Title: The R Interface to 'SyncroSim'
Description: 'SyncroSim' is a generalized framework for managing scenario-based
datasets (<https://syncrosim.com/>). 'rsyncrosim' provides an interface to
'SyncroSim'. Simulation models can be added to 'SyncroSim' in order to
transform these datasets, taking advantage of general features such as
defining scenarios of model inputs, running Monte Carlo simulations, and
summarizing model outputs. 'rsyncrosim' requires 'SyncroSim' 2.3.5 or higher
(API documentation: <https://docs.syncrosim.com/>).
Author: Colin Daniel [aut],
Josie Hughes [aut],
Valentin Lucet [aut],
Alex Embrey [aut],
Katie Birchard [aut, cre],
Leonardo Frid [aut],
Tabitha Kennedy [aut],
Shreeram Senthivasan [aut],
ApexRMS [cph]
Maintainer: Katie Birchard <katie.birchard@apexrms.com>
Diff between rsyncrosim versions 1.5.0 dated 2024-02-01 and 2.0.1 dated 2024-10-14
rsyncrosim-1.5.0/rsyncrosim/R/addon.R |only rsyncrosim-1.5.0/rsyncrosim/R/autogentags.R |only rsyncrosim-1.5.0/rsyncrosim/R/breakpoint.R |only rsyncrosim-1.5.0/rsyncrosim/R/datasheetRaster.R |only rsyncrosim-1.5.0/rsyncrosim/R/deprecated.R |only rsyncrosim-1.5.0/rsyncrosim/R/disableAddon.R |only rsyncrosim-1.5.0/rsyncrosim/R/enableAddon.R |only rsyncrosim-1.5.0/rsyncrosim/R/package.R |only rsyncrosim-1.5.0/rsyncrosim/R/ssimUpdate.R |only rsyncrosim-1.5.0/rsyncrosim/R/updatePackage.R |only rsyncrosim-1.5.0/rsyncrosim/man/addBreakpoint.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/addModule.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/addPackageFile.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/addon.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/autogentags.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/basePackage.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/breakpoint.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/datasheetRaster.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/deleteBreakpoint.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/deleteModule.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/deletePackage.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/disableAddon.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/enableAddon.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/envBeginSimulation.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/envEndSimulation.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/envInputFolder.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/envOutputFolder.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/envReportProgress.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/envStepSimulation.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/envTempFolder.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/model.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/module.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/package.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/runtimeInputFolder.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/runtimeOutputFolder.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/ssimUpdate.Rd |only rsyncrosim-1.5.0/rsyncrosim/man/updatePackage.Rd |only rsyncrosim-2.0.1/rsyncrosim/DESCRIPTION | 46 rsyncrosim-2.0.1/rsyncrosim/MD5 | 227 ++-- rsyncrosim-2.0.1/rsyncrosim/NAMESPACE | 48 rsyncrosim-2.0.1/rsyncrosim/NEWS.md | 26 rsyncrosim-2.0.1/rsyncrosim/R/AAAClassDefinitions.R | 49 rsyncrosim-2.0.1/rsyncrosim/R/addPackage.R | 189 ++- rsyncrosim-2.0.1/rsyncrosim/R/backup.R | 12 rsyncrosim-2.0.1/rsyncrosim/R/chart.R |only rsyncrosim-2.0.1/rsyncrosim/R/chartCriteria.R |only rsyncrosim-2.0.1/rsyncrosim/R/chartData.R |only rsyncrosim-2.0.1/rsyncrosim/R/chartDisagg.R |only rsyncrosim-2.0.1/rsyncrosim/R/chartErrorBar.R |only rsyncrosim-2.0.1/rsyncrosim/R/chartId.R |only rsyncrosim-2.0.1/rsyncrosim/R/chartInclude.R |only rsyncrosim-2.0.1/rsyncrosim/R/chartOptionsFont.R |only rsyncrosim-2.0.1/rsyncrosim/R/chartOptionsFormat.R |only rsyncrosim-2.0.1/rsyncrosim/R/chartOptionsLegend.R |only rsyncrosim-2.0.1/rsyncrosim/R/chartOptionsXAxis.R |only rsyncrosim-2.0.1/rsyncrosim/R/chartOptionsYAxis.R |only rsyncrosim-2.0.1/rsyncrosim/R/command.R | 11 rsyncrosim-2.0.1/rsyncrosim/R/createCondaEnv.R |only rsyncrosim-2.0.1/rsyncrosim/R/datasheet.R | 243 ++-- rsyncrosim-2.0.1/rsyncrosim/R/datasheetSpatRaster.R | 120 +- rsyncrosim-2.0.1/rsyncrosim/R/dateModified.R | 18 rsyncrosim-2.0.1/rsyncrosim/R/delete.R | 268 ++-- rsyncrosim-2.0.1/rsyncrosim/R/deleteLibrary.R |only rsyncrosim-2.0.1/rsyncrosim/R/dependency.R | 226 +--- rsyncrosim-2.0.1/rsyncrosim/R/description.R | 46 rsyncrosim-2.0.1/rsyncrosim/R/folder.R | 88 + rsyncrosim-2.0.1/rsyncrosim/R/folderId.R | 11 rsyncrosim-2.0.1/rsyncrosim/R/info.R | 7 rsyncrosim-2.0.1/rsyncrosim/R/installPackage.R |only rsyncrosim-2.0.1/rsyncrosim/R/internalHelpers.R | 558 +++++++--- rsyncrosim-2.0.1/rsyncrosim/R/internalWrappers.R | 12 rsyncrosim-2.0.1/rsyncrosim/R/name.R | 34 rsyncrosim-2.0.1/rsyncrosim/R/owner.R | 37 rsyncrosim-2.0.1/rsyncrosim/R/packages.R |only rsyncrosim-2.0.1/rsyncrosim/R/parentId.R | 12 rsyncrosim-2.0.1/rsyncrosim/R/print.R | 14 rsyncrosim-2.0.1/rsyncrosim/R/project.R | 64 - rsyncrosim-2.0.1/rsyncrosim/R/projectId.R | 12 rsyncrosim-2.0.1/rsyncrosim/R/readOnly.R | 39 rsyncrosim-2.0.1/rsyncrosim/R/removePackage.R | 111 + rsyncrosim-2.0.1/rsyncrosim/R/rsyncrosim.R | 3 rsyncrosim-2.0.1/rsyncrosim/R/run.R | 291 +---- rsyncrosim-2.0.1/rsyncrosim/R/runLog.R | 12 rsyncrosim-2.0.1/rsyncrosim/R/saveDatasheet.R | 132 +- rsyncrosim-2.0.1/rsyncrosim/R/scenario.R | 43 rsyncrosim-2.0.1/rsyncrosim/R/session.R | 9 rsyncrosim-2.0.1/rsyncrosim/R/sqlStatement.R | 23 rsyncrosim-2.0.1/rsyncrosim/R/ssimEnvironment.R | 50 rsyncrosim-2.0.1/rsyncrosim/R/ssimLibrary.R | 246 +--- rsyncrosim-2.0.1/rsyncrosim/R/uninstallPackage.R |only rsyncrosim-2.0.1/rsyncrosim/R/useConda.R | 20 rsyncrosim-2.0.1/rsyncrosim/README.md | 4 rsyncrosim-2.0.1/rsyncrosim/man/Chart-class.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/Scenario-class.Rd | 2 rsyncrosim-2.0.1/rsyncrosim/man/addPackage.Rd | 68 - rsyncrosim-2.0.1/rsyncrosim/man/backup.Rd | 82 - rsyncrosim-2.0.1/rsyncrosim/man/chart.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/chartCriteria.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/chartData.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/chartDisagg.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/chartErrorBar.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/chartId.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/chartInclude.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/chartOptionsFont.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/chartOptionsFormat.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/chartOptionsLegend.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/chartOptionsXAxis.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/chartOptionsYAxis.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/command.Rd | 8 rsyncrosim-2.0.1/rsyncrosim/man/createCondaEnv.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/datasheet.Rd | 77 - rsyncrosim-2.0.1/rsyncrosim/man/datasheetSpatRaster.Rd | 25 rsyncrosim-2.0.1/rsyncrosim/man/dateModified.Rd | 95 - rsyncrosim-2.0.1/rsyncrosim/man/delete.Rd | 190 +-- rsyncrosim-2.0.1/rsyncrosim/man/deleteLibrary.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/dependency.Rd | 44 rsyncrosim-2.0.1/rsyncrosim/man/description.Rd | 114 -- rsyncrosim-2.0.1/rsyncrosim/man/filepath.Rd | 92 - rsyncrosim-2.0.1/rsyncrosim/man/folder.Rd | 121 +- rsyncrosim-2.0.1/rsyncrosim/man/folderId.Rd | 124 +- rsyncrosim-2.0.1/rsyncrosim/man/ignoreDependencies.Rd | 108 - rsyncrosim-2.0.1/rsyncrosim/man/info.Rd | 5 rsyncrosim-2.0.1/rsyncrosim/man/installPackage.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/mergeDependencies.Rd | 112 +- rsyncrosim-2.0.1/rsyncrosim/man/name.Rd | 164 +- rsyncrosim-2.0.1/rsyncrosim/man/owner.Rd | 132 +- rsyncrosim-2.0.1/rsyncrosim/man/packages.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/parentId.Rd | 12 rsyncrosim-2.0.1/rsyncrosim/man/printCmd.Rd | 74 - rsyncrosim-2.0.1/rsyncrosim/man/project.Rd | 178 +-- rsyncrosim-2.0.1/rsyncrosim/man/projectId.Rd | 99 - rsyncrosim-2.0.1/rsyncrosim/man/readOnly.Rd | 154 +- rsyncrosim-2.0.1/rsyncrosim/man/removePackage.Rd | 52 rsyncrosim-2.0.1/rsyncrosim/man/rsyncrosim.Rd | 66 - rsyncrosim-2.0.1/rsyncrosim/man/run.Rd | 52 rsyncrosim-2.0.1/rsyncrosim/man/runLog.Rd | 12 rsyncrosim-2.0.1/rsyncrosim/man/runtimeDataFolder.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/saveDatasheet.Rd | 39 rsyncrosim-2.0.1/rsyncrosim/man/scenario.Rd | 212 +-- rsyncrosim-2.0.1/rsyncrosim/man/scenarioId.Rd | 78 - rsyncrosim-2.0.1/rsyncrosim/man/session.Rd | 5 rsyncrosim-2.0.1/rsyncrosim/man/silent.Rd | 100 - rsyncrosim-2.0.1/rsyncrosim/man/sqlStatement.Rd | 23 rsyncrosim-2.0.1/rsyncrosim/man/ssimLibrary.Rd | 40 rsyncrosim-2.0.1/rsyncrosim/man/tempfilepath.Rd | 86 - rsyncrosim-2.0.1/rsyncrosim/man/uninstallPackage.Rd |only rsyncrosim-2.0.1/rsyncrosim/man/updateRunLog.Rd | 68 - rsyncrosim-2.0.1/rsyncrosim/man/useConda.Rd | 118 +- rsyncrosim-2.0.1/rsyncrosim/man/version.Rd | 72 - rsyncrosim-2.0.1/rsyncrosim/tests/testthat/test-integration.R | 4 rsyncrosim-2.0.1/rsyncrosim/tests/testthat/test-unit.R | 34 151 files changed, 3428 insertions(+), 3074 deletions(-)
Title: Panomics Marketplace - Quality Control and Statistical Analysis
for Panomics Data
Description: Provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups. Implements methods described in: Webb-Robertson et al. (2014) <doi:10.1074/mcp.M113.030932>. Webb-Robertson et al. (2011) <doi:10.1002/pmic.201100078>. Matzke et al. (2011) <doi:10.1093/bioinformatics/btr479>. Matzke et al. (2013) <doi:10.1002/pmic.201200269>. Polpitiya et al. (2008) <doi:10.1093/bioinformatics/btn217>. Webb-Robertson et al. (2010) <doi:10.1021/pr1005247>.
Author: Lisa Bramer [aut, cre],
Kelly Stratton [aut],
Daniel Claborne [aut],
Evan Glasscock [ctb],
Rachel Richardson [ctb],
David Degnan [ctb],
Evan Martin [ctb]
Maintainer: Lisa Bramer <lisa.bramer@pnnl.gov>
Diff between pmartR versions 2.4.5 dated 2024-05-21 and 2.4.6 dated 2024-10-14
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/applyFilt.R | 18 ++++++------------ R/filter_objects.R | 2 +- R/group_designation.R | 5 +++++ R/protein_quant.R | 6 ++++++ R/seqData_wrappers.R | 11 +++++++++-- README.md | 20 +++++++++++++++++--- src/imd_anova.cpp | 4 ++++ src/kw_rcpp.cpp | 7 ++++++- tests/testthat/test_quant_protein.R | 8 ++++++++ 11 files changed, 76 insertions(+), 33 deletions(-)
Title: 'date' C++ Header Library for Date and Time Functionality
Description: A header-only C++ library is provided with support
for dates, time zones, ISO weeks, Julian dates, and Islamic dates.
'date' offers extensive date and time functionality for the C++11,
C++14 and C++17 standards and was written by Howard Hinnant and released
under the MIT license. A slightly modified version has been accepted
(along with 'tz.h') as part of C++20. This package regroups all
header files from the upstream repository by Howard Hinnant so that
other R packages can use them in their C++ code. At present, few of
the types have explicit 'Rcpp' wrappers though these may be added as
needed.
Author: Dirk Eddelbuettel [aut, cre] ,
Howard Hinnant [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppDate versions 0.0.3 dated 2021-05-19 and 0.0.4 dated 2024-10-14
ChangeLog | 59 ++++++++++++++++++++ DESCRIPTION | 16 +++-- MD5 | 28 ++++----- NAMESPACE | 2 README.md | 7 +- build/partial.rdb |binary inst/NEWS.Rd | 7 ++ inst/include/date.h | 131 ++++++++++++++++++++++++++++++--------------- inst/include/ios.h | 4 - inst/include/iso_week.h | 18 ++++-- inst/include/julian.h | 16 ++--- inst/include/ptz.h | 107 +++++++++++++++++++++++++++++++++--- inst/include/solar_hijri.h | 20 +++--- inst/include/tz.h | 26 +++++++- inst/include/tz_private.h | 3 - 15 files changed, 336 insertions(+), 108 deletions(-)
Title: Efficient Univariate Maximum Mean Discrepancy
Description: Computes maximum mean discrepancy two-sample test for univariate data using the Laplacian kernel, as described in Bodenham and Kawahara (2023) <doi:10.1007/s11222-023-10271-x>. The p-value is computed using permutations. Also includes implementation for computing the robust median difference statistic 'Q_n' from Croux and Rousseeuw (1992) <doi:10.1007/978-3-662-26811-7_58> based on Johnson and Mizoguchi (1978) <doi:10.1137/0207013>.
Author: Dean Bodenham [aut, cre]
Maintainer: Dean Bodenham <deanbodenhampkgs@gmail.com>
Diff between eummd versions 0.1.9 dated 2024-05-21 and 0.2.0 dated 2024-10-14
DESCRIPTION | 10 +- MD5 | 19 ++-- NEWS.md | 5 + R/RcppExports.R | 4 R/meammd.R | 14 ++- man/meammd.Rd | 6 + src/RcppExports.cpp | 9 +- src/interfaceRcpp.cpp | 36 +++++--- src/meammd.cpp | 179 ++++++++++++++++++++++++++++++++++++++++-- src/meammd.h | 9 ++ tests/testthat/test6_meammd.R |only 11 files changed, 252 insertions(+), 39 deletions(-)
Title: Bayesian Hierarchical Analysis of Cognitive Models of Choice
Description: Fit Bayesian (hierarchical) cognitive models
using a linear modeling language interface using particle metropolis Markov
chain Monte Carlo sampling with Gibbs steps. The diffusion decision model (DDM),
linear ballistic accumulator model (LBA), racing diffusion model (RDM), and the lognormal
race model (LNR) are supported. Additionally, users can specify their own likelihood
function and/or choose for non-hierarchical
estimation, as well as for a diagonal, blocked or full multivariate normal
group-level distribution to test individual differences. Prior specification
is facilitated through methods that visualize the (implied) prior.
A wide range of plotting functions assist in assessing model convergence and
posterior inference. Models can be easily evaluated using functions
that plot posterior predictions or using relative model comparison metrics
such as information criteria or Bayes factors.
References: Stevenson et al. (2024) <doi:10.31234/osf.io/2e4dq>.
Author: Niek Stevenson [aut, cre] ,
Michelle Donzallaz [aut],
Andrew Heathcote [aut],
Steven Miletic [ctb],
Raphael Hartmann [ctb],
Karl C. Klauer [ctb],
Steven G. Johnson [ctb],
Jean M. Linhart [ctb],
Brian Gough [ctb],
Gerard Jungman [ctb],
Rudolf Schuerer [...truncated...]
Maintainer: Niek Stevenson <niek.stevenson@gmail.com>
Diff between EMC2 versions 2.0.2 dated 2024-09-10 and 2.1.0 dated 2024-10-14
EMC2-2.0.2/EMC2/man/DDMt0natural.Rd |only EMC2-2.0.2/EMC2/man/IC.Rd |only EMC2-2.0.2/EMC2/man/add_constants.Rd |only EMC2-2.0.2/EMC2/man/auto_burn.Rd |only EMC2-2.0.2/EMC2/man/compare_MLL.Rd |only EMC2-2.0.2/EMC2/man/get_prior_SEM.Rd |only EMC2-2.0.2/EMC2/man/get_prior_blocked.Rd |only EMC2-2.0.2/EMC2/man/get_prior_diag.Rd |only EMC2-2.0.2/EMC2/man/get_prior_factor.Rd |only EMC2-2.0.2/EMC2/man/get_prior_single.Rd |only EMC2-2.0.2/EMC2/man/get_prior_standard.Rd |only EMC2-2.0.2/EMC2/man/make_factor_diagram.Rd |only EMC2-2.0.2/EMC2/man/make_missing.Rd |only EMC2-2.0.2/EMC2/man/plot_fit_choice.Rd |only EMC2-2.0.2/EMC2/man/plot_mcmc.Rd |only EMC2-2.0.2/EMC2/man/plot_mcmc_list.Rd |only EMC2-2.0.2/EMC2/man/probit.Rd |only EMC2-2.0.2/EMC2/man/run_IS2.Rd |only EMC2-2.0.2/EMC2/man/run_adapt.Rd |only EMC2-2.0.2/EMC2/man/run_sample.Rd |only EMC2-2.0.2/EMC2/man/standardize_loadings.Rd |only EMC2-2.0.2/EMC2/src/Parameters_DDM.h |only EMC2-2.0.2/EMC2/tests/testthat/_snaps/Darwin |only EMC2-2.1.0/EMC2/DESCRIPTION | 51 - EMC2-2.1.0/EMC2/MD5 | 124 +-- EMC2-2.1.0/EMC2/NAMESPACE | 19 EMC2-2.1.0/EMC2/NEWS.md |only EMC2-2.1.0/EMC2/R/EMC2-package.R | 10 EMC2-2.1.0/EMC2/R/RcppExports.R | 4 EMC2-2.1.0/EMC2/R/SBC.R |only EMC2-2.1.0/EMC2/R/design.R | 6 EMC2-2.1.0/EMC2/R/factor_analysis.R | 68 -- EMC2-2.1.0/EMC2/R/fitting.R | 130 --- EMC2-2.1.0/EMC2/R/get_type_objects.R | 146 ++-- EMC2-2.1.0/EMC2/R/make_data.R | 19 EMC2-2.1.0/EMC2/R/map.R | 7 EMC2-2.1.0/EMC2/R/model_DDM.R | 124 +-- EMC2-2.1.0/EMC2/R/model_SDT.R | 18 EMC2-2.1.0/EMC2/R/plotting.R | 124 +-- EMC2-2.1.0/EMC2/R/priors.R | 344 ++++++---- EMC2-2.1.0/EMC2/R/sampling.R | 99 +- EMC2-2.1.0/EMC2/R/statistics.R | 115 ++- EMC2-2.1.0/EMC2/R/variant_SEM.R | 35 - EMC2-2.1.0/EMC2/R/variant_blocked.R | 95 +- EMC2-2.1.0/EMC2/R/variant_diag.R | 86 -- EMC2-2.1.0/EMC2/R/variant_diag_gamma.R |only EMC2-2.1.0/EMC2/R/variant_factor.R | 44 - EMC2-2.1.0/EMC2/R/variant_infnt_factor.R | 5 EMC2-2.1.0/EMC2/R/variant_single.R | 38 - EMC2-2.1.0/EMC2/R/variant_standard.R | 91 -- EMC2-2.1.0/EMC2/README.md | 11 EMC2-2.1.0/EMC2/build/vignette.rds |only EMC2-2.1.0/EMC2/inst |only EMC2-2.1.0/EMC2/man/DDM.Rd | 1 EMC2-2.1.0/EMC2/man/EMC2-package.Rd | 20 EMC2-2.1.0/EMC2/man/plot_sbc_ecdf.Rd |only EMC2-2.1.0/EMC2/man/plot_sbc_hist.Rd |only EMC2-2.1.0/EMC2/man/prior.Rd | 11 EMC2-2.1.0/EMC2/man/run_sbc.Rd |only EMC2-2.1.0/EMC2/src/Makevars |only EMC2-2.1.0/EMC2/src/Makevars.win |only EMC2-2.1.0/EMC2/src/RcppExports.cpp | 17 EMC2-2.1.0/EMC2/src/fncs_seven.cpp |only EMC2-2.1.0/EMC2/src/fncs_seven.h |only EMC2-2.1.0/EMC2/src/gauss.h |only EMC2-2.1.0/EMC2/src/hcubature.cpp |only EMC2-2.1.0/EMC2/src/log_likelihood_race.cpp | 16 EMC2-2.1.0/EMC2/src/model_DDM.h | 399 +----------- EMC2-2.1.0/EMC2/src/model_fMRI.h | 84 +- EMC2-2.1.0/EMC2/src/pdf_fncs.cpp |only EMC2-2.1.0/EMC2/src/pdf_fncs.h |only EMC2-2.1.0/EMC2/src/tools.cpp |only EMC2-2.1.0/EMC2/src/tools.h |only EMC2-2.1.0/EMC2/tests/testthat/_snaps/Linux/variant_funs.md | 35 - EMC2-2.1.0/EMC2/tests/testthat/_snaps/compare.md | 4 EMC2-2.1.0/EMC2/tests/testthat/_snaps/model_functions.md | 244 +++---- EMC2-2.1.0/EMC2/tests/testthat/test-model_functions.R | 2 EMC2-2.1.0/EMC2/tests/testthat/test-variant_funs.R | 5 EMC2-2.1.0/EMC2/vignettes |only 79 files changed, 1111 insertions(+), 1540 deletions(-)
Title: Hyperparameter Optimization for 'mlr3'
Description: Hyperparameter optimization package of the 'mlr3' ecosystem.
It features highly configurable search spaces via the 'paradox'
package and finds optimal hyperparameter configurations for any 'mlr3'
learner. 'mlr3tuning' works with several optimization algorithms e.g.
Random Search, Iterated Racing, Bayesian Optimization (in 'mlr3mbo')
and Hyperband (in 'mlr3hyperband'). Moreover, it can automatically
optimize learners and estimate the performance of optimized models
with nested resampling.
Author: Marc Becker [cre, aut] ,
Michel Lang [aut] ,
Jakob Richter [aut] ,
Bernd Bischl [aut] ,
Daniel Schalk [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 1.0.1 dated 2024-09-10 and 1.0.2 dated 2024-10-14
DESCRIPTION | 6 ++--- MD5 | 36 ++++++++++++++++----------------- NEWS.md | 4 +++ R/TuningInstanceAsyncMulticrit.R | 11 +++++++--- R/TuningInstanceAsyncSingleCrit.R | 11 +++++++--- R/TuningInstanceBatchMulticrit.R | 11 +++++++--- R/TuningInstanceBatchSingleCrit.R | 12 ++++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/extending.html | 14 ++++++------ man/ContextAsyncTuning.Rd | 2 - man/TuningInstanceAsyncMultiCrit.Rd | 6 ++--- man/TuningInstanceAsyncSingleCrit.Rd | 6 ++--- man/TuningInstanceBatchMultiCrit.Rd | 11 +++++++--- man/TuningInstanceBatchSingleCrit.Rd | 6 ++--- tests/testthat/test_Tuner.R | 4 +++ tests/testthat/test_TunerBatchCmaes.R | 3 +- tests/testthat/test_TunerBatchNLoptr.R | 2 + tests/testthat/test_mlr_tuners.R | 4 +++ 19 files changed, 95 insertions(+), 54 deletions(-)
Title: Provide Tools to Register Models for Use in 'tidymodels'
Description: An developer focused, low dependency package in 'tidymodels' that
provides functions to register how models are to be used. Functions to
register models are complimented with accessor functions to retrieve
registered model information to aid in model fitting and error handling.
Author: Emil Hvitfeldt [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between modelenv versions 0.1.1 dated 2023-03-08 and 0.2.0 dated 2024-10-14
DESCRIPTION | 10 +- MD5 | 50 +++++----- NAMESPACE | 1 NEWS.md | 4 R/check.R | 108 ++++++++++++++------- R/env-get.R | 9 - R/env.R | 2 R/import-standalone-obj-type.R |only R/import-standalone-types-check.R |only R/modelenv-package.R | 1 R/set_dependency.R | 19 +-- R/set_encoding.R | 57 ++++++----- R/set_fit.R | 88 +++++++++-------- R/set_model_arg.R | 16 +-- R/set_model_engine.R | 17 +-- R/set_new_model.R | 6 - R/set_pred.R | 41 +++++--- man/check_spec_mode_engine_val.Rd | 7 + tests/testthat/_snaps/check.md | 78 ++++++++++----- tests/testthat/_snaps/set_dependency.md | 65 +++++++------ tests/testthat/_snaps/set_encoding.md | 90 +++++++++++------- tests/testthat/_snaps/set_fit.md | 148 ++++++++++++++++++------------ tests/testthat/_snaps/set_model_arg.md | 85 ++++++++++------- tests/testthat/_snaps/set_model_engine.md | 50 ++++++---- tests/testthat/_snaps/set_model_mode.md | 25 +++-- tests/testthat/_snaps/set_new_model.md | 25 +++-- tests/testthat/_snaps/set_pred.md | 100 ++++++++++++-------- 27 files changed, 659 insertions(+), 443 deletions(-)
Title: Automatic Codebooks from Metadata Encoded in Dataset Attributes
Description: Easily automate the following tasks to describe data frames:
Summarise the distributions, and labelled missings of variables graphically
and using descriptive statistics.
For surveys, compute and summarise reliabilities (internal consistencies,
retest, multilevel) for psychological scales.
Combine this information with metadata (such as item labels and labelled
values) that is derived from R attributes.
To do so, the package relies on 'rmarkdown' partials, so you can generate
HTML, PDF, and Word documents.
Codebooks are also available as tables (CSV, Excel, etc.) and in JSON-LD, so
that search engines can find your data and index the metadata.
The metadata are also available at your fingertips via RStudio Addins.
Author: Ruben Arslan [aut, cre]
Maintainer: Ruben Arslan <ruben.arslan@gmail.com>
Diff between codebook versions 0.9.2 dated 2020-06-06 and 0.9.5 dated 2024-10-14
DESCRIPTION | 21 MD5 | 87 - NAMESPACE | 4 NEWS.md | 16 R/codebook.R | 894 +++++++------ R/codebook_table.R | 509 ++++--- R/correct_attributes.R | 4 R/detect_missing.R | 341 +++-- R/detect_scales.R | 102 - R/label_browser.R | 540 ++++---- R/metadata.R | 912 +++++++------- R/misc.R | 460 +++---- R/psych_print.R | 88 - R/reliability.R | 382 +++-- R/rmarkdown_helpers.R | 229 +-- README.md | 39 build/vignette.rds |binary inst/CITATION | 26 inst/_codebook.Rmd | 96 - inst/_codebook_data_info.Rmd | 192 +- inst/_codebook_scale.Rmd | 7 inst/_knit_print_psych.Rmd |only inst/_metadata_jsonld.Rmd | 9 inst/doc/codebook.R | 617 +-------- inst/doc/codebook.Rmd | 190 +- inst/doc/codebook.html | 1405 +++++++++++---------- inst/doc/codebook_qualtrics.R | 28 inst/doc/codebook_qualtrics.html | 450 ++++-- inst/doc/codebook_sav.R | 30 inst/doc/codebook_sav.Rmd | 262 ++-- inst/doc/codebook_sav.html | 503 +++++-- inst/doc/codebook_tutorial.R | 614 +-------- inst/doc/codebook_tutorial.Rmd | 580 ++++----- inst/doc/codebook_tutorial.html | 2511 ++++++++++++++++++++++++--------------- man/codebook.Rd | 2 man/codebook_browser.Rd | 2 man/compute_reliabilities.Rd | 6 man/detect_missing.Rd | 16 man/detect_scales.Rd | 8 man/knit_print.alpha.Rd |only man/plot_labelled.Rd | 2 man/pull_reliability.Rd |only man/reexports.Rd | 4 vignettes/codebook.Rmd | 190 +- vignettes/codebook_sav.Rmd | 262 ++-- vignettes/codebook_tutorial.Rmd | 580 ++++----- 46 files changed, 6764 insertions(+), 6456 deletions(-)
Title: Estimate Brain Networks and Connectivity with ICA and Empirical
Priors
Description: Implements the template ICA (independent components analysis) model
proposed in Mejia et al. (2020) <doi:10.1080/01621459.2019.1679638> and the
spatial template ICA model proposed in proposed in Mejia et al. (2022)
<doi:10.1080/10618600.2022.2104289>. Both models estimate subject-level
brain as deviations from known population-level networks, which are
estimated using standard ICA algorithms. Both models employ an
expectation-maximization algorithm for estimation of the latent brain
networks and unknown model parameters. Includes direct support for 'CIFTI',
'GIFTI', and 'NIFTI' neuroimaging file formats.
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] ,
Daniel Spencer [ctb] ,
Mary Beth Nebel [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between templateICAr versions 0.6.4 dated 2024-01-17 and 0.8.8 dated 2024-10-14
templateICAr-0.6.4/templateICAr/R/dim_reduce_PCA.R |only templateICAr-0.6.4/templateICAr/R/dual_reg.R |only templateICAr-0.6.4/templateICAr/R/templateICAr.R |only templateICAr-0.6.4/templateICAr/man/PCA.Rd |only templateICAr-0.6.4/templateICAr/man/center_Bcols_Param.Rd |only templateICAr-0.6.4/templateICAr/man/detrend_DCT_Param.Rd |only templateICAr-0.6.4/templateICAr/man/dual_reg.Rd |only templateICAr-0.6.4/templateICAr/man/normA_Param.Rd |only templateICAr-0.8.8/templateICAr/DESCRIPTION | 18 templateICAr-0.8.8/templateICAr/MD5 | 128 - templateICAr-0.8.8/templateICAr/NAMESPACE | 25 templateICAr-0.8.8/templateICAr/NEWS.md | 19 templateICAr-0.8.8/templateICAr/R/EM_FCtemplateICA.R | 653 ++++-- templateICAr-0.8.8/templateICAr/R/EM_templateICA.R | 648 +++++- templateICAr-0.8.8/templateICAr/R/INLA_check.R | 11 templateICAr-0.8.8/templateICAr/R/VB_FCtemplateICA.R |only templateICAr-0.8.8/templateICAr/R/activations.R | 283 +- templateICAr-0.8.8/templateICAr/R/activations.methods.R | 201 +- templateICAr-0.8.8/templateICAr/R/activations_utils.R |only templateICAr-0.8.8/templateICAr/R/check_parallel_packages.R |only templateICAr-0.8.8/templateICAr/R/dim_reduce.R |only templateICAr-0.8.8/templateICAr/R/dual_reg2.R |only templateICAr-0.8.8/templateICAr/R/estimate_template.R | 847 ++++++-- templateICAr-0.8.8/templateICAr/R/estimate_template.methods.R | 181 + templateICAr-0.8.8/templateICAr/R/estimate_template.utils.R | 82 templateICAr-0.8.8/templateICAr/R/export_template.R | 116 - templateICAr-0.8.8/templateICAr/R/groupICA.R | 26 templateICAr-0.8.8/templateICAr/R/norm_BOLD.R | 66 templateICAr-0.8.8/templateICAr/R/orthonorm.R |only templateICAr-0.8.8/templateICAr/R/removebs_template.R | 17 templateICAr-0.8.8/templateICAr/R/resample_template.R | 27 templateICAr-0.8.8/templateICAr/R/rm_nuisIC.R | 6 templateICAr-0.8.8/templateICAr/R/rox_args_docs.R | 40 templateICAr-0.8.8/templateICAr/R/templateICA.R | 944 ++++++---- templateICAr-0.8.8/templateICAr/R/templateICA.methods.R | 81 templateICAr-0.8.8/templateICAr/R/templateICAr-package.R |only templateICAr-0.8.8/templateICAr/R/utils.R | 84 templateICAr-0.8.8/templateICAr/README.md | 18 templateICAr-0.8.8/templateICAr/build |only templateICAr-0.8.8/templateICAr/man/Chol_samp_fun.Rd |only templateICAr-0.8.8/templateICAr/man/EM_FCtemplateICA.Rd | 37 templateICAr-0.8.8/templateICAr/man/EM_templateICA.Rd | 31 templateICAr-0.8.8/templateICAr/man/GSR_Param.Rd |only templateICAr-0.8.8/templateICAr/man/IW_var_cor.Rd |only templateICAr-0.8.8/templateICAr/man/LL2_kappa.Rd | 2 templateICAr-0.8.8/templateICAr/man/LL_SQUAREM.Rd | 31 templateICAr-0.8.8/templateICAr/man/TR_param.Rd |only templateICAr-0.8.8/templateICAr/man/UT2mat.Rd |only templateICAr-0.8.8/templateICAr/man/UpdateThetaSQUAREM_templateICA.Rd | 6 templateICAr-0.8.8/templateICAr/man/UpdateTheta_FCtemplateICA.Rd | 6 templateICAr-0.8.8/templateICAr/man/UpdateTheta_templateICA.Rd | 16 templateICAr-0.8.8/templateICAr/man/VB_FCtemplateICA.Rd |only templateICAr-0.8.8/templateICAr/man/activations.Rd | 38 templateICAr-0.8.8/templateICAr/man/add_str.Rd |only templateICAr-0.8.8/templateICAr/man/bdiag_m2.Rd |only templateICAr-0.8.8/templateICAr/man/check_parallel_packages.Rd |only templateICAr-0.8.8/templateICAr/man/compute_LL_FC.Rd |only templateICAr-0.8.8/templateICAr/man/compute_LL_std.Rd |only templateICAr-0.8.8/templateICAr/man/dim_reduce.Rd |only templateICAr-0.8.8/templateICAr/man/dual_reg2.Rd | 59 templateICAr-0.8.8/templateICAr/man/estimate.ESS.Rd |only templateICAr-0.8.8/templateICAr/man/estimate_nu.Rd |only templateICAr-0.8.8/templateICAr/man/estimate_template.Rd | 147 - templateICAr-0.8.8/templateICAr/man/estimate_template_FC.Rd | 6 templateICAr-0.8.8/templateICAr/man/export_template.Rd | 3 templateICAr-0.8.8/templateICAr/man/format_activation_name.Rd |only templateICAr-0.8.8/templateICAr/man/getInvCovAR.Rd |only templateICAr-0.8.8/templateICAr/man/groupICA.cifti.Rd | 17 templateICAr-0.8.8/templateICAr/man/halflogdetX.Rd |only templateICAr-0.8.8/templateICAr/man/hpf_param.Rd |only templateICAr-0.8.8/templateICAr/man/lik.Rd |only templateICAr-0.8.8/templateICAr/man/norm_BOLD.Rd | 33 templateICAr-0.8.8/templateICAr/man/orthonorm.Rd |only templateICAr-0.8.8/templateICAr/man/pw_estimate.Rd |only templateICAr-0.8.8/templateICAr/man/scale_Param.Rd | 8 templateICAr-0.8.8/templateICAr/man/sqrt_XtX.Rd |only templateICAr-0.8.8/templateICAr/man/struct_template.Rd | 13 templateICAr-0.8.8/templateICAr/man/summary.tICA_act.nifti.Rd |only templateICAr-0.8.8/templateICAr/man/templateICA.Rd | 142 + templateICAr-0.8.8/templateICAr/man/templateICAr-package.Rd |only templateICAr-0.8.8/templateICAr/man/update_A.Rd |only templateICAr-0.8.8/templateICAr/man/update_A_Chol.Rd |only templateICAr-0.8.8/templateICAr/man/update_S.Rd |only templateICAr-0.8.8/templateICAr/man/update_tau2.Rd |only templateICAr-0.8.8/templateICAr/man/var_sq_err_constrained.Rd |only templateICAr-0.8.8/templateICAr/src/EM_FCtempICA.cpp | 71 templateICAr-0.8.8/templateICAr/tests/run_templateICAr_tests.R |only templateICAr-0.8.8/templateICAr/tests/testthat/test-misc.R | 8 88 files changed, 3626 insertions(+), 1569 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 10.9.2 dated 2024-09-06 and 10.9.3 dated 2024-10-14
NNS-10.9.2/NNS/man/NNS_bin.Rd |only NNS-10.9.3/NNS/DESCRIPTION | 14 NNS-10.9.3/NNS/MD5 | 51 - NNS-10.9.3/NNS/NAMESPACE | 1 NNS-10.9.3/NNS/R/ARMA_optim.R | 2 NNS-10.9.3/NNS/R/Central_tendencies.R | 115 +-- NNS-10.9.3/NNS/R/Dependence.R | 35 NNS-10.9.3/NNS/R/Partition_Map.R | 383 +++------- NNS-10.9.3/NNS/R/RcppExports.R | 18 NNS-10.9.3/NNS/R/Regression.R | 27 NNS-10.9.3/NNS/R/Uni_Causation.R | 6 NNS-10.9.3/NNS/R/dy_d_wrt.R | 2 NNS-10.9.3/NNS/R/dy_dx.R | 24 NNS-10.9.3/NNS/README.md | 15 NNS-10.9.3/NNS/inst/doc/NNSvignette_Classification.html | 6 NNS-10.9.3/NNS/inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 2 NNS-10.9.3/NNS/inst/doc/NNSvignette_Clustering_and_Regression.html | 14 NNS-10.9.3/NNS/inst/doc/NNSvignette_Correlation_and_Dependence.R | 9 NNS-10.9.3/NNS/inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 20 NNS-10.9.3/NNS/inst/doc/NNSvignette_Correlation_and_Dependence.html | 66 + NNS-10.9.3/NNS/man/NNS.reg.Rd | 2 NNS-10.9.3/NNS/man/PM.matrix.Rd | 2 NNS-10.9.3/NNS/src/partial_moments_rcpp.cpp | 96 -- NNS-10.9.3/NNS/tests/testthat/Rplots.pdf |binary NNS-10.9.3/NNS/vignettes/NNSvignette_Clustering_and_Regression.Rmd | 2 NNS-10.9.3/NNS/vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 20 NNS-10.9.3/NNS/vignettes/images/ARMA_ex.png |only NNS-10.9.3/NNS/vignettes/images/NNS_hex_sticker.png |only 28 files changed, 435 insertions(+), 497 deletions(-)
Title: Generalized Hypergeometric Function with Tunable High Precision
Description: Computation of generalized hypergeometric function with tunable high precision in a vectorized manner, with the floating-point datatypes from 'mpfr' or 'gmp' library. The computation is limited to real numbers.
Author: Xiurui Zhu [aut, cre]
Maintainer: Xiurui Zhu <zxr6@163.com>
Diff between hypergeo2 versions 0.1.0 dated 2024-09-18 and 0.2.0 dated 2024-10-14
DESCRIPTION | 6 +- MD5 | 20 +++++---- NEWS.md | 11 +++++ R/hypergeo.R | 22 +++++++--- README.md | 4 - inst/include/hypergeo2_RcppExports.h | 27 +++++++++++- man/figures/README-toc-1.png |binary man/genhypergeo.Rd | 23 ++++++++--- src/RcppExports.cpp | 47 +++++++++++++++++++++- src/hypergeo.cpp | 73 ++++++++++------------------------- src/hypergeo_impl.cpp |only src/hypergeo_impl.h |only 12 files changed, 150 insertions(+), 83 deletions(-)
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and other displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell V. Lenth [aut, cre, cph],
Balazs Banfai [ctb],
Ben Bolker [ctb],
Paul Buerkner [ctb],
Iago Gine-Vazquez [ctb],
Maxime Herve [ctb],
Maarten Jung [ctb],
Jonathon Love [ctb],
Fernando Miguez [ctb],
Julia Piaskowski [ctb],
Hannes Riebl [ctb],
Hen [...truncated...]
Maintainer: Russell V. Lenth <russell-lenth@uiowa.edu>
Diff between emmeans versions 1.10.4 dated 2024-08-20 and 1.10.5 dated 2024-10-14
DESCRIPTION | 10 +- MD5 | 62 ++++++++-------- NAMESPACE | 1 NEWS.md | 9 ++ R/0nly-internal.R | 2 R/emmGrid-methods.R | 138 +++++++------------------------------ R/helpers.R | 2 R/ref-grid.R | 12 +-- R/summary.R | 2 README.md | 7 + inst/doc/AQuickStart.html | 4 - inst/doc/FAQs.Rmd | 9 ++ inst/doc/FAQs.html | 17 +++- inst/doc/basics.html | 26 +++--- inst/doc/comparisons.html | 14 +-- inst/doc/confidence-intervals.html | 22 ++--- inst/doc/interactions.html | 42 +++++------ inst/doc/messy-data.html | 78 +++++++++----------- inst/doc/models.Rmd | 3 inst/doc/models.html | 10 +- inst/doc/predictions.html | 6 - inst/doc/re-engineering-clds.html | 4 - inst/doc/sophisticated.html | 20 ++--- inst/doc/transformations.html | 22 ++--- inst/doc/utilities.html | 4 - inst/doc/vignette-topics.html | 4 - inst/doc/xplanations.html | 4 - inst/doc/xtending.html | 8 +- man/emm_options.Rd | 14 +++ tests/testthat/test-ref_grid.R | 20 +++++ vignettes/FAQs.Rmd | 9 ++ vignettes/models.Rmd | 3 32 files changed, 295 insertions(+), 293 deletions(-)
Title: Implement Download Buttons in 'rmarkdown'
Description: Implement download buttons in HTML output from 'rmarkdown' without the need for 'runtime:shiny'.
Author: Felipe Mattioni Maturana [aut, cre]
,
John Coene [ctb]
Maintainer: Felipe Mattioni Maturana <felipe.mattioni@med.uni-tuebingen.de>
Diff between downloadthis versions 0.4.0 dated 2024-07-04 and 0.4.1 dated 2024-10-14
DESCRIPTION | 6 +++--- MD5 | 10 ++++++---- NEWS.md | 4 ++++ inst/assets/webfonts/fa-v4compatibility.ttf |only inst/assets/webfonts/fa-v4compatibility.woff2 |only inst/doc/button_types.html | 6 +++--- inst/doc/downloadthis.html | 10 +++++----- 7 files changed, 21 insertions(+), 15 deletions(-)
Title: Split Knockoffs for Structural Sparsity
Description: Split Knockoff is a data adaptive variable selection framework for controlling the
(directional) false discovery rate (FDR) in structural sparsity, where variable
selection on linear transformation of parameters is of concern. This proposed scheme
relaxes the linear subspace constraint to its neighborhood, often known as variable
splitting in optimization.
Simulation experiments can be reproduced following the Vignette.
'Split Knockoffs' is first defined in Cao et al. (2021) <doi:10.48550/arXiv.2103.16159>.
Author: Yuxuan Chen [aut, cre] ,
Haoxue Wang [aut] ,
Yang Cao [aut] ,
Xinwei Sun [aut] ,
Yuan Yao [aut]
Maintainer: Yuxuan Chen <yx.chen@connect.ust.hk>
Diff between SplitKnockoff versions 1.2 dated 2022-03-18 and 2.1 dated 2024-10-14
SplitKnockoff-1.2/SplitKnockoff/R/others.R |only SplitKnockoff-1.2/SplitKnockoff/R/statistics_W.R |only SplitKnockoff-1.2/SplitKnockoff/inst/extdata |only SplitKnockoff-1.2/SplitKnockoff/man/W_sign.Rd |only SplitKnockoff-1.2/SplitKnockoff/man/W_support.Rd |only SplitKnockoff-1.2/SplitKnockoff/man/sk.select.Rd |only SplitKnockoff-1.2/SplitKnockoff/tests |only SplitKnockoff-2.1/SplitKnockoff/DESCRIPTION | 35 SplitKnockoff-2.1/SplitKnockoff/LICENSE | 2 SplitKnockoff-2.1/SplitKnockoff/MD5 | 63 SplitKnockoff-2.1/SplitKnockoff/NAMESPACE | 18 SplitKnockoff-2.1/SplitKnockoff/R/W_fixed.R |only SplitKnockoff-2.1/SplitKnockoff/R/W_path.R |only SplitKnockoff-2.1/SplitKnockoff/R/canonicalSVD.R | 88 SplitKnockoff-2.1/SplitKnockoff/R/create.R | 313 +- SplitKnockoff-2.1/SplitKnockoff/R/cv_all.R |only SplitKnockoff-2.1/SplitKnockoff/R/cv_screen.R |only SplitKnockoff-2.1/SplitKnockoff/R/decompose.R | 48 SplitKnockoff-2.1/SplitKnockoff/R/filter.R | 449 ++- SplitKnockoff-2.1/SplitKnockoff/R/hittingpoint.R |only SplitKnockoff-2.1/SplitKnockoff/R/normc.R |only SplitKnockoff-2.1/SplitKnockoff/R/select.R | 44 SplitKnockoff-2.1/SplitKnockoff/R/threshold.R |only SplitKnockoff-2.1/SplitKnockoff/build/vignette.rds |binary SplitKnockoff-2.1/SplitKnockoff/inst/doc/Splitknockoff.R | 18 SplitKnockoff-2.1/SplitKnockoff/inst/doc/Splitknockoff.Rmd | 1085 +++---- SplitKnockoff-2.1/SplitKnockoff/inst/doc/Splitknockoff.html | 1729 +++++------- SplitKnockoff-2.1/SplitKnockoff/man/canonicalSVD.Rd | 5 SplitKnockoff-2.1/SplitKnockoff/man/cv_all.Rd |only SplitKnockoff-2.1/SplitKnockoff/man/cv_screen.Rd |only SplitKnockoff-2.1/SplitKnockoff/man/hittingpoint.Rd | 6 SplitKnockoff-2.1/SplitKnockoff/man/normc.Rd | 4 SplitKnockoff-2.1/SplitKnockoff/man/select.Rd |only SplitKnockoff-2.1/SplitKnockoff/man/sk.W_fixed.Rd |only SplitKnockoff-2.1/SplitKnockoff/man/sk.W_path.Rd |only SplitKnockoff-2.1/SplitKnockoff/man/sk.create.Rd | 21 SplitKnockoff-2.1/SplitKnockoff/man/sk.decompose.Rd | 13 SplitKnockoff-2.1/SplitKnockoff/man/sk.filter.Rd | 103 SplitKnockoff-2.1/SplitKnockoff/man/threshold.Rd |only SplitKnockoff-2.1/SplitKnockoff/vignettes/Splitknockoff.Rmd | 1085 +++---- 40 files changed, 2563 insertions(+), 2566 deletions(-)
Title: Pedigree-Based Mixed-Effects Models
Description: Fit pedigree-based mixed-effects models.
Author: Douglas Bates [aut],
Ana Ines Vazquez [aut, cre],
Paulino Perez Rodriguez [ctb]
Maintainer: Ana Ines Vazquez <avazquez@msu.edu>
Diff between pedigreemm versions 0.3-4 dated 2023-11-24 and 0.3-5 dated 2024-10-14
ChangeLog | 2 ++ DESCRIPTION | 23 ++++++++++++++++++----- MD5 | 6 +++--- src/pedigree.c | 23 ++++++++++++++++------- 4 files changed, 39 insertions(+), 15 deletions(-)
Title: Prepare and Explore Data for Palaeobiological Analyses
Description: Provides functionality to support data preparation and exploration for
palaeobiological analyses, improving code reproducibility and accessibility. The
wider aim of 'palaeoverse' is to bring the palaeobiological community together
to establish agreed standards. The package currently includes functionality for
data cleaning, binning (time and space), exploration, summarisation and
visualisation. Reference datasets (i.e. Geological Time Scales <https://stratigraphy.org/chart>)
and auxiliary functions are also provided. Details can be found in:
Jones et al., (2023) <doi: 10.1111/2041-210X.14099>.
Author: Lewis A. Jones [aut, cre] ,
William Gearty [aut] ,
Bethany J. Allen [aut] ,
Kilian Eichenseer [aut] ,
Christopher D. Dean [aut] ,
Sofia Galvan [ctb] ,
Miranta Kouvari [ctb] ,
Pedro L. Godoy [ctb] ,
Cecily Nicholl [ctb] ,
Lucas Buffan [ctb] ,
Erin M. [...truncated...]
Maintainer: Lewis A. Jones <LewisA.Jones@outlook.com>
Diff between palaeoverse versions 1.3.0 dated 2024-04-16 and 1.4.0 dated 2024-10-14
palaeoverse-1.3.0/palaeoverse/R/lat_bins.R |only palaeoverse-1.3.0/palaeoverse/tests/testthat/test-lat_bins.R |only palaeoverse-1.4.0/palaeoverse/DESCRIPTION | 14 palaeoverse-1.4.0/palaeoverse/MD5 | 93 +- palaeoverse-1.4.0/palaeoverse/NAMESPACE | 4 palaeoverse-1.4.0/palaeoverse/NEWS.md | 11 palaeoverse-1.4.0/palaeoverse/R/bin_lat.R | 18 palaeoverse-1.4.0/palaeoverse/R/bin_space.R | 9 palaeoverse-1.4.0/palaeoverse/R/bin_time.R | 40 palaeoverse-1.4.0/palaeoverse/R/group_apply.R | 2 palaeoverse-1.4.0/palaeoverse/R/lat_bins_area.R |only palaeoverse-1.4.0/palaeoverse/R/lat_bins_degrees.R |only palaeoverse-1.4.0/palaeoverse/R/look_up.R | 15 palaeoverse-1.4.0/palaeoverse/R/palaeorotate.R | 421 ++++------ palaeoverse-1.4.0/palaeoverse/R/palaeoverse-package.R | 1 palaeoverse-1.4.0/palaeoverse/R/tax_check.R | 35 palaeoverse-1.4.0/palaeoverse/R/tax_expand_lat.R | 14 palaeoverse-1.4.0/palaeoverse/R/tax_expand_time.R | 18 palaeoverse-1.4.0/palaeoverse/R/tax_range_space.R | 21 palaeoverse-1.4.0/palaeoverse/R/tax_range_strat.R | 24 palaeoverse-1.4.0/palaeoverse/R/tax_range_time.R | 12 palaeoverse-1.4.0/palaeoverse/README.md | 2 palaeoverse-1.4.0/palaeoverse/build/partial.rdb |binary palaeoverse-1.4.0/palaeoverse/build/vignette.rds |binary palaeoverse-1.4.0/palaeoverse/inst/CITATION | 7 palaeoverse-1.4.0/palaeoverse/inst/doc/phanerozoic-reefs.Rmd | 67 - palaeoverse-1.4.0/palaeoverse/inst/doc/phanerozoic-reefs.html | 347 ++++---- palaeoverse-1.4.0/palaeoverse/inst/doc/structure-and-standards.html | 140 +-- palaeoverse-1.4.0/palaeoverse/inst/doc/tetrapod-biodiversity.Rmd | 112 +- palaeoverse-1.4.0/palaeoverse/inst/doc/tetrapod-biodiversity.html | 382 ++++----- palaeoverse-1.4.0/palaeoverse/man/bin_lat.Rd | 2 palaeoverse-1.4.0/palaeoverse/man/figures/lifecycle-deprecated.svg |only palaeoverse-1.4.0/palaeoverse/man/figures/lifecycle-experimental.svg |only palaeoverse-1.4.0/palaeoverse/man/figures/lifecycle-stable.svg |only palaeoverse-1.4.0/palaeoverse/man/figures/lifecycle-superseded.svg |only palaeoverse-1.4.0/palaeoverse/man/group_apply.Rd | 2 palaeoverse-1.4.0/palaeoverse/man/lat_bins.Rd | 43 - palaeoverse-1.4.0/palaeoverse/man/lat_bins_area.Rd |only palaeoverse-1.4.0/palaeoverse/man/lat_bins_degrees.Rd |only palaeoverse-1.4.0/palaeoverse/man/look_up.Rd | 4 palaeoverse-1.4.0/palaeoverse/man/palaeorotate.Rd | 165 +-- palaeoverse-1.4.0/palaeoverse/man/palaeoverse-package.Rd | 2 palaeoverse-1.4.0/palaeoverse/man/tax_check.Rd | 2 palaeoverse-1.4.0/palaeoverse/man/tax_expand_lat.Rd | 2 palaeoverse-1.4.0/palaeoverse/tests/testthat/_snaps/lat_bins_area |only palaeoverse-1.4.0/palaeoverse/tests/testthat/test-bin_lat.R | 4 palaeoverse-1.4.0/palaeoverse/tests/testthat/test-lat_bins_area.R |only palaeoverse-1.4.0/palaeoverse/tests/testthat/test-lat_bins_degrees.R |only palaeoverse-1.4.0/palaeoverse/tests/testthat/test-look_up.R | 5 palaeoverse-1.4.0/palaeoverse/tests/testthat/test-palaeorotate.R | 229 +---- palaeoverse-1.4.0/palaeoverse/tests/testthat/test-tax_expand_lat.R | 2 palaeoverse-1.4.0/palaeoverse/vignettes/phanerozoic-reefs.Rmd | 67 - palaeoverse-1.4.0/palaeoverse/vignettes/source |only palaeoverse-1.4.0/palaeoverse/vignettes/tetrapod-biodiversity.Rmd | 112 +- 54 files changed, 1139 insertions(+), 1311 deletions(-)
Title: Multivariate and Propensity Score Matching with Balance
Optimization
Description: Provides functions for multivariate and propensity score matching
and for finding optimal balance based on a genetic search algorithm.
A variety of univariate and multivariate metrics to
determine if balance has been obtained are also provided. For
details, see the paper by Jasjeet Sekhon
(2007, <doi:10.18637/jss.v042.i07>).
Author: Jasjeet Singh Sekhon [aut, cre],
Theo Saarinen [aut]
Maintainer: Jasjeet Singh Sekhon <jas.sekhon@yale.edu>
Diff between Matching versions 4.10-14 dated 2023-09-14 and 4.10-15 dated 2024-10-14
DESCRIPTION | 8 +-- MD5 | 14 ++--- src/Makevars | 2 src/Makevars.win | 2 src/matching.cc | 104 ++++++++++++++++++++--------------------- src/scythematrix.cc | 94 ++++++++++++++++++------------------- src/scythematrix.h | 4 - tests/testthat/test-GenMatch.R | 1 8 files changed, 115 insertions(+), 114 deletions(-)
Title: Boldness-Recalibration of Binary Events
Description: Boldness-recalibration maximally spreads out probability predictions while maintaining a user specified level of calibration, facilitated the brcal() function. Supporting functions to assess calibration via Bayesian and Frequentist approaches, Maximum Likelihood Estimator (MLE) recalibration, Linear in Log Odds (LLO)-adjust via any specified parameters, and visualize results are also provided. Methodological details can be found in Guthrie & Franck (2024) <doi:10.1080/00031305.2024.2339266>.
Author: Adeline P. Guthrie [aut, cre] ,
Christopher T. Franck [aut]
Maintainer: Adeline P. Guthrie <apguthrie47@gmail.com>
Diff between BRcal versions 1.0.0 dated 2024-09-13 and 1.0.1 dated 2024-10-14
BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br90_833624141bc7c2f984bd2a2aa5589f83.RData |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br90_833624141bc7c2f984bd2a2aa5589f83.rdb |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br90_833624141bc7c2f984bd2a2aa5589f83.rdx |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br90_tau_5cbcbb517f5ea9a6a92958ce86c80468.RData |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br90_tau_5cbcbb517f5ea9a6a92958ce86c80468.rdb |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br90_tau_5cbcbb517f5ea9a6a92958ce86c80468.rdx |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_2_bc84195f5545bbeeb9459ba87cee4579.RData |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_2_bc84195f5545bbeeb9459ba87cee4579.rdb |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_2_bc84195f5545bbeeb9459ba87cee4579.rdx |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_3_a15138f2ae67678b519d05efb23146d1.RData |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_3_a15138f2ae67678b519d05efb23146d1.rdb |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_3_a15138f2ae67678b519d05efb23146d1.rdx |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_49c34b170b17be939d8b4874d4c661aa.RData |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_49c34b170b17be939d8b4874d4c661aa.rdb |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_49c34b170b17be939d8b4874d4c661aa.rdx |only BRcal-1.0.1/BRcal/DESCRIPTION | 6 - BRcal-1.0.1/BRcal/MD5 | 36 +++++----- BRcal-1.0.1/BRcal/README.md | 9 +- BRcal-1.0.1/BRcal/inst/CITATION | 27 +++++-- BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br90_9669711251e15d8261f5a1241517b14b.RData |only BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br90_9669711251e15d8261f5a1241517b14b.rdb |only BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br90_9669711251e15d8261f5a1241517b14b.rdx |only BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br90_tau_f1d880055aefb72d287cf2130d71724e.RData |only BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br90_tau_f1d880055aefb72d287cf2130d71724e.rdb |only BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br90_tau_f1d880055aefb72d287cf2130d71724e.rdx |only BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br95_2_1abdd883f300983cf549d2e6f6b4d481.RData |only BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br95_2_1abdd883f300983cf549d2e6f6b4d481.rdb |only BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br95_2_1abdd883f300983cf549d2e6f6b4d481.rdx |only BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br95_3_156a5ac818750136836781152f4f6441.RData |only BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br95_3_156a5ac818750136836781152f4f6441.rdb |only BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br95_3_156a5ac818750136836781152f4f6441.rdx |only BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br95_9d76030cf0a9380056b68ad8c4bd06c7.RData |only BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br95_9d76030cf0a9380056b68ad8c4bd06c7.rdb |only BRcal-1.0.1/BRcal/vignettes/hockey_vignette_cache/html/br95_9d76030cf0a9380056b68ad8c4bd06c7.rdx |only 34 files changed, 48 insertions(+), 30 deletions(-)
Title: Diversity Indices for Numerical Matrices
Description: Provides methods to calculate diversity indices on numerical matrices
based on information theory, as described in Rocchini, Marcantonio and Ricotta (2017) <doi:10.1016/j.ecolind.2016.07.039>,
and Rocchini et al. (2021) <doi:10.1101/2021.01.23.427872>.
Author: Matteo Marcantonio [aut, cre],
Martina Iannacito [aut, ctb],
Elisa Marchetto [ctb],
Elisa Thouverai [aut, ctb],
Michele Torresani [aut, ctb],
Daniele Da Re [aut],
Clara Tattoni [aut],
Giovanni Bacaro [aut],
Saverio Vicario [aut, ctb],
Carlo Ricotta [ [...truncated...]
Maintainer: Matteo Marcantonio <marcantoniomatteo@gmail.com>
Diff between rasterdiv versions 0.3.4 dated 2024-03-04 and 0.3.5 dated 2024-10-14
rasterdiv-0.3.4/rasterdiv/R/load_world.R |only rasterdiv-0.3.4/rasterdiv/R/world.R |only rasterdiv-0.3.4/rasterdiv/man/load_world.Rd |only rasterdiv-0.3.4/rasterdiv/man/world.Rd |only rasterdiv-0.3.5/rasterdiv/DESCRIPTION | 13 + rasterdiv-0.3.5/rasterdiv/MD5 | 66 ++++++--- rasterdiv-0.3.5/rasterdiv/NAMESPACE | 2 rasterdiv-0.3.5/rasterdiv/NEWS.md | 10 + rasterdiv-0.3.5/rasterdiv/R/copNDVI.R | 4 rasterdiv-0.3.5/rasterdiv/R/mdist.R | 13 + rasterdiv-0.3.5/rasterdiv/R/mpaRaoAreaS.R | 41 +++--- rasterdiv-0.3.5/rasterdiv/R/mpaRaoP.R | 56 +++++--- rasterdiv-0.3.5/rasterdiv/R/mpaRaoS.R | 185 ++++++++++++++++------------ rasterdiv-0.3.5/rasterdiv/R/paRao.R | 55 +++++++- rasterdiv-0.3.5/rasterdiv/R/paRaoP.R | 31 ++-- rasterdiv-0.3.5/rasterdiv/R/paRaoS.R | 19 +- rasterdiv-0.3.5/rasterdiv/build |only rasterdiv-0.3.5/rasterdiv/inst/WORDLIST | 4 rasterdiv-0.3.5/rasterdiv/inst/doc |only rasterdiv-0.3.5/rasterdiv/man/Rao.Rd |only rasterdiv-0.3.5/rasterdiv/man/copNDVI.Rd | 4 rasterdiv-0.3.5/rasterdiv/man/mpaRaoP.Rd | 20 ++- rasterdiv-0.3.5/rasterdiv/man/mpaRaoS.Rd | 20 ++- rasterdiv-0.3.5/rasterdiv/man/paRao.Rd | 19 ++ rasterdiv-0.3.5/rasterdiv/man/paRaoP.Rd | 5 rasterdiv-0.3.5/rasterdiv/man/paRaoS.Rd | 5 rasterdiv-0.3.5/rasterdiv/vignettes |only 27 files changed, 387 insertions(+), 185 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Roger Bivand [ctb] ,
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.7-78 dated 2024-05-22 and 1.7-83 dated 2024-10-14
DESCRIPTION | 10 - MD5 | 191 +++++++++++++----------- NAMESPACE | 14 + NEWS.md | 31 ++++ R/Agenerics.R | 10 + R/RcppExports.R | 4 R/SpatRasterDataset.R | 15 + R/SpatVectorCollection.R | 31 +++- R/clip.R | 5 R/coerce.R | 17 ++ R/distance.R | 4 R/extract_single.R | 6 R/focal.R | 3 R/generics.R | 22 ++ R/names.R | 30 +++ R/plot_axes.R | 4 R/plot_legend.R | 49 ++++++ R/plot_let.R | 72 ++++++++- R/plot_raster.R | 40 ++++- R/plot_scale.R | 2 R/plot_vector.R | 34 ++++ R/predict.R | 3 R/princomp.R | 10 + R/rast.R | 1 R/rasterize.R | 23 +-- R/rasterizeWin.R | 2 R/spatvec.R | 6 R/subset.R | 8 - R/tiles.R | 2 R/vect.R | 3 R/watershed.R |only R/zonal.R | 4 inst/ex/elev_vinschgau.tif |only inst/tinytest/test_flowAccumulation.R |only inst/tinytest/test_pitfinder.R |only inst/tinytest/test_rasterize.R |only inst/tinytest/test_vect-geom.R |only man/NIPD.Rd |only man/add_mtext.Rd |only man/as.lines.Rd | 14 + man/box.Rd | 4 man/c.Rd | 4 man/describe.Rd | 2 man/flowAccumulation.Rd |only man/focalCpp.Rd | 2 man/geometry.Rd | 5 man/grid.Rd | 2 man/legend.Rd | 3 man/map_extent.Rd |only man/mappal.Rd | 2 man/mask.Rd | 2 man/pitfinder.Rd |only man/plet.Rd | 4 man/plot.Rd | 14 + man/prcomp.Rd | 3 man/project.Rd | 6 man/rast.Rd | 4 man/resample.Rd | 10 - man/subset_dollar.Rd | 2 man/subset_double.Rd | 2 man/svc.Rd | 2 man/terra-package.Rd | 4 man/terrain.Rd | 2 man/union.Rd | 4 man/vect.Rd | 2 man/vrt.Rd | 4 man/watershed.Rd |only man/writeRaster.Rd | 4 man/writeVector.Rd | 2 man/xyCellFrom.Rd | 10 - src/Makevars.ucrt | 1 src/RcppExports.cpp | 11 + src/RcppFunctions.cpp | 17 ++ src/RcppModule.cpp | 15 + src/arith.cpp | 38 ++-- src/common.h |only src/distRaster.cpp | 209 ++++++++++++++------------- src/file_utils.cpp | 26 +++ src/focal.cpp | 2 src/gdal_algs.cpp | 28 +-- src/gdal_multidimensional.cpp | 4 src/geos_methods.cpp | 27 ++- src/math_utils.cpp | 4 src/memory.cpp | 2 src/raster_methods.cpp | 260 +++++++++++++++++++--------------- src/raster_stats.cpp | 8 - src/rasterize.cpp | 4 src/read.cpp | 35 ++++ src/read_gdal.cpp | 75 ++++++--- src/sample.cpp | 10 - src/spatBase.cpp | 7 src/spatBase.h | 12 - src/spatRaster.cpp | 86 +++++------ src/spatRaster.h | 131 +++++++++-------- src/spatRasterMultiple.cpp | 41 ++++- src/spatRasterMultiple.h | 97 ++++++------ src/spatSources.cpp | 78 +++++----- src/spatVector.cpp | 26 +++ src/spatVector.h | 4 src/vecmath.cpp | 2 src/vecmath.h | 78 +++++++++- src/vector_methods.cpp | 4 src/watershed_internal.cpp |only src/watershed_internal.h |only 104 files changed, 1412 insertions(+), 705 deletions(-)
Title: Easy Access to NetCDF Files with CF Metadata Conventions
Description: Network Common Data Form ('netCDF') files are widely used for
scientific data. Library-level access in R is provided through packages
'RNetCDF' and 'ncdf4'. Package 'ncdfCF' is built on top of 'RNetCDF' and
makes the data and its attributes available as a set of R6 classes that are
informed by the Climate and Forecasting Metadata Conventions. Access to the
data uses standard R subsetting operators and common function forms.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between ncdfCF versions 0.1.1 dated 2024-06-10 and 0.2.1 dated 2024-10-14
ncdfCF-0.1.1/ncdfCF/R/ncdfDataset.R |only ncdfCF-0.1.1/ncdfCF/R/ncdfDimension.R |only ncdfCF-0.1.1/ncdfCF/R/ncdfDimensionCharacter.R |only ncdfCF-0.1.1/ncdfCF/R/ncdfDimensionNumeric.R |only ncdfCF-0.1.1/ncdfCF/R/ncdfDimensionTime.R |only ncdfCF-0.1.1/ncdfCF/R/ncdfObject.R |only ncdfCF-0.1.1/ncdfCF/R/ncdfResource.R |only ncdfCF-0.1.1/ncdfCF/R/ncdfVariable.R |only ncdfCF-0.1.1/ncdfCF/R/zzz.R |only ncdfCF-0.1.1/ncdfCF/inst/extdata/pr_day_EC-Earth3-CC_ssp245_r1i1p1f1_gr_20240101-20241231_vncdfCF.nc |only ncdfCF-0.1.1/ncdfCF/man/attribute-ncdfObject-method.Rd |only ncdfCF-0.1.1/ncdfCF/man/axis-ncdfDimension-method.Rd |only ncdfCF-0.1.1/ncdfCF/man/dimlength.Rd |only ncdfCF-0.1.1/ncdfCF/man/has_bounds-ncdfDimensionNumeric-method.Rd |only ncdfCF-0.1.1/ncdfCF/man/has_bounds-ncdfDimensionTime-method.Rd |only ncdfCF-0.1.1/ncdfCF/man/id-ncdfObject-method.Rd |only ncdfCF-0.1.1/ncdfCF/man/indexOf.Rd |only ncdfCF-0.1.1/ncdfCF/man/length-ncdfDimension-method.Rd |only ncdfCF-0.1.1/ncdfCF/man/name-ncdfObject-method.Rd |only ncdfCF-0.1.1/ncdfCF/man/names-ncdfDataset-method.Rd |only ncdfCF-0.1.1/ncdfCF/man/ncdfDataset-class.Rd |only ncdfCF-0.1.1/ncdfCF/man/ncdfDimension-class.Rd |only ncdfCF-0.1.1/ncdfCF/man/ncdfDimensionCharacter-class.Rd |only ncdfCF-0.1.1/ncdfCF/man/ncdfDimensionGenerics.Rd |only ncdfCF-0.1.1/ncdfCF/man/ncdfDimensionNumeric-class.Rd |only ncdfCF-0.1.1/ncdfCF/man/ncdfDimensionTime-class.Rd |only ncdfCF-0.1.1/ncdfCF/man/ncdfDimnames.Rd |only ncdfCF-0.1.1/ncdfCF/man/ncdfGenerics.Rd |only ncdfCF-0.1.1/ncdfCF/man/ncdfObject-class.Rd |only ncdfCF-0.1.1/ncdfCF/man/ncdfResource-class.Rd |only ncdfCF-0.1.1/ncdfCF/man/ncdfVariable-class.Rd |only ncdfCF-0.1.1/ncdfCF/man/showObject.Rd |only ncdfCF-0.1.1/ncdfCF/man/show_attributes-ncdfObject-method.Rd |only ncdfCF-0.1.1/ncdfCF/man/sub-ncdfVariable-method.Rd |only ncdfCF-0.1.1/ncdfCF/man/sub-sub-ncdfDataset-method.Rd |only ncdfCF-0.1.1/ncdfCF/man/subset-ncdfVariable-method.Rd |only ncdfCF-0.1.1/ncdfCF/man/time-ncdfDimension-method.Rd |only ncdfCF-0.1.1/ncdfCF/man/time-ncdfDimensionTime-method.Rd |only ncdfCF-0.2.1/ncdfCF/DESCRIPTION | 31 ncdfCF-0.2.1/ncdfCF/MD5 | 124 + ncdfCF-0.2.1/ncdfCF/NAMESPACE | 60 ncdfCF-0.2.1/ncdfCF/NEWS.md | 45 ncdfCF-0.2.1/ncdfCF/R/AOI.R |only ncdfCF-0.2.1/ncdfCF/R/AOImethod.R |only ncdfCF-0.2.1/ncdfCF/R/CFAuxiliaryLongLat.R |only ncdfCF-0.2.1/ncdfCF/R/CFAxis.R |only ncdfCF-0.2.1/ncdfCF/R/CFAxisCharacter.R |only ncdfCF-0.2.1/ncdfCF/R/CFAxisDiscrete.R |only ncdfCF-0.2.1/ncdfCF/R/CFAxisLatitude.R |only ncdfCF-0.2.1/ncdfCF/R/CFAxisLongitude.R |only ncdfCF-0.2.1/ncdfCF/R/CFAxisNumeric.R |only ncdfCF-0.2.1/ncdfCF/R/CFAxisScalar.R |only ncdfCF-0.2.1/ncdfCF/R/CFAxisTime.R |only ncdfCF-0.2.1/ncdfCF/R/CFAxisVertical.R |only ncdfCF-0.2.1/ncdfCF/R/CFBounds.R |only ncdfCF-0.2.1/ncdfCF/R/CFData.R |only ncdfCF-0.2.1/ncdfCF/R/CFDataset.R |only ncdfCF-0.2.1/ncdfCF/R/CFGridMapping.R |only ncdfCF-0.2.1/ncdfCF/R/CFObject.R |only ncdfCF-0.2.1/ncdfCF/R/CFResource.R |only ncdfCF-0.2.1/ncdfCF/R/CFVariable.R |only ncdfCF-0.2.1/ncdfCF/R/CFread.R |only ncdfCF-0.2.1/ncdfCF/R/MemoryGroup.R |only ncdfCF-0.2.1/ncdfCF/R/NCDimension.R |only ncdfCF-0.2.1/ncdfCF/R/NCGroup.R |only ncdfCF-0.2.1/ncdfCF/R/NCObject.R |only ncdfCF-0.2.1/ncdfCF/R/NCUDT.R |only ncdfCF-0.2.1/ncdfCF/R/NCVariable.R |only ncdfCF-0.2.1/ncdfCF/R/ncdfCF-package.R | 190 ++ ncdfCF-0.2.1/ncdfCF/R/sysdata.rda |only ncdfCF-0.2.1/ncdfCF/R/utils.R | 52 ncdfCF-0.2.1/ncdfCF/R/wkt2.R |only ncdfCF-0.2.1/ncdfCF/README.md | 314 ++-- ncdfCF-0.2.1/ncdfCF/TODO | 47 ncdfCF-0.2.1/ncdfCF/build/vignette.rds |binary ncdfCF-0.2.1/ncdfCF/inst/doc/Using_ncdfCF.R | 82 - 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Title: Armadillo Client for the Armadillo Service
Description: A set of functions to manage data shared on a
'MOLGENIS Armadillo' server.
Author: Mariska Slofstra [aut, cre] ,
Sido Haakma [aut] ,
Tommy de Boer [aut] ,
Fleur Kelpin [aut] ,
Morris Swertz [aut] ,
Tim Cadman [aut]
Maintainer: Mariska Slofstra <m.k.slofstra@umcg.nl>
Diff between MolgenisArmadillo versions 2.6.3 dated 2024-06-13 and 2.7.0 dated 2024-10-14
DESCRIPTION | 8 ++--- MD5 | 40 +++++++++++++------------ NAMESPACE | 2 + R/names.R | 2 - R/object.R | 51 +++++++++++++++++++++++++++++---- R/project.R | 22 +++++++++++++- R/resource.R | 2 - R/subset.R | 18 +++++++++++ R/table.R | 10 +++--- R/utils.R | 12 +++++++ inst/doc/MolgenisArmadillo.html | 14 +++++++-- inst/doc/create_resources.html | 14 +++++++-- inst/doc/creating_data_subsets.html | 14 +++++++-- inst/doc/install_packages.html | 14 +++++++-- man/armadillo.delete_project_folder.Rd |only man/dot-add_slash_if_missing.Rd |only tests/testthat/test-object.R | 47 +++++++++++++++++++++++++++--- tests/testthat/test-project.R | 19 ++++++++++++ tests/testthat/test-resource.R | 4 +- tests/testthat/test-subset.R | 13 ++++++++ tests/testthat/test-table.R | 4 +- tests/testthat/test-utils.R | 19 ++++++++++++ 22 files changed, 271 insertions(+), 58 deletions(-)
More information about MolgenisArmadillo at CRAN
Permanent link
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' <https://libgit2.org> with
support for SSH and HTTPS remotes. All functions in 'gert' use basic R data
types (such as vectors and data-frames) for their arguments and return values.
User credentials are shared with command line 'git' through the git-credential
store and ssh keys stored on disk or ssh-agent.
Author: Jeroen Ooms [aut, cre] ,
Jennifer Bryan [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between gert versions 2.1.3 dated 2024-10-13 and 2.1.4 dated 2024-10-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/gert.html | 19 +++++++++---------- src/utils.h | 2 +- 4 files changed, 16 insertions(+), 17 deletions(-)
Title: Visualization of a Correlation Matrix
Description: Provides a visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.
Author: Taiyun Wei [cre, aut],
Viliam Simko [aut],
Michael Levy [ctb],
Yihui Xie [ctb],
Yan Jin [ctb],
Jeff Zemla [ctb],
Moritz Freidank [ctb],
Jun Cai [ctb],
Tomas Protivinsky [ctb]
Maintainer: Taiyun Wei <weitaiyun@gmail.com>
Diff between corrplot versions 0.94 dated 2024-08-17 and 0.95 dated 2024-10-14
DESCRIPTION | 8 LICENSE | 4 MD5 | 74 - NAMESPACE | 28 NEWS.md | 343 ++--- R/colorlegend.R | 216 +-- R/colors.R | 190 +-- R/cor-mtest.R | 100 - R/corrMatOrder.R | 154 +- R/corrRect.R | 274 ++-- R/corrRect.hclust.R | 92 - R/corrplot-package.R | 86 - R/corrplot.R | 2191 ++++++++++++++++++------------------ R/corrplot.mixed.R | 178 +- README.md | 122 +- inst/CITATION | 48 inst/doc/corrplot-intro.Rmd | 1062 ++++++++--------- inst/doc/corrplot-intro.html | 28 man/colorlegend.Rd | 224 +-- man/cor.mtest.Rd | 70 - man/corrMatOrder.Rd | 160 +- man/corrRect.Rd | 246 ++-- man/corrRect.hclust.Rd | 154 +- man/corrplot-package.Rd | 80 - man/corrplot.Rd | 1118 +++++++++--------- man/corrplot.mixed.Rd | 150 +- tests/testthat.R | 8 tests/testthat/test-colorlegend.R | 114 - tests/testthat/test-cor-mtest.R | 50 tests/testthat/test-corrRect.R | 126 +- tests/testthat/test-corrplot.R | 576 ++++----- vignettes/corrplot-intro.Rmd | 1062 ++++++++--------- vignettes/example-colorlegend.R | 108 - vignettes/example-corrMatOrder.R | 56 vignettes/example-corrRect.R | 130 +- vignettes/example-corrRect.hclust.R | 70 - vignettes/example-corrplot.R | 458 +++---- vignettes/example-corrplot.mixed.R | 26 38 files changed, 5096 insertions(+), 5088 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-15 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-05 2.16.11
Title: High Throughput Phenotyping (HTP) Data Analysis
Description: Phenotypic analysis of data coming from high throughput
phenotyping (HTP) platforms, including different types of outlier detection,
spatial analysis, and parameter estimation. The package is being developed
within the EPPN2020 project (<https://eppn2020.plant-phenotyping.eu/>).
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r/>).
Author: Emilie J Millet [aut] ,
Maria Xose Rodriguez Alvarez [aut]
,
Diana Marcela Perez Valencia [aut]
,
Isabelle Sanchez [aut],
Nadine Hilgert [aut],
Bart-Jan van Rossum [aut, cre]
,
Fred van Eeuwijk [aut] ,
Martin Boer [aut]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenHTP versions 1.0.6.1 dated 2023-04-14 and 1.0.7 dated 2024-10-14
DESCRIPTION | 12 MD5 | 96 +++---- NEWS.md | 3 R/fitModels.R | 2 R/fitSplineHDM.R | 5 R/predict.psHDM.R | 5 R/utils.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview_HTP.html | 495 +++++++++++++++++++------------------- inst/tinytest/coefDat |binary inst/tinytest/corr1Comp |binary inst/tinytest/corr2Comp |binary inst/tinytest/corr3Comp |binary inst/tinytest/corr4Comp |binary inst/tinytest/corr5Comp |binary inst/tinytest/corr6Comp |binary inst/tinytest/effDims1Comp |binary inst/tinytest/effDims2Comp |binary inst/tinytest/effRats1Comp |binary inst/tinytest/effRats2Comp |binary inst/tinytest/genoLevel |binary inst/tinytest/gp1Comp |binary inst/tinytest/gp2Comp |binary inst/tinytest/gp3Comp |binary inst/tinytest/gp4CheckComp |binary inst/tinytest/gp4Comp |binary inst/tinytest/gp5Comp |binary inst/tinytest/gp6CheckComp |binary inst/tinytest/gp6Comp |binary inst/tinytest/plotLevel |binary inst/tinytest/popLevel |binary inst/tinytest/predDat |binary inst/tinytest/predHDM |binary inst/tinytest/predHDMse |binary inst/tinytest/serieOut |binary inst/tinytest/splineEst |binary inst/tinytest/splineEstHDM |binary inst/tinytest/test_fitModPlots.R | 3 inst/tinytest/test_fitSplineHDM.R | 6 inst/tinytest/test_getHerit.R | 6 inst/tinytest/var1Comp |binary inst/tinytest/var2Comp |binary inst/tinytest/var3Comp |binary inst/tinytest/var4Comp |binary man/fitSplineHDM.Rd | 3 man/plot.singleOut.Rd | 2 man/removeSingleOut.Rd | 2 man/statgenHTP-package.Rd | 2 49 files changed, 326 insertions(+), 318 deletions(-)
Title: Generalized Network-Based Dimensionality Reduction and Analysis
Description: Non-parametric dimensionality reduction function. Reduction with and without feature selection. Plot functions. Automated feature selections. Kosztyan et. al. (2024) <doi:10.1016/j.eswa.2023.121779>.
Author: Zsolt T. Kosztyan [aut, cre],
Marcell T. Kurbucz [aut],
Attila I. Katona [aut],
Zahid Khan [aut]
Maintainer: Zsolt T. Kosztyan <kosztyan.zsolt@gtk.uni-pannon.hu>
Diff between nda versions 0.1.13 dated 2023-09-27 and 0.1.15 dated 2024-10-14
DESCRIPTION | 17 ++- MD5 | 56 ++++++------ NAMESPACE | 1 R/biplot.nda.R | 110 ++++++++++++------------ R/dCor.R | 93 +++++++++++--------- R/dCov.R | 85 +++++++++--------- R/data_gen.R | 115 ++++++++++++------------- R/fs.KMO.R | 100 +++++++++++---------- R/fs.dimred.R | 241 ++++++++++++++++++++++++++--------------------------- R/nda.R | 211 ++++++++++++++++++++++++++++++++-------------- R/ndr.R | 91 ++++++++++---------- R/normalize.R | 77 ++++++++-------- R/pdCor.R | 118 +++++++++++++------------ R/plot.nda.R | 40 +++----- R/print.nda.R |only R/spdCor.R | 118 +++++++++++++------------ R/summary.nda.R | 89 ++++++++++--------- README.md | 69 +++++++-------- inst/CITATION | 10 +- inst/NEWS | 8 + man/biplot.nda.Rd | 4 man/dCor.Rd | 8 - man/dCov.Rd | 8 - man/fs.dmred.Rd | 4 man/nda.Rd | 4 man/ndr.Rd | 168 ++++++++++++++++++------------------ man/normalize.Rd | 4 man/plot.nda.Rd | 115 +++++++++++++------------ man/print.nda.Rd |only man/summary.nda.Rd | 18 +++ 30 files changed, 1072 insertions(+), 910 deletions(-)
Title: Modular Cohort-Building Framework for Analytical Dashboards
Description: You can easily add advanced cohort-building component
to your analytical dashboard or simple 'Shiny' app.
Then you can instantly start building cohorts using multiple
filters of different types, filtering datasets, and filtering steps.
Filters can be complex and data-specific, and together
with multiple filtering steps you can use complex filtering rules.
The cohort-building sidebar panel allows you to easily
work with filters, add and remove filtering steps.
It helps you with handling missing values during filtering,
and provides instant filtering feedback with filter feedback plots.
The GUI panel is not only compatible with native shiny
bookmarking, but also provides reproducible R code.
Author: Krystian Igras [cre, aut],
Kamil Wais [aut],
Adam Forys [ctb]
Maintainer: Krystian Igras <krystian8207@gmail.com>
Diff between shinyCohortBuilder versions 0.3.0 dated 2024-09-27 and 0.3.1 dated 2024-10-14
DESCRIPTION | 6 ++--- MD5 | 10 ++++----- NEWS.md | 4 +++ R/filter_discrete.R | 40 ++++++++++++++++++--------------------- README.md | 2 - inst/doc/shinyCohortBuilder.html | 10 ++++----- 6 files changed, 37 insertions(+), 35 deletions(-)
More information about shinyCohortBuilder at CRAN
Permanent link
Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing
with meteorological data in the tidy data framework. Extends 'ggplot2'
for better plotting of scalar and vector fields and provides commonly
used analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between metR versions 0.15.0 dated 2024-02-08 and 0.16.0 dated 2024-10-14
metR-0.15.0/metR/R/guide_vector.R |only metR-0.15.0/metR/man/guide_vector.Rd |only metR-0.15.0/metR/tests/testthat/_snaps |only metR-0.15.0/metR/tests/testthat/test-GetSMNData.R |only metR-0.16.0/metR/DESCRIPTION | 12 metR-0.16.0/metR/MD5 | 150 ++------- metR-0.16.0/metR/NAMESPACE | 4 metR-0.16.0/metR/NEWS.md | 15 metR-0.16.0/metR/R/EOF.R | 27 + metR-0.16.0/metR/R/GetSMNData.R | 175 ---------- metR-0.16.0/metR/R/ReadNetCDF.R | 5 metR-0.16.0/metR/R/WriteNetCDF.R |only metR-0.16.0/metR/R/geom_arrow.R | 350 +++++++++++---------- metR-0.16.0/metR/R/geom_contour_fill.R | 4 metR-0.16.0/metR/R/geom_contour_tanaka.R | 2 metR-0.16.0/metR/R/geom_streamline.R | 1 metR-0.16.0/metR/R/label-scales.R | 4 metR-0.16.0/metR/R/metR-package.R | 6 metR-0.16.0/metR/R/scale_vector.R | 72 ---- metR-0.16.0/metR/R/stat_contour2.r | 32 + metR-0.16.0/metR/R/stat_contour_fill.R | 32 + metR-0.16.0/metR/README.md | 21 - metR-0.16.0/metR/build/partial.rdb |binary metR-0.16.0/metR/build/vignette.rds |binary metR-0.16.0/metR/inst/doc/Visualization-tools.html | 83 ++-- metR-0.16.0/metR/inst/doc/Working-with-data.R | 7 metR-0.16.0/metR/inst/doc/Working-with-data.Rmd | 13 metR-0.16.0/metR/inst/doc/Working-with-data.html | 30 - metR-0.16.0/metR/man/EOF.Rd | 7 metR-0.16.0/metR/man/GetSMNData.Rd | 51 --- metR-0.16.0/metR/man/discretised_scale.Rd | 65 +-- metR-0.16.0/metR/man/figures/field-1.png |binary metR-0.16.0/metR/man/geom_arrow.Rd | 69 +++- metR-0.16.0/metR/man/geom_contour2.Rd | 86 ++++- metR-0.16.0/metR/man/geom_contour_fill.Rd | 87 ++++- metR-0.16.0/metR/man/geom_contour_tanaka.Rd | 71 +++- metR-0.16.0/metR/man/geom_relief.Rd | 63 +++ metR-0.16.0/metR/man/geom_streamline.Rd | 82 +++- metR-0.16.0/metR/man/geom_text_contour.Rd | 62 +++ metR-0.16.0/metR/man/guide_colourstrip.Rd | 50 --- metR-0.16.0/metR/man/label_scales.Rd | 31 - metR-0.16.0/metR/man/metR.Rd | 9 metR-0.16.0/metR/man/scale_divergent.Rd | 43 -- metR-0.16.0/metR/man/scale_longitude.Rd | 16 metR-0.16.0/metR/man/scale_mag.Rd | 61 +-- metR-0.16.0/metR/man/stat_na.Rd | 62 +++ metR-0.16.0/metR/man/stat_subset.Rd | 62 +++ metR-0.16.0/metR/tests/testthat/Rplots.pdf |binary metR-0.16.0/metR/tests/testthat/test-eof.R | 10 metR-0.16.0/metR/tests/testthat/test-vis-arrow.R | 4 metR-0.16.0/metR/vignettes/Working-with-data.Rmd | 13 51 files changed, 1036 insertions(+), 1013 deletions(-)
Title: Get Images Out of DICOM Format Quickly
Description: Provides tools to sort DICOM-format medical image files, and
convert them to NIfTI-1 format.
Author: Jon Clayden [aut, cre] ,
Chris Rorden [aut],
Martin J Fiedler [cph],
Cong Xu [cph],
Pascal Gloor [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between divest versions 1.0.0 dated 2024-02-12 and 1.1.0 dated 2024-10-14
DESCRIPTION | 10 MD5 | 61 NAMESPACE | 1 NEWS | 11 R/zzz.R | 26 README.md | 24 build/partial.rdb |binary configure | 566 ++-- configure.ac | 23 inst/tinytest/test-05-read.R | 3 inst/tinytest/test-20-qa.R | 17 man/bidsJson.Rd | 10 man/divest.capabilities.Rd |only man/imageAttributes.Rd | 18 man/readDicom.Rd | 14 src/dcm2niix/jpg_0XC3.cpp | 331 +- src/dcm2niix/jpg_0XC3.h | 24 src/dcm2niix/nifti1_io_core.cpp | 1550 ++++++----- src/dcm2niix/nifti1_io_core.h | 125 src/dcm2niix/nii_dicom.cpp | 3947 ++++++++++++++++------------- src/dcm2niix/nii_dicom.h | 427 +-- src/dcm2niix/nii_dicom_batch.cpp | 5136 +++++++++++++++++++++------------------ src/dcm2niix/nii_dicom_batch.h | 112 src/dcm2niix/nii_foreign.cpp | 76 src/dcm2niix/nii_foreign.h | 12 src/dcm2niix/nii_ortho.cpp | 116 src/dcm2niix/nii_ortho.h | 10 src/dcm2niix/print.h | 140 - src/dcm2niix/tinydir.h | 148 - src/main.cpp | 26 src/ujpeg/ujpeg.cpp | 1310 +++++---- src/ujpeg/ujpeg.h | 20 32 files changed, 7762 insertions(+), 6532 deletions(-)
Title: 'Praat Picture' Style Plots of Acoustic Data
Description: Quickly and easily generate plots of acoustic data aligned with transcriptions similar to those made in 'Praat' using either derived signals generated directly in R with 'wrassp' or imported derived signals from 'Praat'. Provides easy and fast out-of-the-box solutions but also a high extent of flexibility. Also provides options for embedding audio in figures and animating figures.
Author: Rasmus Puggaard-Rode [aut, cre, cph]
Maintainer: Rasmus Puggaard-Rode <r.puggaard@phonetik.uni-muenchen.de>
Diff between praatpicture versions 1.2.0 dated 2024-05-22 and 1.3.0 dated 2024-10-14
DESCRIPTION | 6 MD5 | 38 - NEWS.md | 52 ++ R/emupicture.R | 25 - R/formantplot.R | 303 +++++++------- R/intensityplot.R | 6 R/pitchplot.R | 262 ++++++------ R/praatpicture.R | 109 ++++- R/specplot.R | 698 ++++++++++++++++----------------- R/tgplot.R | 4 R/waveplot.R | 228 +++++----- inst/shiny/shiny_praatpicture/server.R | 25 + inst/shiny/shiny_praatpicture/ui.R | 24 - man/emupicture.Rd | 14 man/formantplot.Rd | 12 man/intensityplot.Rd | 6 man/pitchplot.Rd | 12 man/praatpicture.Rd | 48 +- man/specplot.Rd | 21 man/waveplot.Rd | 4 20 files changed, 1094 insertions(+), 803 deletions(-)
Title: Simple Functions to Save Time and Memory
Description: Fast and memory-efficient (or 'cheap') tools to facilitate
efficient programming, saving time and memory. It aims to provide
'cheaper' alternatives to common base R functions, as well as some
additional functions.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cheapr versions 0.9.8 dated 2024-10-02 and 0.9.9 dated 2024-10-14
cheapr-0.9.8/cheapr/R/comparison.R |only cheapr-0.9.8/cheapr/src/comparison.cpp |only cheapr-0.9.9/cheapr/DESCRIPTION | 6 cheapr-0.9.9/cheapr/MD5 | 56 +++--- cheapr-0.9.9/cheapr/NAMESPACE | 3 cheapr-0.9.9/cheapr/NEWS.md | 15 + cheapr-0.9.9/cheapr/R/as_discrete.R | 80 ++++++++- cheapr-0.9.9/cheapr/R/bin.R | 5 cheapr-0.9.9/cheapr/R/cpp11.R | 8 cheapr-0.9.9/cheapr/R/extras.R | 53 +++++- cheapr-0.9.9/cheapr/R/get_breaks.R | 189 +++++++++++++++-------- cheapr-0.9.9/cheapr/R/sset.R | 5 cheapr-0.9.9/cheapr/R/utils.R | 23 -- cheapr-0.9.9/cheapr/README.md | 114 ++++++------- cheapr-0.9.9/cheapr/man/as_discrete.Rd | 51 +++++- cheapr-0.9.9/cheapr/man/bin.Rd | 6 cheapr-0.9.9/cheapr/man/extras.Rd | 20 +- cheapr-0.9.9/cheapr/man/get_breaks.Rd | 43 +++-- cheapr-0.9.9/cheapr/src/altrep.cpp | 18 ++ cheapr-0.9.9/cheapr/src/attrs.cpp | 36 +++- cheapr-0.9.9/cheapr/src/cheapr_cpp.h | 4 cheapr-0.9.9/cheapr/src/cpp11.cpp | 16 - cheapr-0.9.9/cheapr/src/int64.cpp | 4 cheapr-0.9.9/cheapr/src/lists.cpp | 2 cheapr-0.9.9/cheapr/src/nas.cpp | 8 cheapr-0.9.9/cheapr/src/scalars.cpp | 127 +++++++++++++-- cheapr-0.9.9/cheapr/src/sset.cpp | 15 - cheapr-0.9.9/cheapr/src/utils.cpp | 171 +++++++++++++++++++- cheapr-0.9.9/cheapr/src/which.cpp | 2 cheapr-0.9.9/cheapr/tests/testthat/test-extras.R |only cheapr-0.9.9/cheapr/tests/testthat/test_bin.R |only 31 files changed, 798 insertions(+), 282 deletions(-)
Title: Single Trial Analysis (STA) of Field Trials
Description: Phenotypic analysis of field trials using mixed models with and
without spatial components. One of a series of statistical genetic packages
for streamlining the analysis of typical plant breeding experiments developed
by Biometris.
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r/>).
Author: Bart-Jan van Rossum [aut, cre]
,
Fred van Eeuwijk [ctb] ,
Martin Boer [ctb] ,
Marcos Malosetti [ctb] ,
Daniela Bustos-Korts [ctb] ,
Emilie J. Millet [ctb] ,
Joao Paulo [ctb] ,
Maikel Verouden [ctb] ,
Willem Kruijer [ctb] ,
Ron Wehrens [ctb] ,
Choazhi [...truncated...]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenSTA versions 1.0.13 dated 2024-05-06 and 1.0.14 dated 2024-10-14
DESCRIPTION | 12 +- MD5 | 68 +++++------ NEWS.md | 5 R/createSTA.R | 32 +++-- R/extractSTA.R | 65 ++--------- R/fitTD.R | 2 R/fitTDAsreml.R | 6 - R/fitTDLme4.R | 3 R/fitTDSpATS.R | 4 R/layoutPlot.R | 6 - R/sysdata.rda |binary README.md | 2 build/partial.rdb |binary build/vignette.rds |binary data/TDHeat05.rda |binary data/TDMaize.rda |binary inst/doc/statgenSTA.R | 4 inst/doc/statgenSTA.Rmd | 4 inst/doc/statgenSTA.html | 83 +++++++------- inst/reports/modelReport.Rnw | 5 man/extractSTA.Rd | 4 man/figures/README-basePlot-1.png |binary man/figures/README-layoutPlot-1.png |binary man/figures/README-mapPlot-1.png |binary man/figures/README-scatterPlot-1.png |binary man/figures/README-spatialPlot-1.png |binary man/fitTD.Rd | 2 man/statgenSTA-package.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test-ExtractSpATS.R | 200 +++++++++++++++++------------------ tests/testthat/test-STA.R | 11 + tests/testthat/test-fitTDAsreml.R | 9 - tests/testthat/test-fitTDLme4.R | 5 tests/testthat/test-fitTDSpATS.R | 5 vignettes/statgenSTA.Rmd | 4 35 files changed, 265 insertions(+), 278 deletions(-)
Title: Dynamic Multi-Species Size Spectrum Modelling
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Gustav Delius [cre, aut, cph] ,
Finlay Scott [aut, cph],
Julia Blanchard [aut, cph] ,
Ken Andersen [aut, cph] ,
Richard Southwell [ctb, cph]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 2.5.1 dated 2024-03-08 and 2.5.2 dated 2024-10-14
mizer-2.5.1/mizer/tests/testthat/_snaps/plots/plotpredmort-truncated.new.svg |only mizer-2.5.1/mizer/tests/testthat/_snaps/plots/plotpredmort-truncated.svg |only mizer-2.5.2/mizer/DESCRIPTION | 15 mizer-2.5.2/mizer/MD5 | 268 ++++---- mizer-2.5.2/mizer/NAMESPACE | 3 mizer-2.5.2/mizer/NEWS.md | 39 + mizer-2.5.2/mizer/R/MizerParams-class.R | 216 +++---- mizer-2.5.2/mizer/R/age_mat.R | 4 mizer-2.5.2/mizer/R/calibrate.R | 13 mizer-2.5.2/mizer/R/compareParams.R | 74 +- mizer-2.5.2/mizer/R/data.R | 6 mizer-2.5.2/mizer/R/extension.R | 1 mizer-2.5.2/mizer/R/helpers.R | 16 mizer-2.5.2/mizer/R/manipulate_species.R | 44 - mizer-2.5.2/mizer/R/match.R | 17 mizer-2.5.2/mizer/R/matchGrowth.R | 4 mizer-2.5.2/mizer/R/newMultispeciesParams.R | 17 mizer-2.5.2/mizer/R/plotBiomassObservedVsModel.R | 4 mizer-2.5.2/mizer/R/plots.R | 17 mizer-2.5.2/mizer/R/selectivity_funcs.R | 44 - mizer-2.5.2/mizer/R/setBevertonHolt.R | 4 mizer-2.5.2/mizer/R/setColours.R | 10 mizer-2.5.2/mizer/R/setExtEncounter.R | 4 mizer-2.5.2/mizer/R/setFishing.R | 103 ++- mizer-2.5.2/mizer/R/setInitialValues.R | 2 mizer-2.5.2/mizer/R/setMetadata.R | 5 mizer-2.5.2/mizer/R/setPredKernel.R | 8 mizer-2.5.2/mizer/R/setReproduction.R | 56 + mizer-2.5.2/mizer/R/species_params.R | 218 ------- mizer-2.5.2/mizer/R/steady.R | 43 + mizer-2.5.2/mizer/R/steadySingleSpecies.R | 8 mizer-2.5.2/mizer/R/summary_methods.R | 41 - mizer-2.5.2/mizer/R/validSpeciesParams.R |only mizer-2.5.2/mizer/R/wrapper_functions.R | 1 mizer-2.5.2/mizer/build/vignette.rds |binary mizer-2.5.2/mizer/data/NS_params.rda |binary mizer-2.5.2/mizer/inst/WORDLIST | 2 mizer-2.5.2/mizer/inst/doc/mizer.Rmd | 6 mizer-2.5.2/mizer/inst/doc/mizer.html | 10 mizer-2.5.2/mizer/man/NS_species_params.Rd | 3 mizer-2.5.2/mizer/man/NS_species_params_gears.Rd | 3 mizer-2.5.2/mizer/man/calc_selectivity.Rd |only mizer-2.5.2/mizer/man/calibrateYield.Rd | 13 mizer-2.5.2/mizer/man/completeSpeciesParams.Rd | 73 +- mizer-2.5.2/mizer/man/double_sigmoid_length.Rd | 23 mizer-2.5.2/mizer/man/gear_params.Rd | 3 mizer-2.5.2/mizer/man/getDiet.Rd | 32 - mizer-2.5.2/mizer/man/initialN-set.Rd | 3 mizer-2.5.2/mizer/man/initialNOther-set.Rd | 3 mizer-2.5.2/mizer/man/initialNResource-set.Rd | 3 mizer-2.5.2/mizer/man/knife_edge.Rd | 5 mizer-2.5.2/mizer/man/l2w.Rd | 16 mizer-2.5.2/mizer/man/matchGrowth.Rd | 3 mizer-2.5.2/mizer/man/matchYields.Rd | 17 mizer-2.5.2/mizer/man/newMultispeciesParams.Rd | 41 - mizer-2.5.2/mizer/man/plotBiomassObservedVsModel.Rd | 4 mizer-2.5.2/mizer/man/plotGrowthCurves.Rd | 6 mizer-2.5.2/mizer/man/plotYieldGear.Rd | 4 mizer-2.5.2/mizer/man/setExtEncounter.Rd | 3 mizer-2.5.2/mizer/man/setFishing.Rd | 7 mizer-2.5.2/mizer/man/setMetadata.Rd | 3 mizer-2.5.2/mizer/man/setParams.Rd | 39 - mizer-2.5.2/mizer/man/setReproduction.Rd | 31 - mizer-2.5.2/mizer/man/sigmoid_length.Rd | 12 mizer-2.5.2/mizer/man/sigmoid_weight.Rd | 5 mizer-2.5.2/mizer/man/species_params.Rd | 11 mizer-2.5.2/mizer/man/validParams.Rd | 9 mizer-2.5.2/mizer/man/validSpeciesParams.Rd | 51 + mizer-2.5.2/mizer/man/valid_gears_arg.Rd |only mizer-2.5.2/mizer/tests/testthat.R | 8 mizer-2.5.2/mizer/tests/testthat/Rplots.pdf |binary mizer-2.5.2/mizer/tests/testthat/_snaps/age_mat.md | 12 mizer-2.5.2/mizer/tests/testthat/_snaps/backwards_compatibility.md |only mizer-2.5.2/mizer/tests/testthat/_snaps/plots/plot-single-growth-curve.svg | 6 mizer-2.5.2/mizer/tests/testthat/_snaps/project.md |only mizer-2.5.2/mizer/tests/testthat/_snaps/project_methods.md |only mizer-2.5.2/mizer/tests/testthat/_snaps/steady.md | 4 mizer-2.5.2/mizer/tests/testthat/_snaps/summary_methods.md |only mizer-2.5.2/mizer/tests/testthat/helper.R | 5 mizer-2.5.2/mizer/tests/testthat/test-MizerParams-class.R | 10 mizer-2.5.2/mizer/tests/testthat/test-MizerSim-class.R | 2 mizer-2.5.2/mizer/tests/testthat/test-age_mat.R | 4 mizer-2.5.2/mizer/tests/testthat/test-analytic_results.R | 21 mizer-2.5.2/mizer/tests/testthat/test-animateSpectra.R | 1 mizer-2.5.2/mizer/tests/testthat/test-backwards_compatibility.R | 301 +++++----- mizer-2.5.2/mizer/tests/testthat/test-calibrate.R | 32 - mizer-2.5.2/mizer/tests/testthat/test-compareParams.R | 28 mizer-2.5.2/mizer/tests/testthat/test-data.R | 4 mizer-2.5.2/mizer/tests/testthat/test-get_initial_n.R | 4 mizer-2.5.2/mizer/tests/testthat/test-manipulate_species.R | 104 ++- mizer-2.5.2/mizer/tests/testthat/test-match.R | 42 - mizer-2.5.2/mizer/tests/testthat/test-matchGrowth.R | 2 mizer-2.5.2/mizer/tests/testthat/test-newMultispeciesParams.R | 39 - mizer-2.5.2/mizer/tests/testthat/test-plotBiomassObservedVsModel.R | 10 mizer-2.5.2/mizer/tests/testthat/test-plotYieldObservedVsModel.R | 6 mizer-2.5.2/mizer/tests/testthat/test-plots.R | 8 mizer-2.5.2/mizer/tests/testthat/test-project.R | 21 mizer-2.5.2/mizer/tests/testthat/test-project_methods.R | 69 +- mizer-2.5.2/mizer/tests/testthat/test-rate_functions.R | 10 mizer-2.5.2/mizer/tests/testthat/test-resource_logistic.R | 2 mizer-2.5.2/mizer/tests/testthat/test-resource_semichemostat.R | 2 mizer-2.5.2/mizer/tests/testthat/test-selectivity_funcs.R | 4 mizer-2.5.2/mizer/tests/testthat/test-setBevertonHolt.R | 17 mizer-2.5.2/mizer/tests/testthat/test-setColours.R | 8 mizer-2.5.2/mizer/tests/testthat/test-setExtEncounter.R | 5 mizer-2.5.2/mizer/tests/testthat/test-setExtMort.R | 7 mizer-2.5.2/mizer/tests/testthat/test-setFishing.R | 12 mizer-2.5.2/mizer/tests/testthat/test-setInitialValues.R | 8 mizer-2.5.2/mizer/tests/testthat/test-setInteraction.R | 1 mizer-2.5.2/mizer/tests/testthat/test-setMaxIntakeRate.R | 6 mizer-2.5.2/mizer/tests/testthat/test-setMetabolicRate.R | 1 mizer-2.5.2/mizer/tests/testthat/test-setMetadata.R | 2 mizer-2.5.2/mizer/tests/testthat/test-setPredKernel.R | 34 - mizer-2.5.2/mizer/tests/testthat/test-setReproduction.R | 2 mizer-2.5.2/mizer/tests/testthat/test-setResource.R | 1 mizer-2.5.2/mizer/tests/testthat/test-setSearchVolume.R | 3 mizer-2.5.2/mizer/tests/testthat/test-single_species.R | 6 mizer-2.5.2/mizer/tests/testthat/test-species_params.R | 61 -- mizer-2.5.2/mizer/tests/testthat/test-steady.R | 5 mizer-2.5.2/mizer/tests/testthat/test-steadySingleSpecies.R | 6 mizer-2.5.2/mizer/tests/testthat/test-summary_methods.R | 92 +-- mizer-2.5.2/mizer/tests/testthat/test-upgrade.R | 33 - mizer-2.5.2/mizer/tests/testthat/test-validSpeciesParams.R |only mizer-2.5.2/mizer/tests/testthat/test-wrapper_functions.R | 15 mizer-2.5.2/mizer/tests/testthat/values/getCommunitySlope |binary mizer-2.5.2/mizer/tests/testthat/values/getERepro |binary mizer-2.5.2/mizer/tests/testthat/values/getFMort |binary mizer-2.5.2/mizer/tests/testthat/values/getFMortGear |binary mizer-2.5.2/mizer/tests/testthat/values/getMeanMaxWeight |binary mizer-2.5.2/mizer/tests/testthat/values/getMeanWeight |binary mizer-2.5.2/mizer/tests/testthat/values/getMort |binary mizer-2.5.2/mizer/tests/testthat/values/getN |binary mizer-2.5.2/mizer/tests/testthat/values/getProportionOfLargeFish |binary mizer-2.5.2/mizer/tests/testthat/values/getRDD |binary mizer-2.5.2/mizer/tests/testthat/values/getRDI |binary mizer-2.5.2/mizer/tests/testthat/values/getYield |binary mizer-2.5.2/mizer/tests/testthat/values/getYieldGear |binary mizer-2.5.2/mizer/tests/testthat/values/set_community_phi_prey |binary mizer-2.5.2/mizer/tests/testthat/values/set_multispecies_model_phi_prey |binary mizer-2.5.2/mizer/vignettes/mizer.Rmd | 6 140 files changed, 1557 insertions(+), 1284 deletions(-)
Title: Behavior-Driven Development for R
Description: Write executable specifications in a natural language that describes how your code should behave.
Write specifications in feature files using 'Gherkin' language and execute them using functions implemented in R.
Use them as an extension to your 'testthat' tests to provide a high level description of how your code works.
Author: Jakub Sobolewski [aut, cre]
Maintainer: Jakub Sobolewski <jakupsob@gmail.com>
Diff between cucumber versions 1.0.4 dated 2024-06-29 and 1.1.0 dated 2024-10-14
cucumber-1.0.4/cucumber/inst/doc/how-it-works.R |only cucumber-1.0.4/cucumber/inst/doc/how-it-works.Rmd |only cucumber-1.0.4/cucumber/inst/doc/how-it-works.html |only cucumber-1.1.0/cucumber/DESCRIPTION | 13 +- cucumber-1.1.0/cucumber/MD5 | 41 ++++--- cucumber-1.1.0/cucumber/NAMESPACE | 4 cucumber-1.1.0/cucumber/NEWS.md | 6 + cucumber-1.1.0/cucumber/R/hooks.R |only cucumber-1.1.0/cucumber/R/parse_token.R | 12 +- cucumber-1.1.0/cucumber/R/run.R | 5 cucumber-1.1.0/cucumber/R/test.R | 1 cucumber-1.1.0/cucumber/R/tokenize.R | 4 cucumber-1.1.0/cucumber/build/vignette.rds |binary cucumber-1.1.0/cucumber/inst/doc/bdd.R |only cucumber-1.1.0/cucumber/inst/doc/bdd.html |only cucumber-1.1.0/cucumber/inst/doc/bdd.qmd |only cucumber-1.1.0/cucumber/inst/examples/comments/tests/testthat/guess_the_word.feature | 7 + cucumber-1.1.0/cucumber/inst/examples/comments/tests/testthat/steps/steps.R | 5 cucumber-1.1.0/cucumber/inst/examples/hooks |only cucumber-1.1.0/cucumber/man/hook.Rd |only cucumber-1.1.0/cucumber/tests/testthat/_snaps/examples.md | 13 ++ cucumber-1.1.0/cucumber/tests/testthat/test-examples.R | 4 cucumber-1.1.0/cucumber/tests/testthat/test-hooks.R |only cucumber-1.1.0/cucumber/tests/testthat/test-run.R | 57 ++++++++++ cucumber-1.1.0/cucumber/tests/testthat/test-tokenize.R | 56 +++++++++ cucumber-1.1.0/cucumber/vignettes/bdd.qmd |only 26 files changed, 198 insertions(+), 30 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-12 0.1.0
2024-01-12 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-26 0.9.100.1
2022-04-22 0.9.100
2020-10-30 0.9.99
2020-09-18 0.9.98
2020-06-09 0.9.97
2020-05-19 0.9.96
2020-04-27 0.9.95
2020-04-01 0.9.94
2020-03-20 0.9.93
2020-02-12 0.9.92
2019-11-15 0.9.91
2019-10-17 0.9.9
2019-06-28 0.9.8
2019-05-09 0.9.7
2019-02-24 0.9.6
2019-01-30 0.9.5
2018-07-24 0.9.4
2018-03-20 0.9.3
2018-03-01 0.9.2
2017-09-28 0.9.0
2017-07-11 0.8.9
2017-07-01 0.8.8
2017-01-19 0.8.4
2016-12-16 0.8.0
2016-07-23 0.7.9
2016-06-17 0.7.8
2016-05-11 0.7.6
2016-04-06 0.7.5
2016-03-08 0.7.4
2015-11-30 0.7.0
2015-10-01 0.6.6
2015-08-07 0.6.2
2015-06-13 0.6.0
2014-12-19 0.5.2
2014-09-09 0.4.0
2014-05-20 0.3.0
2014-03-02 0.2.2
2014-02-17 0.2.0
2013-12-27 0.1.8
2013-11-19 0.1.5
2013-10-27 0.1.0
2013-08-01 0.0.6
2013-02-19 0.0.5
2013-01-31 0.0.4
2013-01-30 0.0.3
2012-12-07 0.0.2
2012-12-04 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-17 0.5.1
2020-08-27 0.5.0
2019-06-29 0.4.2
2019-06-07 0.4.0
2017-09-22 0.3.0
2016-03-18 0.2.0
2015-09-12 0.1.2
2015-06-12 0.1.0
Title: Helper Tools for Australian Hydrologists
Description: Functions to speed up work flow for hydrological analysis.
Focused on Australian climate data (SILO climate data), hydrological models (eWater Source) and in particular South Australia (<https://water.data.sa.gov.au> hydrological data).
Author: Matt Gibbs [aut, cre]
Maintainer: Matt Gibbs <gibbs.ms@gmail.com>
Diff between SWTools versions 1.0.3 dated 2024-05-24 and 1.1.0 dated 2024-10-14
SWTools-1.0.3/SWTools/man/SWTools.Rd |only SWTools-1.1.0/SWTools/DESCRIPTION | 10 +-- SWTools-1.1.0/SWTools/MD5 | 50 ++++++++------- SWTools-1.1.0/SWTools/NAMESPACE | 1 SWTools-1.1.0/SWTools/NEWS.md | 4 + SWTools-1.1.0/SWTools/R/DEWAquarius.R | 2 SWTools-1.1.0/SWTools/R/HydstraSiteDetails.R |only SWTools-1.1.0/SWTools/R/SILO.R | 7 -- SWTools-1.1.0/SWTools/R/SILOCheckConsistency.R | 4 - SWTools-1.1.0/SWTools/R/SILOCorrectSite.R | 2 SWTools-1.1.0/SWTools/R/SILOFindSitesByShapefile.R | 2 SWTools-1.1.0/SWTools/R/SWTools.R | 11 ++- SWTools-1.1.0/SWTools/README.md | 2 SWTools-1.1.0/SWTools/inst/extdata/quality_codes |only SWTools-1.1.0/SWTools/man/AQWPDownload.Rd | 2 SWTools-1.1.0/SWTools/man/HydstraSiteDetails.Rd |only SWTools-1.1.0/SWTools/man/SILOCheckConsistency.Rd | 10 +-- SWTools-1.1.0/SWTools/man/SILOCorrectSite.Rd | 2 SWTools-1.1.0/SWTools/man/SILOImport.Rd | 4 - SWTools-1.1.0/SWTools/man/SILOLoad.Rd | 4 - SWTools-1.1.0/SWTools/man/SILOMortonQualityCodes.Rd | 2 SWTools-1.1.0/SWTools/man/SILOReport.Rd | 4 - SWTools-1.1.0/SWTools/man/SILOThiessenShp.Rd | 16 +++- SWTools-1.1.0/SWTools/man/SILOWriteFunctionsforSource.Rd | 8 +- SWTools-1.1.0/SWTools/man/SWTools-package.Rd |only SWTools-1.1.0/SWTools/man/VeneerGetTS.Rd | 12 ++- SWTools-1.1.0/SWTools/man/WritepwtoIS.Rd | 4 - 27 files changed, 94 insertions(+), 69 deletions(-)
Title: Nonparametric and Semiparametric Proportional Hazards Model
Description: An estimation procedure for the analysis of nonparametric proportional hazards model (e.g. h(t) = h0(t)exp(b(t)'Z)), providing estimation of b(t) and its pointwise standard errors, and semiparametric proportional hazards model (e.g. h(t) = h0(t)exp(b(t)'Z1 + c*Z2)), providing estimation of b(t), c and their standard errors. More details can be found in Lu Tian et al. (2005) <doi:10.1198/016214504000000845>.
Author: Qi Yang [aut, cre],
Kuan Yang [aut],
Xiaoxuan Liu [ctb],
Xinyuan Song [ctb]
Maintainer: Qi Yang <qiyang-sdu@outlook.com>
Diff between NPCox versions 1.2 dated 2023-11-13 and 1.3 dated 2024-10-14
DESCRIPTION | 10 ++-- MD5 | 24 +++++----- NAMESPACE | 4 + R/bandselect.R |only R/npcox.R | 53 +++++++++++++++------- R/npplot.R | 2 R/npsimu.R | 4 - R/spcox.R | 129 +++++++++++++++++++++++------------------------------- man/bandselect.Rd |only man/npcox.Rd | 6 +- man/npplot.Rd | 2 man/npsimu.Rd | 2 man/pbc.Rd | 89 +++++++++++++++++++++++++------------ man/spcox.Rd | 6 +- 14 files changed, 186 insertions(+), 145 deletions(-)