Title: Export Emissions to Atmospheric Models
Description: Emissions are the mass of pollutants released into the atmosphere. Air quality models need emissions data, with spatial and temporal distribution, to represent air pollutant concentrations. This package, eixport, creates inputs for the air quality models 'WRF-Chem' Grell et al (2005) <doi:10.1016/j.atmosenv.2005.04.027>, 'MUNICH' Kim et al (2018) <doi:10.5194/gmd-11-611-2018> , 'BRAMS-SPM' Freitas et al (2005) <doi:10.1016/j.atmosenv.2005.07.017> and 'RLINE' Snyder et al (2013) <doi:10.1016/j.atmosenv.2013.05.074>. See the 'eixport' website (<https://atmoschem.github.io/eixport/>) for more information, documentations and examples. More details in Ibarra-Espinosa et al (2018) <doi:10.21105/joss.00607>.
Author: Sergio Ibarra-Espinosa [aut, cre]
,
Daniel Schuch [aut] ,
Edmilson Freitas [ths]
Maintainer: Sergio Ibarra-Espinosa <zergioibarra@gmail.com>
Diff between eixport versions 0.6.0 dated 2023-10-04 and 0.6.2 dated 2024-09-22
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ R/Lights.R | 2 +- R/sfx_explode.R | 2 +- R/to_as4wrf.R | 6 ++++-- R/to_wrf.R | 6 ++++-- R/wrf_raster.R | 14 +++++++++----- build/partial.rdb |binary man/Lights.Rd | 2 +- man/sfx_explode.Rd | 2 +- man/to_as4wrf.Rd | 6 ++++-- man/to_wrf.Rd | 3 +++ man/wrf_raster.Rd | 5 ++++- 13 files changed, 49 insertions(+), 33 deletions(-)
Title: Estimation and Additional Tools for Alternative Shared Frailty
Models
Description: Provide estimation and data generation tools for some new multivariate frailty models.
This version includes the gamma, inverse Gaussian, weighted Lindley, Birnbaum-Saunders,
truncated normal, mixture of inverse Gaussian and mixture of Birnbaum-Saunders as the
distribution for the frailty terms. For the basal model, it is considered a parametric
approach based on the exponential, Weibull and the piecewise exponential distributions
as well as a semiparametric approach.
For details, see Gallardo and Bourguignon (2022) <doi:10.48550/arXiv.2206.12973> and
Gallardo et al. (2024) <doi:10.1007/s11222-024-10458-w>.
Author: Diego Gallardo [aut, cre],
Marcelo Bourguignon [aut]
Maintainer: Diego Gallardo <dgallardo@ubiobio.cl>
Diff between extrafrail versions 1.11 dated 2024-09-02 and 1.12 dated 2024-09-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/frailty.fit.R | 21 ++++++++++++--------- 4 files changed, 23 insertions(+), 16 deletions(-)
Title: Simultaneous Multi-Bias Adjustment
Description: Quantify the causal effect of a binary exposure on a binary
outcome with adjustment for multiple biases. The functions can
simultaneously adjust for any combination of uncontrolled confounding,
exposure/outcome misclassification, and selection bias.
The underlying method generalizes the concept of combining inverse
probability of selection weighting with predictive value weighting.
Simultaneous multi-bias analysis can be used to enhance the validity
and transparency of real-world evidence obtained from observational,
longitudinal studies. Based on the work from Paul Brendel, Aracelis Torres,
and Onyebuchi Arah (2023) <doi:10.1093/ije/dyad001>.
Author: Paul Brendel [aut, cre, cph]
Maintainer: Paul Brendel <pcbrendel@gmail.com>
Diff between multibias versions 1.5.2 dated 2024-08-21 and 1.5.3 dated 2024-09-22
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Title: Time Series Methods
Description: Generic methods for use in a time series probabilistic framework, allowing for a common calling convention across packages. Additional methods for time series prediction ensembles and probabilistic plotting of predictions is included. A more detailed description is available at <https://www.nopredict.com/packages/tsmethods> which shows the currently implemented methods in the 'tsmodels' framework.
Author: Alexios Galanos [aut, cre, cph]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between tsmethods versions 1.0.1 dated 2024-03-18 and 1.0.2 dated 2024-09-22
DESCRIPTION | 15 ++++---- MD5 | 19 +++++++---- NAMESPACE | 7 ++++ NEWS.md | 11 ++++++ R/convert.R |only R/methods.R | 58 ++++++++++++++++++++++++++++++++++ R/multivariate.R |only R/tsmethods-package.R | 1 man/distribution_list.Rd |only man/tscokurt.Rd |only man/tsconvert.tsmodel.distribution.Rd |only man/tsconvolve.Rd |only man/tscoskew.Rd |only man/tsmethods-package.Rd | 2 - 14 files changed, 99 insertions(+), 14 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 3.0.0 dated 2024-09-18 and 3.0.1 dated 2024-09-22
DESCRIPTION | 6 MD5 | 22 +- NEWS.md | 4 R/rxode2_md5.R | 2 inst/doc/rxode2-syntax.Rmd | 15 + inst/doc/rxode2-syntax.html | 262 ++++++++++++++++------------------ inst/include/rxode2parseVer.h | 4 man/rmdhunks/rxode2-create-models.Rmd | 16 +- src/genModelVars.h | 3 tests/testthat/test-000-modelVars.R | 1 tests/testthat/test-phi.R | 200 ++++++++++++------------- vignettes/rxode2-syntax.Rmd | 15 + 12 files changed, 272 insertions(+), 278 deletions(-)
Title: 'Rcpp' Tic-Toc Timer with 'OpenMP' Support
Description: Provides 'Rcpp' bindings for 'cpptimer', a simple tic-toc timer class for benchmarking 'C++' code <https://github.com/BerriJ/cpptimer>. It's not just simple, it's blazing fast! This sleek tic-toc timer class supports overlapping timers as well as 'OpenMP' parallelism <https://www.openmp.org/>. It boasts a nanosecond-level time resolution. We did not find any overhead of the timer itself at this resolution. Results (with summary statistics) are automatically passed back to 'R' as a data frame.
Author: Jonathan Berrisch [aut, cre]
Maintainer: Jonathan Berrisch <Jonathan@Berrisch.biz>
Diff between rcpptimer versions 1.2.0 dated 2024-09-20 and 1.2.1 dated 2024-09-22
DESCRIPTION | 8 ++--- MD5 | 24 +++++++-------- NEWS.md | 6 +++ README.md | 2 - inst/doc/advanced.html | 32 ++++++++++---------- inst/doc/autoreturn.html | 18 +++++------ inst/doc/packages.html | 4 +- inst/doc/rcpptimer.Rmd | 16 +++++----- inst/doc/rcpptimer.html | 62 +++++++++++++++++++-------------------- inst/doc/sourceCpp.html | 4 +- inst/include/cpptimer/cpptimer.h | 2 - inst/include/rcpptimer.h | 4 +- vignettes/rcpptimer.Rmd | 16 +++++----- 13 files changed, 102 insertions(+), 96 deletions(-)
Title: The Matrix-Normal Inverse-Wishart Distribution
Description: Density evaluation and random number generation for the Matrix-Normal Inverse-Wishart (MNIW) distribution, as well as the the Matrix-Normal, Matrix-T, Wishart, and Inverse-Wishart distributions. Core calculations are implemented in a portable (header-only) C++ library, with matrix manipulations using the 'Eigen' library for linear algebra. Also provided is a Gibbs sampler for Bayesian inference on a random-effects model with multivariate normal observations.
Author: Martin Lysy [aut, cre],
Bryan Yates [aut]
Maintainer: Martin Lysy <mlysy@uwaterloo.ca>
Diff between mniw versions 1.0.1 dated 2022-08-22 and 1.0.2 dated 2024-09-22
mniw-1.0.1/mniw/R/MNIW.R |only mniw-1.0.1/mniw/R/MatrixNormal.R |only mniw-1.0.1/mniw/R/MatrixT.R |only mniw-1.0.1/mniw/R/MultiNormal.R |only mniw-1.0.1/mniw/R/Wishart.R |only mniw-1.0.1/mniw/data/Hospitals.RData |only mniw-1.0.1/mniw/man/MNIW.Rd |only mniw-1.0.1/mniw/man/MatrixNormal.Rd |only mniw-1.0.1/mniw/man/MatrixT.Rd |only mniw-1.0.1/mniw/man/MultiNormal.Rd |only mniw-1.0.1/mniw/man/Wishart.Rd |only mniw-1.0.2/mniw/DESCRIPTION | 12 mniw-1.0.2/mniw/MD5 | 55 +-- mniw-1.0.2/mniw/NEWS.md |only mniw-1.0.2/mniw/R/Hierarchical.R | 22 - mniw-1.0.2/mniw/R/MNIW-dist.R |only mniw-1.0.2/mniw/R/MatrixNormal-dist.R |only mniw-1.0.2/mniw/R/MatrixT-dist.R |only mniw-1.0.2/mniw/R/MultiNormal-dist.R |only mniw-1.0.2/mniw/R/RandomEffects.R | 12 mniw-1.0.2/mniw/R/Wishart-dist.R |only mniw-1.0.2/mniw/R/crossprodV.R | 12 mniw-1.0.2/mniw/R/hospitals.R | 10 mniw-1.0.2/mniw/R/mniw-format.R | 41 +- mniw-1.0.2/mniw/build/vignette.rds |binary mniw-1.0.2/mniw/data/Hospitals.rda |only mniw-1.0.2/mniw/inst/doc/mniw-distributions.Rmd | 160 +++----- mniw-1.0.2/mniw/inst/doc/mniw-distributions.html | 420 +++++++++++++++-------- mniw-1.0.2/mniw/inst/include/mniw/TriUtils.h | 30 - mniw-1.0.2/mniw/man/Hospitals.Rd | 8 mniw-1.0.2/mniw/man/MNIW-dist.Rd |only mniw-1.0.2/mniw/man/MatrixNormal-dist.Rd |only mniw-1.0.2/mniw/man/MatrixT-dist.Rd |only mniw-1.0.2/mniw/man/MultiNormal-dist.Rd |only mniw-1.0.2/mniw/man/RxNormLM.Rd | 16 mniw-1.0.2/mniw/man/Wishart-dist.Rd |only mniw-1.0.2/mniw/man/crossprodV.Rd | 10 mniw-1.0.2/mniw/man/mniw-package.Rd | 1 mniw-1.0.2/mniw/man/rRxNorm.Rd | 8 mniw-1.0.2/mniw/vignettes/mniw-distributions.Rmd | 160 +++----- 40 files changed, 541 insertions(+), 436 deletions(-)
Title: Download Geographic Data on Various Topics Provided and Managed
by the Spatial Data Infrastructure of Peru
Description: Provides R users with easy access to official cartographic data from Peru across a range of topics, including society, transport, environment, agriculture, climate, and more.
It also includes data from regional government entities and technical-scientific institutions, all managed by Peru's Spatial Data Infrastructure.
For more information, please visit: <https://www.geoidep.gob.pe/catalogos-de-metadatos>.
Author: antony barja [aut, cre, cph]
Maintainer: antony barja <geografo.pe@gmail.com>
Diff between geoidep versions 0.2.0 dated 2024-09-19 and 0.3.0 dated 2024-09-22
DESCRIPTION | 9 ++-- MD5 | 53 +++++++++++++++----------- NAMESPACE | 2 NEWS.md | 40 +++++++++++++++++-- R/get_data_sources.R | 2 R/get_departaments.R | 2 R/get_districts.R | 2 R/get_forest_fire_data.R |only R/get_hotspots_data.R |only R/get_providers.R | 4 - R/get_provinces.R | 2 R/get_sernanp_data.R | 2 R/utils.R | 38 +++++++++++++++++- R/zzz.R | 2 build/vignette.rds |binary inst/doc/article.R |only inst/doc/article.Rmd |only inst/doc/article.html |only inst/doc/geoidep.Rmd | 8 +++ inst/doc/geoidep.html | 69 +++++++++++++++------------------- inst/sources-idep/sources_geoidep.csv | 2 man/as_data_time.Rd |only man/get_departaments.Rd | 60 ++++++++++++++--------------- man/get_districts.Rd | 60 ++++++++++++++--------------- man/get_forest_fire_data.Rd |only man/get_forest_fire_link.Rd |only man/get_heat_spot_link.Rd |only man/get_hotspots_data.Rd |only man/get_providers.Rd | 46 +++++++++++----------- man/get_provinces.Rd | 60 ++++++++++++++--------------- man/get_sernanp_data.Rd | 64 +++++++++++++++---------------- vignettes/article.Rmd |only vignettes/geoidep.Rmd | 8 +++ 33 files changed, 310 insertions(+), 225 deletions(-)
Title: Structure Optimized Proximity Scaling
Description: Methods that use flexible variants of multidimensional scaling (MDS) which incorporate parametric nonlinear distance transformations and trade-off the goodness-of-fit fit with structure considerations to find optimal hyperparameters, also known as structure optimized proximity scaling (STOPS) (Rusch, Mair & Hornik, 2023,<doi:10.1007/s11222-022-10197-w>). The package contains various functions, wrappers, methods and classes for fitting, plotting and displaying different 1-way MDS models with ratio, interval, ordinal optimal scaling in a STOPS framework. These cover essentially the functionality of the package smacofx, including Torgerson (classical) scaling with power transformations of dissimilarities, SMACOF MDS with powers of dissimilarities, Sammon mapping with powers of dissimilarities, elastic scaling with powers of dissimilarities, spherical SMACOF with powers of dissimilarities, (ALSCAL) s-stress MDS with powers of dissimilarities, r-stress MDS, MDS with powers of diss [...truncated...]
Author: Thomas Rusch [aut, cre] ,
Patrick Mair [aut] ,
Kurt Hornik [ctb]
Maintainer: Thomas Rusch <thomas.rusch@wu.ac.at>
Diff between stops versions 1.6-2 dated 2024-06-28 and 1.8-2 dated 2024-09-22
DESCRIPTION | 10 - MD5 | 168 ++++++++++----------- NAMESPACE | 3 NEWS | 12 + R/biplotmds.stops.R |only R/jackmds.stops.R | 6 R/stop_apstress.R | 5 R/stop_bcmds.R | 7 R/stop_clca.R | 7 R/stop_clda.R | 14 + R/stop_cmdscale.R | 7 R/stop_elastic.R | 6 R/stop_isomap.R | 10 - R/stop_lmds.R | 7 R/stop_powerelastic.R | 7 R/stop_powermds.R | 6 R/stop_powersammon.R | 7 R/stop_powerstress.R | 7 R/stop_rpowerstress.R | 5 R/stop_rstress.R | 6 R/stop_sammon.R | 6 R/stop_sammon2.R | 7 R/stop_smacofSphere.R | 7 R/stop_smacofSym.R | 6 R/stop_smdda.R | 13 + R/stop_smds.R | 7 R/stop_spmdda.R | 12 + R/stop_spmds.R | 7 R/stop_sstress.R | 6 R/stoploss.R | 254 ++++++++++++++++++-------------- R/stops-package.R | 1 R/stops.R | 42 ++--- R/structurednessindices.R | 80 ++++++---- R/zzz.R |only man/biplotmds.stops.Rd |only man/c_association.Rd | 2 man/c_clumpiness.Rd | 2 man/c_clusteredness.Rd | 3 man/c_complexity.Rd | 2 man/c_convexity.Rd | 2 man/c_dependence.Rd | 2 man/c_faithfulness.Rd | 4 man/c_functionality.Rd | 2 man/c_hierarchy.Rd | 4 man/c_inequality.Rd | 4 man/c_linearity.Rd | 2 man/c_manifoldness.Rd | 2 man/c_nonmonotonicity.Rd | 2 man/c_outlying.Rd | 2 man/c_regularity.Rd | 3 man/c_shepardness.Rd | 4 man/c_skinniness.Rd | 2 man/c_sparsity.Rd | 2 man/c_striatedness.Rd | 2 man/c_stringiness.Rd | 2 man/jackmds.stops.Rd | 6 man/match_partial_ignorecase_nopunct.Rd |only man/stop_apstress.Rd | 5 man/stop_bcmds.Rd | 5 man/stop_clca.Rd | 5 man/stop_cldae.Rd | 5 man/stop_cldak.Rd | 5 man/stop_cmdscale.Rd | 7 man/stop_elastic.Rd | 5 man/stop_isomap1.Rd | 5 man/stop_isomap2.Rd | 5 man/stop_lmds.Rd | 5 man/stop_powerelastic.Rd | 5 man/stop_powermds.Rd | 5 man/stop_powersammon.Rd | 5 man/stop_powerstress.Rd | 5 man/stop_rpowerstress.Rd | 5 man/stop_rstress.Rd | 5 man/stop_sammon.Rd | 5 man/stop_sammon2.Rd | 5 man/stop_smacofSphere.Rd | 5 man/stop_smacofSym.Rd | 5 man/stop_smddae.Rd | 5 man/stop_smddak.Rd | 5 man/stop_smds.Rd | 5 man/stop_spmddae.Rd | 5 man/stop_spmddak.Rd | 5 man/stop_spmds.Rd | 5 man/stop_sstress.Rd | 5 man/stoploss.Rd | 10 - man/stops-package.Rd | 1 man/stops.Rd | 3 87 files changed, 579 insertions(+), 376 deletions(-)
Title: Pseudo-Value Regression Approach for Network Analysis (PRANA)
Description: A novel pseudo-value regression approach for the differential co-expression network analysis in expression data, which can incorporate additional clinical variables in the model. This is a direct regression modeling for the differential network analysis, and it is therefore computationally amenable for the most users. The full methodological details can be found in Ahn S et al (2023) <doi:10.1186/s12859-022-05123-w>.
Author: Seungjun Ahn [cre, aut, trl] ,
Somnath Datta [ctb, ths]
Maintainer: Seungjun Ahn <seungjun.ahn@mountsinai.org>
Diff between PRANA versions 1.0.5 dated 2024-07-27 and 1.0.6 dated 2024-09-22
DESCRIPTION | 6 +-- MD5 | 6 +-- R/PRANA.R | 2 - inst/doc/UserManualPRANA.html | 68 +++++++++++++++++++++--------------------- 4 files changed, 41 insertions(+), 41 deletions(-)
Title: Cross-Validating Regression Models
Description: Cross-validation methods of regression models that exploit features of various
modeling functions to improve speed. Some of the methods implemented in the package are
novel, as described in the package vignettes; for general introductions to cross-validation,
see, for example, Gareth James, Daniela Witten, Trevor Hastie, and Robert Tibshirani
(2021, ISBN 978-1-0716-1417-4, Secs. 5.1, 5.3), "An Introduction to Statistical Learning with
Applications in R, Second Edition", and Trevor Hastie, Robert Tibshirani,
and Jerome Friedman (2009, ISBN 978-0-387-84857-0, Sec. 7.10), "The Elements of Statistical
Learning, Second Edition".
Author: John Fox [aut] ,
Georges Monette [aut, cre]
Maintainer: Georges Monette <georges+cv@yorku.ca>
Diff between cv versions 2.0.2 dated 2024-08-18 and 2.0.3 dated 2024-09-22
cv-2.0.2/cv/vignettes/cv-selection_cache/html/cvSelect-artificial-data_b2b776816415afbf66d17287d64b4dfa.RData |only cv-2.0.2/cv/vignettes/cv-selection_cache/html/cvSelect-artificial-data_b2b776816415afbf66d17287d64b4dfa.rdb |only cv-2.0.2/cv/vignettes/cv-selection_cache/html/cvSelect-artificial-data_b2b776816415afbf66d17287d64b4dfa.rdx |only cv-2.0.3/cv/DESCRIPTION | 18 cv-2.0.3/cv/MD5 | 82 cv-2.0.3/cv/NAMESPACE | 10 cv-2.0.3/cv/NEWS.md | 14 cv-2.0.3/cv/R/cost-functions.R | 6 cv-2.0.3/cv/R/cv-mixed-models.R | 85 cv-2.0.3/cv/R/cv-select.R | 64 cv-2.0.3/cv/R/cv-utilities.R | 25 cv-2.0.3/cv/R/cv.R | 311 ++ cv-2.0.3/cv/R/cv.modList.R | 55 cv-2.0.3/cv/inst/WORDLIST | 4 cv-2.0.3/cv/inst/doc/cv-extend.R | 28 cv-2.0.3/cv/inst/doc/cv-extend.Rmd | 30 cv-2.0.3/cv/inst/doc/cv-extend.html | 128 cv-2.0.3/cv/inst/doc/cv-mixed.R | 23 cv-2.0.3/cv/inst/doc/cv-mixed.Rmd | 23 cv-2.0.3/cv/inst/doc/cv-mixed.html | 60 cv-2.0.3/cv/inst/doc/cv-notes.R | 18 cv-2.0.3/cv/inst/doc/cv-notes.Rmd | 18 cv-2.0.3/cv/inst/doc/cv-notes.html | 35 cv-2.0.3/cv/inst/doc/cv-selection.R | 39 cv-2.0.3/cv/inst/doc/cv-selection.Rmd | 42 cv-2.0.3/cv/inst/doc/cv-selection.html | 116 cv-2.0.3/cv/inst/doc/cv.R | 40 cv-2.0.3/cv/inst/doc/cv.Rmd | 60 cv-2.0.3/cv/inst/doc/cv.html | 1378 +++++----- cv-2.0.3/cv/man/cost-functions.Rd | 6 cv-2.0.3/cv/man/cv.Rd | 123 cv-2.0.3/cv/man/cv.function.Rd | 50 cv-2.0.3/cv/man/cv.merMod.Rd | 38 cv-2.0.3/cv/man/cv.modList.Rd | 29 cv-2.0.3/cv/man/cvCompute.Rd | 4 cv-2.0.3/cv/tests/testthat/test-cvSelect.R | 18 cv-2.0.3/cv/vignettes/cv-extend.Rmd | 30 cv-2.0.3/cv/vignettes/cv-mixed.Rmd | 23 cv-2.0.3/cv/vignettes/cv-notes.Rmd | 18 cv-2.0.3/cv/vignettes/cv-selection.Rmd | 42 cv-2.0.3/cv/vignettes/cv-selection_cache/html/__packages | 17 cv-2.0.3/cv/vignettes/cv-selection_cache/html/cvSelect-artificial-data_9ad06ef148cf54d6b84209620167407e.RData |only cv-2.0.3/cv/vignettes/cv-selection_cache/html/cvSelect-artificial-data_9ad06ef148cf54d6b84209620167407e.rdb |only cv-2.0.3/cv/vignettes/cv-selection_cache/html/cvSelect-artificial-data_9ad06ef148cf54d6b84209620167407e.rdx |only cv-2.0.3/cv/vignettes/cv.Rmd | 60 45 files changed, 1935 insertions(+), 1235 deletions(-)
Title: 'airGR' Integrated Water Resource Management
Description: Semi-distributed Precipitation-Runoff Modeling based on
'airGR' package models integrating human infrastructures and their
managements.
Author: David Dorchies [aut, cre] ,
Olivier Delaigue [ctb] ,
Guillaume Thirel [ctb]
Maintainer: David Dorchies <david.dorchies@inrae.fr>
Diff between airGRiwrm versions 0.6.2 dated 2023-10-24 and 0.7.0 dated 2024-09-22
airGRiwrm-0.6.2/airGRiwrm/R/RunModel.SD.R |only airGRiwrm-0.6.2/airGRiwrm/R/utils.R |only airGRiwrm-0.6.2/airGRiwrm/inst/doc/airgriwrm.R |only airGRiwrm-0.6.2/airGRiwrm/inst/doc/airgriwrm.Rmd |only airGRiwrm-0.6.2/airGRiwrm/inst/doc/airgriwrm.html |only airGRiwrm-0.6.2/airGRiwrm/inst/vignettes/ParamV03.RDS |only airGRiwrm-0.6.2/airGRiwrm/man/RunModel.SD.Rd |only airGRiwrm-0.6.2/airGRiwrm/tests/testthat/helper_RunModel.R |only airGRiwrm-0.6.2/airGRiwrm/tests/testthat/test-plot.R |only airGRiwrm-0.6.2/airGRiwrm/vignettes/airgriwrm.Rmd |only airGRiwrm-0.7.0/airGRiwrm/DESCRIPTION | 21 airGRiwrm-0.7.0/airGRiwrm/MD5 | 231 airGRiwrm-0.7.0/airGRiwrm/NAMESPACE | 118 airGRiwrm-0.7.0/airGRiwrm/NEWS.md | 384 - airGRiwrm-0.7.0/airGRiwrm/R/Calibration.GRiwrmInputsModel.R | 236 airGRiwrm-0.7.0/airGRiwrm/R/Calibration.InputsModel.R | 38 airGRiwrm-0.7.0/airGRiwrm/R/Calibration.R | 72 airGRiwrm-0.7.0/airGRiwrm/R/ConvertMeteoSD.R | 177 airGRiwrm-0.7.0/airGRiwrm/R/CreateCalibOptions.GRiwrmInputsModel.R | 80 airGRiwrm-0.7.0/airGRiwrm/R/CreateCalibOptions.R | 154 airGRiwrm-0.7.0/airGRiwrm/R/CreateController.R | 183 airGRiwrm-0.7.0/airGRiwrm/R/CreateGRiwrm.R | 514 + airGRiwrm-0.7.0/airGRiwrm/R/CreateInputsCrit.GRiwrmInputsModel.R | 262 airGRiwrm-0.7.0/airGRiwrm/R/CreateInputsCrit.InputsModel.R | 18 airGRiwrm-0.7.0/airGRiwrm/R/CreateInputsCrit.R | 84 airGRiwrm-0.7.0/airGRiwrm/R/CreateInputsModel.GRiwrm.R | 779 +- airGRiwrm-0.7.0/airGRiwrm/R/CreateInputsModel.R | 44 airGRiwrm-0.7.0/airGRiwrm/R/CreateRunOptions.GRiwrmInputsModel.R | 27 airGRiwrm-0.7.0/airGRiwrm/R/CreateRunOptions.R | 126 airGRiwrm-0.7.0/airGRiwrm/R/CreateSupervisor.R | 151 airGRiwrm-0.7.0/airGRiwrm/R/RunModel.GR.R | 62 airGRiwrm-0.7.0/airGRiwrm/R/RunModel.GRiwrmInputsModel.R | 163 airGRiwrm-0.7.0/airGRiwrm/R/RunModel.InputsModel.R | 164 airGRiwrm-0.7.0/airGRiwrm/R/RunModel.R | 20 airGRiwrm-0.7.0/airGRiwrm/R/RunModel.Supervisor.R | 292 airGRiwrm-0.7.0/airGRiwrm/R/RunModel_Reservoir.R |only airGRiwrm-0.7.0/airGRiwrm/R/RunModel_Routing.R |only airGRiwrm-0.7.0/airGRiwrm/R/Severn.R | 22 airGRiwrm-0.7.0/airGRiwrm/R/UpdateQsimUpstream.R | 45 airGRiwrm-0.7.0/airGRiwrm/R/airGRiwrm-package.R |only airGRiwrm-0.7.0/airGRiwrm/R/getNodeProperties.R |only airGRiwrm-0.7.0/airGRiwrm/R/getNodeRanking.R |only airGRiwrm-0.7.0/airGRiwrm/R/plot.GRiwrm.R | 371 + airGRiwrm-0.7.0/airGRiwrm/R/plot.GRiwrmOutputsModel.R | 87 airGRiwrm-0.7.0/airGRiwrm/R/plot.OutputsModelReservoir.R |only airGRiwrm-0.7.0/airGRiwrm/R/plot.Qm3s.R | 143 airGRiwrm-0.7.0/airGRiwrm/R/utils.Calibration.R |only airGRiwrm-0.7.0/airGRiwrm/R/utils.CreateInputsModel.R |only airGRiwrm-0.7.0/airGRiwrm/R/utils.GRiwrm.R |only airGRiwrm-0.7.0/airGRiwrm/R/utils.RunModel.R |only airGRiwrm-0.7.0/airGRiwrm/R/utils.Supervisor.R |only airGRiwrm-0.7.0/airGRiwrm/README.md | 106 airGRiwrm-0.7.0/airGRiwrm/build/partial.rdb |binary airGRiwrm-0.7.0/airGRiwrm/build/vignette.rds |binary airGRiwrm-0.7.0/airGRiwrm/data/Severn.rda |binary airGRiwrm-0.7.0/airGRiwrm/inst/CITATION |only airGRiwrm-0.7.0/airGRiwrm/inst/WORDLIST | 313 - airGRiwrm-0.7.0/airGRiwrm/inst/doc/V01_Structure_SD_model.R | 1 airGRiwrm-0.7.0/airGRiwrm/inst/doc/V01_Structure_SD_model.Rmd | 243 airGRiwrm-0.7.0/airGRiwrm/inst/doc/V01_Structure_SD_model.html | 2587 -------- airGRiwrm-0.7.0/airGRiwrm/inst/doc/V02_Calibration_SD_model.R | 7 airGRiwrm-0.7.0/airGRiwrm/inst/doc/V02_Calibration_SD_model.Rmd | 326 - airGRiwrm-0.7.0/airGRiwrm/inst/doc/V02_Calibration_SD_model.html | 373 - airGRiwrm-0.7.0/airGRiwrm/inst/doc/V03_Open-loop_influenced_flow.R | 18 airGRiwrm-0.7.0/airGRiwrm/inst/doc/V03_Open-loop_influenced_flow.Rmd | 316 - airGRiwrm-0.7.0/airGRiwrm/inst/doc/V03_Open-loop_influenced_flow.html | 2696 -------- airGRiwrm-0.7.0/airGRiwrm/inst/doc/V04_Closed-loop_regulated_withdrawal.R | 48 airGRiwrm-0.7.0/airGRiwrm/inst/doc/V04_Closed-loop_regulated_withdrawal.Rmd | 783 +- airGRiwrm-0.7.0/airGRiwrm/inst/doc/V04_Closed-loop_regulated_withdrawal.html | 3047 ---------- airGRiwrm-0.7.0/airGRiwrm/inst/doc/V05_Modelling_ungauged_nodes.R |only airGRiwrm-0.7.0/airGRiwrm/inst/doc/V05_Modelling_ungauged_nodes.Rmd |only airGRiwrm-0.7.0/airGRiwrm/inst/doc/V05_Modelling_ungauged_nodes.html |only airGRiwrm-0.7.0/airGRiwrm/inst/doc/V06_Modelling_regulated_diversion.R |only airGRiwrm-0.7.0/airGRiwrm/inst/doc/V06_Modelling_regulated_diversion.Rmd |only airGRiwrm-0.7.0/airGRiwrm/inst/doc/V06_Modelling_regulated_diversion.html |only airGRiwrm-0.7.0/airGRiwrm/inst/doc/airGRiwrm.R |only airGRiwrm-0.7.0/airGRiwrm/inst/doc/airGRiwrm.Rmd |only airGRiwrm-0.7.0/airGRiwrm/inst/doc/airGRiwrm.html |only airGRiwrm-0.7.0/airGRiwrm/inst/vignettes/ParamV02.RDS |only airGRiwrm-0.7.0/airGRiwrm/man/Calibration.Rd | 131 airGRiwrm-0.7.0/airGRiwrm/man/ConvertMeteoSD.Rd | 75 airGRiwrm-0.7.0/airGRiwrm/man/CreateCalibOptions.Rd | 105 airGRiwrm-0.7.0/airGRiwrm/man/CreateController.Rd | 117 airGRiwrm-0.7.0/airGRiwrm/man/CreateGRiwrm.Rd | 297 airGRiwrm-0.7.0/airGRiwrm/man/CreateInputsCrit.Rd | 148 airGRiwrm-0.7.0/airGRiwrm/man/CreateInputsModel.GRiwrm.Rd | 266 airGRiwrm-0.7.0/airGRiwrm/man/CreateInputsModel.Rd | 47 airGRiwrm-0.7.0/airGRiwrm/man/CreateRunOptions.Rd | 189 airGRiwrm-0.7.0/airGRiwrm/man/CreateSupervisor.Rd | 76 airGRiwrm-0.7.0/airGRiwrm/man/RunModel.GR.Rd | 57 airGRiwrm-0.7.0/airGRiwrm/man/RunModel.GRiwrmInputsModel.Rd | 363 - 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Title: Explanation Groves
Description: Compute surrogate explanation groves for predictive machine learning models and analyze complexity vs. explanatory power of an explanation according to Szepannek, G. and von Holt, B. (2023) <doi:10.1007/s41237-023-00205-2>.
Author: Gero Szepannek [aut, cre]
Maintainer: Gero Szepannek <gero.szepannek@web.de>
Diff between xgrove versions 0.1-12 dated 2024-09-15 and 0.1-13 dated 2024-09-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 1 + R/xgrove.R | 31 +++++++++++++++---------------- 4 files changed, 23 insertions(+), 23 deletions(-)
Title: Tools for Summarising and Analysing Soundscape Data
Description: A variety of tools relevant to the analysis
of marine soundscape data. There are tools for downloading AIS (automatic identification system)
data from Marine Cadastre <https://hub.marinecadastre.gov>,
connecting AIS data to GPS coordinates, plotting summaries of various soundscape
measurements, and downloading relevant environmental variables (wind, swell height) from the
National Center for Atmospheric Research data server <https://rda.ucar.edu/datasets/ds084.1/>.
Most tools were developed to work well with output from 'Triton' software, but can be adapted
to work with any similar measurements.
Author: Taiki Sakai [aut, cre],
Anne Simonis [ctb],
Shannon Rankin [ctb],
Megan McKenna [ctb],
Kaitlin Palmer [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PAMscapes versions 0.6.0 dated 2024-07-09 and 0.7.0 dated 2024-09-22
DESCRIPTION | 14 - MD5 | 62 ++++-- NAMESPACE | 42 ++++ NEWS.md | 31 +++ R/binSoundscapeData.R |only R/checkSoundscapeInput.R | 60 +++++- R/createOctaveLevel.R | 25 ++ R/downloadMarCadAIS.R | 23 +- R/loadMantaNc.R | 34 --- R/matchSeascape.R |only R/plotAcousticScene.R | 104 +++++++++-- R/plotHourlyLevel.R | 36 +++ R/plotLTSA.R | 104 +++++++---- R/plotPSD.R | 373 ++++++++++++++++++++++++++++++----------- R/plotScaledTimeseries.R | 27 ++ R/plotTimeseries.R | 18 + R/readLocalAIS.R | 17 + R/runSoundscapeExplorer.R |only R/utils.R | 136 +++++++++++--- README.md | 2 inst/images |only man/binSoundscapeData.Rd |only man/checkSoundscapeInput.Rd | 23 ++ man/createOctaveLevel.Rd | 2 man/downloadMarCadAIS.Rd | 3 man/matchSeascape.Rd |only man/plotAcousticScene.Rd | 14 + man/plotHourlyLevel.Rd | 9 man/plotLTSA.Rd | 16 + man/plotPSD.Rd | 17 + man/runSoundscapeExplorer.Rd |only tests/testthat/test-dataprep.R | 26 +- 32 files changed, 894 insertions(+), 324 deletions(-)
Title: Flexible Multidimensional Scaling and 'smacof' Extensions
Description: Flexible multidimensional scaling (MDS) methods and extensions to the package 'smacof'. This package contains various functions, wrappers, methods and classes for fitting, plotting and displaying a large number of different flexible MDS models (some as of yet unpublished). These are: Torgerson scaling (Torgerson, 1958, ISBN:978-0471879459) with powers, Sammon mapping (Sammon, 1969, <doi:10.1109/T-C.1969.222678>) with ratio and interval optimal scaling, Multiscale MDS (Ramsay, 1977, <doi:10.1007/BF02294052>) with ratio and interval optimal scaling, S-stress MDS (ALSCAL; Takane, Young & De Leeuw, 1977, <doi:10.1007/BF02293745>) with ratio and interval optimal scaling, elastic scaling (McGee, 1966, <doi:10.1111/j.2044-8317.1966.tb00367.x>) with ratio and interval optimal scaling, r-stress MDS (De Leeuw, Groenen & Mair, 2016, <https://rpubs.com/deleeuw/142619>) with ratio, interval and non-metric optimal scaling, power-stress MDS (POST-MDS; Buja & [...truncated...]
Author: Thomas Rusch [aut, cre] ,
Jan de Leeuw [aut],
Lisha Chen [aut],
Patrick Mair [aut]
Maintainer: Thomas Rusch <thomas.rusch@wu.ac.at>
Diff between smacofx versions 1.5-3 dated 2024-06-19 and 1.6-1 dated 2024-09-22
DESCRIPTION | 6 - MD5 | 40 ++++----- NEWS | 4 R/alscal.R | 195 --------------------------------------------- R/apStressMin.R | 2 R/elscal.R | 198 ---------------------------------------------- R/multiscale.R | 209 ++----------------------------------------------- R/powerStressMin.R | 185 +------------------------------------------ R/rStressMin.R | 8 + R/rpowerStressMin.R | 2 R/sammonmap.R | 206 ------------------------------------------------ R/spmds.R | 8 - man/alscal.Rd | 2 man/apStressMin.Rd | 2 man/elscal.Rd | 2 man/multiscale.Rd | 6 - man/powerStressMin.Rd | 2 man/rStressMin.Rd | 2 man/rpowerStressMin.Rd | 2 man/sammonmap.Rd | 2 man/spmds.Rd | 2 21 files changed, 74 insertions(+), 1011 deletions(-)
Title: Extension to 'ggplot2' for Plotting Stats
Description: Provides new statistics, new geometries and new positions for
'ggplot2' and a suite of functions to facilitate the creation of
statistical plots.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between ggstats versions 0.6.0 dated 2024-04-05 and 0.7.0 dated 2024-09-22
ggstats-0.6.0/ggstats/man/reexports.Rd |only ggstats-0.7.0/ggstats/DESCRIPTION | 21 ggstats-0.7.0/ggstats/MD5 | 104 ++-- ggstats-0.7.0/ggstats/NAMESPACE | 25 - ggstats-0.7.0/ggstats/NEWS.md | 28 + ggstats-0.7.0/ggstats/R/geom_diverging.R |only ggstats-0.7.0/ggstats/R/geom_stripped_rows.R | 24 ggstats-0.7.0/ggstats/R/ggcascade.R |only ggstats-0.7.0/ggstats/R/ggcoef_model.R | 20 ggstats-0.7.0/ggstats/R/gglikert.R | 245 ++++++---- ggstats-0.7.0/ggstats/R/ggstats-package.R | 5 ggstats-0.7.0/ggstats/R/hex_bw.R | 33 + ggstats-0.7.0/ggstats/R/pal_extender.R |only ggstats-0.7.0/ggstats/R/position_likert.R | 108 ++-- ggstats-0.7.0/ggstats/R/scale_fill_likert.R |only ggstats-0.7.0/ggstats/R/stat_cross.R | 14 ggstats-0.7.0/ggstats/R/stat_prop.R | 162 +++++- ggstats-0.7.0/ggstats/R/symmetric_limits.R |only ggstats-0.7.0/ggstats/R/weighted_sum.R |only ggstats-0.7.0/ggstats/README.md | 17 ggstats-0.7.0/ggstats/build/vignette.rds |binary ggstats-0.7.0/ggstats/inst/WORDLIST | 8 ggstats-0.7.0/ggstats/inst/doc/geom_diverging.R |only ggstats-0.7.0/ggstats/inst/doc/geom_diverging.Rmd |only ggstats-0.7.0/ggstats/inst/doc/geom_diverging.html |only ggstats-0.7.0/ggstats/inst/doc/ggcoef_model.R | 6 ggstats-0.7.0/ggstats/inst/doc/ggcoef_model.Rmd | 7 ggstats-0.7.0/ggstats/inst/doc/ggcoef_model.html | 89 +-- ggstats-0.7.0/ggstats/inst/doc/gglikert.R | 28 - ggstats-0.7.0/ggstats/inst/doc/gglikert.Rmd | 41 + ggstats-0.7.0/ggstats/inst/doc/gglikert.html | 195 ++++--- ggstats-0.7.0/ggstats/inst/doc/stat_cross.html | 2 ggstats-0.7.0/ggstats/inst/doc/stat_prop.R | 33 + ggstats-0.7.0/ggstats/inst/doc/stat_prop.Rmd | 45 + ggstats-0.7.0/ggstats/inst/doc/stat_prop.html | 56 +- ggstats-0.7.0/ggstats/inst/doc/stat_weighted_mean.html | 2 ggstats-0.7.0/ggstats/man/figures/README-unnamed-chunk-11-1.png |only ggstats-0.7.0/ggstats/man/figures/README-unnamed-chunk-6-1.png |binary ggstats-0.7.0/ggstats/man/geom_diverging.Rd |only ggstats-0.7.0/ggstats/man/geom_stripped_rows.Rd | 63 ++ ggstats-0.7.0/ggstats/man/ggcascade.Rd |only ggstats-0.7.0/ggstats/man/ggcoef_model.Rd | 63 +- ggstats-0.7.0/ggstats/man/gglikert.Rd | 47 + ggstats-0.7.0/ggstats/man/hex_bw.Rd | 22 ggstats-0.7.0/ggstats/man/pal_extender.Rd |only ggstats-0.7.0/ggstats/man/position_likert.Rd | 75 ++- ggstats-0.7.0/ggstats/man/scale_fill_likert.Rd |only ggstats-0.7.0/ggstats/man/stat_cross.Rd | 47 + ggstats-0.7.0/ggstats/man/stat_prop.Rd | 133 ++++- ggstats-0.7.0/ggstats/man/stat_weighted_mean.Rd | 47 + ggstats-0.7.0/ggstats/man/symmetric_limits.Rd |only ggstats-0.7.0/ggstats/man/weighted.sum.Rd |only ggstats-0.7.0/ggstats/tests/spelling.R | 3 ggstats-0.7.0/ggstats/tests/testthat/test-ggcascade.R |only ggstats-0.7.0/ggstats/tests/testthat/test-gglikert.R | 35 + ggstats-0.7.0/ggstats/tests/testthat/test-pal_extender.R |only ggstats-0.7.0/ggstats/tests/testthat/test-position_likert.R | 43 + ggstats-0.7.0/ggstats/tests/testthat/test-stat_prop.R | 59 ++ ggstats-0.7.0/ggstats/tests/testthat/test-utilities.R | 11 ggstats-0.7.0/ggstats/vignettes/geom_diverging.Rmd |only ggstats-0.7.0/ggstats/vignettes/ggcoef_model.Rmd | 7 ggstats-0.7.0/ggstats/vignettes/gglikert.Rmd | 41 + ggstats-0.7.0/ggstats/vignettes/stat_prop.Rmd | 45 + 63 files changed, 1512 insertions(+), 547 deletions(-)
Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also
translating queries the retired classic interface), the
'ISRCTN' (<http://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Documents in registers associated with trials can also be downloaded.
Other functions identify deduplicated records,
easily find and extract variables (fields) of interest even
from complex nested data as used by the registers,
merge variables and update queries.
The package can be used for meta-analysis and trend-analysis of
the design and cond [...truncated...]
Author: Ralf Herold [aut, cre]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.19.2 dated 2024-08-28 and 1.19.3 dated 2024-09-22
DESCRIPTION | 6 MD5 | 60 - NEWS.md | 7 R/ctrFindActiveSubstanceSynonyms.R | 2 R/ctrGetQueryUrl.R | 13 R/ctrLoadQueryIntoDb.R | 8 R/ctrLoadQueryIntoDbCtgov2.R | 26 R/ctrLoadQueryIntoDbCtis.R | 88 -- R/ctrLoadQueryIntoDbEuctr.R | 14 R/ctrLoadQueryIntoDbIsrctn.R | 18 R/ctrRerunQuery.R | 5 R/ctrdata-registers.R | 4 R/dbFindIdsUniqueTrials.R | 930 ++++++++++++------------- R/dbGetFieldsIntoDf.R | 4 R/dbQueryHistory.R | 2 R/dfTrials2Long.R | 5 R/util_fields.R | 3 R/util_functions.R | 90 +- README.md | 87 +- inst/WORDLIST | 1 inst/tinytest/ctrdata_ctgov.R | 14 inst/tinytest/ctrdata_ctgov2.R | 10 inst/tinytest/ctrdata_ctis.R | 86 +- inst/tinytest/ctrdata_euctr.R | 12 inst/tinytest/ctrdata_isrctn.R | 6 inst/tinytest/more_test_ctrdata_duckdb_euctr.R | 2 inst/tinytest/test_ctrdata_other_functions.R | 7 man/ctrLoadQueryIntoDb.Rd | 10 man/ctrdata-registers.Rd | 4 vignettes/ctrdata_retrieve.Rmd | 10 vignettes/ctrdata_summarise.Rmd | 43 - 31 files changed, 822 insertions(+), 755 deletions(-)
Title: Cluster Optimized Proximity Scaling
Description: Multidimensional scaling (MDS) methods that aim at pronouncing the clustered appearance of the configuration (Rusch, Mair & Hornik, 2021, <doi:10.1080/10618600.2020.1869027>). They achieve this by transforming proximities/distances with explicit power functions and penalizing the fitting criterion with a clusteredness index, the OPTICS Cordillera (Rusch, Hornik & Mair, 2018, <doi:10.1080/10618600.2017.1349664>). There are two variants: One for finding the configuration directly (COPS-C) with given explicit power transformations and implicit ratio, interval and non-metric optimal scaling transformations (Borg & Groenen, 2005, ISBN:978-0-387-28981-6), and one for using the augmented fitting criterion to find optimal hyperparameters for the explicit transformations (P-COPS). The package contains various functions, wrappers, methods and classes for fitting, plotting and displaying a large number of different MDS models (most of the functionality in smacofx) in the C [...truncated...]
Author: Thomas Rusch [aut, cre] ,
Patrick Mair [aut] ,
Kurt Hornik [ctb]
Maintainer: Thomas Rusch <thomas.rusch@wu.ac.at>
Diff between cops versions 1.11-3 dated 2024-06-27 and 1.12-1 dated 2024-09-22
DESCRIPTION | 6 +++--- MD5 | 14 +++++++++----- NAMESPACE | 3 +++ NEWS | 6 ++++++ R/biplotmds.pcops.R |only R/biplotmds.stops.R |only R/copstressMin.R | 7 +++---- man/biplotmds.pcops.Rd |only man/biplotmds.stops.Rd |only man/copstressMin.Rd | 2 +- 10 files changed, 25 insertions(+), 13 deletions(-)
Title: Calculation of the OPTICS Cordillera
Description: Functions for calculating the OPTICS Cordillera. The OPTICS Cordillera measures the amount of 'clusteredness' in a numeric data matrix within a distance-density based framework for a given minimum number of points comprising a cluster, as described in Rusch, Hornik, Mair (2018) <doi:10.1080/10618600.2017.1349664>. We provide an R native version with methods for printing, summarizing, and plotting the result.
Author: Thomas Rusch [aut, cre] ,
Patrick Mair [ctb] ,
Kurt Hornik [ctb]
Maintainer: Thomas Rusch <thomas.rusch@wu.ac.at>
Diff between cordillera versions 1.0-0 dated 2023-01-17 and 1.0-3 dated 2024-09-22
cordillera-1.0-0/cordillera/man/oldcordilleraplot.Rd |only cordillera-1.0-3/cordillera/DESCRIPTION | 18 - cordillera-1.0-3/cordillera/MD5 | 25 +- cordillera-1.0-3/cordillera/NAMESPACE | 1 cordillera-1.0-3/cordillera/NEWS | 6 cordillera-1.0-3/cordillera/R/CAClimateIndicatorsCountyMedian-data.R | 2 cordillera-1.0-3/cordillera/R/cordillera-package.R | 5 cordillera-1.0-3/cordillera/R/cordillera.R | 120 ---------- cordillera-1.0-3/cordillera/build/partial.rdb |binary cordillera-1.0-3/cordillera/build/vignette.rds |binary cordillera-1.0-3/cordillera/inst/CITATION | 19 + cordillera-1.0-3/cordillera/man/CAClimateIndicatorsCountyMedian.Rd | 2 cordillera-1.0-3/cordillera/man/cordillera-package.Rd | 18 + cordillera-1.0-3/cordillera/man/cordillera.Rd | 6 14 files changed, 72 insertions(+), 150 deletions(-)
Title: Tools for Supply Chain Management, Demand and Supply Planning
Description: Perform flexible and quick calculations for Demand and Supply Planning, such as projected inventories and coverages, as well as replenishment plan. For any time bucket, daily, weekly or monthly, and any granularity level, product or group of products.
Author: Nicolas Nguyen [aut, cre]
Maintainer: Nicolas Nguyen <nikonguyen@yahoo.fr>
Diff between planr versions 0.4.1 dated 2024-05-22 and 0.4.2 dated 2024-09-22
DESCRIPTION | 6 ++-- MD5 | 13 +++++--- NAMESPACE | 2 + R/month_to_weekx.R |only README.md | 5 ++- inst/doc/get_started.html | 24 ++++++++-------- inst/doc/user_cases.html | 52 +++++++++++++++++------------------ man/month_to_weekx.Rd |only tests/testthat/test-month_to_weekx.R |only 9 files changed, 55 insertions(+), 47 deletions(-)
Title: Minimal Examples of Using Rust Code in R
Description: Template R package with minimal setup to use Rust code in R without
hacks or frameworks. Includes basic examples of importing cargo dependencies,
spawning threads and passing numbers or strings from Rust to R. Cargo crates
are automatically 'vendored' in the R source package to support offline
installation. The GitHub repository for this package has more details and also
explains how to set up CI. This project was first presented at 'Erum2018' to
showcase R-Rust integration <https://jeroen.github.io/erum2018/>; for a real
world use-case, see the 'gifski' package on 'CRAN'.
Author: Jeroen Ooms [aut, cre] ,
Authors of the dependency Rust crates [aut]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between hellorust versions 1.2.1 dated 2024-09-20 and 1.2.2 dated 2024-09-22
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 3 +++ inst/AUTHORS | 2 +- src/Makevars | 2 +- src/myrustlib/vendor.tar.xz |binary 6 files changed, 13 insertions(+), 10 deletions(-)
Title: A S3 Class for Vectors of 64bit Integers
Description: Package 'bit64' provides serializable S3 atomic 64bit (signed) integers.
These are useful for handling database keys and exact counting in +-2^63.
WARNING: do not use them as replacement for 32bit integers, integer64 are not
supported for subscripting by R-core and they have different semantics when
combined with double, e.g. integer64 + double => integer64.
Class integer64 can be used in vectors, matrices, arrays and data.frames.
Methods are available for coercion from and to logicals, integers, doubles,
characters and factors as well as many elementwise and summary functions.
Many fast algorithmic operations such as 'match' and 'order' support inter-
active data exploration and manipulation and optionally leverage caching.
Author: Jens Oehlschlaegel [aut, cre],
Leonardo Silvestri [ctb],
Ofek Shilon [ctb]
Maintainer: Jens Oehlschlaegel <Jens.Oehlschlaegel@truecluster.com>
Diff between bit64 versions 4.0.5 dated 2020-08-30 and 4.5.2 dated 2024-09-22
DESCRIPTION | 23 ++- MD5 | 42 +++--- NAMESPACE | 16 +- NEWS | 43 ++++++ R/cache.R | 8 - R/highlevel64.R | 2 R/integer64.R | 227 +++++++++++++++++++++++++++------- R/sort64.R | 12 - R/zzz.R | 15 +- inst/doc/ANNOUNCEMENT-0.9-Details.txt | 50 +++++++ man/as.character.integer64.rd | 2 man/bit64-package.rd | 225 ++++++++++++++++----------------- man/cache.rd | 4 man/hashcache.rd | 4 man/identical.integer64.rd | 13 + man/keypos.rd | 2 man/ramsort.integer64.rd | 8 - man/sort.integer64.rd | 4 man/xor.integer64.rd | 12 + src/init.c | 4 src/integer64.c | 75 ++++++++--- src/integer64.h | 21 ++- 22 files changed, 576 insertions(+), 236 deletions(-)
Title: Fast and Memory Efficient Data Operations in Tidy Syntax
Description: Tidy syntax for 'data.table', using modification by reference whenever possible.
This toolkit is designed for big data analysis in high-performance desktop or laptop computers.
The syntax of the package is similar or identical to 'tidyverse'.
It is user friendly, memory efficient and time saving. For more information,
check its ancestor package 'tidyfst'.
Author: Tian-Yuan Huang [aut, cre]
Maintainer: Tian-Yuan Huang <huang.tian-yuan@qq.com>
Diff between tidyft versions 0.5.7 dated 2023-01-08 and 0.9.20 dated 2024-09-22
DESCRIPTION | 14 MD5 | 14 NAMESPACE | 15 build/vignette.rds |binary inst/doc/Introduction.R | 111 - inst/doc/Introduction.Rmd | 121 - inst/doc/Introduction.html | 4874 ++------------------------------------------- vignettes/Introduction.Rmd | 121 - 8 files changed, 490 insertions(+), 4780 deletions(-)
Title: Standardized Moderation Effect and Its Confidence Interval
Description: Functions for computing a standardized moderation effect
in moderated regression and forming its confidence interval
by nonparametric bootstrapping as proposed in
Cheung, Cheung, Lau, Hui, and Vong (2022)
<doi:10.1037/hea0001188>. Also includes simple-to-use
functions for computing conditional effects (unstandardized
or standardized) and plotting moderation effects.
Author: Shu Fai Cheung [aut, cre] ,
David Weng Ngai Vong [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between stdmod versions 0.2.10 dated 2024-02-22 and 0.2.11 dated 2024-09-22
stdmod-0.2.10/stdmod/vignettes/numerical_example_01.html |only stdmod-0.2.11/stdmod/DESCRIPTION | 10 stdmod-0.2.11/stdmod/MD5 | 225 +- stdmod-0.2.11/stdmod/NAMESPACE | 50 stdmod-0.2.11/stdmod/NEWS.md | 367 +-- stdmod-0.2.11/stdmod/R/add1_stdmod.R | 40 stdmod-0.2.11/stdmod/R/coef_condeff.R | 104 - stdmod-0.2.11/stdmod/R/coef_stdmod_lavaan.R | 122 - stdmod-0.2.11/stdmod/R/condeff.R | 516 ++--- stdmod-0.2.11/stdmod/R/condeff_boot.R | 398 ++-- stdmod-0.2.11/stdmod/R/confint_condeff.R | 258 +- stdmod-0.2.11/stdmod/R/confint_stdmod.R | 278 +- stdmod-0.2.11/stdmod/R/confint_stdmod_lavaan.R | 156 - stdmod-0.2.11/stdmod/R/data.R | 94 stdmod-0.2.11/stdmod/R/data_2.R | 68 stdmod-0.2.11/stdmod/R/data_3.R | 98 - stdmod-0.2.11/stdmod/R/data_4.R | 52 stdmod-0.2.11/stdmod/R/helpers.R | 18 stdmod-0.2.11/stdmod/R/plotmod.R | 958 +++++----- stdmod-0.2.11/stdmod/R/plotmod_helpers.R | 254 +- stdmod-0.2.11/stdmod/R/plotmod_helpers_2.R | 64 stdmod-0.2.11/stdmod/R/print_cond_eff.R | 406 ++-- stdmod-0.2.11/stdmod/R/print_stdmod.R | 98 - stdmod-0.2.11/stdmod/R/print_stdmod_lavaan.R | 260 +- stdmod-0.2.11/stdmod/R/print_summary_stdmod.R | 632 +++--- stdmod-0.2.11/stdmod/R/std_selected.R | 452 ++-- stdmod-0.2.11/stdmod/R/std_selected_boot.R | 360 +-- stdmod-0.2.11/stdmod/R/stdmod-package.R | 18 stdmod-0.2.11/stdmod/R/stdmod.R | 276 +- stdmod-0.2.11/stdmod/R/stdmod_bootci.R | 174 - stdmod-0.2.11/stdmod/R/stdmod_lavaan.R | 884 ++++----- stdmod-0.2.11/stdmod/R/summary_stdmod.R | 200 +- stdmod-0.2.11/stdmod/R/sweep2.R | 46 stdmod-0.2.11/stdmod/R/update_stdmod.R | 162 - stdmod-0.2.11/stdmod/R/vcov_stdmod.R | 166 - stdmod-0.2.11/stdmod/README.md | 186 - stdmod-0.2.11/stdmod/build/partial.rdb |binary stdmod-0.2.11/stdmod/build/vignette.rds |binary stdmod-0.2.11/stdmod/inst/CITATION | 42 stdmod-0.2.11/stdmod/inst/doc/cond_effect.Rmd | 522 ++--- stdmod-0.2.11/stdmod/inst/doc/cond_effect.html | 210 +- stdmod-0.2.11/stdmod/inst/doc/moderation.Rmd | 488 ++--- stdmod-0.2.11/stdmod/inst/doc/moderation.html | 406 ++-- stdmod-0.2.11/stdmod/inst/doc/plotmod.Rmd | 688 +++---- stdmod-0.2.11/stdmod/inst/doc/plotmod.html | 214 +- stdmod-0.2.11/stdmod/inst/doc/std_selected.Rmd | 652 +++--- stdmod-0.2.11/stdmod/inst/doc/std_selected.html | 422 ++-- stdmod-0.2.11/stdmod/inst/doc/stdmod.Rmd | 630 +++--- stdmod-0.2.11/stdmod/inst/doc/stdmod.html | 590 +++--- stdmod-0.2.11/stdmod/inst/doc/stdmod_lavaan.Rmd | 364 +-- stdmod-0.2.11/stdmod/inst/doc/stdmod_lavaan.html | 270 +- stdmod-0.2.11/stdmod/man/add1.std_selected.Rd | 52 stdmod-0.2.11/stdmod/man/coef.cond_effect.Rd | 112 - stdmod-0.2.11/stdmod/man/coef.stdmod_lavaan.Rd | 132 - stdmod-0.2.11/stdmod/man/cond_effect.Rd | 522 ++--- stdmod-0.2.11/stdmod/man/confint.cond_effect.Rd | 150 - stdmod-0.2.11/stdmod/man/confint.std_selected.Rd | 214 +- stdmod-0.2.11/stdmod/man/confint.stdmod_lavaan.Rd | 134 - stdmod-0.2.11/stdmod/man/plotmod.Rd | 484 ++--- stdmod-0.2.11/stdmod/man/print.cond_effect.Rd | 174 - stdmod-0.2.11/stdmod/man/print.std_selected.Rd | 96 - stdmod-0.2.11/stdmod/man/print.stdmod_lavaan.Rd | 142 - stdmod-0.2.11/stdmod/man/print.summary.std_selected.Rd | 210 +- stdmod-0.2.11/stdmod/man/sleep_emo_con.Rd | 50 stdmod-0.2.11/stdmod/man/std_selected.Rd | 468 ++-- stdmod-0.2.11/stdmod/man/stdmod-package.Rd | 58 stdmod-0.2.11/stdmod/man/stdmod.Rd | 364 +-- stdmod-0.2.11/stdmod/man/stdmod_lavaan.Rd | 428 ++-- stdmod-0.2.11/stdmod/man/summary.std_selected.Rd | 108 - stdmod-0.2.11/stdmod/man/test_mod1.Rd | 64 stdmod-0.2.11/stdmod/man/test_mod2.Rd | 64 stdmod-0.2.11/stdmod/man/test_mod3_miss.Rd | 68 stdmod-0.2.11/stdmod/man/test_x_1_w_1_v_1_cat1_n_500.Rd | 52 stdmod-0.2.11/stdmod/man/test_x_1_w_1_v_1_cat1_xw_cov_n_500.Rd | 50 stdmod-0.2.11/stdmod/man/test_x_1_w_1_v_1_cat1_xw_cov_wcat3_n_500.Rd | 54 stdmod-0.2.11/stdmod/man/test_x_1_w_1_v_2_n_500.Rd | 46 stdmod-0.2.11/stdmod/man/update.std_selected.Rd | 112 - stdmod-0.2.11/stdmod/man/vcov.std_selected.Rd | 138 - stdmod-0.2.11/stdmod/tests/testthat.R | 8 stdmod-0.2.11/stdmod/tests/testthat/test_condeff.R | 405 ++-- stdmod-0.2.11/stdmod/tests/testthat/test_condeff_boot.R | 184 - stdmod-0.2.11/stdmod/tests/testthat/test_condeff_boot_methods.R | 112 - stdmod-0.2.11/stdmod/tests/testthat/test_condeff_methods.R | 234 +- stdmod-0.2.11/stdmod/tests/testthat/test_condeff_user_value.R | 130 - stdmod-0.2.11/stdmod/tests/testthat/test_methods_stdmod_lavaan.R | 190 + stdmod-0.2.11/stdmod/tests/testthat/test_plotmod.R | 831 ++++---- stdmod-0.2.11/stdmod/tests/testthat/test_plotmod_percentile_more_levels.R | 62 stdmod-0.2.11/stdmod/tests/testthat/test_plotmod_tumble.R | 434 ++-- stdmod-0.2.11/stdmod/tests/testthat/test_plotmod_user_value.R | 116 - stdmod-0.2.11/stdmod/tests/testthat/test_stdmod.R | 182 - stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_cat.R | 182 - stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_lavaan.R | 172 - stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_lavaan2.R | 274 +- stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_lavaan3_warning.R | 111 - stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_lavaan_2.R | 178 - stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_selected.R | 262 +- stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_selected_boot.R | 258 +- stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_selected_boot_fac.R | 285 +- stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_selected_confint.R | 112 - stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_selected_fac.R | 262 +- stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_selected_print_summary.R | 86 stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_selected_print_summary_rsq.R | 102 - stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_selected_update.R | 318 +-- stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_selected_vcov.R | 114 - stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_selectedj_to_std.R | 254 +- stdmod-0.2.11/stdmod/tests/testthat/test_stdmod_update.R | 90 stdmod-0.2.11/stdmod/tests/testthat/test_sweep2.R | 44 stdmod-0.2.11/stdmod/vignettes/cond_effect.Rmd | 522 ++--- stdmod-0.2.11/stdmod/vignettes/cond_effect.Rmd.original | 424 ++-- stdmod-0.2.11/stdmod/vignettes/moderation.Rmd | 488 ++--- stdmod-0.2.11/stdmod/vignettes/plotmod.Rmd | 688 +++---- stdmod-0.2.11/stdmod/vignettes/std_selected.Rmd | 652 +++--- stdmod-0.2.11/stdmod/vignettes/stdmod.Rmd | 630 +++--- stdmod-0.2.11/stdmod/vignettes/stdmod_lavaan.Rmd | 364 +-- 114 files changed, 14218 insertions(+), 14036 deletions(-)
Title: Financial Time Series Objects (Rmetrics)
Description: 'S4' classes and various tools for financial time series:
Basic functions such as scaling and sorting, subsetting,
mathematical operations and statistical functions.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Martin Maechler [ctb] ,
Georgi N. Boshnakov [cre, aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between timeSeries versions 4041.110 dated 2024-09-16 and 4041.111 dated 2024-09-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 10 +--------- NEWS.md | 9 +++++++++ inst/doc/timeSeriesPlot.pdf |binary inst/doc/timeSeriesRefCard.pdf |binary 6 files changed, 19 insertions(+), 18 deletions(-)
Title: Rmetrics - Chronological and Calendar Objects
Description: The 'timeDate' class fulfils the conventions of the ISO 8601
standard as well as of the ANSI C and POSIX standards. Beyond
these standards it provides the "Financial Center" concept
which allows to handle data records collected in different time
zones and mix them up to have always the proper time stamps with
respect to your personal financial center, or alternatively to the GMT
reference time. It can thus also handle time stamps from historical
data records from the same time zone, even if the financial
centers changed day light saving times at different calendar
dates.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Martin Maechler [ctb] ,
Joe W. Byers [ctb],
Georgi N. Boshnakov [cre, aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between timeDate versions 4032.109 dated 2023-12-14 and 4041.110 dated 2024-09-22
DESCRIPTION | 6 - MD5 | 158 ++++++++++++++++---------------- NAMESPACE | 102 ++++++++------------ NEWS.md | 35 +++++++ R/AllClass.R | 9 - R/AllGeneric.R | 11 -- R/calendar-atoms.R | 181 ++++++++++++++++++++++++++++--------- R/calendar-isDaily.R | 16 ++- R/calendar-julian.R | 11 -- R/holiday-Dates.R | 95 ++++++++++--------- R/holiday-Listing.R | 26 ++--- R/methods-show.R | 13 +- R/stats-frequency.R | 17 ++- R/timeDate.R | 23 +++- README.md | 2 inst/_pkgdown.yml | 3 inst/pkgdown.yml | 6 - man/00timeDate-package.Rd | 2 man/base-c.Rd | 41 +++----- man/base-diff.Rd | 77 ++++++--------- man/base-difftimeDate.Rd | 48 ++++----- man/base-format.Rd | 46 ++++----- man/base-length.Rd | 10 -- man/base-rep.Rd | 18 +-- man/base-rev.Rd | 5 - man/base-round.Rd | 12 -- man/base-sample.Rd | 43 +++----- man/base-sort.Rd | 57 +++++------ man/base-start.Rd | 37 +++---- man/base-subset.Rd | 18 +-- man/base-summary.Rd | 5 - man/base-unique.Rd | 54 +++++------ man/calendar-Easter.Rd | 19 +-- man/calendar-align.Rd | 20 +--- man/calendar-dayOfWeek.Rd | 14 -- man/calendar-dayOfYear.Rd | 14 -- man/calendar-endpoints.Rd | 12 -- man/calendar-firstDay.Rd | 67 ++++++------- man/calendar-isBizday.Rd | 21 ++-- man/calendar-isRegular.Rd | 20 ++-- man/calendar-isWeekday.Rd | 25 ++--- man/calendar-julian.Rd | 107 +++++++++++++++++---- man/calendar-nDay.Rd | 12 +- man/calendar-onOrAfter.Rd | 16 +-- man/calendar-periods.Rd | 24 +--- man/class-timeDate.Rd | 46 ++++----- man/earlyCloseNYSE.Rd | 10 -- man/graphics-plot.Rd | 32 ++---- man/holiday-Dates.Rd | 13 +- man/holiday-LONDON.Rd | 6 - man/holiday-Listing.Rd | 27 ++--- man/holiday-NERC.Rd | 13 +- man/holiday-NYSE.Rd | 9 - man/holiday-TSX.Rd | 11 -- man/holiday-ZURICH.Rd | 23 +--- man/holiday.Rd | 31 ++---- man/methods-as.Rd | 85 ++++------------- man/methods-mathOps.Rd | 26 ++--- man/methods-names.Rd | 5 - man/methods-show.Rd | 6 - man/options-RmetricsOptions.Rd | 1 man/options-currentYear.Rd | 8 - man/options-myFinCenter.Rd | 15 +-- man/options-myUnits.Rd | 5 - man/specialHolidayGB.Rd | 4 man/stats-blockStart.Rd | 17 +-- man/stats-kurtosis.Rd | 19 +-- man/stats-na-fail.Rd | 2 man/stats-skewness.Rd | 18 +-- man/stats-window.Rd | 35 +++---- man/timeDate-Calendar.Rd | 31 ++---- man/timeDate-DaylightSavingTime.Rd | 10 -- man/timeDate-Sequence.Rd | 20 ++-- man/timeDate-Sys.timeDate.Rd | 14 +- man/timeDate-finCenter.Rd | 1 man/timeDate-listFinCenter.Rd | 26 ++--- man/timeDate-midnightStandard.Rd | 16 +-- man/timeDate-rulesFinCenter.Rd | 9 - man/timeDate-whichFormat.Rd | 10 -- man/timeDate.Rd | 138 +++++++++++++++++----------- 80 files changed, 1134 insertions(+), 1166 deletions(-)
Title: Rapid Manipulation of the Variant Call Format (VCF)
Description: The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.
Author: Zilong Li [aut, cre] ,
Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and
Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies,
Robert M [cph]
Maintainer: Zilong Li <zilong.dk@gmail.com>
Diff between vcfppR versions 0.4.6 dated 2024-05-24 and 0.5.0 dated 2024-09-22
DESCRIPTION | 6 MD5 | 30 +-- NEWS.md | 8 R/RcppExports.R | 3 R/vcf-compare.R | 33 ++- R/vcf-popgen.R | 4 README.md | 23 ++ man/vcfcomp.Rd | 6 man/vcfreader.Rd | 4 src/vcf-popgen.cpp | 2 src/vcf-reader.cpp | 117 +++++++++---- src/vcf-table.cpp | 40 ++-- src/vcfpp.h | 341 ++++++++++++++++++++++++++++++++------- tests/testthat/test-modify-vcf.R | 56 ++++++ tests/testthat/test-vcf-comp.R | 26 ++ tests/testthat/test-vcf-reader.R | 47 +++++ 16 files changed, 581 insertions(+), 165 deletions(-)
Title: Breiman and Cutlers Random Forests for Classification and
Regression
Description: Classification and regression based on a forest of trees using random inputs, based on Breiman (2001) <DOI:10.1023/A:1010933404324>.
Author: Leo Breiman [aut] ,
Adele Cutler [aut] ,
Andy Liaw [aut, cre] ,
Matthew Wiener [aut]
Maintainer: Andy Liaw <andy_liaw@merck.com>
Diff between randomForest versions 4.7-1.1 dated 2022-05-23 and 4.7-1.2 dated 2024-09-22
DESCRIPTION | 24 ++++++++++++++++++------ MD5 | 21 +++++++++++---------- NAMESPACE | 5 +++++ build |only data/imports85.rda |binary inst/CITATION | 17 +++++------------ man/imports85.Rd | 4 ++-- src/classTree.c | 10 +++++----- src/regTree.c | 44 ++++++++++++++++++++++---------------------- src/regrf.c | 4 ++-- src/rf.c | 4 ++-- src/rfutils.c | 24 ++++++++++++------------ 12 files changed, 84 insertions(+), 73 deletions(-)
Title: Error Detection in Science
Description: Test published summary statistics for consistency
(Brown and Heathers, 2017, <doi:10.1177/1948550616673876>;
Allard, 2018, <https://aurelienallard.netlify.app/post/anaytic-grimmer-possibility-standard-deviations/>;
Heathers and Brown, 2019, <https://osf.io/5vb3u/>).
The package also provides infrastructure for implementing new
error detection techniques.
Author: Lukas Jung [aut, cre],
Aurelien Allard [ctb]
Maintainer: Lukas Jung <jung-lukas@gmx.net>
Diff between scrutiny versions 0.4.0 dated 2024-02-23 and 0.5.0 dated 2024-09-22
scrutiny-0.4.0/scrutiny/man/audit_list.Rd |only scrutiny-0.5.0/scrutiny/DESCRIPTION | 22 scrutiny-0.5.0/scrutiny/LICENSE |only scrutiny-0.5.0/scrutiny/MD5 | 181 ++-- scrutiny-0.5.0/scrutiny/NAMESPACE | 2 scrutiny-0.5.0/scrutiny/NEWS.md | 46 + scrutiny-0.5.0/scrutiny/R/audit.R | 36 scrutiny-0.5.0/scrutiny/R/before-inside-parens.R | 16 scrutiny-0.5.0/scrutiny/R/debit-map.R | 4 scrutiny-0.5.0/scrutiny/R/debit.R | 2 scrutiny-0.5.0/scrutiny/R/duplicate-count-colpair.R | 13 scrutiny-0.5.0/scrutiny/R/duplicate-count.R | 20 scrutiny-0.5.0/scrutiny/R/duplicate-detect.R | 31 scrutiny-0.5.0/scrutiny/R/function-factory-helpers.R | 45 - scrutiny-0.5.0/scrutiny/R/function-map-seq.R | 18 scrutiny-0.5.0/scrutiny/R/function-map-total-n.R | 4 scrutiny-0.5.0/scrutiny/R/grim-granularity.R | 16 scrutiny-0.5.0/scrutiny/R/grim-map-seq-debug.R |only scrutiny-0.5.0/scrutiny/R/grim-map.R | 106 +- scrutiny-0.5.0/scrutiny/R/grim-stats.R | 104 +- scrutiny-0.5.0/scrutiny/R/grim.R | 2 scrutiny-0.5.0/scrutiny/R/grimmer-map-seq.R | 7 scrutiny-0.5.0/scrutiny/R/grimmer-map-total-n.R | 7 scrutiny-0.5.0/scrutiny/R/grimmer-map.R | 63 + scrutiny-0.5.0/scrutiny/R/grimmer-rsprite2.R |only scrutiny-0.5.0/scrutiny/R/grimmer.R | 191 ++-- scrutiny-0.5.0/scrutiny/R/method-grim-map.R | 14 scrutiny-0.5.0/scrutiny/R/restore-zeros.R | 32 scrutiny-0.5.0/scrutiny/R/row-to-colnames.R | 2 scrutiny-0.5.0/scrutiny/R/seq-predicates.R | 127 +- scrutiny-0.5.0/scrutiny/R/split-by-parens.R | 2 scrutiny-0.5.0/scrutiny/R/subset-superset.R | 91 ++ scrutiny-0.5.0/scrutiny/R/utils.R | 180 ---- scrutiny-0.5.0/scrutiny/README.md | 52 - scrutiny-0.5.0/scrutiny/build/partial.rdb |binary scrutiny-0.5.0/scrutiny/build/vignette.rds |binary scrutiny-0.5.0/scrutiny/inst/doc/consistency-tests-in-depth.html | 9 scrutiny-0.5.0/scrutiny/inst/doc/consistency-tests-simple.html | 2 scrutiny-0.5.0/scrutiny/inst/doc/debit.Rmd | 4 scrutiny-0.5.0/scrutiny/inst/doc/debit.html | 34 scrutiny-0.5.0/scrutiny/inst/doc/devtools.html | 5 scrutiny-0.5.0/scrutiny/inst/doc/duplicates.html | 2 scrutiny-0.5.0/scrutiny/inst/doc/grim.R | 18 scrutiny-0.5.0/scrutiny/inst/doc/grim.Rmd | 65 - scrutiny-0.5.0/scrutiny/inst/doc/grim.html | 303 +++---- scrutiny-0.5.0/scrutiny/inst/doc/grimmer.R | 76 - scrutiny-0.5.0/scrutiny/inst/doc/grimmer.Rmd | 96 +- scrutiny-0.5.0/scrutiny/inst/doc/grimmer.html | 431 +++++----- scrutiny-0.5.0/scrutiny/inst/doc/related.Rmd | 4 scrutiny-0.5.0/scrutiny/inst/doc/related.html | 5 scrutiny-0.5.0/scrutiny/inst/doc/rounding-in-depth.R | 2 scrutiny-0.5.0/scrutiny/inst/doc/rounding-in-depth.Rmd | 4 scrutiny-0.5.0/scrutiny/inst/doc/rounding-in-depth.html | 65 - scrutiny-0.5.0/scrutiny/inst/doc/rounding-options.Rmd | 2 scrutiny-0.5.0/scrutiny/inst/doc/rounding-options.html | 6 scrutiny-0.5.0/scrutiny/inst/doc/wrangling.Rmd | 8 scrutiny-0.5.0/scrutiny/inst/doc/wrangling.html | 16 scrutiny-0.5.0/scrutiny/man/debit.Rd | 2 scrutiny-0.5.0/scrutiny/man/debit_map.Rd | 4 scrutiny-0.5.0/scrutiny/man/duplicate_count.Rd | 17 scrutiny-0.5.0/scrutiny/man/duplicate_count_colpair.Rd | 9 scrutiny-0.5.0/scrutiny/man/duplicate_detect.Rd | 5 scrutiny-0.5.0/scrutiny/man/figures/README-unnamed-chunk-5-1.png |binary scrutiny-0.5.0/scrutiny/man/figures/README-unnamed-chunk-6-1.png |binary scrutiny-0.5.0/scrutiny/man/grim-stats.Rd | 53 - scrutiny-0.5.0/scrutiny/man/grim_granularity.Rd | 11 scrutiny-0.5.0/scrutiny/man/grim_map.Rd | 23 scrutiny-0.5.0/scrutiny/man/grim_ratio_upper.Rd |only scrutiny-0.5.0/scrutiny/man/grimmer.Rd | 32 scrutiny-0.5.0/scrutiny/man/grimmer_map.Rd | 51 - scrutiny-0.5.0/scrutiny/man/grimmer_map_seq.Rd | 7 scrutiny-0.5.0/scrutiny/man/grimmer_map_total_n.Rd | 7 scrutiny-0.5.0/scrutiny/man/restore_zeros.Rd | 12 scrutiny-0.5.0/scrutiny/man/row_to_colnames.Rd | 2 scrutiny-0.5.0/scrutiny/man/seq-predicates.Rd | 2 scrutiny-0.5.0/scrutiny/man/split_by_parens.Rd | 2 scrutiny-0.5.0/scrutiny/man/subset-superset.Rd | 15 scrutiny-0.5.0/scrutiny/tests/testthat/test-grim-map-seq.R | 127 +- scrutiny-0.5.0/scrutiny/tests/testthat/test-grim-map-total-n.R | 20 scrutiny-0.5.0/scrutiny/tests/testthat/test-grim-map.R | 49 - scrutiny-0.5.0/scrutiny/tests/testthat/test-grim-stats.R | 27 scrutiny-0.5.0/scrutiny/tests/testthat/test-grimmer-map.R | 10 scrutiny-0.5.0/scrutiny/tests/testthat/test-grimmer.R | 226 +++++ scrutiny-0.5.0/scrutiny/tests/testthat/test-method-audit-seq.R | 24 scrutiny-0.5.0/scrutiny/tests/testthat/test-method-audit-total-n.R | 12 scrutiny-0.5.0/scrutiny/tests/testthat/test-seq-predicates.R | 3 scrutiny-0.5.0/scrutiny/tests/testthat/test-utils.R | 12 scrutiny-0.5.0/scrutiny/vignettes/debit.Rmd | 4 scrutiny-0.5.0/scrutiny/vignettes/grim.Rmd | 65 - scrutiny-0.5.0/scrutiny/vignettes/grimmer.Rmd | 96 +- scrutiny-0.5.0/scrutiny/vignettes/related.Rmd | 4 scrutiny-0.5.0/scrutiny/vignettes/rounding-in-depth.Rmd | 4 scrutiny-0.5.0/scrutiny/vignettes/rounding-options.Rmd | 2 scrutiny-0.5.0/scrutiny/vignettes/wrangling.Rmd | 8 94 files changed, 1882 insertions(+), 1658 deletions(-)
Title: Partially Separable Quasi-Newton
Description: Provides quasi-Newton methods to minimize partially separable
functions. The methods are largely described by
Nocedal and Wright (2006) <doi:10.1007/978-0-387-40065-5>.
Author: Benjamin Christoffersen [cre, aut]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between psqn versions 0.3.1 dated 2022-03-02 and 0.3.2 dated 2024-09-22
DESCRIPTION | 7 - MD5 | 36 +++---- NEWS | 4 build/vignette.rds |binary inst/doc/psqn.html | 134 +++++++++++++-------------- inst/doc/quick-intro.html | 4 inst/include/psqn-bfgs.h | 9 + inst/include/psqn.h | 22 ---- inst/mlogit-ex.cpp | 2 inst/poly-ex.cpp | 2 src/Makevars | 2 tests/testthat/helper.R | 16 +++ tests/testthat/psqn_generic-glm-hess-res.RDS |binary tests/testthat/psqn_generic-glm-res-mask.RDS |binary tests/testthat/psqn_generic-glm-res.RDS |binary tests/testthat/psqn_generic-hess-res.RDS |binary tests/testthat/test-cpp-api.R | 1 tests/testthat/test-poly-ex.R | 1 tests/testthat/test-psqn-generic.R | 6 - 19 files changed, 126 insertions(+), 120 deletions(-)
Title: Simulate DNA Methylation Dynamics on Different Genomic
Structures along Genealogies
Description: DNA methylation is an epigenetic modification involved in genomic stability,
gene regulation, development and disease.
DNA methylation occurs mainly through the addition of a methyl group to cytosines,
for example to cytosines in a CpG dinucleotide context (CpG stands for a cytosine followed by a guanine).
Tissue-specific methylation patterns lead to genomic regions with different characteristic
methylation levels.
E.g. in vertebrates CpG islands (regions with high CpG content) that are associated to promoter regions of
expressed genes tend to be unmethylated.
'MethEvolSIM' is a model-based simulation software for the generation and modification
of cytosine methylation patterns along a given tree, which can be a genealogy of
cells within an organism, a coalescent tree of DNA sequences sampled from a population, or a species tree.
The simulations are based on an extension of the model of
Grosser & Metzler (2020) <doi:10.1186/s12859-020-3438-5> and allows for changes of
the met [...truncated...]
Author: Sara Castillo Vicente [aut, cre],
Dirk Metzler [aut, ths]
Maintainer: Sara Castillo Vicente <castillo@bio.lmu.de>
Diff between MethEvolSIM versions 0.1.6 dated 2024-09-09 and 0.1.7 dated 2024-09-22
DESCRIPTION | 6 MD5 | 10 R/multiRegion_SIM.R | 191 +++++++--- inst/doc/intro-vignette.html | 49 +- man/singleStructureGenerator.Rd | 43 ++ tests/testthat/test-multiRegion_SIM.R | 642 +++++++++++++++++++++++++++++++++- 6 files changed, 843 insertions(+), 98 deletions(-)
Title: Graphical Independence Networks
Description: Probability propagation in Bayesian networks, also known as graphical independence networks. Documentation
of the package is provided in vignettes included in the package and in
the paper by Højsgaard (2012, <doi:10.18637/jss.v046.i10>).
See 'citation("gRain")' for details.
Author: Soeren Hoejsgaard [aut, cre]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between gRain versions 1.4.1 dated 2023-11-21 and 1.4.2 dated 2024-09-22
gRain-1.4.1/gRain/R/evidence_joint.R |only gRain-1.4.1/gRain/R/grain_data.R |only gRain-1.4.1/gRain/data |only gRain-1.4.1/gRain/inst/doc/grain_intro.R |only gRain-1.4.1/gRain/inst/doc/grain_intro.Rnw |only gRain-1.4.1/gRain/inst/doc/grain_intro.pdf |only gRain-1.4.1/gRain/man/chest.Rd |only gRain-1.4.1/gRain/man/evidence_object.Rd |only gRain-1.4.1/gRain/man/get_superset_list.Rd |only gRain-1.4.1/gRain/man/grain_joint_evidence.Rd |only gRain-1.4.1/gRain/man/grass.Rd |only gRain-1.4.1/gRain/man/replace-cpt.Rd |only gRain-1.4.1/gRain/vignettes/figures/grain-chest-LS-1.pdf |only gRain-1.4.1/gRain/vignettes/figures/grain-unnamed-chunk-32-1.pdf |only gRain-1.4.1/gRain/vignettes/figures/grain-unnamed-chunk-33-1.pdf |only gRain-1.4.1/gRain/vignettes/figures/grain-unnamed-chunk-34-1.pdf |only gRain-1.4.1/gRain/vignettes/figures/grain-unnamed-chunk-35-1.pdf |only gRain-1.4.1/gRain/vignettes/figures/grain-unnamed-chunk-36-1.pdf |only gRain-1.4.1/gRain/vignettes/figures/grain-unnamed-chunk-37-1.pdf |only gRain-1.4.1/gRain/vignettes/figures/grain-unnamed-chunk-38-1.pdf |only gRain-1.4.1/gRain/vignettes/figures/grain-unnamed-chunk-39-1.pdf |only gRain-1.4.1/gRain/vignettes/figures/grain-unnamed-chunk-40-1.pdf |only gRain-1.4.1/gRain/vignettes/figures/grain-unnamed-chunk-41-1.pdf |only gRain-1.4.1/gRain/vignettes/figures/grain-unnamed-chunk-42-1.pdf |only gRain-1.4.1/gRain/vignettes/figures/grain-unnamed-chunk-43-1.pdf |only gRain-1.4.1/gRain/vignettes/figures/grain-unnamed-chunk-44-1.pdf |only gRain-1.4.1/gRain/vignettes/figures/grain-unnamed-chunk-45-1.pdf |only gRain-1.4.1/gRain/vignettes/grain_intro.Rnw |only gRain-1.4.2/gRain/DESCRIPTION | 25 gRain-1.4.2/gRain/MD5 | 138 +-- gRain-1.4.2/gRain/NAMESPACE | 29 gRain-1.4.2/gRain/R/DATA_grain.R |only gRain-1.4.2/gRain/R/NAMESPACE.R | 12 gRain-1.4.2/gRain/R/cpt_pot_extract.R | 119 +- gRain-1.4.2/gRain/R/cpt_pot_gather.R | 47 - gRain-1.4.2/gRain/R/cptable_create.R | 9 gRain-1.4.2/gRain/R/cptable_special.R | 29 gRain-1.4.2/gRain/R/display.R | 34 gRain-1.4.2/gRain/R/evidence.R | 416 +++------- gRain-1.4.2/gRain/R/evidence_objects.R | 199 ++-- gRain-1.4.2/gRain/R/finding.R | 24 gRain-1.4.2/gRain/R/generics.R | 25 gRain-1.4.2/gRain/R/grain_compile.R | 64 - gRain-1.4.2/gRain/R/grain_internal.R | 4 gRain-1.4.2/gRain/R/grain_main.R | 23 gRain-1.4.2/gRain/R/grain_simulate.R | 10 gRain-1.4.2/gRain/R/grain_utilities.R | 67 + gRain-1.4.2/gRain/R/predict.R | 7 gRain-1.4.2/gRain/R/propagate.R | 45 - gRain-1.4.2/gRain/R/querygrain.R | 105 +- gRain-1.4.2/gRain/R/repeat_pattern.R | 4 gRain-1.4.2/gRain/R/replace_cpt.R | 21 gRain-1.4.2/gRain/R/zzz.R | 12 gRain-1.4.2/gRain/README.md | 23 gRain-1.4.2/gRain/build/vignette.rds |binary gRain-1.4.2/gRain/inst/doc/grain.R |only gRain-1.4.2/gRain/inst/doc/grain.pdf |only gRain-1.4.2/gRain/inst/doc/grain.rmd |only gRain-1.4.2/gRain/man/components_extract.Rd | 14 gRain-1.4.2/gRain/man/components_gather.Rd | 8 gRain-1.4.2/gRain/man/cpt.Rd | 6 gRain-1.4.2/gRain/man/example_chest.Rd |only gRain-1.4.2/gRain/man/example_grass.Rd |only gRain-1.4.2/gRain/man/finding.Rd | 17 gRain-1.4.2/gRain/man/generics.Rd | 15 gRain-1.4.2/gRain/man/grain-main.Rd | 4 gRain-1.4.2/gRain/man/grain-simulate.Rd | 2 gRain-1.4.2/gRain/man/grain_compile.Rd | 2 gRain-1.4.2/gRain/man/grain_evidence.Rd | 98 -- gRain-1.4.2/gRain/man/grain_predict.Rd | 4 gRain-1.4.2/gRain/man/grain_propagate.Rd | 5 gRain-1.4.2/gRain/man/internal-grain.Rd | 1 gRain-1.4.2/gRain/man/logical.Rd | 16 gRain-1.4.2/gRain/man/old_components_extract.Rd |only gRain-1.4.2/gRain/man/old_components_gather.Rd |only gRain-1.4.2/gRain/man/old_grain_evidence.Rd |only gRain-1.4.2/gRain/man/old_repeat_pattern.Rd |only gRain-1.4.2/gRain/man/old_replace_cpt.Rd |only gRain-1.4.2/gRain/man/querygrain.Rd | 4 gRain-1.4.2/gRain/man/repeat_pattern.Rd | 3 gRain-1.4.2/gRain/man/replace_cpt.Rd |only gRain-1.4.2/gRain/src/RcppExports.cpp | 1 gRain-1.4.2/gRain/tests |only gRain-1.4.2/gRain/vignettes/figures/grain-bn1-1.png |only gRain-1.4.2/gRain/vignettes/figures/grain-bn2-1.png |only gRain-1.4.2/gRain/vignettes/figures/grain-chest-LS-1.png |only gRain-1.4.2/gRain/vignettes/figures/grain-unnamed-chunk-35-1.png |only gRain-1.4.2/gRain/vignettes/figures/grain-unnamed-chunk-36-1.png |only gRain-1.4.2/gRain/vignettes/figures/grain-unnamed-chunk-39-1.png |only gRain-1.4.2/gRain/vignettes/figures/grain-unnamed-chunk-4-1.png |only gRain-1.4.2/gRain/vignettes/figures/grain-unnamed-chunk-52-1.png |only gRain-1.4.2/gRain/vignettes/figures/grain-unnamed-chunk-53-1.png |only gRain-1.4.2/gRain/vignettes/figures/grain-unnamed-chunk-57-1.png |only gRain-1.4.2/gRain/vignettes/figures/grain-unnamed-chunk-58-1.png |only gRain-1.4.2/gRain/vignettes/grain.html |only gRain-1.4.2/gRain/vignettes/grain.rmd |only 96 files changed, 768 insertions(+), 923 deletions(-)
Title: Fast Nearest Neighbor Search Algorithms and Applications
Description: Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications
including KNN classification, regression and information measures are implemented.
Author: Alina Beygelzimer [aut] ,
Sham Kakadet [aut] ,
John Langford [aut] ,
Sunil Arya [aut] ,
David Mount [aut] ,
Shengqiao Li [aut, cre]
Maintainer: Shengqiao Li <lishengqiao@yahoo.com>
Diff between FNN versions 1.1.4 dated 2024-01-12 and 1.1.4.1 dated 2024-09-22
DESCRIPTION | 28 ++++++++++++++++++++++------ MD5 | 14 +++++++------- src/KNN_ANN.cpp | 24 ++++++++++++------------ src/KNN_correlation_distance.cpp | 4 ++-- src/KNN_cover_tree.cpp | 4 ++-- src/KNN_mutual_information.cpp | 4 ++-- src/include/ANN/ANN.h | 2 +- src/label_point.h | 2 +- 8 files changed, 49 insertions(+), 33 deletions(-)
Title: A Tidy Format Datasets of Dengue by Country
Description: Provides a weekly, monthly, yearly summary of dengue cases by state/ province/ country.
Author: Thiyanga S. Talagala [aut, cre]
Maintainer: Thiyanga S. Talagala <ttalagala@sjp.ac.lk>
Diff between denguedatahub versions 1.0.4 dated 2023-05-15 and 2.1.1 dated 2024-09-22
DESCRIPTION | 15 +- MD5 | 89 ++++++++++---- NAMESPACE | 18 ++ R/americas_annual_data.R | 26 ++-- R/cdc_casesby_week.R |only R/cdc_dengue_agesex.R |only R/cdc_dengue_casesbyjurisdiction.R |only R/cdc_dengue_countyyear.R |only R/cdc_local_dengue_cases.R |only R/cdc_travel_associated_dengue_cases.R |only R/cdc_usa_dengue_infection.R | 28 ++-- R/china_annual_data.R | 26 ++-- R/convert_slwer_to_tidy.R |only R/convert_srilanka_wer_to_tidy.R |only R/download_pdfwer_srilanka.R |only R/filter_year_wer_link.R |only R/get_addresses.R |only R/get_pdflinks_srilanka.R |only R/global.R | 6 R/india_annual_data.R | 26 ++-- R/korea_dengue.R |only R/level_of_risk.R | 23 +-- R/min_max.R | 94 +++++++------- R/philippines_daily_data.R | 26 ++-- R/singapore_weekly_data.R | 22 +-- R/sl_annual.R |only R/sl_dengue_serotype.R |only R/sl_sites.R |only R/srilanka_weekly_data.R | 28 ++-- R/taiwan_dengue.R |only R/world_annual.R | 30 ++-- README.md | 177 ++++++++++++++-------------- data/cdc_casesby_week.rda |only data/cdc_dengue_agesex.rda |only data/cdc_dengue_casesbyjurisdiction.rda |only data/cdc_dengue_countyyear.rda |only data/cdc_local_dengue_cases.rda |only data/cdc_travel_associated_dengue_cases.rda |only data/korea_dengue.rda |only data/level_of_risk.rda |binary data/philippines_daily_data.rda |binary data/sl_annual.rda |only data/sl_dengue_serotype.rda |only data/sl_sites.rda |only data/srilanka_weekly_data.rda |binary data/taiwan_dengue.rda |only data/world_annual.rda |binary man/cdc_casesby_week.Rd |only man/cdc_dengue_agesex.Rd |only man/cdc_dengue_casesbyjurisdiction.Rd |only man/cdc_dengue_countyyear.Rd |only man/cdc_local_dengue_cases.Rd |only man/cdc_travel_associated_dengue_cases.Rd |only man/china_annual_data.Rd | 2 man/convert_slwer_to_tidy.Rd |only man/convert_srilanka_wer_to_tidy.Rd |only man/download_pdfwer_srilanka.Rd |only man/filter_year_wer.Rd |only man/get_addresses.Rd |only man/get_pdflinks_srilanka.Rd |only man/korea_dengue.Rd |only man/level_of_risk.Rd | 7 - man/sl_annual.Rd |only man/sl_dengue_serotype.Rd |only man/sl_sites.Rd |only man/srilanka_weekly_data.Rd | 4 man/taiwan_dengue.Rd |only man/world_annual.Rd | 8 + 68 files changed, 373 insertions(+), 282 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-12 0.1.0
Title: A Tool for Downloading Functional Traits Data for Plant Species
Description: Plant ecologists often need to collect "traits" data
about plant species which are often scattered among various
databases: TR8 contains a set of tools which take care of
automatically retrieving some of those functional traits data
for plant species from publicly available databases (The Ecological Flora
of the British Isles, LEDA traitbase, Ellenberg
values for Italian Flora, Mycorrhizal intensity databases, BROT,
PLANTS, Jepson Flora Project).
The TR8 name, inspired by "car plates" jokes, was chosen since
it both reminds of the main object of the package and is
extremely short to type.
Author: Gionata Bocci [aut, cre]
Maintainer: Gionata Bocci <boccigionata@gmail.com>
Diff between TR8 versions 0.9.22 dated 2020-12-01 and 0.9.23 dated 2024-09-22
TR8-0.9.22/TR8/data/column_list.R |only TR8-0.9.22/TR8/data/imkerbond_data.R |only TR8-0.9.22/TR8/data/leda_lookup.R |only TR8-0.9.22/TR8/data/traits_Biolflor.R |only TR8-0.9.22/TR8/data/traits_eco.R |only TR8-0.9.23/TR8/DESCRIPTION | 20 TR8-0.9.23/TR8/MD5 | 61 +- TR8-0.9.23/TR8/NAMESPACE | 2 TR8-0.9.23/TR8/R/PLANTS_download.R | 7 TR8-0.9.23/TR8/R/Pignatti.R | 21 TR8-0.9.23/TR8/R/catminat.R | 12 TR8-0.9.23/TR8/R/generate_biolflor_lu.R | 104 ++-- TR8-0.9.23/TR8/R/leda_download.R | 5 TR8-0.9.23/TR8/R/local_storage.R | 20 TR8-0.9.23/TR8/R/myco.R | 8 TR8-0.9.23/TR8/R/tr8.R | 466 ++++++++++--------- TR8-0.9.23/TR8/R/tr8_gui.R | 13 TR8-0.9.23/TR8/R/tr8_setup.R | 2 TR8-0.9.23/TR8/build/vignette.rds |binary TR8-0.9.23/TR8/data/column_list.rda |only TR8-0.9.23/TR8/data/imkerbond_data.rda |only TR8-0.9.23/TR8/data/leda_lookup.rda |only TR8-0.9.23/TR8/data/traits_Biolflor.rda |only TR8-0.9.23/TR8/data/traits_eco.rda |only TR8-0.9.23/TR8/inst/CITATION | 21 TR8-0.9.23/TR8/inst/doc/Expanding_TR8.pdf |binary TR8-0.9.23/TR8/inst/doc/TR8.R | 23 TR8-0.9.23/TR8/inst/doc/TR8.Rnw | 291 ++++++------ TR8-0.9.23/TR8/inst/doc/TR8.pdf |binary TR8-0.9.23/TR8/inst/doc/TR8_workflow.R | 21 TR8-0.9.23/TR8/inst/doc/TR8_workflow.Rnw | 490 ++++++++++----------- TR8-0.9.23/TR8/inst/doc/TR8_workflow.pdf |binary TR8-0.9.23/TR8/inst/shiny_interface/myApp/server.R | 8 TR8-0.9.23/TR8/inst/shiny_interface/myApp/ui.R | 38 - TR8-0.9.23/TR8/vignettes/TR8.Rnw | 291 ++++++------ TR8-0.9.23/TR8/vignettes/TR8_workflow.Rnw | 490 ++++++++++----------- TR8-0.9.23/TR8/vignettes/_region_.tex |only 37 files changed, 1228 insertions(+), 1186 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 3.1-1 dated 2024-07-15 and 3.2-1 dated 2024-09-22
DESCRIPTION | 16 ++--- MD5 | 48 ++++++++--------- NAMESPACE | 3 + NEWS | 19 ++++++ R/changes.R |only inst/doc/bugfixes.pdf |binary inst/doc/datasets.pdf |binary inst/doc/fv.R | 114 +++++++++++++++++++++-------------------- inst/doc/fv.Rnw | 42 +++++---------- inst/doc/fv.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 1 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/spatstatKnetsize.txt | 5 + inst/doc/spatstatguisize.txt | 5 - inst/doc/spatstatlocalsize.txt | 4 - inst/doc/updates.Rnw | 56 +++++++++++++++++--- inst/doc/updates.pdf |binary inst/info/packagesizes.txt | 1 man/bugfixes.Rd | 2 man/latest.changes.Rd |only man/spatstat-internal.Rd | 2 man/spatstat-package.Rd | 11 +++ vignettes/fv.Rnw | 42 +++++---------- vignettes/updates.Rnw | 56 +++++++++++++++++--- 26 files changed, 270 insertions(+), 157 deletions(-)
Title: Univariate GARCH Models
Description: ARFIMA, in-mean, external regressors and various GARCH flavors, with methods for fit, forecast, simulation, inference and plotting.
Author: Alexios Galanos [aut, cre],
Tobias Kley [ctb]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between rugarch versions 1.5-2 dated 2024-08-19 and 1.5-3 dated 2024-09-22
rugarch-1.5-2/rugarch/src/fracimport.f |only rugarch-1.5-3/rugarch/ChangeLog | 6 + rugarch-1.5-3/rugarch/DESCRIPTION | 10 +- rugarch-1.5-3/rugarch/MD5 | 13 +-- rugarch-1.5-3/rugarch/NAMESPACE | 1 rugarch-1.5-3/rugarch/R/rugarch-cwrappers.R | 35 +++------- rugarch-1.5-3/rugarch/inst/doc/Introduction_to_the_rugarch_package.pdf |binary rugarch-1.5-3/rugarch/src/rugarch.c | 8 -- 8 files changed, 30 insertions(+), 43 deletions(-)
Title: Generalized Linear Mixed Models via Monte Carlo Likelihood
Approximation
Description: Approximates the likelihood of a generalized linear mixed model using Monte Carlo likelihood approximation. Then maximizes the likelihood approximation to return maximum likelihood estimates, observed Fisher information, and other model information.
Author: Christina Knudson [aut, cre],
Charles J. Geyer [ctb],
Sydney Benson [ctb]
Maintainer: Christina Knudson <drchristinaknudson@gmail.com>
Diff between glmm versions 1.4.4 dated 2022-10-09 and 1.4.5 dated 2024-09-22
DESCRIPTION | 10 +++---- MD5 | 26 +++++++++---------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/vignettes.pdf |binary src/distRand.c | 10 +++---- src/distRand3c.c | 8 ++--- src/elGH.c | 28 ++++++++++---------- src/elc.c | 32 +++++++++++------------ src/elval.c | 8 ++--- src/hess.c | 66 ++++++++++++++++++++++++------------------------- src/mcse.c | 52 +++++++++++++++++++------------------- src/t.c | 4 +- src/valgrad.c | 44 ++++++++++++++++---------------- 14 files changed, 144 insertions(+), 144 deletions(-)