0.0 dated 2023-08-16 and 1.0.2 dated 2024-07-24
DESCRIPTION | 8 ++-- MD5 | 9 ++--- build |only man/psp.Rd | 2 - man/pspGlobal.Rd | 93 +++++++++++++++++++++++------------------------------- src/pspGlobal.cpp | 4 +- 6 files changed, 54 insertions(+), 62 deletions(-)
Title: Functional Analysis of Phenotypic Growth Data to Smooth and
Extract Traits
Description: Assists in the plotting and functional smoothing of traits
measured over time and the extraction of features from these traits,
implementing the SET (Smoothing and Extraction of Traits) method
described in Brien et al. (2020) Plant Methods, 16. Smoothing of
growth trends for individual plants using natural cubic smoothing
splines or P-splines is available for removing transient effects and
segmented smoothing is available to deal with discontinuities in
growth trends. There are graphical tools for assessing the adequacy
of trait smoothing, both when using this and other packages, such as
those that fit nonlinear growth models. A range of per-unit (plant,
pot, plot) growth traits or features can be extracted from the
data, including single time points, interval growth rates and other
growth statistics, such as maximum growth or days to maximum growth.
The package also has tools adapted to inputting data from
high-throughput phenotyping facilities, such from a Lemna-Tec
Scananalyzer 3D ( [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between growthPheno versions 2.1.24 dated 2024-02-28 and 2.1.25 dated 2024-07-24
DESCRIPTION | 8 ++-- MD5 | 60 ++++++++++++++++++------------------- R/byIndv4Times.r | 7 ++++ R/traitSmooth.r | 2 + build/partial.rdb |binary build/vignette.rds |binary inst/News.Rd | 5 +++ inst/doc/Rice.pdf |binary inst/doc/Tomato.pdf |binary inst/doc/growthPheno-manual.pdf |binary man/args4chosen_plot.Rd | 12 +++---- man/args4devnboxes_plot.Rd | 16 ++++----- man/args4meddevn_plot.Rd | 17 +++++----- man/args4profile_plot.Rd | 16 ++++----- man/byIndv4Times_GRsDiff.Rd | 5 +++ man/plotAnom.Rd | 2 - man/plotCorrmatrix.Rd | 17 +++++----- man/plotDeviationsBoxes.Rd | 21 ++++++------ man/plotImagetimes.Rd | 13 ++++---- man/plotLongitudinal.Rd | 21 ++++++------ man/plotMedianDeviations.Rd | 21 ++++++------ man/plotProfiles.Rd | 21 ++++++------ man/plotSmoothsComparison.Rd | 12 +++---- man/plotSmoothsDevnBoxplots.Rd | 10 +++--- man/plotSmoothsMedianDevns.Rd | 4 +- man/probeSmoothing.Rd | 22 ++++++------- man/probeSmooths.Rd | 4 +- man/traitSmooth.Rd | 2 - tests/testthat/testProbeSmooths.r | 6 +-- tests/testthat/testTraitWrappers.r | 8 ++-- tests/testthat/testexampleData.r | 4 +- 31 files changed, 181 insertions(+), 155 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 2.4.3 dated 2024-06-02 and 2.4.5 dated 2024-07-24
DESCRIPTION | 17 +++--- MD5 | 98 +++++++++++++++++------------------ NAMESPACE | 1 R/add_forests.R | 14 ++--- R/add_soilgrids.R | 8 +- R/add_topography.R | 10 +-- R/create_management_scenario.R | 4 - R/dataset_documentation.R | 10 +-- R/default_volume_function.R | 2 R/dispersal.R | 9 +-- R/extract_variables.R | 10 +-- R/fire_regime_instance.R | 4 - R/fordyn_scenario.R | 18 +++--- R/impute_forests.R | 84 ++++++++++++++++++------------ R/initialize_landscape.R | 26 +++++---- R/landscape_summary.R | 10 +-- R/medfateland-package.R | 5 + R/model_land.R | 55 ++++++++++--------- R/model_spatial.R | 26 ++++----- R/model_spatial_day.R | 12 ++-- R/parse_forestable.R |only R/plot_summary.R | 6 +- R/shinyplot_land.R | 8 +- R/simulation_summary.R | 6 +- R/sysdata.rda |binary R/update_landscape.R | 4 - man/add_forests.Rd | 15 +++-- man/add_topography.Rd | 10 +-- man/create_management_scenario.Rd | 4 - man/defaultPrescriptionsBySpecies.Rd | 4 - man/default_volume_function.Rd | 2 man/dispersal.Rd | 8 +- man/example_ifn.Rd | 2 man/example_watershed.Rd | 4 - man/extract_variables.Rd | 10 +-- man/fire_regime_instance.Rd | 4 - man/fordyn_scenario.Rd | 18 +++--- man/forest_parametrization.Rd | 41 ++++++++------ man/initialize_landscape.Rd | 26 +++++---- man/landscape_summary.Rd | 10 +-- man/medfateland-package.Rd | 5 + man/parse_forestable.Rd |only man/plot_summary.Rd | 6 +- man/shinyplot_land.Rd | 8 +- man/simulation_summary.Rd | 6 +- man/soil_parametrization.Rd | 8 +- man/spwb_land.Rd | 41 +++++++------- man/spwb_land_day.Rd | 14 ++--- man/spwb_spatial.Rd | 26 ++++----- man/spwb_spatial_day.Rd | 12 ++-- man/update_landscape.Rd | 4 - 51 files changed, 400 insertions(+), 335 deletions(-)
Title: Compact Standard for Australian Phone Numbers
Description: Phone numbers are often represented as strings because there
is no obvious and suitable native representation for them. This leads
to high memory use and a lack of standard representation. The package
provides integer representation of Australian phone numbers with optional
raw vector calling code. The package name is an extension of 'au' and 'ph'.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between dauphin versions 0.3.1 dated 2023-11-28 and 0.3.2 dated 2024-07-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/CMobileCleaning.c | 8 ++++---- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: An R Package to Extend 'ACER ConQuest'
Description: Extends 'ACER ConQuest' through a family of functions
designed to improve graphical outputs and help with advanced analysis
(e.g., differential item functioning). Allows R users to call
'ACER ConQuest' from within R and read 'ACER ConQuest' System Files
(generated by the command `put` <https://conquestmanual.acer.org/s4-00.html#put>).
Requires 'ACER ConQuest' version 5.39 or later.
A demonstration version can be downloaded from <https://shop.acer.org/acer-conquest-5.html>.
Author: Dan Cloney [aut, cre] ,
Ray Adams [aut]
Maintainer: Dan Cloney <dan.cloney@acer.org>
Diff between conquestr versions 1.3.0 dated 2024-02-17 and 1.3.4 dated 2024-07-24
DESCRIPTION | 16 - MD5 | 42 +- NAMESPACE | 3 R/ReadConQuestState_createDF.R | 4 R/conquestr.R | 10 R/conquestrFunc.R | 80 ++--- R/generateHelpers.R | 65 +++- R/itanalHelpers.R | 6 R/plotRout.R | 45 +++ build/vignette.rds |binary inst/doc/data-cleaning-functions-in-conquestr.html | 40 +- inst/doc/generateResponses.html | 59 ++- inst/doc/intro-to-conquestr.html | 312 ++++++++++----------- inst/doc/itanal-in-conquestr.html | 40 +- inst/doc/plotting.html | 16 - inst/doc/responseProbs.html | 6 inst/doc/test_item_review_sheet_markdown.html | 34 +- inst/extdata/myicc.rout |binary inst/extdata/mysysfile.cqs |binary man/genResponses.Rd | 17 - man/plotRout.Rd | 3 man/transformPvs.Rd | 18 - 22 files changed, 458 insertions(+), 358 deletions(-)