Title: Subgroup Identification Based on Quantitative Objectives
Description: A subgroup identification method for precision medicine based on
quantitative objectives. This method can handle continuous, binary and
survival endpoint for both prognostic and predictive case. For the
predictive case, the method aims at identifying a subgroup for which
treatment is better than control by at least a pre-specified or
auto-selected constant. For the prognostic case, the method aims at
identifying a subgroup that is at least better than a
pre-specified/auto-selected constant. The derived signature is a linear
combination of predictors, and the selected subgroup are subjects with
the signature > 0. The false discover rate when no true subgroup exists
is controlled at a user-specified level.
Author: YAN SUN [aut, cre, cph],
LING CHENG [aut],
A.S. HEDAYAT [aut]
Maintainer: YAN SUN <sunyanrobin@gmail.com>
Diff between squant versions 1.1.5 dated 2024-06-02 and 1.1.7 dated 2024-08-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/SQUANT_pred.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: JSON for R
Description: Converts R object into JSON objects and vice-versa.
Author: Alex Couture-Beil [aut, cre]
Maintainer: Alex Couture-Beil <rjson_pkg@mofo.ca>
Diff between rjson versions 0.2.21 dated 2022-01-08 and 0.2.22 dated 2024-08-19
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/json_rpc_server.pdf |binary src/dump.cpp | 24 ++++++++++++------------ 5 files changed, 22 insertions(+), 22 deletions(-)
Title: Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations
Description: Simulate dose regimens for pharmacokinetic-pharmacodynamic (PK-PD)
models described by differential equation (DE) systems. Simulation using
ADVAN-style analytical equations is also supported (Abuhelwa et al. (2015)
<doi:10.1016/j.vascn.2015.03.004>).
Author: Ron Keizer [aut, cre],
Jasmine Hughes [aut],
Dominic Tong [aut],
Kara Woo [aut],
Jordan Brooks [aut],
InsightRX [cph, fnd]
Maintainer: Ron Keizer <ron@insight-rx.com>
Diff between PKPDsim versions 1.3.0 dated 2023-03-02 and 1.4.0 dated 2024-08-19
DESCRIPTION | 16 - MD5 | 237 ++++++++-------- NAMESPACE | 11 NEWS.md | 27 + R/PKPDsim-package.R | 3 R/advan.R | 2 R/apply_duration_scale.R |only R/calc_auc_analytic.R |only R/calculate_parameters.R | 56 ++- R/compile_sim_cpp.R | 10 R/create_event_table.R | 27 + R/define_tdm_init_model.R | 2 R/get_fixed_parameters.R | 14 R/get_model_info.R |only R/get_t_obs_from_regimen.R | 6 R/install_default_literature_model.R |only R/join_regimen.R | 2 R/merge_regimen.R | 2 R/new_covariate.R | 71 +++- R/new_ode_model.R | 18 - R/new_regimen.R | 27 - R/regimen_to_nm.R | 27 + R/sim.R | 13 R/sim_core.R | 6 README.md | 15 + inst/cpp/sim.cpp | 15 - inst/doc/covariates.Rmd | 2 inst/doc/covariates.html | 120 ++++---- inst/doc/example-absorption-models.html | 120 ++++---- inst/doc/export-model.html | 44 +- inst/doc/model.Rmd | 2 inst/doc/model.html | 134 ++++----- inst/doc/output.html | 90 +++--- inst/doc/parameters.html | 14 inst/doc/regimen.Rmd | 2 inst/doc/regimen.html | 70 ++-- inst/doc/simulation.html | 60 ++-- inst/models/pk_busulfan_mccune.json5 |only inst/models/pk_busulfan_shukla.json5 |only inst/models/pk_pegasparaginase_modified_wurthwein.json5 |only inst/models/pk_vanco_anderson.json5 | 1 inst/models/pk_vanco_capparelli.json5 | 3 inst/models/pk_vanco_dao.json5 | 1 inst/models/pk_vanco_frymoyer.json5 | 1 inst/models/pk_vanco_germovsek.json5 | 1 inst/models/pk_vanco_le.json5 | 1 inst/models/pk_voriconazole_friberg.json5 | 12 inst/models/pkpd_neutropenia_template1.json5 | 3 inst/template/R/model.R | 7 man/OneCompIVbolus.Rd | 14 man/PKPDsim-package.Rd | 9 man/add_quotes.Rd | 2 man/add_ruv.Rd | 2 man/add_ruv_to_quantile.Rd | 2 man/adherence_binomial.Rd | 4 man/adherence_markov.Rd | 4 man/advan.Rd | 2 man/advan_process_infusion_doses.Rd | 6 man/analytical_eqn_wrapper.Rd | 4 man/apply_duration_scale.Rd |only man/apply_lagtime.Rd | 2 man/available_default_literature_models.Rd |only man/bioavailability_to_R_code.Rd | 2 man/calc_auc_analytic.Rd |only man/calc_ss_analytic.Rd | 4 man/calculate_parameters.Rd | 21 + man/check_iov_specification.Rd | 2 man/check_mixture_model.Rd | 2 man/check_obs_input.Rd | 2 man/covariates_table_to_list.Rd | 6 man/define_tdm_init_model.Rd | 4 man/get_fixed_parameters.Rd | 7 man/get_model_info.Rd |only man/get_t_obs_from_regimen.Rd | 6 man/get_var_y.Rd | 18 - man/install_default_literature_model.Rd |only man/join_cov_and_par.Rd | 2 man/merge_regimen.Rd | 4 man/mvrnorm2.Rd | 2 man/new_adherence.Rd | 4 man/new_covariate.Rd | 34 +- man/new_ode_model.Rd | 22 - man/new_regimen.Rd | 12 man/nlmixr_parse_parameters.Rd | 2 man/parse_obs_types.Rd | 4 man/pkpdsim_to_nlmixr.Rd | 10 man/pop_regimen.Rd | 2 man/regimen_to_nm.Rd | 17 - man/reparametrize.Rd | 2 man/search_replace_in_file.Rd | 2 man/shift_regimen.Rd | 2 man/sim.Rd | 22 - man/sim_core.Rd | 2 man/translate_ode.Rd | 4 src/pk_1cmt_iv_bolus.cpp | 1 src/pk_1cmt_iv_bolus_covariates.cpp | 4 src/pk_1cmt_iv_infusion.cpp | 1 src/pk_1cmt_oral.cpp | 1 src/pk_2cmt_iv_bolus.cpp | 1 src/pk_2cmt_iv_infusion.cpp | 1 src/pk_2cmt_oral.cpp | 3 src/pk_3cmt_iv_bolus.cpp | 1 src/pk_3cmt_iv_infusion.cpp | 1 src/pk_3cmt_oral.cpp | 5 tests/testthat/sample_json/test_1cmt_iv.json5 | 1 tests/testthat/setup.R | 18 - tests/testthat/test_apply_duration_scale.R |only tests/testthat/test_calc_auc_analytic.R |only tests/testthat/test_calc_parameters.R | 29 + tests/testthat/test_create_event_table.R | 73 ++++ tests/testthat/test_get_fixed_parameters.R | 20 - tests/testthat/test_get_model_info.R |only tests/testthat/test_get_t_obs_from_regimen.R |only tests/testthat/test_install_default_literature_model.R |only tests/testthat/test_iov.R | 54 +++ tests/testthat/test_join_regimen.R | 17 + tests/testthat/test_merge_regimen.R | 11 tests/testthat/test_model_from_api.R | 6 tests/testthat/test_new_covariate.R | 60 ++++ tests/testthat/test_new_ode_model.R | 20 + tests/testthat/test_new_regimen.R | 61 +++- tests/testthat/test_overlapping_doses.R | 6 tests/testthat/test_regimen_to_nm.R | 111 +++++++ tests/testthat/test_t_init.R | 45 +-- tests/testthat/test_timevar_cov.R | 107 ++++++- vignettes/covariates.Rmd | 2 vignettes/model.Rmd | 2 vignettes/regimen.Rmd | 2 128 files changed, 1474 insertions(+), 759 deletions(-)
Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of regular vine copula
models, see Aas et al. (2009) <doi:10.1016/j.insmatheco.2007.02.001> and
Dissman et al. (2013) <doi:10.1016/j.csda.2012.08.010>.
The package includes tools for parameter estimation, model selection,
simulation, goodness-of-fit tests, and visualization. Tools for estimation,
selection and exploratory data analysis of bivariate copula models are also
provided.
Author: Thomas Nagler [aut, cre],
Ulf Schepsmeier [aut],
Jakob Stoeber [aut],
Eike Christian Brechmann [aut],
Benedikt Graeler [aut],
Tobias Erhardt [aut],
Carlos Almeida [ctb],
Aleksey Min [ctb, ths],
Claudia Czado [ctb, ths],
Mathias Hofmann [ctb],
Matthia [...truncated...]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between VineCopula versions 2.5.0 dated 2023-07-10 and 2.5.1 dated 2024-08-19
DESCRIPTION | 8 +- MD5 | 80 +++++++++++++-------------- NEWS.md | 12 ++++ R/BiCop.R | 5 + R/BiCopKDE.R | 2 R/BiCopName.R | 2 R/RVineClarkeTest.R | 7 +- R/RVineCopSelect.R | 2 R/RVineMatrix.R | 14 +++- R/RVineSeqEst.R | 2 R/RVineStructureSelect.R | 4 - R/VineCopula-package.R | 3 - R/as.copuladata.R | 7 ++ R/plot.BiCop.R | 4 - R/pobs.R | 2 build/partial.rdb |binary inst/include/VineCopula/vine.h | 17 +++-- man/BiCopKDE.Rd | 2 man/RVineClarkeTest.Rd | 7 +- man/RVineCopSelect.Rd | 2 man/RVineMatrix.Rd | 8 +- man/RVineSeqEst.Rd | 2 man/RVineStructureSelect.Rd | 2 man/VineCopula-package.Rd | 32 ++++++++++ man/plot.BiCop.Rd | 4 - man/pobs.Rd | 2 src/cdvine.c | 4 - src/deriv.c | 2 src/hfunc.c | 48 ++++++++-------- src/hfuncderiv.c | 2 src/incompleteBeta.c | 48 ++++++++-------- src/likelihood.c | 108 ++++++++++++++++++------------------ src/logderiv.c | 16 ++--- src/memoryhandling.c | 42 +++++++------- src/rvine.c | 12 ++-- src/rvinederiv.c | 26 ++++---- src/rvinederiv2.c | 120 ++++++++++++++++++++--------------------- src/rvinesample.c | 7 -- src/tcopuladeriv.c | 104 +++++++++++++++++------------------ src/tcopuladeriv_new.c | 16 ++--- src/tools.c | 17 ++--- 41 files changed, 428 insertions(+), 376 deletions(-)
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'.
For example, the 'parallelFor()' function can be used to convert the work of
a standard serial "for" loop into a parallel one and the 'parallelReduce()'
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut],
Romain Francois [aut, cph],
Kevin Ushey [aut, cre],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] ,
Hamada S. Badr [ctb] ,
Posit, PBC [cph],
Intel [aut, cph] ,
Microsoft [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between RcppParallel versions 5.1.8 dated 2024-07-06 and 5.1.9 dated 2024-08-19
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/tbb.R | 3 ++- src/Makevars.in | 6 +++++- tools/config/configure.R | 1 + 6 files changed, 22 insertions(+), 10 deletions(-)
Title: Multiple Criteria Optimization Algorithms and Related Functions
Description: A collection of function to solve multiple criteria optimization problems
using genetic algorithms (NSGA-II). Also included is a collection of test functions.
Author: Olaf Mersmann [aut, cre],
Heike Trautmann [ctb],
Detlef Steuer [ctb],
Bernd Bischl [ctb],
Kalyanmoy Deb [cph]
Maintainer: Olaf Mersmann <olafm@p-value.net>
Diff between mco versions 1.16 dated 2024-01-11 and 1.17 dated 2024-08-19
mco-1.16/mco/build/mco.pdf |only mco-1.17/mco/DESCRIPTION | 8 ++-- mco-1.17/mco/MD5 | 13 +++---- mco-1.17/mco/build/stage23.rdb |binary mco-1.17/mco/src/eps_ind.c | 4 ++ mco-1.17/mco/src/hv.c | 2 + mco-1.17/mco/src/hv_interface.c | 2 + mco-1.17/mco/src/nsga2.c | 67 ++++++++++++++++++++-------------------- 8 files changed, 53 insertions(+), 43 deletions(-)
Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser
desorption/ionization-time-of-flight (MALDI-TOF) and other
two-dimensional mass spectrometry data. In addition to commonly
used plotting and processing methods it includes distinctive
features, namely baseline subtraction methods such as
morphological filters (TopHat) or the statistics-sensitive
non-linear iterative peak-clipping algorithm (SNIP), peak
alignment using warping functions, handling of replicated
measurements as well as allowing spectra with different
resolutions.
Author: Sebastian Gibb [aut, cre] ,
Korbinian Strimmer [ths] ,
Sigurdur Smarason [ctb],
Laurent Gatto [ctb] ,
Paolo Inglese [ctb]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquant versions 1.22.2 dated 2024-01-22 and 1.22.3 dated 2024-08-19
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS | 14 ++++++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 -- inst/doc/MALDIquant-intro.pdf |binary man/MALDIquant-package.Rd | 8 ++++---- man/fiedler2009subset.Rd | 3 +-- src/lowerConvexHull.c | 4 ++-- 10 files changed, 35 insertions(+), 24 deletions(-)
Title: Extra Functionality for 'leaflet' Package
Description: The 'leaflet' JavaScript library provides many plugins some of which
are available in the core 'leaflet' package, but there are many more. It is not
possible to support them all in the core 'leaflet' package. This package serves
as an add-on to the 'leaflet' package by providing extra functionality via 'leaflet'
plugins.
Author: Sebastian Gatscha [aut, cre],
Bhaskar Karambelkar [aut],
Barret Schloerke [aut],
Bangyou Zheng [ctb] ,
Robin Cura [ctb] ,
Markus Voge [ctb] ,
Markus Dumke [ctb] ,
Mapbox [ctb, cph] ,
Henry Thasler [ctb, cph] ,
Dennis Wilhelm [ctb, cph] ,
Kirollos Ris [...truncated...]
Maintainer: Sebastian Gatscha <sebastian_gatscha@gmx.at>
Diff between leaflet.extras versions 2.0.0 dated 2024-06-10 and 2.0.1 dated 2024-08-19
DESCRIPTION | 6 MD5 | 52 +++--- NAMESPACE | 2 NEWS.md | 9 + R/draw.R | 10 + R/drawOptions.R | 75 +++++++++- R/heatmap.R | 21 -- R/omnivore.R | 33 ---- R/webGLHeatmap.R | 19 -- R/wms-legend.R | 13 + inst/examples/shiny/bouncemarkers.R | 4 inst/examples/shiny/search/app.R | 4 inst/examples/shiny/search/features_app.R | 4 inst/examples/webglHeatmaps.R | 2 inst/htmlwidgets/build/lfx-draw/lfx-draw-bindings.js | 2 inst/htmlwidgets/build/lfx-wms-legend/lfx-wms-legend-bindings.js | 2 man/addBounceMarkers.Rd | 12 - man/draw.Rd | 6 man/edithandlersOptions.Rd |only man/edittoolbarOptions.Rd |only man/geodesics.Rd | 16 +- man/handlersOptions.Rd | 5 man/heatmap.Rd | 6 man/omnivore.Rd | 23 +-- man/pulseMarkers.Rd | 14 - man/weatherMarkers.Rd | 12 - man/webglheatmap.Rd | 4 man/wms-legend.Rd | 20 ++ 28 files changed, 221 insertions(+), 155 deletions(-)
More information about leaflet.extras at CRAN
Permanent link
Title: Extracting and Visualizing Output from 'jagsUI'
Description: Tools are provided to streamline Bayesian analyses in 'JAGS' using
the 'jagsUI' package. Included are functions for extracting output in
simpler format, functions for streamlining assessment of convergence, and
functions for producing summary plots of output. Also included is a
function that provides a simple template for running 'JAGS' from 'R'.
Referenced materials can be found at <DOI:10.1214/ss/1177011136>.
Author: Matt Tyers [aut, cre]
Maintainer: Matt Tyers <matttyersstat@gmail.com>
Diff between jagshelper versions 0.3.1 dated 2024-07-30 and 0.3.2 dated 2024-08-19
DESCRIPTION | 8 - MD5 | 20 +-- NEWS.md | 4 R/diagnostic_plots.R | 1 build/vignette.rds |binary inst/doc/jagshelper-vignette.html | 6 man/asdf_prior_jags_out.Rd | 34 ++--- man/comparepriors.Rd | 84 ++++++------- man/jagshelper-package.Rd | 4 man/plot_postpred.Rd | 240 +++++++++++++++++++------------------- man/ts_postpred.Rd | 196 +++++++++++++++---------------- 11 files changed, 301 insertions(+), 296 deletions(-)
Title: GLCM Textures of Raster Layers
Description: Calculates grey level co-occurrence matrix (GLCM) based texture measures (Hall-Beyer (2017) <https://prism.ucalgary.ca/bitstream/handle/1880/51900/texture%20tutorial%20v%203_0%20180206.pdf>; Haralick et al. (1973) <doi:10.1109/TSMC.1973.4309314>) of raster layers using a sliding rectangular window. It also includes functions to quantize a raster into grey levels as well as tabulate a glcm and calculate glcm texture metrics for a matrix.
Author: Alexander Ilich [aut, cre]
Maintainer: Alexander Ilich <ailich@usf.edu>
Diff between GLCMTextures versions 0.4.1 dated 2024-01-22 and 0.4.2 dated 2024-08-19
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/quantize_raster.R | 2 +- inst/doc/README.html | 10 +++++----- man/quantize_raster.Rd | 2 +- 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Global Envelopes
Description: Implementation of global envelopes for a set of general d-dimensional vectors T
in various applications. A 100(1-alpha)% global envelope is a band bounded by two
vectors such that the probability that T falls outside this envelope in any of the d
points is equal to alpha. Global means that the probability is controlled simultaneously
for all the d elements of the vectors. The global envelopes can be used for graphical
Monte Carlo and permutation tests where the test statistic is a multivariate vector or
function (e.g. goodness-of-fit testing for point patterns and random sets, functional
analysis of variance, functional general linear model, n-sample test of correspondence
of distribution functions), for central regions of functional or multivariate data (e.g.
outlier detection, functional boxplot) and for global confidence and prediction bands
(e.g. confidence band in polynomial regression, Bayesian posterior prediction). See
Myllymäki and Mrkvička (2023) <doi:10.48550/arXiv.1911.0 [...truncated...]
Author: Mari Myllymaeki [aut, cre],
Tomas Mrkvicka [aut],
Mikko Kuronen [ctb],
Jiri Dvorak [ctb],
Pavel Grabarnik [ctb],
Ute Hahn [ctb],
Michael Rost [ctb],
Henri Seijo [ctb]
Maintainer: Mari Myllymaeki <mari.myllymaki@luke.fi>
Diff between GET versions 1.0-2 dated 2024-05-01 and 1.0-3 dated 2024-08-19
DESCRIPTION | 19 +- MD5 | 44 ++--- NAMESPACE | 2 NEWS | 4 R/appl_ecdf.r | 316 ++++++++++++++++++++++++++++++++-------- R/fclustering.r | 2 R/geom_central_region.R | 6 README.md | 3 inst/CITATION | 63 +++++-- inst/doc/FDRenvelopes.pdf |binary inst/doc/GET.pdf |binary inst/doc/GET.tex.rsp | 5 inst/doc/HotSpots.pdf |binary inst/doc/HotSpots.tex.rsp | 5 inst/doc/QuantileRegression.pdf |binary inst/doc/pointpatterns.pdf |binary man/GET.distrequal.Rd | 127 ++++++++++++---- man/fclustering.Rd | 2 man/geom_central_region.Rd | 6 vignettes/GET.Rnw.orig | 5 vignettes/GET.tex.rsp | 5 vignettes/HotSpots.Rnw.orig | 5 vignettes/HotSpots.tex.rsp | 5 23 files changed, 462 insertions(+), 162 deletions(-)
Title: Plots of the Empirical Attainment Function
Description: Computation and visualization of the empirical attainment function (EAF) for the analysis of random sets in multi-criterion optimization. M. López-Ibáñez, L. Paquete, and T. Stützle (2010) <doi:10.1007/978-3-642-02538-9_9>.
Author: Manuel Lopez-Ibanez [aut, cre]
,
Marco Chiarandini [aut],
Carlos Fonseca [aut],
Luis Paquete [aut],
Thomas Stuetzle [aut],
Mickael Binois [ctb]
Maintainer: Manuel Lopez-Ibanez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between eaf versions 2.5 dated 2023-11-28 and 2.5.1 dated 2024-08-19
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 4 ++++ R/eafplot.R | 46 +++++++++++++++++++++++----------------------- build/partial.rdb |binary cleanup | 8 +++++++- inst/REFERENCES.bib | 2 +- man/eafdiffplot.Rd | 2 +- man/eafplot.Rd | 10 +++++----- src/Makevars.in | 14 +------------- src/Makevars.win | 16 +--------------- src/eaf/eaf_main.c | 12 +++++++----- src/eaf/svn_version | 2 +- src/install.libs.R | 19 +++++-------------- 14 files changed, 73 insertions(+), 96 deletions(-)
Title: Complete Change Point Analysis
Description: Provides a comprehensive approach for identifying and estimating change points in multivariate time series through various statistical methods. Implements the multiple change point detection methodology from Ryan & Killick (2023) <doi:10.1080/00401706.2023.2183261> and a novel estimation methodology from Fotopoulos et al. (2023) <doi:10.1007/s00362-023-01495-0> generalized to fit the detection methodologies. Performs both detection and estimation of change points, providing visualization and summary information of the estimation process for each detected change point.
Author: Vasileios Pavlopoulos [cre, aut],
Hieu Pham [aut, ctb],
Paras Bhatt [aut, ctb],
Yi Tan [aut, ctb],
Ravi Patnayakuni [aut, ctb]
Maintainer: Vasileios Pavlopoulos <vasileios.pavlopoulos@uah.edu>
Diff between decp versions 0.1.0 dated 2024-07-09 and 0.1.1 dated 2024-08-19
decp-0.1.0/decp/man/plot_change_points.Rd |only decp-0.1.0/decp/man/plot_mle_change_point.Rd |only decp-0.1.1/decp/DESCRIPTION | 6 - decp-0.1.1/decp/MD5 | 19 ++-- decp-0.1.1/decp/NAMESPACE | 16 +-- decp-0.1.1/decp/R/decp.R | 56 +++++++++++- decp-0.1.1/decp/R/mle_change_point.R | 3 decp-0.1.1/decp/R/plotting.R | 86 ++++++++----------- decp-0.1.1/decp/man/decp.Rd | 2 decp-0.1.1/decp/man/plot.decp_result.Rd |only decp-0.1.1/decp/man/plot.mle_change_point_result.Rd |only decp-0.1.1/decp/man/print.decp_result.Rd |only decp-0.1.1/decp/man/print.mle_change_point_result.Rd |only decp-0.1.1/decp/man/summary.decp_result.Rd |only 14 files changed, 110 insertions(+), 78 deletions(-)
Title: Satellite Image Time Series Analysis for Earth Observation Data
Cubes
Description: An end-to-end toolkit for land use and land cover classification
using big Earth observation data, based on machine learning methods
applied to satellite image data cubes, as described in Simoes et al (2021) <doi:10.3390/rs13132428>.
Builds regular data cubes from collections in AWS, Microsoft Planetary Computer,
Brazil Data Cube, Copernicus Data Space Environment (CDSE), Digital Earth Africa, Digital Earth Australia,
NASA HLS using the Spatio-temporal Asset Catalog (STAC)
protocol (<https://stacspec.org/>) and the 'gdalcubes' R package
developed by Appel and Pebesma (2019) <doi:10.3390/data4030092>.
Supports visualization methods for images and time series and
smoothing filters for dealing with noisy time series.
Includes functions for quality assessment of training samples using self-organized maps
as presented by Santos et al (2021) <doi:10.1016/j.isprsjprs.2021.04.014>.
Provides machine learning methods including support vector machines,
random forests, extr [...truncated...]
Author: Rolf Simoes [aut],
Gilberto Camara [aut, cre, ths],
Felipe Souza [aut],
Felipe Carlos [aut],
Lorena Santos [ctb],
Karine Ferreira [ctb, ths],
Charlotte Pelletier [ctb],
Pedro Andrade [ctb],
Alber Sanchez [ctb],
Gilberto Queiroz [ctb]
Maintainer: Gilberto Camara <gilberto.camara.inpe@gmail.com>
Diff between sits versions 1.5.0 dated 2024-05-09 and 1.5.1 dated 2024-08-19
sits-1.5.0/sits/R/sits_resnet.R |only sits-1.5.0/sits/demo/classify_raster_rfor.R |only sits-1.5.0/sits/demo/classify_ts.R |only sits-1.5.0/sits/demo/evaluate_samples_Kohonen.R |only sits-1.5.0/sits/inst/extdata/skater |only sits-1.5.0/sits/inst/extdata/srr |only sits-1.5.0/sits/man/sits_resnet.Rd |only sits-1.5.0/sits/tests/testthat/test-parallel.R |only sits-1.5.1/sits/DESCRIPTION | 132 - sits-1.5.1/sits/MD5 | 465 ++--- sits-1.5.1/sits/NAMESPACE | 81 sits-1.5.1/sits/NEWS.md | 22 sits-1.5.1/sits/R/RcppExports.R | 8 sits-1.5.1/sits/R/api_accessors.R | 2 sits-1.5.1/sits/R/api_accuracy.R | 68 sits-1.5.1/sits/R/api_apply.R | 4 sits-1.5.1/sits/R/api_band.R | 4 sits-1.5.1/sits/R/api_check.R | 109 - sits-1.5.1/sits/R/api_chunks.R | 14 sits-1.5.1/sits/R/api_classify.R | 66 sits-1.5.1/sits/R/api_colors.R | 5 sits-1.5.1/sits/R/api_combine_predictions.R | 16 sits-1.5.1/sits/R/api_conf.R | 250 ++ sits-1.5.1/sits/R/api_crop.R |only sits-1.5.1/sits/R/api_csv.R | 27 sits-1.5.1/sits/R/api_cube.R | 293 ++- sits-1.5.1/sits/R/api_data.R | 136 + sits-1.5.1/sits/R/api_download.R | 16 sits-1.5.1/sits/R/api_file.R | 12 sits-1.5.1/sits/R/api_file_info.R | 4 sits-1.5.1/sits/R/api_gdal.R | 40 sits-1.5.1/sits/R/api_gdalcubes.R | 28 sits-1.5.1/sits/R/api_label_class.R | 12 sits-1.5.1/sits/R/api_mixture_model.R | 6 sits-1.5.1/sits/R/api_ml_model.R | 36 sits-1.5.1/sits/R/api_mosaic.R | 4 sits-1.5.1/sits/R/api_opensearch.R | 8 sits-1.5.1/sits/R/api_patterns.R |only sits-1.5.1/sits/R/api_period.R | 34 sits-1.5.1/sits/R/api_plot_raster.R | 505 +++-- sits-1.5.1/sits/R/api_plot_time_series.R | 9 sits-1.5.1/sits/R/api_plot_vector.R | 119 - 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sits-1.5.1/sits/src/softmax.cpp |only sits-1.5.1/sits/tests/testthat/Rplots.pdf |only sits-1.5.1/sits/tests/testthat/test-accuracy.R | 21 sits-1.5.1/sits/tests/testthat/test-active_learning.R | 16 sits-1.5.1/sits/tests/testthat/test-apply.R | 10 sits-1.5.1/sits/tests/testthat/test-bands.R | 2 sits-1.5.1/sits/tests/testthat/test-check.R | 4 sits-1.5.1/sits/tests/testthat/test-combine_predictions.R | 2 sits-1.5.1/sits/tests/testthat/test-config.R | 31 sits-1.5.1/sits/tests/testthat/test-cube-aws.R | 23 sits-1.5.1/sits/tests/testthat/test-cube-bdc.R | 277 ++- sits-1.5.1/sits/tests/testthat/test-cube-cdse.R | 1 sits-1.5.1/sits/tests/testthat/test-cube-deafrica.R | 141 + sits-1.5.1/sits/tests/testthat/test-cube-deaustralia.R |only sits-1.5.1/sits/tests/testthat/test-cube-mpc.R | 183 ++ sits-1.5.1/sits/tests/testthat/test-cube-terrascope.R |only sits-1.5.1/sits/tests/testthat/test-cube.R | 8 sits-1.5.1/sits/tests/testthat/test-cube_copy.R | 154 - sits-1.5.1/sits/tests/testthat/test-data.R | 214 ++ sits-1.5.1/sits/tests/testthat/test-debug.R | 1 sits-1.5.1/sits/tests/testthat/test-file_info.R | 69 sits-1.5.1/sits/tests/testthat/test-labels.R | 63 sits-1.5.1/sits/tests/testthat/test-ml.R | 25 sits-1.5.1/sits/tests/testthat/test-mosaic.R | 103 - 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Title: Tide Heights
Description: Calculates tide heights based on tide station harmonics. It
includes the harmonics data for 637 US stations. The harmonics data
was converted from
<https://github.com/poissonconsulting/rtide/blob/main/data-raw/harmonics-dwf-20151227-free.tar.bz2>,
NOAA web site data processed by David Flater for 'XTide'. The code to
calculate tide heights from the harmonics is based on 'XTide'.
Author: Joe Thorley [aut] ,
Luke Miller [aut, cre],
Abram Fleishman [aut],
Poisson Consulting [cph]
Maintainer: Luke Miller <contact@lukemiller.org>
Diff between rtide versions 0.0.9 dated 2021-05-29 and 0.0.10 dated 2024-08-19
rtide-0.0.10/rtide/DESCRIPTION | 47 ++--- rtide-0.0.10/rtide/MD5 | 46 ++--- rtide-0.0.10/rtide/NEWS.md | 7 rtide-0.0.10/rtide/R/rtide-package.R | 5 rtide-0.0.10/rtide/R/tide-height.R | 7 rtide-0.0.10/rtide/R/tide-slack.R | 2 rtide-0.0.10/rtide/README.md | 46 ++--- rtide-0.0.10/rtide/data/brandywine.rda |binary rtide-0.0.10/rtide/data/monterey.rda |binary rtide-0.0.10/rtide/inst/WORDLIST | 4 rtide-0.0.10/rtide/man/figures/README-unnamed-chunk-4-1.png |binary rtide-0.0.10/rtide/man/figures/README-unnamed-chunk-6-1.png |only rtide-0.0.10/rtide/man/figures/README-unnamed-chunk-7-1.png |only rtide-0.0.10/rtide/man/figures/lifecycle-deprecated.svg |only rtide-0.0.10/rtide/man/figures/lifecycle-experimental.svg |only rtide-0.0.10/rtide/man/figures/lifecycle-stable.svg |only rtide-0.0.10/rtide/man/figures/lifecycle-superseded.svg |only rtide-0.0.10/rtide/man/rtide-package.Rd | 12 - rtide-0.0.10/rtide/tests/spelling.R |only rtide-0.0.10/rtide/tests/testthat.R | 8 rtide-0.0.10/rtide/tests/testthat/test-data.R | 2 rtide-0.0.10/rtide/tests/testthat/test-tide-harmonics.R |only rtide-0.0.10/rtide/tests/testthat/test-tide-height.R | 99 ++++++++++- rtide-0.0.10/rtide/tests/testthat/test-tide-slack.R |only rtide-0.0.9/rtide/R/namespace.R |only rtide-0.0.9/rtide/tests/testthat/test-harmonics.R |only rtide-0.0.9/rtide/tests/testthat/test-hours-year.R |only rtide-0.0.9/rtide/tests/testthat/test-subset.R |only rtide-0.0.9/rtide/tests/testthat/test-tide-datetimes.R |only rtide-0.0.9/rtide/tests/testthat/test-tide-height-data.R |only rtide-0.0.9/rtide/tests/testthat/test-tide-slack-data.R |only rtide-0.0.9/rtide/tests/testthat/test-tide-stations.R |only rtide-0.0.9/rtide/tests/testthat/test-years-tide-harmonics.R |only 33 files changed, 194 insertions(+), 91 deletions(-)
Title: Visualizing Topological Loops and Voids
Description: Visualizations to explain the results of a topological
data analysis. The goal of topological data analysis is to identify
persistent topological structures, such as loops (topological circles)
and voids (topological spheres), in data sets. The output of an
analysis using the 'TDA' package is a Rips diagram (named after the
mathematician Eliyahu Rips). The goal of 'RPointCloud' is to fill in
these holes in the data by providing tools to visualize the features
that help explain the structures found in the Rips diagram. See McGee
and colleagues (2024) <doi:10.1101/2024.05.16.593927>.
Author: Kevin R. Coombes [aut, cre],
Jake Reed [aut],
RB McGee [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between RPointCloud versions 0.6.2 dated 2024-06-25 and 0.8.0 dated 2024-08-19
RPointCloud-0.6.2/RPointCloud/R/09-significance.R |only RPointCloud-0.6.2/RPointCloud/tests/test-signif.R |only RPointCloud-0.6.2/RPointCloud/tests/test-signif.Rout.save |only RPointCloud-0.8.0/RPointCloud/DESCRIPTION | 12 RPointCloud-0.8.0/RPointCloud/MD5 | 33 +- RPointCloud-0.8.0/RPointCloud/NAMESPACE | 10 RPointCloud-0.8.0/RPointCloud/R/05-HigherD.R | 93 ++++--- RPointCloud-0.8.0/RPointCloud/build/vignette.rds |binary RPointCloud-0.8.0/RPointCloud/data/CLL.rda |binary RPointCloud-0.8.0/RPointCloud/data/cytof.rda |binary RPointCloud-0.8.0/RPointCloud/data/treg.rda |binary RPointCloud-0.8.0/RPointCloud/inst/doc/clinical.R | 2 RPointCloud-0.8.0/RPointCloud/inst/doc/clinical.Rmd | 2 RPointCloud-0.8.0/RPointCloud/inst/doc/clinical.html | 172 +++++++------- RPointCloud-0.8.0/RPointCloud/inst/doc/cytof.html | 140 ++++++----- RPointCloud-0.8.0/RPointCloud/inst/doc/treg.html | 2 RPointCloud-0.8.0/RPointCloud/man/m07-EBexpo-class.Rd | 45 ++- RPointCloud-0.8.0/RPointCloud/tests/test-EBexpo.R |only RPointCloud-0.8.0/RPointCloud/tests/test-EBexpo.Rout.save |only RPointCloud-0.8.0/RPointCloud/vignettes/clinical.Rmd | 2 20 files changed, 283 insertions(+), 230 deletions(-)
Title: Tidy Quantitative Financial Analysis
Description: Bringing business and financial analysis to the 'tidyverse'. The 'tidyquant'
package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR'
and 'PerformanceAnalytics' package
functions and returns the objects in the tidy 'tibble' format. The main
advantage is being able to use quantitative functions with the 'tidyverse'
functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See
the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between tidyquant versions 1.0.7 dated 2023-03-31 and 1.0.8 dated 2024-08-19
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tidyquant-1.0.8/tidyquant/tests/testthat/test-tq_performance.R | 112 tidyquant-1.0.8/tidyquant/tests/testthat/test-tq_portfolio.R | 150 tidyquant-1.0.8/tidyquant/tests/testthat/test-tq_transmute.R | 380 - tidyquant-1.0.8/tidyquant/vignettes/TQ00-introduction-to-tidyquant.Rmd | 243 tidyquant-1.0.8/tidyquant/vignettes/TQ01-core-functions-in-tidyquant.Rmd | 852 +- tidyquant-1.0.8/tidyquant/vignettes/TQ02-quant-integrations-in-tidyquant.Rmd | 1117 +-- tidyquant-1.0.8/tidyquant/vignettes/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 656 +- tidyquant-1.0.8/tidyquant/vignettes/TQ04-charting-with-tidyquant.Rmd | 1002 +-- tidyquant-1.0.8/tidyquant/vignettes/TQ05-performance-analysis-with-tidyquant.Rmd | 1406 ++-- tidyquant-1.0.8/tidyquant/vignettes/TQ06-excel-in-r.Rmd | 62 112 files changed, 24022 insertions(+), 23843 deletions(-)
Title: Complement to 'Modern Data Science with R'
Description: A complement to all editions of *Modern Data
Science with R*
(ISBN: 978-0367191498, publisher URL:
<https://www.routledge.com/Modern-Data-Science-with-R/Baumer-Kaplan-Horton/p/book/9780367191498>).
This package contains data and code to complete exercises and
reproduce examples from the text. It also facilitates connections
to the SQL database server used in the book. All editions of the book are
supported by this package.
Author: Benjamin S. Baumer [aut, cre] ,
Nicholas Horton [aut] ,
Daniel Kaplan [aut]
Maintainer: Benjamin S. Baumer <ben.baumer@gmail.com>
Diff between mdsr versions 0.2.7 dated 2023-01-06 and 0.2.8 dated 2024-08-19
DESCRIPTION | 22 +-- MD5 | 76 +++++----- NEWS.md | 8 + R/BabynameDist.R | 28 ++-- R/NCI60.R | 4 R/Rnw2Rmd.R | 6 R/data.R | 314 ++++++++++++++++++++++----------------------- R/macros.R | 9 + R/scidb.R | 84 ++++++++++-- R/themes.R | 18 +- R/webshot.R | 21 +-- README.md | 7 - build/partial.rdb |binary inst/CITATION | 23 --- man/CIACountries.Rd | 6 man/Cherry.Rd | 43 +++--- man/CholeraDeaths.Rd | 4 man/DataSciencePapers.Rd | 9 - man/Elections.Rd | 31 ++-- man/Emails_train.Rd | 15 +- man/Headlines_train.Rd | 6 man/MLB_teams.Rd | 38 ++--- man/MedicareCharges.Rd | 20 +- man/MedicareProviders.Rd | 30 ++-- man/Minneapolis2013.Rd | 14 +- man/NCI60_tiny.Rd | 23 +-- man/SAT_2010.Rd | 26 +-- man/Violations.Rd | 60 ++++---- man/Votes.Rd | 26 +-- man/etl_NCI60.Rd | 6 man/macros.Rd | 9 + man/make_babynames_dist.Rd | 4 man/mdsr_table.Rd | 2 man/ordway_birds.Rd | 54 +++---- man/saratoga_houses.Rd | 38 ++--- man/save_webshot.Rd | 21 ++- man/src_scidb.Rd | 67 ++++++++- man/world_cities.Rd | 10 - tests/testthat/tests.R | 14 +- 39 files changed, 665 insertions(+), 531 deletions(-)
Title: 'hms' Based Timer
Description: Tracks elapsed clock time using a `hms::hms()` scalar.
It was was originally developed to time Bayesian model runs.
It should not be used to estimate how long extremely fast code takes to execute
as the package code adds a small time cost.
Author: Joe Thorley [aut, cre] ,
Kirill Mueller [aut] ,
Nadine Hussein [ctb] ,
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between hmstimer versions 0.2.1 dated 2022-09-20 and 0.3.0 dated 2024-08-19
hmstimer-0.2.1/hmstimer/R/internal.R |only hmstimer-0.2.1/hmstimer/R/namespace.R |only hmstimer-0.3.0/hmstimer/DESCRIPTION | 29 +- hmstimer-0.3.0/hmstimer/LICENSE | 2 hmstimer-0.3.0/hmstimer/MD5 | 92 ++++--- hmstimer-0.3.0/hmstimer/NAMESPACE | 6 hmstimer-0.3.0/hmstimer/NEWS.md | 20 + hmstimer-0.3.0/hmstimer/R/ceiling.R | 3 hmstimer-0.3.0/hmstimer/R/chk.R | 36 ++- hmstimer-0.3.0/hmstimer/R/floor.R | 3 hmstimer-0.3.0/hmstimer/R/format.R | 13 - hmstimer-0.3.0/hmstimer/R/hmstimer-package.R | 4 hmstimer-0.3.0/hmstimer/R/is-titled.R |only hmstimer-0.3.0/hmstimer/R/local-timer.R |only hmstimer-0.3.0/hmstimer/R/params.R | 33 ++ hmstimer-0.3.0/hmstimer/R/print.R | 24 +- hmstimer-0.3.0/hmstimer/R/reset.R | 3 hmstimer-0.3.0/hmstimer/R/round.R | 3 hmstimer-0.3.0/hmstimer/R/start.R | 7 hmstimer-0.3.0/hmstimer/R/stop.R | 2 hmstimer-0.3.0/hmstimer/R/timer.R | 12 - hmstimer-0.3.0/hmstimer/R/title.R |only hmstimer-0.3.0/hmstimer/R/utils.R | 11 hmstimer-0.3.0/hmstimer/R/with-timer.R |only hmstimer-0.3.0/hmstimer/README.md | 118 ++++++++-- hmstimer-0.3.0/hmstimer/man/figures/lifecycle-deprecated.svg | 22 + hmstimer-0.3.0/hmstimer/man/figures/lifecycle-experimental.svg | 22 + hmstimer-0.3.0/hmstimer/man/figures/lifecycle-stable.svg | 30 ++ hmstimer-0.3.0/hmstimer/man/figures/lifecycle-superseded.svg | 22 + hmstimer-0.3.0/hmstimer/man/hmstimer-package.Rd | 16 + hmstimer-0.3.0/hmstimer/man/local_timer.Rd |only hmstimer-0.3.0/hmstimer/man/params.Rd | 36 ++- hmstimer-0.3.0/hmstimer/man/tmr_format.Rd | 8 hmstimer-0.3.0/hmstimer/man/tmr_is_titled.Rd |only hmstimer-0.3.0/hmstimer/man/tmr_print.Rd | 6 hmstimer-0.3.0/hmstimer/man/tmr_round.Rd | 2 hmstimer-0.3.0/hmstimer/man/tmr_start.Rd | 6 hmstimer-0.3.0/hmstimer/man/tmr_timer.Rd | 15 - hmstimer-0.3.0/hmstimer/man/tmr_title-set.Rd |only hmstimer-0.3.0/hmstimer/man/tmr_title.Rd |only hmstimer-0.3.0/hmstimer/man/with_timer.Rd |only hmstimer-0.3.0/hmstimer/tests/testthat/test-ceiling.R | 5 hmstimer-0.3.0/hmstimer/tests/testthat/test-elapsed.R |only hmstimer-0.3.0/hmstimer/tests/testthat/test-floor.R | 5 hmstimer-0.3.0/hmstimer/tests/testthat/test-format.R | 15 + hmstimer-0.3.0/hmstimer/tests/testthat/test-is-started.R |only hmstimer-0.3.0/hmstimer/tests/testthat/test-is-stopped.R |only hmstimer-0.3.0/hmstimer/tests/testthat/test-is-titled.R |only hmstimer-0.3.0/hmstimer/tests/testthat/test-local-timer.R |only hmstimer-0.3.0/hmstimer/tests/testthat/test-print.R | 40 +++ hmstimer-0.3.0/hmstimer/tests/testthat/test-reset.R | 5 hmstimer-0.3.0/hmstimer/tests/testthat/test-round.R | 5 hmstimer-0.3.0/hmstimer/tests/testthat/test-start.R |only hmstimer-0.3.0/hmstimer/tests/testthat/test-stop.R |only hmstimer-0.3.0/hmstimer/tests/testthat/test-timer.R | 90 ------- hmstimer-0.3.0/hmstimer/tests/testthat/test-title.R |only hmstimer-0.3.0/hmstimer/tests/testthat/test-with-timer.R |only 57 files changed, 552 insertions(+), 219 deletions(-)
Title: Inspect, Read, Edit and Run 'APSIM' "Next Generation" and
'APSIM' Classic
Description: The functions in this package inspect, read, edit and run files for 'APSIM' "Next Generation" ('JSON')
and 'APSIM' "Classic" ('XML'). The files with an 'apsim' extension correspond to
'APSIM' Classic (7.x) - Windows only - and the ones with an 'apsimx' extension correspond to 'APSIM' "Next Generation".
For more information about 'APSIM' see (<https://www.apsim.info/>) and for 'APSIM'
next generation (<https://apsimnextgeneration.netlify.app/>).
Author: Fernando Miguez [aut, cre]
Maintainer: Fernando Miguez <femiguez@iastate.edu>
Diff between apsimx versions 2.7.7 dated 2024-05-06 and 2.8.0 dated 2024-08-19
DESCRIPTION | 13 MD5 | 103 +- NAMESPACE | 6 NEWS.md | 19 R/apsim_met.R | 17 R/apsim_version.R | 2 R/apsimx.R | 423 ++++++++++ R/apsimx_soil_profile.R | 67 + R/compare_apsim.R | 168 +++- R/compare_apsim_met.R | 66 + R/edit_apsim_replace_soil_profile.R | 51 + R/edit_apsimx_json.R | 100 +- R/edit_apsimx_replace_soil_profile.R | 610 ++++++++------- R/extract_data_apsimx.R | 127 ++- R/get_gsod_apsim_met.R | 28 R/get_isric_soil_profile.R | 4 R/get_ssurgo_soil_profile.R | 2 R/get_worldmodeler_soil_profile.R | 318 +++---- R/inspect_apsimx_json.R | 675 +++++++++------- R/inspect_apsimx_replacement.R | 67 + R/optim_apsimx.R | 1401 +++++++++++++++++------------------ R/sens_apsimx.R | 133 ++- R/ssurgo2sp.R | 5 inst/doc/apsimx-scripts.Rmd | 2 inst/doc/apsimx-scripts.html | 12 inst/doc/apsimx.html | 12 inst/doc/optim-apsim.html | 6 inst/doc/sensitivity-apsim.html | 18 man/apsimx.options.Rd | 2 man/apsimx_options.Rd | 5 man/apsimx_soil_profile.Rd | 5 man/check_apsimx.Rd |only man/compare_apsim.Rd | 27 man/compare_apsim_soil_profile.Rd | 4 man/edit_apsimx.Rd | 8 man/extract_data_apsimx.Rd | 6 man/get_gsod_apsim_met.Rd | 3 man/get_isric_soil_profile.Rd | 3 man/inspect_apsimx.Rd | 36 man/inspect_apsimx_json.Rd | 2 man/inspect_apsimx_replacement.Rd | 4 man/optim_apsimx.Rd | 20 man/sens_apsimx.Rd | 32 man/solutes_parms.Rd |only tests/test_allow_path_spaces.R |only tests/test_apsim_met.R | 22 tests/test_check_apsimx.R |only tests/test_compare_apsim.R | 13 tests/test_cores_sens_apsimx.R | 415 +++++----- tests/test_edit.R | 68 + tests/test_examples.R | 11 tests/test_extract_data.R | 70 + tests/test_initialwater.R |only tests/test_inspect.R | 64 + vignettes/apsimx-scripts.Rmd | 2 55 files changed, 3364 insertions(+), 1913 deletions(-)
Title: Detecting Anomalies in Data
Description: Implements Collective And Point Anomaly (CAPA) Fisch, Eckley, and Fearnhead (2022) <doi:10.1002/sam.11586>, Multi-Variate Collective And Point Anomaly (MVCAPA) Fisch, Eckley, and Fearnhead (2021) <doi:10.1080/10618600.2021.1987257>, Proportion Adaptive Segment Selection (PASS) Jeng, Cai, and Li (2012) <doi:10.1093/biomet/ass059>, and Bayesian Abnormal Region Detector (BARD) Bardwell and Fearnhead (2015) <doi:10.1214/16-BA998>. These methods are for the detection of anomalies in time series data. Further information regarding the use of this package along with detailed examples can be found in Fisch, Grose, Eckley, Fearnhead, and Bardwell (2024) <doi:10.18637/jss.v110.i01>.
Author: Alex Fisch [aut],
Daniel Grose [aut, cre],
Lawrence Bardwell [aut, ctb],
Idris Eckley [aut, ths],
Paul Fearnhead [aut, ths]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between anomaly versions 4.3.2 dated 2023-11-23 and 4.3.3 dated 2024-08-19
anomaly-4.3.2/anomaly/README.md |only anomaly-4.3.3/anomaly/DESCRIPTION | 12 +++++------ anomaly-4.3.3/anomaly/MD5 | 28 +++++++++++++-------------- anomaly-4.3.3/anomaly/NEWS.md | 5 +++- anomaly-4.3.3/anomaly/R/bard.R | 3 ++ anomaly-4.3.3/anomaly/R/capa.R | 1 anomaly-4.3.3/anomaly/R/pass.R | 1 anomaly-4.3.3/anomaly/build/partial.rdb |binary anomaly-4.3.3/anomaly/inst/CITATION |only anomaly-4.3.3/anomaly/inst/REFERENCES.bib | 12 +++++++++++ anomaly-4.3.3/anomaly/man/anomaly-package.Rd | 2 + anomaly-4.3.3/anomaly/man/bard.Rd | 2 + anomaly-4.3.3/anomaly/man/capa.Rd | 2 + anomaly-4.3.3/anomaly/man/pass.Rd | 2 + anomaly-4.3.3/anomaly/man/plot-methods.Rd | 2 - anomaly-4.3.3/anomaly/man/sampler.Rd | 2 + 16 files changed, 52 insertions(+), 22 deletions(-)
Title: A Tool for Automating the Statistical Disclosure Control of
Research Outputs
Description: Assists researchers and output checkers by distinguishing between research output that is safe to publish, output that requires further analysis, and output that cannot be published because of substantial disclosure risk. A paper about the tool was presented at the UNECE Expert Meeting on Statistical Data Confidentiality 2023; see <https://uwe-repository.worktribe.com/output/11060964>.
Author: Jim Smith [cre, ctb] ,
Maha Albashir [aut, ctb],
Richard John Preen [ctb]
Maintainer: Jim Smith <James.Smith@uwe.ac.uk>
Diff between acro versions 0.1.1 dated 2023-12-01 and 0.1.2 dated 2024-08-19
DESCRIPTION | 12 +++--- LICENSE | 2 - MD5 | 55 +++++++++++++++------------ NEWS.md |only R/acro_init.R | 4 +- R/acro_regression.R | 14 +++---- R/acro_tables.R | 57 +++++++++++++--------------- R/create_virtualenv.R | 34 +++++++++++------ R/output_commands.R | 21 +++------- README.md | 61 ++++++++++++++++++++----------- inst/Images |only inst/WORDLIST | 23 ++++++++--- man/install_acro.Rd | 10 ++--- tests/spelling.R | 9 +++- tests/testthat/Rplots.pdf |only tests/testthat/test-acro_add_comments.R | 6 +-- tests/testthat/test-acro_add_exception.R | 4 +- tests/testthat/test-acro_crosstab.R | 4 +- tests/testthat/test-acro_custom_output.R | 2 - tests/testthat/test-acro_finalise.R | 2 - tests/testthat/test-acro_glm.R | 36 +++++++++--------- tests/testthat/test-acro_hist.R | 3 - tests/testthat/test-acro_lm.R | 23 +++++------ tests/testthat/test-acro_pivot_table.R | 11 ++--- tests/testthat/test-acro_print_outputs.R | 8 ++-- tests/testthat/test-acro_remove_output.R | 6 +-- tests/testthat/test-acro_rename_output.R | 4 +- tests/testthat/test-acro_surv_func.R | 8 ++-- tests/testthat/test-acro_table.R | 20 +++++----- 29 files changed, 238 insertions(+), 201 deletions(-)
Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other
'dplyr' inspired syntactic style when calculating summary statistics on survey
data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre],
Thomas Lumley [ctb],
Tomasz Zoltak [ctb],
Ben Schneider [aut, ctb],
Pavel N. Krivitsky [ctb]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>
Diff between srvyr versions 1.2.0 dated 2023-02-20 and 1.3.0 dated 2024-08-19
DESCRIPTION | 11 MD5 | 74 ++--- NAMESPACE | 3 NEWS.md | 13 + R/as_survey.r | 13 + R/as_survey_design.r | 4 R/as_survey_rep.r | 13 - R/lazy_tbl.r | 20 + R/manip.r | 15 - R/srvyr.r | 3 R/subset_svy_vars.R | 24 + R/summarise.r | 10 R/survey_statistics.r | 27 ++ R/survey_statistics_helpers.R | 50 ++-- R/survey_vars.r | 19 - R/tbl-svy.r | 7 README.md | 175 +++++++------- build/vignette.rds |binary inst/WORDLIST | 6 inst/doc/extending-srvyr.html | 142 +++++------ inst/doc/srvyr-database.R | 2 inst/doc/srvyr-database.Rmd | 4 inst/doc/srvyr-database.html | 384 +++++++++++++++---------------- inst/doc/srvyr-vs-survey.R | 32 +- inst/doc/srvyr-vs-survey.Rmd | 4 inst/doc/srvyr-vs-survey.html | 286 +++++++++++------------ man/as_survey_rep.Rd | 7 man/get_var_est.Rd | 4 man/srvyr.Rd | 26 ++ man/survey_mean.Rd | 16 + tests/testthat/test_as_survey_design.r | 56 ++-- tests/testthat/test_as_survey_rep.r | 15 + tests/testthat/test_database.R | 34 ++ tests/testthat/test_dplyr_verbs.R | 53 +++- tests/testthat/test_survey_mean_factor.r | 13 + tests/testthat/test_survey_statistics.r | 71 +++++ vignettes/srvyr-database.Rmd | 4 vignettes/srvyr-vs-survey.Rmd | 4 38 files changed, 991 insertions(+), 653 deletions(-)
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <https://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey [aut],
Cory Nathe [cre]
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 3.2.3 dated 2024-06-28 and 3.3.0 dated 2024-08-19
DESCRIPTION | 20 +++++++++++++------ MD5 | 11 +++++----- NAMESPACE | 1 NEWS | 3 ++ R/labkey.experiment.R | 40 +++++++++++++++++++++++++++++++++++++++ man/Rlabkey-package.Rd | 4 +-- man/labkey.experiment.lineage.Rd |only 7 files changed, 66 insertions(+), 13 deletions(-)
Title: Multilevel B-Spline Approximation
Description: Functions to interpolate irregularly and regularly spaced data using Multilevel B-spline Approximation (MBA). Functions call portions of the SINTEF Multilevel B-spline Library written by Øyvind Hjelle which implements methods developed by Lee, Wolberg and Shin (1997; <doi:10.1109/2945.620490>).
Author: Andrew Finley [aut, cre],
Sudipto Banerjee [aut],
Oeyvind Hjelle [aut],
Roger Bivand [ctb]
Maintainer: Andrew Finley <finleya@msu.edu>
Diff between MBA versions 0.1-0 dated 2022-11-29 and 0.1-1 dated 2024-08-19
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- man/mba.points.Rd | 30 +++++++++++++++++++----------- man/mba.surf.Rd | 27 +++++++++++++++------------ src/MBA.cpp | 10 +++++++--- src/MBAPoints.cpp | 14 +++++++------- src/MBASurf.cpp | 26 +++++++++++++------------- src/include/RMBA.h | 4 ++++ 8 files changed, 76 insertions(+), 57 deletions(-)
Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a unified
interface for model fitting, prediction, performance assessment, and
presentation of results. Approaches for model fitting and prediction of
numerical, categorical, or censored time-to-event outcomes include
traditional regression models, regularization methods, tree-based methods,
support vector machines, neural networks, ensembles, data preprocessing,
filtering, and model tuning and selection. Performance metrics are provided
for model assessment and can be estimated with independent test sets, split
sampling, cross-validation, or bootstrap resampling. Resample estimation
can be executed in parallel for faster processing and nested in cases of
model tuning and selection. Modeling results can be summarized with
descriptive statistics; calibration curves; variable importance; partial
dependence plots; confusion matrices; and ROC, lift, and other performance
curves.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between MachineShop versions 3.7.0 dated 2023-09-18 and 3.8.0 dated 2024-08-19
DESCRIPTION | 10 MD5 | 112 NAMESPACE | 2 NEWS.md | 13 R/MLControl.R | 9 R/MLOptimization.R | 2 R/ML_AdaBagModel.R | 2 R/ML_AdaBoostModel.R | 2 R/ML_BARTMachineModel.R | 11 R/ML_BlackBoostModel.R | 2 R/ML_C50Model.R | 3 R/ML_CForestModel.R | 7 R/ML_EarthModel.R | 7 R/ML_GAMBoostModel.R | 2 R/ML_GBMModel.R | 5 R/ML_GLMBoostModel.R | 2 R/ML_GLMNetModel.R | 13 R/ML_LMModel.R | 2 R/ML_NNetModel.R | 2 R/ML_PLSModel.R | 2 R/ML_POLRModel.R | 4 R/ML_RFSRCModel.R | 38 R/ML_RPartModel.R | 12 R/ML_RandomForestModel.R | 9 R/ML_RangerModel.R | 2 R/ML_StackedModel.R | 6 R/ML_SuperModel.R | 4 R/ML_XGBModel.R | 32 R/TrainedInputs.R | 2 R/TrainingParams.R | 15 R/classes.R | 6 R/combine.R | 13 R/dependence.R | 7 R/diff.R | 4 R/plot.R | 9 R/predict.R | 16 R/print.R | 7 R/resample.R | 9 R/rfe.R | 2 R/settings.R | 6 R/varimp.R | 172 - build/vignette.rds |binary inst/doc/MLModels.html | 6 inst/doc/UserGuide.R | 42 inst/doc/UserGuide.Rmd | 44 inst/doc/UserGuide.html | 2619 ++++++++-------- man/RFSRCModel.Rd | 12 man/predict.Rd | 6 man/t.test.Rd | 4 man/varimp.Rd | 41 tests/testthat/Rplots.pdf |binary tests/testthat/helper-models.R | 5 tests/testthat/test-ML_ParsnipModel.R | 2 tests/testthat/test-survival.txt | 3974 ++++++++++++------------- vignettes/UserGuide.Rmd | 44 vignettes/img/using_strategies_tune_plot-1.png |binary vignettes/setup.R | 3 57 files changed, 3817 insertions(+), 3570 deletions(-)
Title: Gibbs Sea Water Functions
Description: Provides an interface to the Gibbs 'SeaWater' ('TEOS-10') C library, version 3.06-16-0 (commit '657216dd4f5ea079b5f0e021a4163e2d26893371', dated 2022-10-11, available at <https://github.com/TEOS-10/GSW-C>, which stems from 'Matlab' and other code written by members of Working Group 127 of 'SCOR'/'IAPSO' (Scientific Committee on Oceanic Research / International Association for the Physical Sciences of the Oceans).
Author: Dan Kelley [aut, cre, cph] ,
Clark Richards [aut, cph] ,
WG127 SCOR/IAPSO [aut, cph]
Maintainer: Dan Kelley <dan.kelley@dal.ca>
Diff between gsw versions 1.1-1 dated 2022-10-16 and 1.2-0 dated 2024-08-19
DESCRIPTION | 12 MD5 | 331 ++++++------ NAMESPACE | 1 NEWS.md | 39 - R/gsw.R | 62 ++ README.md | 27 build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/gsw.Rmd | 4 inst/doc/gsw.html | 233 ++++---- man/gsw.Rd | 20 man/gsw_CT_first_derivatives.Rd | 7 man/gsw_CT_first_derivatives_wrt_t_exact.Rd | 7 man/gsw_CT_freezing.Rd | 7 man/gsw_CT_freezing_first_derivatives.Rd | 7 man/gsw_CT_freezing_first_derivatives_poly.Rd | 7 man/gsw_CT_freezing_poly.Rd | 7 man/gsw_CT_from_enthalpy.Rd | 23 man/gsw_CT_from_entropy.Rd | 7 man/gsw_CT_from_pt.Rd | 7 man/gsw_CT_from_rho.Rd | 20 man/gsw_CT_from_t.Rd | 7 man/gsw_CT_maxdensity.Rd | 20 man/gsw_CT_second_derivatives.Rd | 7 man/gsw_C_from_SP.Rd | 9 man/gsw_Fdelta.Rd | 4 man/gsw_Helmholtz_energy_ice.Rd | 4 man/gsw_IPV_vs_fNsquared_ratio.Rd | 9 man/gsw_Nsquared.Rd | 9 man/gsw_O2sol.Rd | 9 man/gsw_O2sol_SP_pt.Rd | 7 man/gsw_SAAR.Rd | 4 man/gsw_SA_freezing_from_CT.Rd | 6 man/gsw_SA_freezing_from_CT_poly.Rd | 6 man/gsw_SA_freezing_from_t.Rd | 4 man/gsw_SA_freezing_from_t_poly.Rd | 4 man/gsw_SA_from_SP.Rd | 7 man/gsw_SA_from_SP_Baltic.Rd | 7 man/gsw_SA_from_Sstar.Rd | 6 man/gsw_SA_from_rho.Rd | 19 man/gsw_SP_from_C.Rd | 6 man/gsw_SP_from_SA.Rd | 9 man/gsw_SP_from_SK.Rd | 2 man/gsw_SP_from_SR.Rd | 6 man/gsw_SP_from_Sstar.Rd | 6 man/gsw_SP_salinometer.Rd | 4 man/gsw_SR_from_SP.Rd | 9 man/gsw_Sstar_from_SA.Rd | 9 man/gsw_Sstar_from_SP.Rd | 9 man/gsw_Turner_Rsubrho.Rd | 9 man/gsw_adiabatic_lapse_rate_from_CT.Rd | 9 man/gsw_adiabatic_lapse_rate_ice.Rd | 4 man/gsw_alpha.Rd | 20 man/gsw_alpha_on_beta.Rd | 22 man/gsw_alpha_wrt_t_exact.Rd | 20 man/gsw_alpha_wrt_t_ice.Rd | 17 man/gsw_beta.Rd | 20 man/gsw_beta_const_t_exact.Rd | 18 man/gsw_cabbeling.Rd | 9 man/gsw_chem_potential_water_ice.Rd | 4 man/gsw_chem_potential_water_t_exact.Rd | 7 man/gsw_cp_ice.Rd | 4 man/gsw_cp_t_exact.Rd | 7 man/gsw_deltaSA_from_SP.Rd | 9 man/gsw_dilution_coefficient_t_exact.Rd | 7 man/gsw_dynamic_enthalpy.Rd | 25 man/gsw_enthalpy.Rd | 23 man/gsw_enthalpy_CT_exact.Rd | 25 man/gsw_enthalpy_diff.Rd | 25 man/gsw_enthalpy_first_derivatives.Rd | 23 man/gsw_enthalpy_first_derivatives_CT_exact.Rd | 23 man/gsw_enthalpy_ice.Rd | 20 man/gsw_enthalpy_second_derivatives.Rd | 9 man/gsw_enthalpy_second_derivatives_CT_exact.Rd | 9 man/gsw_enthalpy_t_exact.Rd | 23 man/gsw_entropy_first_derivatives.Rd | 9 man/gsw_entropy_from_pt.Rd | 7 man/gsw_entropy_from_t.Rd | 7 man/gsw_entropy_ice.Rd | 4 man/gsw_entropy_second_derivatives.Rd | 9 man/gsw_frazil_properties.Rd | 4 man/gsw_frazil_properties_potential.Rd | 18 man/gsw_frazil_properties_potential_poly.Rd | 18 man/gsw_frazil_ratios_adiabatic.Rd | 7 man/gsw_frazil_ratios_adiabatic_poly.Rd | 7 man/gsw_geo_strf_dyn_height.Rd | 9 man/gsw_geo_strf_dyn_height_1.Rd | 9 man/gsw_geo_strf_dyn_height_pc.Rd | 9 man/gsw_gibbs.Rd | 7 man/gsw_gibbs_ice.Rd | 4 man/gsw_grav.Rd | 4 man/gsw_ice_fraction_to_freeze_seawater.Rd | 9 man/gsw_infunnel.Rd |only man/gsw_internal_energy.Rd | 9 man/gsw_internal_energy_ice.Rd | 4 man/gsw_kappa.Rd | 9 man/gsw_kappa_const_t_ice.Rd | 8 man/gsw_kappa_ice.Rd | 8 man/gsw_kappa_t_exact.Rd | 11 man/gsw_latentheat_evap_CT.Rd | 9 man/gsw_latentheat_evap_t.Rd | 7 man/gsw_latentheat_melting.Rd | 7 man/gsw_melting_ice_SA_CT_ratio.Rd | 9 man/gsw_melting_ice_SA_CT_ratio_poly.Rd | 9 man/gsw_melting_ice_equilibrium_SA_CT_ratio.Rd | 7 man/gsw_melting_ice_equilibrium_SA_CT_ratio_poly.Rd | 7 man/gsw_melting_ice_into_seawater.Rd | 9 man/gsw_melting_seaice_into_seawater.Rd | 9 man/gsw_p_from_z.Rd | 4 man/gsw_pot_enthalpy_from_pt_ice.Rd | 18 man/gsw_pot_enthalpy_from_pt_ice_poly.Rd | 18 man/gsw_pot_enthalpy_ice_freezing.Rd | 23 man/gsw_pot_enthalpy_ice_freezing_first_derivatives.Rd | 7 man/gsw_pot_enthalpy_ice_freezing_first_derivatives_poly.Rd | 7 man/gsw_pot_enthalpy_ice_freezing_poly.Rd | 21 man/gsw_pot_rho_t_exact.Rd | 20 man/gsw_pressure_coefficient_ice.Rd | 4 man/gsw_pressure_freezing_CT.Rd | 9 man/gsw_pt0_from_t.Rd | 7 man/gsw_pt0_from_t_ice.Rd | 4 man/gsw_pt_first_derivatives.Rd | 9 man/gsw_pt_from_CT.Rd | 9 man/gsw_pt_from_entropy.Rd | 7 man/gsw_pt_from_pot_enthalpy_ice.Rd | 18 man/gsw_pt_from_pot_enthalpy_ice_poly.Rd | 18 man/gsw_pt_from_t.Rd | 7 man/gsw_pt_from_t_ice.Rd | 4 man/gsw_pt_second_derivatives.Rd | 9 man/gsw_rho.Rd | 20 man/gsw_rho_alpha_beta.Rd | 22 man/gsw_rho_first_derivatives.Rd | 20 man/gsw_rho_first_derivatives_wrt_enthalpy.Rd | 20 man/gsw_rho_ice.Rd | 17 man/gsw_rho_second_derivatives.Rd | 9 man/gsw_rho_second_derivatives_wrt_enthalpy.Rd | 9 man/gsw_rho_t_exact.Rd | 20 man/gsw_seaice_fraction_to_freeze_seawater.Rd | 9 man/gsw_sigma0.Rd | 22 man/gsw_sigma1.Rd | 22 man/gsw_sigma2.Rd | 22 man/gsw_sigma3.Rd | 22 man/gsw_sigma4.Rd | 22 man/gsw_sound_speed.Rd | 9 man/gsw_sound_speed_ice.Rd | 8 man/gsw_sound_speed_t_exact.Rd | 11 man/gsw_specvol.Rd | 18 man/gsw_specvol_alpha_beta.Rd | 22 man/gsw_specvol_anom_standard.Rd | 22 man/gsw_specvol_first_derivatives.Rd | 21 man/gsw_specvol_first_derivatives_wrt_enthalpy.Rd | 21 man/gsw_specvol_ice.Rd | 17 man/gsw_specvol_second_derivatives.Rd | 9 man/gsw_specvol_second_derivatives_wrt_enthalpy.Rd | 9 man/gsw_specvol_t_exact.Rd | 20 man/gsw_spiciness0.Rd | 9 man/gsw_spiciness1.Rd | 9 man/gsw_spiciness2.Rd | 9 man/gsw_t_deriv_chem_potential_water_t_exact.Rd | 7 man/gsw_t_freezing.Rd | 7 man/gsw_t_freezing_first_derivatives.Rd | 7 man/gsw_t_freezing_first_derivatives_poly.Rd | 7 man/gsw_t_from_CT.Rd | 9 man/gsw_t_from_pt0_ice.Rd | 4 man/gsw_thermobaric.Rd | 9 man/gsw_z_from_p.Rd | 4 src/wrappers.c | 26 vignettes/gsw.Rmd | 4 167 files changed, 1349 insertions(+), 1121 deletions(-)
Title: A General Framework for Combining Ecosystem Models
Description: Fit and sample from the ensemble model described in Spence et al (2018): "A general framework for combining ecosystem models"<doi:10.1111/faf.12310>.
Author: Michael A. Spence [aut, cre] ,
James A. Martindale [aut] ,
Michael J. Thomson [aut]
Maintainer: Michael A. Spence <michael.spence@cefas.gov.uk>
Diff between EcoEnsemble versions 1.0.5 dated 2023-09-18 and 1.1.0 dated 2024-08-19
DESCRIPTION | 20 - MD5 | 107 +++-- NAMESPACE | 1 R/DiscrepancyPrior-IndSTPrior-class.R | 19 R/EcoEnsemble-package.R | 54 +- R/EnsembleData-class.R | 22 - R/EnsemblePrior-class.R | 17 R/Prior_sampling.R | 46 +- R/fit_ensemble.R | 69 ++- R/fit_ensemble_withdrivers.R |only R/generate_simulator_stan_data_withdrivers.R |only R/get_stan_outputs.R | 7 R/get_stan_outputs_withdrivers.R |only R/plot_functions.R | 28 + R/plot_functions_withdrivers.R |only R/prior_functions.R | 8 R/stanmodels.R | 6 R/validation_functions_withdrivers.R |only R/validation_prior_functions.R | 8 build/vignette.rds |binary inst/CITATION |only inst/doc/BetaConjugatePrior.R |only inst/doc/BetaConjugatePrior.Rmd |only inst/doc/BetaConjugatePrior.html |only inst/doc/EcoEnsemble.R | 16 inst/doc/EcoEnsemble.Rmd | 4 inst/doc/EcoEnsemble.html | 120 +++--- inst/doc/ExploringPriors.R | 2 inst/doc/ExploringPriors.html | 280 +++++++------- inst/doc/IncludingDrivers.R |only inst/doc/IncludingDrivers.Rmd |only inst/doc/IncludingDrivers.html |only inst/doc/SyntheticData.R | 2 inst/doc/SyntheticData.html | 325 ++++++++--------- inst/stan/ensemble_model.stan | 1 inst/stan/ensemble_model_hierarchical.stan | 37 + inst/stan/ensemble_model_hierarchical_withdrivers.stan |only inst/stan/ensemble_model_withdrivers.stan |only inst/stan/ensemble_prior_hierarchical.stan | 35 + inst/stan/ensemble_prior_hierarchical_withdrivers.stan |only inst/stan/ensemble_prior_withdrivers.stan |only man/EcoEnsemble-package.Rd | 18 man/EnsembleData.Rd | 6 man/IndSTPrior-class.Rd | 2 man/PriorConstructorFunctions.Rd | 29 - man/fit_ensemble_model.Rd | 6 man/get_mcmc_ensemble_model.Rd | 13 man/get_stan_outputs.Rd | 6 man/prior_ensemble_model.Rd | 5 man/sample_prior.Rd | 3 src/RcppExports.cpp | 8 tests/testthat/test-Prior_sampling.R | 1 tests/testthat/test-get_stanmodel.R |only tests/testthat/test-post_process_withdrivers.R |only tests/testthat/test-prior_coms.R | 185 +++++++++ tests/testthat/test-prior_functions.R | 21 + vignettes/BetaConjugatePrior.Rmd |only vignettes/EcoEnsemble.Rmd | 4 vignettes/IncludingDrivers.Rmd |only vignettes/data/bgplot.png |only vignettes/data/drivers_trace.png |only vignettes/data/obsplot.png |only vignettes/data/output_plot.png |only vignettes/data/p_priors_beta_conj.png |only vignettes/data/p_truth_withdrivers.png |only vignettes/data/rhomeanplot.png |only vignettes/data/rhoplot.png |only vignettes/data/rhoplot1.png |only vignettes/data/rhoplot2.png |only vignettes/data/rhovarplot.png |only 70 files changed, 989 insertions(+), 552 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Description: Bayesian network structure learning, parameter learning and inference.
This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC,
Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu
Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete,
Gaussian and conditional Gaussian networks, along with many score functions and
conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented.
Some utility functions (model comparison and manipulation, random data generation, arc
orientation testing, simple and advanced plots) are included, as well as support for
parameter estimation (maximum likelihood and Bayesian) and inference, conditional
probability queries, cross-validation, bootstrap and model averaging.
Development snapshots with the latest bugfixes are available from <https://www.bnlearn.com/>.
Author: Marco Scutari [aut, cre],
Tomi Silander [ctb]
Maintainer: Marco Scutari <scutari@bnlearn.com>
Diff between bnlearn versions 5.0 dated 2024-07-30 and 5.0.1 dated 2024-08-19
Changelog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/math/linear.algebra.c | 4 ++-- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Bayesian Aoristic Analyses
Description: Provides an alternative approach to aoristic analyses for archaeological datasets by fitting Bayesian parametric growth models and non-parametric random-walk Intrinsic Conditional Autoregressive (ICAR) models on time frequency data (Crema (2024)<doi:10.1111/arcm.12984>). It handles event typo-chronology based timespans defined by start/end date as well as more complex user-provided vector of probabilities.
Author: Enrico Crema [aut, cre]
Maintainer: Enrico Crema <enrico.crema@gmail.com>
Diff between baorista versions 0.2.0 dated 2024-07-30 and 0.2.1 dated 2024-08-19
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 3 +++ R/plotmcsim.R | 6 ++++-- README.md | 2 +- inst/doc/using_baorista.html | 4 ++-- man/plot.mcsimres.Rd | 3 +++ 7 files changed, 22 insertions(+), 14 deletions(-)
Title: Wavelets Statistics and Transforms
Description: Performs 1, 2 and 3D real and complex-valued wavelet transforms,
nondecimated transforms, wavelet packet transforms, nondecimated
wavelet packet transforms, multiple wavelet transforms,
complex-valued wavelet transforms, wavelet shrinkage for
various kinds of data, locally stationary wavelet time series,
nonstationary multiscale transfer function modeling, density
estimation.
Author: Guy Nason [aut, cre],
Stuart Barber [ctb],
Tim Downie [ctb],
Piotr Frylewicz [ctb],
Arne Kovac [ctb],
Todd Ogden [ctb],
Bernard Silverman [ctb]
Maintainer: Guy Nason <g.nason@imperial.ac.uk>
Diff between wavethresh versions 4.7.2 dated 2022-11-16 and 4.7.3 dated 2024-08-19
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- build/partial.rdb |binary inst/CHANGES | 4 ++++ man/accessC.wst.rd | 2 +- man/griddata.rd | 2 +- man/makegrid.rd | 2 +- man/makewpstDO.rd | 2 +- man/wd.object.rd | 2 +- src/WAVDE.c | 48 ++++++++++++++++++++++++++---------------------- 10 files changed, 48 insertions(+), 40 deletions(-)
Title: Infrastructure for Ordering Objects Using Seriation
Description: Infrastructure for ordering objects with an implementation of several
seriation/sequencing/ordination techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also provides (optimally) reordered heatmaps,
color images and clustering visualizations like dissimilarity plots, and
visual assessment of cluster tendency plots (VAT and iVAT). Hahsler et al (2008) <doi:10.18637/jss.v025.i03>.
Author: Michael Hahsler [aut, cre, cph]
,
Christian Buchta [aut, cph],
Kurt Hornik [aut, cph] ,
David Barnett [ctb],
Michael Brusco [ctb, cph],
Michael Friendly [ctb],
Hans-Friedrich Koehn [ctb, cph],
Fionn Murtagh [ctb, cph],
Stephanie Stahl [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between seriation versions 1.5.5 dated 2024-04-17 and 1.5.6 dated 2024-08-19
seriation-1.5.5/seriation/R/bea.R |only seriation-1.5.5/seriation/src/bea.f |only seriation-1.5.6/seriation/DESCRIPTION | 21 seriation-1.5.6/seriation/MD5 | 80 +- seriation-1.5.6/seriation/NEWS.md | 18 seriation-1.5.6/seriation/R/AAA_check_installed.R | 8 seriation-1.5.6/seriation/R/AAA_color_palette.R | 6 seriation-1.5.6/seriation/R/AAA_registry_criterion.R | 43 + seriation-1.5.6/seriation/R/AAA_registry_seriate.R | 51 + seriation-1.5.6/seriation/R/AAA_seriation-package.R | 4 seriation-1.5.6/seriation/R/Townships.R | 4 seriation-1.5.6/seriation/R/criterion.matrix.R | 45 - seriation-1.5.6/seriation/R/gghmap.R | 2 seriation-1.5.6/seriation/R/register_DendSer.R | 10 seriation-1.5.6/seriation/R/register_tsne.R | 4 seriation-1.5.6/seriation/R/register_umap.R | 8 seriation-1.5.6/seriation/R/ser_dist.R | 66 +- seriation-1.5.6/seriation/R/seriate.R | 40 - seriation-1.5.6/seriation/R/seriate_AOE.R | 2 seriation-1.5.6/seriation/R/seriate_BEA.R | 37 - seriation-1.5.6/seriation/R/seriate_CA.R | 2 seriation-1.5.6/seriation/R/seriate_QAP.R | 4 seriation-1.5.6/seriation/README.md | 255 ++++----- seriation-1.5.6/seriation/build/partial.rdb |binary seriation-1.5.6/seriation/build/vignette.rds |binary seriation-1.5.6/seriation/inst/doc/seriation.pdf |binary seriation-1.5.6/seriation/man/Townships.Rd | 4 seriation-1.5.6/seriation/man/hmap.Rd | 2 seriation-1.5.6/seriation/man/palette.Rd | 5 seriation-1.5.6/seriation/man/register_umap.Rd | 4 seriation-1.5.6/seriation/man/registry_for_seriaiton_methods.Rd | 17 seriation-1.5.6/seriation/man/ser_dist.Rd | 59 +- seriation-1.5.6/seriation/man/seriate.Rd | 41 + seriation-1.5.6/seriation/man/seriation-package.Rd | 4 seriation-1.5.6/seriation/src/criterion.c | 46 + seriation-1.5.6/seriation/src/dist.c | 2 seriation-1.5.6/seriation/src/init.c | 10 seriation-1.5.6/seriation/src/lt.h | 4 seriation-1.5.6/seriation/src/optimal.c | 46 - seriation-1.5.6/seriation/src/pathdist.c | 2 seriation-1.5.6/seriation/src/stress.c | 280 +++++----- seriation-1.5.6/seriation/tests/testthat/test-zzz_seriate_extra.R | 8 42 files changed, 701 insertions(+), 543 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 1.5-1 dated 2023-09-19 and 1.5-2 dated 2024-08-19
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/rugarch-tests.R | 2 +- README.md | 2 ++ build/vignette.rds |binary inst/doc/Introduction_to_the_rugarch_package.pdf |binary src/distributions.c | 20 ++++++++++---------- 8 files changed, 29 insertions(+), 22 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014
<DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic
analysis of functional data through phase and amplitude separation.
Author: J. Derek Tucker [aut, cre] ,
Aymeric Stamm [ctb]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 2.3.1 dated 2024-07-18 and 2.3.2 dated 2024-08-19
DESCRIPTION | 8 MD5 | 51 +-- NAMESPACE | 5 NEWS.md | 5 R/geometry.R | 92 +++++ R/jointfPCA.R | 517 +++++++++++++++++++++++-------- R/multiple_align_functions.R | 183 ++++++---- R/plot.fdawarp.R | 10 R/plot.hfpca.R | 71 ++-- R/plot.jfpca.R | 74 +++- R/plot.jfpcah.R |only R/plot.vfpca.R | 124 +++++-- R/predict.hfpca.R | 39 +- R/predict.jfpca.R | 52 +-- R/predict.jfpcah.R |only R/predict.vfpca.R | 37 +- R/time-warping.R | 134 ++++---- README.md | 4 man/figures/README-1d_aligned_plot-1.png |binary man/figures/README-1d_aligned_plot-2.png |binary man/figures/README-1d_aligned_plot-3.png |binary man/figures/README-1d_aligned_plot-4.png |binary man/figures/README-1d_aligned_plot-5.png |binary man/figures/README-1d_aligned_plot-6.png |only man/figures/README-1d_curve_plot-1.png |binary man/gam_to_h.Rd |only man/h_to_gam.Rd |only man/jointFPCAh.Rd |only man/predict.jfpcah.Rd |only man/v_to_gam.Rd | 2 30 files changed, 981 insertions(+), 427 deletions(-)
Title: Tukey g-&-h Distribution
Description: Functions for density, cumulative density, quantile and simulation
of Tukey g-and-h (1977) distributions. The quantile-based
transformation (Hoaglin 1985 <doi:10.1002/9781118150702.ch11>) and its
reverse transformation, as well as the letter-value based estimates
(Hoaglin 1985), are also provided.
Author: Tingting Zhan [aut, cre, cph],
Inna Chervoneva [ctb, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between TukeyGH77 versions 0.1.2 dated 2024-04-30 and 0.1.3 dated 2024-08-19
DESCRIPTION | 32 ++++++++++++++------------------ MD5 | 8 ++++---- R/vuniroot2.R | 3 --- build/partial.rdb |binary man/vuniroot2.Rd | 1 - 5 files changed, 18 insertions(+), 26 deletions(-)
Title: Spatial Regression Analysis
Description: A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal data using spatial weights matrices) contained up to now in 'spdep'. These model fitting functions include maximum likelihood methods for cross-sectional models proposed by 'Cliff' and 'Ord' (1973, ISBN:0850860369) and (1981, ISBN:0850860814), fitting methods initially described by 'Ord' (1975) <doi:10.1080/01621459.1975.10480272>. The models are further described by 'Anselin' (1988) <doi:10.1007/978-94-015-7799-1>. Spatial two stage least squares and spatial general method of moment models initially proposed by 'Kelejian' and 'Prucha' (1998) <doi:10.1023/A:1007707430416> and (1999) <doi:10.1111/1468-2354.00027> are provided. Impact methods and MCMC fitting methods proposed by 'LeSage' and 'Pace' (2009) <doi:10.1201/9781420064254> are implemented for the family of cross-sectional spatial regression models. Methods for fitting the log determinant term in maximu [...truncated...]
Author: Roger Bivand [cre, aut] ,
Gianfranco Piras [aut],
Luc Anselin [ctb],
Andrew Bernat [ctb],
Eric Blankmeyer [ctb],
Yongwan Chun [ctb],
Virgilio Gomez-Rubio [ctb],
Daniel Griffith [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
James LeSage [ctb],
Ange [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spatialreg versions 1.3-4 dated 2024-06-10 and 1.3-5 dated 2024-08-19
DESCRIPTION | 8 +-- MD5 | 40 +++++++-------- NEWS.md | 12 ++++ R/cyclical.R | 7 +- R/eigenw.R | 3 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/nb_igraph.R | 2 inst/doc/nb_igraph.Rmd | 5 + inst/doc/nb_igraph.html | 41 ++++++++++++---- inst/doc/sids_models.R | 6 +- inst/doc/sids_models.Rmd | 6 +- inst/doc/sids_models.html | 9 ++- man/SpatialFiltering.Rd | 2 man/eigenw.Rd | 3 - man/impacts.Rd | 2 man/invIrM.Rd | 4 - man/trW.Rd | 2 src/ml_sse.c | 116 +++++++++++++++++++++++----------------------- vignettes/nb_igraph.Rmd | 5 + vignettes/sids_models.Rmd | 6 +- 21 files changed, 170 insertions(+), 109 deletions(-)
Title: Network Visualization Using 'sigma.js'
Description: Interactive visualizations of graphs created with the 'igraph' package using a 'htmlwidgets' wrapper for the 'sigma.js' network visualization v2.4.0 <https://www.sigmajs.org/>, enabling to display several thousands of nodes. While several 'R' packages have been developed to interface 'sigma.js', all were developed for v1.x.x and none have migrated to v2.4.0 nor are they planning to. This package builds upon the 'sigmaNet' package, and users familiar with it will recognize the similar design approach. Two extensions have been added to the classic 'sigma.js' visualizations by overriding the underlying 'JavaScript' code, enabling to draw a frame around node labels, and to display labels on multiple lines by parsing line breaks. Other additional functionalities that did not require overriding 'sigma.js' code include toggling node visibility when clicked using a node attribute and highlighting specific edges. 'sigma.js' is currently preparing a stable release v3.0.0, and this package [...truncated...]
Author: Thomas Charlon [aut, cre] ,
CELEHS [aut] ,
PARSE Health [aut]
Maintainer: Thomas Charlon <charlon@protonmail.com>
Diff between sgraph versions 1.0.0 dated 2024-05-27 and 1.1.0 dated 2024-08-19
DESCRIPTION | 10 +++---- MD5 | 37 ++++++++++++++++----------- NAMESPACE | 6 ++++ NEWS.md |only R/kgraph_fit_example.R | 22 ++++++++++++++-- R/legend.R | 16 ++++++++++++ R/package.R | 2 - R/scale_graph.R |only R/sgraph_utils.R | 26 ++++++++----------- R/sigma_attrs.R | 17 ++++++++++++ R/sigma_shiny.R | 4 +-- build/vignette.rds |binary inst/doc/sgraph.Rmd | 6 ++-- inst/doc/sgraph.html | 60 +++++++++++++++------------------------------ inst/htmlwidgets/sgraph.js | 4 +-- man/add_listener.Rd |only man/get_color_map.Rd |only man/get_legend.Rd |only man/kgraph_to_lgraph.Rd |only man/l_graph_to_igraph.Rd |only man/scale_graph.Rd | 13 ++++++--- man/sigma_from_igraph.Rd | 4 +-- vignettes/sgraph.Rmd | 6 ++-- 23 files changed, 137 insertions(+), 96 deletions(-)
Title: Bayesian Graphical Models using MCMC
Description: Interface to the JAGS MCMC library.
Author: Martyn Plummer [aut, cre],
Alexey Stukalov [ctb],
Matt Denwood [ctb]
Maintainer: Martyn Plummer <martyn.plummer@gmail.com>
Diff between rjags versions 4-15 dated 2023-11-30 and 4-16 dated 2024-08-19
DESCRIPTION | 8 MD5 | 10 configure | 3256 +++++++++++++++++++++++++++++++------------------------- configure.ac | 6 src/jags.cc | 191 +-- src/parallel.cc | 29 6 files changed, 1956 insertions(+), 1544 deletions(-)
Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots.
Author: Myles Lewis [aut, cre]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between locuszoomr versions 0.3.1 dated 2024-07-03 and 0.3.2 dated 2024-08-19
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 3 +++ NEWS.md | 10 ++++++++++ R/link_LD.R | 10 ++++++---- R/locus.R | 27 ++++++++++++++++++++------- README.md | 6 ++++-- build/vignette.rds |binary inst/doc/locuszoomr.R | 11 ++++++++++- inst/doc/locuszoomr.Rmd | 22 ++++++++++++++++++---- inst/doc/locuszoomr.html | 32 +++++++++++++++++++++++--------- man/link_LD.Rd | 7 ++++--- man/locus.Rd | 8 ++++++-- vignettes/locuszoomr.Rmd | 22 ++++++++++++++++++---- 14 files changed, 139 insertions(+), 53 deletions(-)
Title: Design and Analysis of Hierarchical Composite Endpoints
Description: Simulate and analyze hierarchical composite endpoints. Win odds is the main analysis method, but other win statistics (win ratio, net benefit) are implemented as well in case of no censoring. See Gasparyan SB et al (2023) "Hierarchical Composite Endpoints in COVID-19: The DARE-19 Trial." Case Studies in Innovative Clinical Trials, 95-148. Chapman; Hall/CRC. <doi:10.1201/9781003288640-7>.
Author: Samvel B. Gasparyan [aut, cre]
Maintainer: Samvel B. Gasparyan <gasparyan.co@gmail.com>
Diff between hce versions 0.6.0 dated 2024-03-12 and 0.6.3 dated 2024-08-19
DESCRIPTION | 8 ++--- MD5 | 68 +++++++++++++++++++++++------------------- NAMESPACE | 2 + NEWS.md |only R/data.R | 32 ++++++++++++-------- R/simADHCE.R |only R/simHCE.R | 41 +++++++++++-------------- R/simORD.R |only build/vignette.rds |binary data/HCE1.rda |binary data/HCE2.rda |binary data/HCE3.rda |binary data/HCE4.rda |binary inst/doc/Introduction.R | 3 + inst/doc/Introduction.Rmd | 12 +++++-- inst/doc/Introduction.html | 72 +++++++++++++++++++++++++++------------------ inst/doc/Wins.R | 3 + inst/doc/Wins.Rmd | 4 ++ inst/doc/Wins.html | 3 + inst/doc/hce.R | 3 + inst/doc/hce.Rmd | 4 ++ inst/doc/hce.html | 3 + inst/doc/maraca.R | 3 + inst/doc/maraca.Rmd | 4 ++ inst/doc/maraca.html | 3 + man/HCE1.Rd | 8 +++-- man/HCE2.Rd | 8 +++-- man/HCE3.Rd | 8 +++-- man/HCE4.Rd | 8 +++-- man/simADHCE.Rd |only man/simHCE.Rd | 13 +++++--- man/simORD.Rd |only vignettes/Introduction.Rmd | 12 +++++-- vignettes/REFERENCES.bib | 11 ++++++ vignettes/Wins.Rmd | 4 ++ vignettes/hce.Rmd | 4 ++ vignettes/hex-hce.png |only vignettes/maraca.Rmd | 4 ++ 38 files changed, 223 insertions(+), 125 deletions(-)
Title: Matrix Exponential, Log, 'etc'
Description: Computation of the matrix exponential, logarithm, sqrt,
and related quantities, using traditional and modern methods.
Author: Martin Maechler [aut, cre] ,
Christophe Dutang [aut] ,
Vincent Goulet [aut] ,
Douglas Bates [ctb] ,
David Firth [ctb] ),
Marina Shapira [ctb] ),
Michael Stadelmann [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between expm versions 0.999-9 dated 2024-01-11 and 1.0-0 dated 2024-08-19
ChangeLog | 23 ++++++ DESCRIPTION | 8 +- MD5 | 66 ++++++++--------- NAMESPACE | 1 R/balance.R | 12 ++- R/expm.R | 58 +++++++++------ R/expm2.R | 4 - build/partial.rdb |binary build/vignette.rds |binary demo/balanceTst.R | 21 +++++ demo/exact-fn.R | 11 +- demo/expm.R | 24 ++++-- inst/doc/expm.pdf |binary inst/test-tools.R | 19 +++++ man/balance.Rd | 14 ++- man/expAtv.Rd | 3 man/expm.Higham08.Rd | 2 man/expm.Rd | 50 ++++++++++--- man/matpow.Rd | 9 ++ src/Makevars | 4 + src/R_dgebal.c | 84 ++++++++++++++++++++-- src/expm-eigen.c | 2 src/expm.c | 9 +- src/expm.h | 1 src/init.c | 1 src/logm-eigen.c | 2 src/matexp_MH09.c | 65 ++++++++++++----- src/matpow.c | 65 +++++++++++++++-- src/matpow.h | 4 - tests/bal-ex.R | 4 - tests/ex.R | 10 ++ tests/ex2.R | 33 ++++++++ tests/exact-ex.R | 191 +++++++++++++++++++++++++++++++++++++-------------- tests/matpow-ex.R | 3 34 files changed, 612 insertions(+), 191 deletions(-)
Title: The MCFS-ID Algorithm for Feature Selection and Interdependency
Discovery
Description: MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data. M. Draminski, J. Koronacki (2018) <doi:10.18637/jss.v085.i12>.
Author: Michal Draminski [aut, cre],
Jacek Koronacki [aut],
Julian Zubek [ctb]
Maintainer: Michal Draminski <michal.draminski@ipipan.waw.pl>
Diff between rmcfs versions 1.3.5 dated 2021-09-18 and 1.3.6 dated 2024-08-19
DESCRIPTION | 13 +- MD5 | 67 ++++++------ NAMESPACE | 1 NEWS.md | 6 + R/onLoad.R | 2 R/rmcfs.R | 38 +++--- R/rmcfs.plot.R | 16 +- R/utils.R | 10 - build/partial.rdb |only build/vignette.rds |binary inst/java/dmLab.jar |binary java/src/dmLab/DMLabInfo.java | 4 java/src/dmLab/array/FArray.java | 7 + java/src/dmLab/array/saver/Array2ADX.java | 31 ++++- java/src/dmLab/array/saver/Array2String.java | 21 +++ java/src/dmLab/experiment/ExperimentParams.java | 3 java/src/dmLab/mcfs/MCFS.java | 2 java/src/dmLab/mcfs/mcfsEngine/MCFSExperiment.java | 49 ++++++-- java/src/dmLab/mcfs/mcfsEngine/arrays/MCFSArrays.java | 12 +- java/src/dmLab/mcfs/mcfsEngine/framework/MCFSFramework.java | 4 java/src/dmLab/mcfs/mcfsEngine/modules/Projection.java | 3 java/src/dmLab/mcfs/mcfsEngine/modules/Split.java | 13 +- java/src/dmLab/utils/FileUtils.java | 38 +++++- java/src/dmLab/utils/GeneralUtils.java | 37 +++++- man/build.idgraph.Rd | 2 man/mcfs.Rd | 21 +++ man/plot.mcfs.Rd | 2 man/write.arff.Rd | 2 tests/testthat/test-io.R | 3 tests/testthat/test-man.build.idgraph.R | 3 tests/testthat/test-man.mcfs.R | 3 tests/testthat/test-man.plot.idgraph.R | 1 tests/testthat/test-mcfs.M5.R | 3 tests/testthat/test-mcfs.R | 4 tests/testthat/test-mcfs.mode2.R | 5 35 files changed, 294 insertions(+), 132 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that
the user is probably willing to make: 'import()' and 'export()' determine
the data format from the file extension, reasonable defaults are used for
data import and export, web-based import is natively supported (including
from SSL/HTTPS), compressed files can be read directly, and fast import
packages are used where appropriate. An additional convenience function,
'convert()', provides a simple method for converting between file types.
Author: Jason Becker [aut],
Chung-hong Chan [aut, cre] ,
David Schoch [aut] ,
Geoffrey CH Chan [ctb],
Thomas J. Leeper [aut] ,
Christopher Gandrud [ctb],
Andrew MacDonald [ctb],
Ista Zahn [ctb],
Stanislaus Stadlmann [ctb],
Ruaridh Williamson [ctb],
Patrick K [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between rio versions 1.2.1 dated 2024-07-26 and 1.2.2 dated 2024-08-19
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++++----- NEWS.md | 4 ++++ inst/doc/extension.Rmd |only inst/doc/labelled.Rmd |only inst/doc/labelled.html | 4 ++-- inst/doc/philosophy.Rmd |only inst/doc/remap.Rmd |only inst/doc/rio.Rmd |only inst/doc/rio.html | 6 +++--- vignettes/rio.Rmd | 2 +- 11 files changed, 23 insertions(+), 14 deletions(-)
Title: Manage Spatial Metadata for Known Locations
Description: Utility functions for discovering and managing metadata
associated with spatially unique "known locations". Applications include
all fields of environmental monitoring (e.g. air and water quality) where
data are collected at stationary sites.
Author: Jonathan Callahan [aut, cre],
Eli Grosman [ctb],
Oliver Fogelin [ctb]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaLocationUtils versions 0.4.3 dated 2024-01-24 and 0.4.4 dated 2024-08-19
DESCRIPTION | 6 +++--- MD5 | 21 +++++++++++---------- NEWS.md | 7 ++++++- R/clusterByDistance.R | 23 ++++++++++++++++++++--- build/vignette.rds |binary data/id_monitors_500.rda |binary data/or_monitors_500.rda |binary data/wa_airfire_meta.rda |binary data/wa_monitors_500.rda |binary inst/doc/MazamaLocationUtils.R | 2 +- inst/doc/MazamaLocationUtils.html | 4 ++-- tests/testthat/test-clusterByDistance.R |only 12 files changed, 43 insertions(+), 20 deletions(-)
More information about MazamaLocationUtils at CRAN
Permanent link
Title: Multiple RMST-Based Tests in General Factorial Designs
Description: We implemented multiple tests based on the restricted mean survival time (RMST) for general factorial designs as described in Munko et al. (2024) <doi:10.1002/sim.10017>. Therefore, an asymptotic test, a groupwise bootstrap test, and a permutation test are incorporated with a Wald-type test statistic. The asymptotic and groupwise bootstrap test take the asymptotic exact dependence structure of the test statistics into account to gain more power. Furthermore, confidence intervals for RMST contrasts can be calculated and plotted and a stepwise extension that can improve the power of the multiple tests is available.
Author: Marc Ditzhaus [aut],
Dennis Dobler [aut],
Marc Kindop [aut],
Merle Munko [aut, cre]
Maintainer: Merle Munko <merle.munko@ovgu.de>
Diff between GFDrmst versions 0.1.0 dated 2024-03-04 and 0.1.1 dated 2024-08-19
DESCRIPTION | 6 - MD5 | 10 +- R/GFDrmstGUI.R | 22 +++++- R/Hilfsfunktionen.R | 181 ++++++++++++++++++++++++++++++++++++++++++---------- R/test_functions.R | 162 ++++++++++++++++++++++++++++++++++++++-------- man/RMST.test.Rd | 18 ++++- 6 files changed, 327 insertions(+), 72 deletions(-)
Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation of hash
digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32',
'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128'
algorithms) permitting easy comparison of R language objects, as well as functions
such as'hmac()' to create hash-based message authentication code. Please note that
this package is not meant to be deployed for cryptographic purposes for which more
comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.
Author: Dirk Eddelbuettel [aut, cre] ,
Antoine Lucas [ctb],
Jarek Tuszynski [ctb],
Henrik Bengtsson [ctb] ,
Simon Urbanek [ctb] ,
Mario Frasca [ctb],
Bryan Lewis [ctb],
Murray Stokely [ctb],
Hannes Muehleisen [ctb],
Duncan Murdoch [ctb],
Jim Hester [ctb],
Wu [...truncated...]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between digest versions 0.6.36 dated 2024-06-23 and 0.6.37 dated 2024-08-19
ChangeLog | 18 ++++++ DESCRIPTION | 99 ++++++++++++++++++++++++++++++---- MD5 | 10 +-- README.md | 4 - inst/doc/sha1.html | 150 +++++++++++++++++++++++++++-------------------------- src/raes.c | 8 +- 6 files changed, 194 insertions(+), 95 deletions(-)
Title: Bayesian Deep Gaussian Processes using MCMC
Description: Performs Bayesian posterior inference for deep Gaussian processes
following Sauer, Gramacy, and Higdon (2023, <doi:10.48550/arXiv.2012.08015>). See Sauer
(2023, <http://hdl.handle.net/10919/114845>) for comprehensive methodological
details and <https://bitbucket.org/gramacylab/deepgp-ex/> for a variety of
coding examples. Models are trained through MCMC including elliptical
slice sampling of latent Gaussian layers and Metropolis-Hastings
sampling of kernel hyperparameters. Vecchia-approximation for faster
computation is implemented following Sauer, Cooper, and Gramacy
(2023, <doi:10.48550/arXiv.2204.02904>). Optional monotonic warpings are implemented
following Barnett et al. (2024, <doi:10.48550/arXiv.2408.01540>). Downstream tasks include sequential design
through active learning Cohn/integrated mean squared error
(ALC/IMSE; Sauer, Gramacy, and Higdon, 2023), optimization through
expected improvement (EI; Gramacy, Sauer, and Wycoff, 2022 <doi:10.4 [...truncated...]
Author: Annie S. Booth [aut, cre]
Maintainer: Annie S. Booth <annie_booth@ncsu.edu>
Diff between deepgp versions 1.1.2 dated 2024-04-28 and 1.1.3 dated 2024-08-19
deepgp-1.1.2/deepgp/R/general.R |only deepgp-1.1.2/deepgp/src/general.c |only deepgp-1.1.2/deepgp/src/general.h |only deepgp-1.1.3/deepgp/DESCRIPTION | 19 + deepgp-1.1.3/deepgp/MD5 | 89 ++++---- deepgp-1.1.3/deepgp/NAMESPACE | 1 deepgp-1.1.3/deepgp/R/ALC.R | 10 deepgp-1.1.3/deepgp/R/IMSE.R | 7 deepgp-1.1.3/deepgp/R/RcppExports.R | 4 deepgp-1.1.3/deepgp/R/checks.R | 92 ++++++-- deepgp-1.1.3/deepgp/R/continue.R | 145 +++++++++---- deepgp-1.1.3/deepgp/R/deepgp-package.R | 14 - deepgp-1.1.3/deepgp/R/fit.R | 282 ++++++++++++++++----------- deepgp-1.1.3/deepgp/R/gibbs.R | 123 ++++++++++- deepgp-1.1.3/deepgp/R/gibbs_vecchia.R | 114 +++++++++- deepgp-1.1.3/deepgp/R/mcmc.R | 124 +++++++++-- deepgp-1.1.3/deepgp/R/mcmc_vecchia.R | 89 +++++++- deepgp-1.1.3/deepgp/R/misc.R |only deepgp-1.1.3/deepgp/R/plot.R | 276 ++++++++++++++------------ deepgp-1.1.3/deepgp/R/predict.R | 140 ++++++++----- deepgp-1.1.3/deepgp/R/predict_vecchia.R | 183 +++++++++++------ deepgp-1.1.3/deepgp/R/trim.R | 15 + deepgp-1.1.3/deepgp/README.md | 14 + deepgp-1.1.3/deepgp/inst/doc/deepgp.R | 31 ++ deepgp-1.1.3/deepgp/inst/doc/deepgp.Rmd | 75 ++++++- deepgp-1.1.3/deepgp/inst/doc/deepgp.html | 219 +++++++++++++------- deepgp-1.1.3/deepgp/man/ALC.Rd | 6 deepgp-1.1.3/deepgp/man/IMSE.Rd | 7 deepgp-1.1.3/deepgp/man/continue.Rd | 2 deepgp-1.1.3/deepgp/man/crps.Rd | 7 deepgp-1.1.3/deepgp/man/deepgp-package.Rd | 12 - deepgp-1.1.3/deepgp/man/fit_one_layer.Rd | 53 ++--- deepgp-1.1.3/deepgp/man/fit_three_layer.Rd | 47 ++-- deepgp-1.1.3/deepgp/man/fit_two_layer.Rd | 98 +++++---- deepgp-1.1.3/deepgp/man/plot.Rd | 22 +- deepgp-1.1.3/deepgp/man/predict.Rd | 9 deepgp-1.1.3/deepgp/man/rmse.Rd | 7 deepgp-1.1.3/deepgp/man/score.Rd | 7 deepgp-1.1.3/deepgp/man/sq_dist.Rd | 2 deepgp-1.1.3/deepgp/man/trim.Rd | 4 deepgp-1.1.3/deepgp/src/RcppExports.cpp | 14 + deepgp-1.1.3/deepgp/src/alc.c | 2 deepgp-1.1.3/deepgp/src/approx.cpp |only deepgp-1.1.3/deepgp/src/imspe.c | 2 deepgp-1.1.3/deepgp/src/invdet.c | 2 deepgp-1.1.3/deepgp/src/misc.c |only deepgp-1.1.3/deepgp/src/misc.h |only deepgp-1.1.3/deepgp/vignettes/deepgp.Rmd | 75 ++++++- deepgp-1.1.3/deepgp/vignettes/references.bib | 39 ++- 49 files changed, 1703 insertions(+), 780 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: Hierarchical continuous (and discrete) time state space modelling, for linear
and nonlinear systems measured by continuous variables, with limited support for
binary data. The subject specific dynamic system is modelled as a stochastic
differential equation (SDE) or difference equation, measurement models are typically multivariate normal factor models.
Linear mixed effects SDE's estimated via maximum likelihood and optimization are the default.
Nonlinearities, (state dependent parameters) and random effects on all parameters
are possible, using either max likelihood / max a posteriori optimization
(with optional importance sampling) or Stan's Hamiltonian Monte Carlo sampling.
See <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf>
for details. Priors may be used. For the conceptual overview of the hierarchical Bayesian
linear SDE approach,
see <https://www.researchgate.net/publication/324093594_Hierarchical_Bayesian_Continuous_Time_Dynamic_Mod [...truncated...]
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph],
Trustees of Columbia University [cph]
Maintainer: Charles Driver <charles.driver2@uzh.ch>
Diff between ctsem versions 3.10.0 dated 2024-05-09 and 3.10.1 dated 2024-08-19
DESCRIPTION | 8 MD5 | 85 +- NAMESPACE | 2 NEWS.md | 8 R/covml.R | 78 +- R/ctCheckFit.R | 10 R/ctDiscretePars.R | 15 R/ctFitMultiModel.R | 19 R/ctKalman.R | 201 ++++-- R/ctStanData.R | 40 - R/ctStanFit.R | 21 R/ctStanKalman.R | 2 R/ctStanModel.R | 4 R/ctStanModelWriter.R | 182 ++--- R/ctSummarise.R | 62 +- R/ctsem-package.R | 27 R/sgd.R | 2 R/stanoptimis.R | 5 build/vignette.rds |binary data/ctstantestdat.rda |binary data/ctstantestfit.rda |binary inst/CITATION | 30 inst/doc/hierarchicalmanual.pdf |binary inst/stan/cov.stan | 104 +-- inst/stan/ctsm.stan | 150 +--- inst/stan/ctsmgen.stan | 150 +--- man/ctFitMultiModel.Rd | 8 man/ctKalman.Rd | 2 man/ctPredictTIP.Rd |only man/ctStanDiscretePars.Rd | 11 man/ctStanDiscreteParsPlot.Rd | 2 man/ctStanFit.Rd | 3 man/test_isclose.Rd |only tests/testthat/ctBinaryGaussianMix.R |only tests/testthat/test-corrcheck.R | 16 tests/testthat/test-ctLOO.R | 20 tests/testthat/test-ctRaschExampleTest.R | 19 tests/testthat/test-dtVct.R | 8 tests/testthat/test-knownFits.R | 4 tests/testthat/test-stantipred.R | 12 tests/testthat/test-sunspots.R | 6 tests/testthat/test-tdeffectvariation_covtest.R | 729 +++++++++++------------- tests/testthat/test-timevarying.R | 56 - tests/testthat/test-ukfpoptest.R | 15 tests/testthat/test_behavGenNLcor.R | 4 45 files changed, 1034 insertions(+), 1086 deletions(-)
Title: Likelihood Based Inference for ARIMA Modeling
Description: Estimating and analyzing auto regressive integrated moving average
(ARIMA) models. The primary function in this package is arima(), which fits
an ARIMA model to univariate time series data using a random restart
algorithm. This approach frequently leads to models that have model
likelihood greater than or equal to that of the likelihood obtained by
fitting the same model using the arima() function from the 'stats' package.
This package enables proper optimization of model likelihoods, which is a
necessary condition for performing likelihood ratio tests. This package
relies heavily on the source code of the arima() function of the 'stats'
package. For more information, please see Jesse Wheeler and Edward L.
Ionides (2023) <doi:10.48550/arXiv.2310.01198>.
Author: Jesse Wheeler [aut, cre, cph],
Noel McAllister [aut],
Dhajanae Sylvertooth [aut],
Edward Ionides [ctb],
Brian Ripley [ctb] ,
R Core Team [cph]
Maintainer: Jesse Wheeler <jeswheel@umich.edu>
Diff between arima2 versions 3.1.0 dated 2023-11-16 and 3.3.0 dated 2024-08-19
arima2-3.1.0/arima2/man/figures/README-example-1.png |only arima2-3.1.0/arima2/man/figures/README-pressure-1.png |only arima2-3.1.0/arima2/man/figures/README-unnamed-chunk-4-1.png |only arima2-3.1.0/arima2/man/figures/README-unnamed-chunk-5-1.png |only arima2-3.3.0/arima2/DESCRIPTION | 10 arima2-3.3.0/arima2/MD5 | 28 - arima2-3.3.0/arima2/NEWS.md | 16 arima2-3.3.0/arima2/R/arima.R | 8 arima2-3.3.0/arima2/R/data.R | 6 arima2-3.3.0/arima2/R/sample_ARMA_coef.R | 295 +++-------- arima2-3.3.0/arima2/README.md | 46 - arima2-3.3.0/arima2/man/figures/README-PlotARMAresults-1.png |binary arima2-3.3.0/arima2/man/figures/README-PlotARMAresults-2.png |binary arima2-3.3.0/arima2/man/miHuron_level.Rd | 4 arima2-3.3.0/arima2/man/sample_ARMA_coef.Rd | 17 arima2-3.3.0/arima2/tests/testthat/test-ARMApolyroots.R | 3 arima2-3.3.0/arima2/tests/testthat/test-sample_ARMA_coef.R | 30 - 17 files changed, 197 insertions(+), 266 deletions(-)
Title: Constructing and Interacting with Databases of Presentations
Description: Provides methods for constructing and maintaining a database of presentations in R. The presentations are either ones that the user gives or gave or presentations at a particular event or event series. The package also provides a plot method for the interactive mapping of the presentations using 'leaflet' by grouping them according to country, city, year and other presentation attributes. The markers on the map come with popups providing presentation details (title, institution, event, links to materials and events, and so on).
Author: Ioannis Kosmidis [aut, cre]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between semnar versions 0.8.1 dated 2022-11-03 and 0.8.2 dated 2024-08-19
DESCRIPTION | 10 +- MD5 | 16 +-- NEWS.md | 7 + R/add_presentation.R | 6 - R/complete_geo.R | 16 ++- R/semnar-package.R | 3 README.md | 165 ++++++++++++++++--------------------- inst/tinytest/test-guess_address.R | 6 - man/semnar-package.Rd | 4 9 files changed, 116 insertions(+), 117 deletions(-)
Title: Smooth Survival Models, Including Generalized Survival Models
Description: R implementation of generalized survival models (GSMs), smooth accelerated failure time (AFT) models and Markov multi-state models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth <doi:10.1177/0962280216664760>. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects <doi:10.1002/sim.7451>, and copulas. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0 [...truncated...]
Author: Mark Clements [aut, cre],
Xing-Rong Liu [aut],
Benjamin Christoffersen [aut],
Paul Lambert [ctb],
Lasse Hjort Jakobsen [ctb],
Alessandro Gasparini [ctb],
Gordon Smyth [cph],
Patrick Alken [cph],
Simon Wood [cph],
Rhys Ulerich [cph]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between rstpm2 versions 1.6.3 dated 2023-12-05 and 1.6.4 dated 2024-08-19
DESCRIPTION | 13 +- MD5 | 64 +++++----- NAMESPACE | 3 R/RcppExports.R | 8 + R/aft.R | 140 ++++++++++++++++------- R/multistate.R | 5 R/pm2-3.R | 13 +- R/vuniroot.R | 13 +- build/vignette.rds |binary inst/doc/Introduction.pdf |binary inst/doc/SimpleGuide.pdf |binary inst/doc/equations.pdf |binary inst/doc/multistate.pdf |binary inst/doc/predictnl.pdf |binary inst/working_code.R | 108 +++++++++++++++++- man/aft-class.Rd | 4 man/aft.Rd | 6 - man/cox.tvc.Rd | 2 man/gsm.Rd | 4 man/markov_msm.Rd | 252 +++++++++++++++++++++--------------------- man/nsx.Rd | 2 man/nsxD.Rd | 2 man/predict-methods.Rd | 6 - man/pstpm2-class.Rd | 2 man/stpm2-class.Rd | 2 man/tvcCoxph-class.Rd | 4 src/RcppExports.cpp | 31 +++++ src/aft.cpp | 5 src/package_init.c | 8 - src/vuniroot.cpp | 38 ++---- tests/testthat/test_base.R | 22 +++ tests/testthat/test_delayed.R | 19 +++ tests/testthat/test_missing.R | 62 ++++++++++ 33 files changed, 572 insertions(+), 266 deletions(-)
Title: 'HydroPortail' Statistical Functions
Description: Statistical functions used in the French 'HydroPortail' <https://hydro.eaufrance.fr/>.
This includes functions to estimate distributions, quantile curves and uncertainties, along with various other utilities.
Technical details are available (in French) in Renard (2016) <https://hal.inrae.fr/hal-02605318>.
Author: Benjamin Renard [aut, cre, cph]
,
INRAE [fnd],
Ministere de la Transition Ecologique - SCHAPI [fnd],
European Commission [fnd]
Maintainer: Benjamin Renard <benjamin.renard@inrae.fr>
Diff between HydroPortailStats versions 1.0.3 dated 2023-05-25 and 1.1.0 dated 2024-08-19
DESCRIPTION | 8 ++-- MD5 | 25 ++++++++----- NAMESPACE | 7 +++ NEWS.md | 12 +++++- R/Distributions_lib.R | 81 ++++++++++++++++++++++++++++++++++++++++++-- R/Estimation_BAY.R | 11 ++--- R/Estimation_HBay.R |only R/Hydro3Stats.R | 10 +++-- README.md | 16 ++++---- data/distInfo.RData |binary man/GenerateWithinBounds.Rd |only man/GetEstimate_BAY.Rd | 2 - man/GetEstimate_HBay.Rd |only man/HBay_Plot.Rd |only man/Hydro3_HBay.Rd |only man/Import_HBayConfig.Rd |only man/readme/logo.png |only 17 files changed, 138 insertions(+), 34 deletions(-)
More information about HydroPortailStats at CRAN
Permanent link
Title: DPQ (Density, Probability, Quantile) Distribution Computations
using MPFR
Description: An extension to the 'DPQ' package with computations for 'DPQ'
(Density (pdf), Probability (cdf) and Quantile) functions, where
the functions here partly use the 'Rmpfr' package and hence the
underlying 'MPFR' and 'GMP' C libraries.
Author: Martin Maechler [aut, cre]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between DPQmpfr versions 0.3-2 dated 2023-12-05 and 0.3-3 dated 2024-08-19
DESCRIPTION | 13 - MD5 | 32 ++- NAMESPACE | 20 ++ R/dpoisEr.R | 14 + R/dpq-mpfrized.R | 31 +++ R/hyperDist.R | 26 ++- R/t-nonc.R | 438 +++++++++++++++++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary inst/NEWS.Rd | 38 ++++ man/algdivM.Rd |only man/dnt.Rd | 87 ++++++---- man/gam1M.Rd |only man/lgamma1pM.Rd |only man/pbetaD94.Rd | 2 man/pbeta_ser.Rd |only man/pnormLU.Rd | 2 man/stirlerrM.Rd | 108 +++++++----- man/utils.Rd | 2 tests/beta-Ding94.R | 2 19 files changed, 696 insertions(+), 119 deletions(-)
Title: Augments 'ASReml-R' in Fitting Mixed Models and Packages
Generally in Exploring Prediction Differences
Description: Assists in automating the selection of terms to include in mixed models when
'asreml' is used to fit the models. Procedures are available for choosing models that
conform to the hierarchy or marginality principle, for fitting and choosing between
two-dimensional spatial models using correlation, natural cubic smoothing spline and
P-spline models. A history of the fitting of a sequence of models is kept in a data frame.
Also used to compute functions and contrasts of, to investigate differences between and
to plot predictions obtained using any model fitting function. The content falls into
the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model
selection and description functions, (iv) Model diagnostics and simulation functions,
(v) Prediction production and presentation functions, (vi) Response transformation
functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions
(for further details see 'asremlPlus-package' in help). The [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between asremlPlus versions 4.4.35 dated 2024-06-19 and 4.4.38 dated 2024-08-19
asremlPlus-4.4.35/asremlPlus/R/spatial.utilities.v1.r |only asremlPlus-4.4.38/asremlPlus/DESCRIPTION | 8 asremlPlus-4.4.38/asremlPlus/MD5 | 50 - asremlPlus-4.4.38/asremlPlus/R/REMLRTIC.v4.r | 5 asremlPlus-4.4.38/asremlPlus/R/alldiffs.v4.r | 9 asremlPlus-4.4.38/asremlPlus/R/asrem.R |only asremlPlus-4.4.38/asremlPlus/R/asremlPlusObjUtils.r |only asremlPlus-4.4.38/asremlPlus/R/asremlPlusUtilities.r | 294 ------- asremlPlus-4.4.38/asremlPlus/R/reml4.v11.r | 372 --------- asremlPlus-4.4.38/asremlPlus/R/spatial.funcs.v8.r | 398 +++++++--- asremlPlus-4.4.38/asremlPlus/R/spatial.funcs.v9.r |only asremlPlus-4.4.38/asremlPlus/R/spatial.utilities.v2.r |only asremlPlus-4.4.38/asremlPlus/build/partial.rdb |binary asremlPlus-4.4.38/asremlPlus/inst/NEWS.Rd | 18 asremlPlus-4.4.38/asremlPlus/inst/doc/Ladybird.asreml.pdf |binary asremlPlus-4.4.38/asremlPlus/inst/doc/Ladybird.lm.pdf |binary asremlPlus-4.4.38/asremlPlus/inst/doc/Wheat.analysis.pdf |binary asremlPlus-4.4.38/asremlPlus/inst/doc/Wheat.infoCriteria.pdf |binary asremlPlus-4.4.38/asremlPlus/inst/doc/WheatSpatialModels.pdf |binary asremlPlus-4.4.38/asremlPlus/inst/doc/asremlPlus-manual.pdf |binary asremlPlus-4.4.38/asremlPlus/man/addSpatialModel.asrtests.Rd | 9 asremlPlus-4.4.38/asremlPlus/man/addSpatialModelOnIC.asrtests.Rd | 9 asremlPlus-4.4.38/asremlPlus/man/chooseSpatialModelOnIC.asrtests.Rd | 8 asremlPlus-4.4.38/asremlPlus/man/pickLSDstatistics.alldiffs.Rd | 20 asremlPlus-4.4.38/asremlPlus/tests/testthat/data/summ703.rda |binary asremlPlus-4.4.38/asremlPlus/tests/testthat/test42SpatialModels.r | 33 asremlPlus-4.4.38/asremlPlus/tests/testthat/test42WheatSpatialVignette.r | 3 asremlPlus-4.4.38/asremlPlus/tests/testthat/test42alldiffsasr.r | 7 asremlPlus-4.4.38/asremlPlus/tests/testthat/testthat-problems.rds |only 29 files changed, 454 insertions(+), 789 deletions(-)
Title: Robust PCA by Projection Pursuit
Description: Provides functions for robust PCA by projection pursuit.
The methods are described in Croux et al. (2006) <doi:10.2139/ssrn.968376>,
Croux et al. (2013) <doi:10.1080/00401706.2012.727746>,
Todorov and Filzmoser (2013) <doi:10.1007/978-3-642-33042-1_31>.
Author: Peter Filzmoser [aut],
Heinrich Fritz [aut],
Klaudius Kalcher [aut],
Valentin Todorov [cre]
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between pcaPP versions 2.0-4-1 dated 2024-08-09 and 2.0-5 dated 2024-08-19
ChangeLog | 19 +++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- src/L1Median_VardiZhang.cpp | 3 +++ src/R_meal.cpp | 8 ++++++-- src/R_meal.h | 4 +++- 6 files changed, 40 insertions(+), 12 deletions(-)
Title: Discrete Event Simulation in R and C++, with Tools for
Cost-Effectiveness Analysis
Description: Discrete event simulation using both R and C++ (Karlsson et al 2016; <doi:10.1109/eScience.2016.7870915>). The C++ code is adapted from the SSIM library <https://www.inf.usi.ch/carzaniga/ssim/>, allowing for event-oriented simulation. The code includes a SummaryReport class for reporting events and costs by age and other covariates. The C++ code is available as a static library for linking to other packages. A priority queue implementation is given in C++ together with an S3 closure and a reference class implementation. Finally, some tools are provided for cost-effectiveness analysis.
Author: Mark Clements [aut, cre, cph],
Alexandra Jauhiainen [aut],
Andreas Karlsson [aut],
Antonio Carzaniga [cph],
University of Colorado [cph],
Pierre L'Ecuyer [cph]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between microsimulation versions 1.4.3 dated 2023-07-19 and 1.4.4 dated 2024-08-19
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/rcpp_hello_world.R | 17 ++++++++--------- inst/include/gsm.h | 6 ++++-- inst/include/microsimulation.h | 8 ++++++++ man/RNGStream.Rd | 12 ++++++------ man/microsimulation-package.Rd | 2 +- src/gsm.cpp | 26 ++++++++++++++++++++++++-- 8 files changed, 63 insertions(+), 32 deletions(-)
More information about microsimulation at CRAN
Permanent link
Title: Utility Functions, Datasets and Extended Examples for Survival
Analysis
Description: Utility functions, datasets and extended examples for survival analysis. This extends a range of other packages, some simple wrappers for time-to-event analyses, datasets, and extensive examples in HTML with R scripts. The package also supports the course Biostatistics III entitled "Survival analysis for epidemiologists in R".
Author: Annika Tillander [ctb],
Andreas Karlsson [aut],
Johan Zetterqvist [ctb],
Peter Strom [ctb],
Benedicte Delcoigne [ctb],
Mark Clements [aut, cre]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between biostat3 versions 0.1.9 dated 2023-10-27 and 0.2.1 dated 2024-08-19
DESCRIPTION | 12 ++++++------ MD5 | 37 ++++++++++++++++++++++++++----------- NAMESPACE | 7 +++++-- R/muhaz2.R | 26 +++++++++++++++++++++++--- build/partial.rdb |binary inst/doc/q1.R | 13 +++++++++++-- inst/doc/q10.R | 7 ++++--- inst/doc/q3.R | 9 +++++++-- inst/doc/q9.R | 8 +++++--- inst/doc/solutions/_extensions |only inst/doc/solutions/q1.qmd |only man/coxphHaz.Rd | 2 +- man/muhaz2.Rd | 21 +++++++++++++++++---- man/survrate.Rd | 4 ++-- 14 files changed, 107 insertions(+), 39 deletions(-)
Title: Scalable Joint Species Distribution Modeling
Description: A scalable and fast method for estimating joint Species Distribution Models (jSDMs) for big community data, including eDNA data. The package estimates a full (i.e. non-latent) jSDM with different response distributions (including the traditional multivariate probit model). The package allows to perform variation partitioning (VP) / ANOVA on the fitted models to separate the contribution of environmental, spatial, and biotic associations. In addition, the total R-squared can be further partitioned per species and site to reveal the internal metacommunity structure, see Leibold et al., <doi:10.1111/oik.08618>. The internal structure can then be regressed against environmental and spatial distinctiveness, richness, and traits to analyze metacommunity assembly processes. The package includes support for accounting for spatial autocorrelation and the option to fit responses using deep neural networks instead of a standard linear predictor. As described in Pichler & Hartig (2021) [...truncated...]
Author: Maximilian Pichler [aut, cre] ,
Florian Hartig [aut] ,
Wang Cai [ctb]
Maintainer: Maximilian Pichler <maximilian.pichler@biologie.uni-regensburg.de>
Diff between sjSDM versions 1.0.5 dated 2023-06-17 and 1.0.6 dated 2024-08-19
sjSDM-1.0.5/sjSDM/build/sjSDM.pdf |only sjSDM-1.0.5/sjSDM/inst/doc/Dependencies.R |only sjSDM-1.0.5/sjSDM/inst/doc/Dependencies.Rmd |only sjSDM-1.0.5/sjSDM/inst/doc/Dependencies.html |only sjSDM-1.0.5/sjSDM/inst/doc/sjSDM_Introduction.R |only sjSDM-1.0.5/sjSDM/man/plotInternalStructure.Rd |only sjSDM-1.0.5/sjSDM/tests/testthat/Rplots.pdf |only sjSDM-1.0.5/sjSDM/tests/testthat/testthat-problems.rds |only sjSDM-1.0.5/sjSDM/vignettes/Dependencies.Rmd |only sjSDM-1.0.5/sjSDM/vignettes/VENN.png |only sjSDM-1.0.5/sjSDM/vignettes/importance.png |only sjSDM-1.0.5/sjSDM/vignettes/internal.png |only sjSDM-1.0.6/sjSDM/DESCRIPTION | 17 sjSDM-1.0.6/sjSDM/MD5 | 124 sjSDM-1.0.6/sjSDM/NAMESPACE | 8 sjSDM-1.0.6/sjSDM/NEWS.md | 7 sjSDM-1.0.6/sjSDM/R/Rsquared.R | 5 sjSDM-1.0.6/sjSDM/R/anova.R | 496 +-- sjSDM-1.0.6/sjSDM/R/data.R |only sjSDM-1.0.6/sjSDM/R/importance.R | 11 sjSDM-1.0.6/sjSDM/R/install.R | 10 sjSDM-1.0.6/sjSDM/R/installation_help.R | 3 sjSDM-1.0.6/sjSDM/R/internalStructure.R |only sjSDM-1.0.6/sjSDM/R/plot.R | 4 sjSDM-1.0.6/sjSDM/R/sjSDM.R | 105 sjSDM-1.0.6/sjSDM/R/sjSDM_cv.R | 4 sjSDM-1.0.6/sjSDM/README.md | 351 -- sjSDM-1.0.6/sjSDM/build/stage23.rdb |binary sjSDM-1.0.6/sjSDM/build/vignette.rds |binary sjSDM-1.0.6/sjSDM/data |only sjSDM-1.0.6/sjSDM/inst/doc/sjSDM_Introduction.Rmd | 1186 +++----- sjSDM-1.0.6/sjSDM/inst/doc/sjSDM_Introduction.html | 1380 ++++------ sjSDM-1.0.6/sjSDM/inst/examples/Anova-example.R |only sjSDM-1.0.6/sjSDM/inst/examples/butterflies-example.R |only sjSDM-1.0.6/sjSDM/inst/examples/eucalypts-example.R |only sjSDM-1.0.6/sjSDM/inst/examples/importance-example.R | 2 sjSDM-1.0.6/sjSDM/inst/examples/plot.sjSDM-example.R | 8 sjSDM-1.0.6/sjSDM/inst/examples/predict-example.R |only sjSDM-1.0.6/sjSDM/inst/examples/sjSDM-example.R | 55 sjSDM-1.0.6/sjSDM/inst/python/sjSDM_py/__pycache__/__init__.cpython-310.pyc |only sjSDM-1.0.6/sjSDM/inst/python/sjSDM_py/__pycache__/dist_mvp.cpython-310.pyc |only sjSDM-1.0.6/sjSDM/inst/python/sjSDM_py/__pycache__/model_sjSDM.cpython-310.pyc |only sjSDM-1.0.6/sjSDM/inst/python/sjSDM_py/__pycache__/optimizer.cpython-310.pyc |only sjSDM-1.0.6/sjSDM/inst/python/sjSDM_py/__pycache__/utils_fa.cpython-310.pyc |only sjSDM-1.0.6/sjSDM/inst/python/sjSDM_py/model_sjSDM.py | 33 sjSDM-1.0.6/sjSDM/man/DNN.Rd | 55 sjSDM-1.0.6/sjSDM/man/Rsquared.Rd | 6 sjSDM-1.0.6/sjSDM/man/anova.sjSDM.Rd | 66 sjSDM-1.0.6/sjSDM/man/bioticStruct.Rd | 55 sjSDM-1.0.6/sjSDM/man/butterflies.Rd |only sjSDM-1.0.6/sjSDM/man/eucalypts.Rd |only sjSDM-1.0.6/sjSDM/man/getWeights.Rd | 4 sjSDM-1.0.6/sjSDM/man/importance.Rd | 11 sjSDM-1.0.6/sjSDM/man/installation_help.Rd | 66 sjSDM-1.0.6/sjSDM/man/internalStructure.Rd |only sjSDM-1.0.6/sjSDM/man/linear.Rd | 55 sjSDM-1.0.6/sjSDM/man/plot.sjSDM.DNN.Rd | 8 sjSDM-1.0.6/sjSDM/man/plot.sjSDM.Rd | 8 sjSDM-1.0.6/sjSDM/man/plot.sjSDManova.Rd | 20 sjSDM-1.0.6/sjSDM/man/plot.sjSDMinternalStructure.Rd |only sjSDM-1.0.6/sjSDM/man/plotAssemblyEffects.Rd |only sjSDM-1.0.6/sjSDM/man/plotsjSDMcoef.Rd | 10 sjSDM-1.0.6/sjSDM/man/predict.sjSDM.Rd | 27 sjSDM-1.0.6/sjSDM/man/print.sjSDManova.Rd | 58 sjSDM-1.0.6/sjSDM/man/print.sjSDMinternalStructure.Rd |only sjSDM-1.0.6/sjSDM/man/residuals.sjSDM.Rd |only sjSDM-1.0.6/sjSDM/man/simulate.sjSDM.Rd | 4 sjSDM-1.0.6/sjSDM/man/sjSDM.Rd | 102 sjSDM-1.0.6/sjSDM/man/summary.sjSDManova.Rd |only sjSDM-1.0.6/sjSDM/tests/testthat/test-1-anova.R | 16 sjSDM-1.0.6/sjSDM/tests/testthat/test-4-sjSDM.R | 14 sjSDM-1.0.6/sjSDM/tests/testthat/test-5-importance.R | 2 sjSDM-1.0.6/sjSDM/tests/testthat/test-7-plotsjSDM.R | 2 sjSDM-1.0.6/sjSDM/vignettes/build.R |only sjSDM-1.0.6/sjSDM/vignettes/jSDM-ANOVA.png |only sjSDM-1.0.6/sjSDM/vignettes/jSDM-structure.png |only sjSDM-1.0.6/sjSDM/vignettes/sjSDM_Introduction.Rmd | 1186 +++----- sjSDM-1.0.6/sjSDM/vignettes/sjSDM_Introduction.orig |only sjSDM-1.0.6/sjSDM/vignettes/unnamed-chunk-12-1.png |only sjSDM-1.0.6/sjSDM/vignettes/unnamed-chunk-13-1.png |only sjSDM-1.0.6/sjSDM/vignettes/unnamed-chunk-15-1.png |only sjSDM-1.0.6/sjSDM/vignettes/unnamed-chunk-17-1.png |only sjSDM-1.0.6/sjSDM/vignettes/unnamed-chunk-18-1.png |only 83 files changed, 2530 insertions(+), 3054 deletions(-)
Title: Scalable Robust Estimators with High Breakdown Point
Description: Robust Location and Scatter Estimation and Robust
Multivariate Analysis with High Breakdown Point:
principal component analysis (Filzmoser and Todorov (2013), <doi:10.1016/j.ins.2012.10.017>),
linear and quadratic discriminant analysis (Todorov and Pires (2007)),
multivariate tests (Todorov and Filzmoser (2010) <doi:10.1016/j.csda.2009.08.015>),
outlier detection (Todorov et al. (2010) <doi:10.1007/s11634-010-0075-2>).
See also Todorov and Filzmoser (2009) <urn:isbn:978-3838108148>,
Todorov and Filzmoser (2010) <doi:10.18637/jss.v032.i03> and
Boudt et al. (2019) <doi:10.1007/s11222-019-09869-x>.
Author: Valentin Todorov [aut, cre]
Maintainer: Valentin Todorov <valentin.todorov@chello.at>
Diff between rrcov versions 1.7-5 dated 2024-01-30 and 1.7-6 dated 2024-08-19
ChangeLog | 8 +++++ DESCRIPTION | 8 ++--- MD5 | 69 +++++++++++++++++++++++++------------------------- R/Pca.R | 6 +--- R/plot-utils.R | 30 ++++++++++++--------- build/partial.rdb |binary build/vignette.rds |only data/Appalachia.rda |binary data/Cars.rda |binary data/Cascades.rda |binary data/OsloTransect.rda |binary data/bus.rda |binary data/bushmiss.rda |binary data/diabetes.rda |binary data/fish.rda |binary data/fruit.rda |binary data/hemophilia.rda |binary data/ionosphere.rda |binary data/lmom32.rda |binary data/lmom33.rda |binary data/machines.rda |binary data/maryo.rda |binary data/octane.rda |binary data/olitos.rda |binary data/pottery.rda |binary data/rice.rda |binary data/salmon.rda |binary data/soil.rda |binary data/un86.rda |binary data/wages.rda |binary data/wolves.rda |binary inst/NEWS.Rd | 9 ++++++ inst/doc/rrcov.pdf |binary man/CovControlMcd.Rd | 2 - man/CovMcd.Rd | 2 - src/sest.c | 22 ++++++++------- 36 files changed, 89 insertions(+), 67 deletions(-)
Title: Bayesian Summary Data Models for Mendelian Randomization Studies
Description: Bayesian estimation of inverse variance weighted (IVW),
Burgess et al. (2013) <doi:10.1002/gepi.21758>, and MR-Egger, Bowden
et al. (2015) <doi:10.1093/ije/dyv080>, summary data models for
Mendelian randomization analyses.
Author: Okezie Uche-Ikonne [aut] ,
Frank Dondelinger [aut] ,
Tom Palmer [aut, cre]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between mrbayes versions 0.5.1 dated 2021-10-02 and 0.5.2 dated 2024-08-19
mrbayes-0.5.1/mrbayes/R/tsmr_mrformat.R |only mrbayes-0.5.2/mrbayes/DESCRIPTION | 66 mrbayes-0.5.2/mrbayes/MD5 | 126 - mrbayes-0.5.2/mrbayes/NAMESPACE | 4 mrbayes-0.5.2/mrbayes/NEWS.md | 26 mrbayes-0.5.2/mrbayes/R/mr_egger_rjags.R | 52 mrbayes-0.5.2/mrbayes/R/mr_egger_stan.R | 32 mrbayes-0.5.2/mrbayes/R/mr_format.R | 15 mrbayes-0.5.2/mrbayes/R/mr_ivw_rjags.R | 66 mrbayes-0.5.2/mrbayes/R/mr_ivw_stan.R | 4 mrbayes-0.5.2/mrbayes/R/mr_radialegger_rjags.R | 59 mrbayes-0.5.2/mrbayes/R/mr_radialegger_stan.R | 28 mrbayes-0.5.2/mrbayes/R/mrbayes-package.r | 5 mrbayes-0.5.2/mrbayes/R/mrinput_mrformat.R | 12 mrbayes-0.5.2/mrbayes/R/mvmr_egger_rjags.R | 136 - mrbayes-0.5.2/mrbayes/R/mvmr_egger_stan.R | 52 mrbayes-0.5.2/mrbayes/R/mvmr_format.R | 16 mrbayes-0.5.2/mrbayes/R/mvmr_ivw_rjags.R | 81 mrbayes-0.5.2/mrbayes/R/mvmr_ivw_stan.R | 36 mrbayes-0.5.2/mrbayes/R/rjags_check.R | 3 mrbayes-0.5.2/mrbayes/R/rstan_check.R | 3 mrbayes-0.5.2/mrbayes/R/stanmodels.R | 2 mrbayes-0.5.2/mrbayes/README.md | 59 mrbayes-0.5.2/mrbayes/build/partial.rdb |binary mrbayes-0.5.2/mrbayes/configure | 3 mrbayes-0.5.2/mrbayes/configure.win | 3 mrbayes-0.5.2/mrbayes/data/bmi_insulin.rda |binary mrbayes-0.5.2/mrbayes/data/dodata.rda |binary mrbayes-0.5.2/mrbayes/inst/CITATION |only mrbayes-0.5.2/mrbayes/man/mr_egger_rjags.Rd | 3 mrbayes-0.5.2/mrbayes/man/mr_egger_stan.Rd | 6 mrbayes-0.5.2/mrbayes/man/mr_format.Rd | 13 mrbayes-0.5.2/mrbayes/man/mr_ivw_rjags.Rd | 5 mrbayes-0.5.2/mrbayes/man/mr_ivw_stan.Rd | 4 mrbayes-0.5.2/mrbayes/man/mr_radialegger_rjags.Rd | 3 mrbayes-0.5.2/mrbayes/man/mr_radialegger_stan.Rd | 8 mrbayes-0.5.2/mrbayes/man/mrbayes-package.Rd | 20 mrbayes-0.5.2/mrbayes/man/mrinput_mr_format.Rd | 12 mrbayes-0.5.2/mrbayes/man/mvmr_egger_rjags.Rd | 17 mrbayes-0.5.2/mrbayes/man/mvmr_egger_stan.Rd | 19 mrbayes-0.5.2/mrbayes/man/mvmr_format.Rd | 13 mrbayes-0.5.2/mrbayes/man/mvmr_ivw_rjags.Rd | 16 mrbayes-0.5.2/mrbayes/man/mvmr_ivw_stan.Rd | 18 mrbayes-0.5.2/mrbayes/src/Makevars | 5 mrbayes-0.5.2/mrbayes/src/Makevars.win | 5 mrbayes-0.5.2/mrbayes/src/stanExports_mregger.cc | 2 mrbayes-0.5.2/mrbayes/src/stanExports_mregger.h | 1244 +++++----- mrbayes-0.5.2/mrbayes/src/stanExports_mrivw.cc | 2 mrbayes-0.5.2/mrbayes/src/stanExports_mrivw.h | 674 +++-- mrbayes-0.5.2/mrbayes/src/stanExports_mrradialegger.cc | 2 mrbayes-0.5.2/mrbayes/src/stanExports_mrradialegger.h | 1203 +++++---- mrbayes-0.5.2/mrbayes/src/stanExports_mvmregger.cc | 2 mrbayes-0.5.2/mrbayes/src/stanExports_mvmregger.h | 974 ++++--- mrbayes-0.5.2/mrbayes/src/stanExports_mvmrivw.cc | 2 mrbayes-0.5.2/mrbayes/src/stanExports_mvmrivw.h | 746 +++-- mrbayes-0.5.2/mrbayes/tests/testthat/test-mr_egger_rjags.R | 2 mrbayes-0.5.2/mrbayes/tests/testthat/test-mr_egger_stan.R | 40 mrbayes-0.5.2/mrbayes/tests/testthat/test-mr_ivw_rjags.R | 1 mrbayes-0.5.2/mrbayes/tests/testthat/test-mr_ivw_stan.R | 30 mrbayes-0.5.2/mrbayes/tests/testthat/test-mr_radialegger_rjags.R | 66 mrbayes-0.5.2/mrbayes/tests/testthat/test-mr_radialegger_stan.R | 56 mrbayes-0.5.2/mrbayes/tests/testthat/test-mvmr_egger_rjags.R | 22 mrbayes-0.5.2/mrbayes/tests/testthat/test-mvmr_egger_stan.R | 106 mrbayes-0.5.2/mrbayes/tests/testthat/test-mvmr_ivw_rjags.R | 21 mrbayes-0.5.2/mrbayes/tests/testthat/test-mvmr_ivw_stan.R | 106 65 files changed, 3483 insertions(+), 2874 deletions(-)
Title: Kinship Analysis with Linked Markers
Description: A 'shiny' application for forensic kinship testing, based on
the 'pedsuite' R packages. 'KLINK' is closely aligned with the (non-R)
software 'Familias' and 'FamLink', but offers several unique features,
including visualisations and automated report generation. The
calculation of likelihood ratios supports pairs of linked markers, and
all common mutation models.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between KLINK versions 1.0.0 dated 2024-07-02 and 1.0.1 dated 2024-08-19
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS.md | 7 +++++++ R/launchApp.R | 21 +++++++++++++++++++-- R/prettyTable.R | 3 +++ R/sysdata.rda |only R/writeResult.R | 7 +++++-- inst/shiny/app.R | 12 +++++------- inst/shiny/www/custom.css | 14 +++++++++----- man/launchApp.Rd | 9 +++++++-- 10 files changed, 67 insertions(+), 29 deletions(-)
Title: Spatial and Spatio-Temporal Models using 'INLA'
Description: Prepare objects to implement models over spatial and
spacetime domains with the 'INLA' package (<https://www.r-inla.org>).
These objects contain data to for the 'cgeneric' interface in
'INLA', enabling fast parallel computations.
We implemented the spatial barrier model, see Bakka et. al. (2019)
<doi:10.1016/j.spasta.2019.01.002>, and some of the spatio-temporal
models proposed in Lindgren et. al. (2023)
<https://www.idescat.cat/sort/sort481/48.1.1.Lindgren-etal.pdf>.
Details are provided in the available vignettes and from the URL bellow.
Author: Elias Teixeira Krainski [cre, aut, cph]
,
Finn Lindgren [aut] ,
Haavard Rue [aut]
Maintainer: Elias Teixeira Krainski <eliaskrainski@gmail.com>
Diff between INLAspacetime versions 0.1.8 dated 2024-04-21 and 0.1.9 dated 2024-08-19
INLAspacetime-0.1.8/INLAspacetime/R/ar2cor.R |only INLAspacetime-0.1.8/INLAspacetime/man/ar2cor.Rd |only INLAspacetime-0.1.8/INLAspacetime/src/INLAspacetime_init.c |only INLAspacetime-0.1.8/INLAspacetime/src/ar2cor.c |only INLAspacetime-0.1.8/INLAspacetime/src/ar2cor.h |only INLAspacetime-0.1.9/INLAspacetime/DESCRIPTION | 9 +- INLAspacetime-0.1.9/INLAspacetime/MD5 | 47 ++++++------- INLAspacetime-0.1.9/INLAspacetime/NAMESPACE | 3 INLAspacetime-0.1.9/INLAspacetime/R/INLAspacetime.R | 2 INLAspacetime-0.1.9/INLAspacetime/R/ar2cov.R |only INLAspacetime-0.1.9/INLAspacetime/R/ar2precision.R | 2 INLAspacetime-0.1.9/INLAspacetime/R/ghcndUtils.R | 2 INLAspacetime-0.1.9/INLAspacetime/R/mesh2fem.R | 27 ++++--- INLAspacetime-0.1.9/INLAspacetime/R/paramsUtils.R | 12 ++- INLAspacetime-0.1.9/INLAspacetime/R/stModel.matrices.R | 11 ++- INLAspacetime-0.1.9/INLAspacetime/R/worldMap.R | 5 - INLAspacetime-0.1.9/INLAspacetime/README.md | 27 +++---- INLAspacetime-0.1.9/INLAspacetime/build/partial.rdb |binary INLAspacetime-0.1.9/INLAspacetime/build/vignette.rds |binary INLAspacetime-0.1.9/INLAspacetime/man/ar2cov.Rd |only INLAspacetime-0.1.9/INLAspacetime/man/ar2precision.Rd | 2 INLAspacetime-0.1.9/INLAspacetime/man/paramsUtils.Rd | 11 ++- INLAspacetime-0.1.9/INLAspacetime/man/worldMap.Rd | 5 - INLAspacetime-0.1.9/INLAspacetime/src/Makevars | 2 INLAspacetime-0.1.9/INLAspacetime/src/ar2cov.c |only INLAspacetime-0.1.9/INLAspacetime/src/ar2cov.h |only INLAspacetime-0.1.9/INLAspacetime/src/cgeneric_ar2ss.c | 5 - INLAspacetime-0.1.9/INLAspacetime/src/cgeneric_barrier.c | 1 INLAspacetime-0.1.9/INLAspacetime/src/cgeneric_sstspde.c | 22 ++++-- 29 files changed, 110 insertions(+), 85 deletions(-)
Title: Scalable Bayesian Disease Mapping Models for High-Dimensional
Data
Description: Implements several spatial and spatio-temporal scalable disease mapping models for high-dimensional count data using the INLA technique for approximate Bayesian inference in latent Gaussian models (Orozco-Acosta et al., 2021 <doi:10.1016/j.spasta.2021.100496>; Orozco-Acosta et al., 2023 <doi:10.1016/j.cmpb.2023.107403> and Vicente et al., 2023 <doi:10.1007/s11222-023-10263-x>). The creation and develpment of this package has been supported by Project MTM2017-82553-R (AEI/FEDER, UE) and Project PID2020-113125RB-I00/MCIN/AEI/10.13039/501100011033. It has also been partially funded by the Public University of Navarra (project PJUPNA2001).
Author: Aritz Adin [aut, cre] ,
Erick Orozco-Acosta [aut] ,
Maria Dolores Ugarte [aut]
Maintainer: Aritz Adin <aritz.adin@unavarra.es>
Diff between bigDM versions 0.5.4 dated 2024-05-30 and 0.5.5 dated 2024-08-19
DESCRIPTION | 10 MD5 | 42 - NEWS | 5 R/Mmodel_icar.R | 48 - R/Mmodel_iid.R | 50 - R/Mmodel_lcar.R | 64 +- R/Mmodel_pcar.R | 60 +- R/STCAR_INLA.R | 1104 ++++++++++++++++++++++---------------------- R/add_neighbour.R | 9 R/clustering_partition.R | 22 R/connect_subgraphs.R | 16 R/divide_carto.R | 15 R/random_partition.R | 68 +- README.md | 5 build/partial.rdb |binary data/Data_MultiCancer.rda |binary inst/CITATION | 4 man/add_neighbour.Rd | 2 man/clustering_partition.Rd | 20 man/connect_subgraphs.Rd | 2 man/divide_carto.Rd | 15 man/random_partition.Rd | 66 +- 22 files changed, 865 insertions(+), 762 deletions(-)
Title: Resolving Plant Taxon Names Using the Australian Plant Census
Description: The process of resolving taxon names is necessary when working with biodiversity data. 'APCalign' uses the Australian Plant Census (APC) and the Australian Plant Name Index (APNI) to align and update plant taxon names to current, accepted standards. 'APCalign' also supplies information about the established status of plant taxa across different states/territories.
Author: Daniel Falster [aut, cre, cph]
,
Elizabeth Wenk [aut, ctb] ,
Will Cornwell [aut, ctb] ,
Fonti Kar [aut, ctb] ,
Carl Boettiger [ctb]
Maintainer: Daniel Falster <daniel.falster@unsw.edu.au>
Diff between APCalign versions 1.0.2 dated 2024-08-17 and 1.1.0 dated 2024-08-19
DESCRIPTION | 6 +-- MD5 | 14 ++++--- NAMESPACE | 1 NEWS.md | 5 ++ R/state_diversity_counts.R | 52 +++++++++++++++++++++++------ README.md | 31 +++++++++++++++-- man/get_apc_genus_family_lookup.Rd |only tests/testthat/benchmarks/family_check.csv |only tests/testthat/test-state_diversity.R | 19 ++++++++++ 9 files changed, 106 insertions(+), 22 deletions(-)
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics.
Tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Martin Maechler [aut, cre] ,
Peter Rousseeuw [ctb] ,
Christophe Croux [ctb] ,
Valentin Todorov [aut] ,
Andreas Ruckstuhl [aut] ,
Matias Salibian-Barrera [aut] ,
Tobias Verbeke [ctb, fnd] ,
Manuel Koller [aut] ,
Eduardo L. T. Conceicao [aut] ,
Maria A [...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between robustbase versions 0.99-3 dated 2024-07-01 and 0.99-4 dated 2024-08-19
DESCRIPTION | 11 +++---- MD5 | 56 ++++++++++++++++++------------------ R/lmrob.MM.R | 51 +++++++++++++++++++-------------- R/psi-rho-funs.R | 9 +++-- TODO | 2 - inst/NEWS.Rd | 24 +++++++++++++++ inst/doc/fastMcd-kmini.Rnw | 2 - inst/doc/fastMcd-kmini.pdf |binary inst/doc/lmrob_simulation.R | 17 +++++------ inst/doc/lmrob_simulation.Rnw | 19 +++++------- inst/doc/lmrob_simulation.pdf |binary inst/doc/psi_functions.R | 2 - inst/doc/psi_functions.Rnw | 11 +++---- inst/doc/psi_functions.pdf |binary inst/doc/simulation.functions.R | 4 +- inst/xtraR/platform-sessionInfo.R | 1 inst/xtraR/plot-psiFun.R | 2 - man/huberM.Rd | 2 - man/lmrob.fit.Rd | 7 +++- src/lmrob.c | 16 +++++----- src/mc.c | 1 src/robustbase.h | 2 + tests/lmrob-psifns.R | 30 +++++++++++++++++++ tests/lmrob-psifns.Rout.save | 58 ++++++++++++++++++++++++++++++++++---- tests/psi-rho-etc.R | 12 ++----- tests/psi-rho-etc.Rout.save | 26 +++++------------ vignettes/fastMcd-kmini.Rnw | 2 - vignettes/lmrob_simulation.Rnw | 19 +++++------- vignettes/psi_functions.Rnw | 11 +++---- 29 files changed, 250 insertions(+), 147 deletions(-)
Title: Multivariate Data Analysis for Chemometrics
Description: Projection based methods for preprocessing, exploring and analysis of multivariate data used in chemometrics. S. Kucheryavskiy (2020) <doi:10.1016/j.chemolab.2020.103937>.
Author: Sergey Kucheryavskiy [aut, cre]
Maintainer: Sergey Kucheryavskiy <svkucheryavski@gmail.com>
Diff between mdatools versions 0.14.1 dated 2023-08-12 and 0.14.2 dated 2024-08-19
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/constraints.R | 16 ++++++++++------ R/misc.R | 6 ++++++ R/prep.R | 1 + README.md | 2 +- 7 files changed, 35 insertions(+), 18 deletions(-)
Title: High-Performance Stemmer, Tokenizer, and Spell Checker
Description: Low level spell checker and morphological analyzer based on the
famous 'hunspell' library <https://hunspell.github.io>. The package can analyze
or check individual words as well as parse text, latex, html or xml documents.
For a more user-friendly interface use the 'spelling' package which builds on
this package to automate checking of files, documentation and vignettes in all
common formats.
Author: Jeroen Ooms [aut, cre],
Authors of libhunspell [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between hunspell versions 3.0.3 dated 2023-10-06 and 3.0.4 dated 2024-08-19
hunspell-3.0.3/hunspell/inst/doc/intro.R |only hunspell-3.0.4/hunspell/DESCRIPTION | 9 hunspell-3.0.4/hunspell/MD5 | 21 hunspell-3.0.4/hunspell/NEWS | 3 hunspell-3.0.4/hunspell/R/hunspell.R | 4 hunspell-3.0.4/hunspell/build/vignette.rds |binary hunspell-3.0.4/hunspell/inst/doc/intro.Rmd | 263 + hunspell-3.0.4/hunspell/inst/doc/intro.html | 2356 ---------------- hunspell-3.0.4/hunspell/man/hunspell.Rd | 4 hunspell-3.0.4/hunspell/tests/testthat/test-encodings.R | 4 hunspell-3.0.4/hunspell/vignettes/intro.Rmd | 263 + hunspell-3.0.4/hunspell/vignettes/intro.Rmd.in |only hunspell-3.0.4/hunspell/vignettes/knit.R |only 13 files changed, 529 insertions(+), 2398 deletions(-)
Title: Access Finnish Geospatial Data
Description: Designed to simplify geospatial data access from the Statistics Finland Web Feature Service API <https://geo.stat.fi/geoserver/index.html>, the geofi package offers researchers and analysts a set of tools to obtain and harmonize administrative spatial data for a wide range of applications, from urban planning to environmental research. The package contains annually updated time series of municipality key datasets that can be used for data aggregation and language translations.
Author: Markus Kainu [aut, cre] ,
Joona Lehtomaki [aut] ,
Juuso Parkkinen [ctb] ,
Jani Miettinen [ctb],
Pyry Kantanen [ctb],
Sampo Vesanen [ctb],
Leo Lahti [aut]
Maintainer: Markus Kainu <markus.kainu@kapsi.fi>
Diff between geofi versions 1.0.15 dated 2024-03-13 and 1.0.16 dated 2024-08-19
DESCRIPTION | 12 MD5 | 90 ++--- NEWS.md | 5 R/data.R | 444 +++++++++++++++-------------- R/get_municipalities.R | 2 R/get_municipality_pop.R | 2 R/get_population_grid.R | 2 R/get_statistical_grid.R | 2 R/get_zipcodes.R | 2 README.md | 8 build/vignette.rds |binary data/municipality_key.rda |binary data/municipality_key_2013.rda |binary data/municipality_key_2014.rda |binary data/municipality_key_2015.rda |binary data/municipality_key_2016.rda |binary data/municipality_key_2017.rda |binary data/municipality_key_2018.rda |binary data/municipality_key_2019.rda |binary data/municipality_key_2020.rda |binary data/municipality_key_2021.rda |binary data/municipality_key_2022.rda |binary data/municipality_key_2023.rda |binary data/municipality_key_2024.rda |binary inst/doc/geofi_datasets.Rmd | 6 inst/doc/geofi_datasets.html | 76 ++-- inst/doc/geofi_joining_attribute_data.html | 6 inst/doc/geofi_making_maps.html | 68 ++-- inst/doc/geofi_spatial_analysis.Rmd | 4 inst/doc/geofi_spatial_analysis.html | 24 - man/figures/readme_map-1.png |binary man/get_municipalities.Rd | 2 man/get_municipality_pop.Rd | 2 man/get_population_grid.Rd | 4 man/get_statistical_grid.Rd | 2 man/get_zipcodes.Rd | 2 man/municipality_key.Rd | 8 man/municipality_key_2013.Rd | 72 ++-- man/municipality_key_2014.Rd | 80 ++--- man/municipality_key_2015.Rd | 80 ++--- man/municipality_key_2016.Rd | 80 ++--- man/municipality_key_2017.Rd | 110 +++---- man/municipality_key_2023.Rd | 6 man/municipality_key_2024.Rd | 6 vignettes/geofi_datasets.Rmd | 6 vignettes/geofi_spatial_analysis.Rmd | 4 46 files changed, 643 insertions(+), 574 deletions(-)
Title: Estimation of Fuzzy Poverty Measures
Description: Estimates fuzzy measures of poverty and deprivation. It also estimates the sampling variance of these measures using bootstrap or jackknife repeated replications.
Author: Federico Crescenzi [aut, cre] ,
Lorenzo Mori [aut] ,
Gianni Betti [ctb]
Maintainer: Federico Crescenzi <federico.crescenzi@unitus.it>
Diff between FuzzyPovertyR versions 2.1.0 dated 2024-05-29 and 3.0.0 dated 2024-08-19
FuzzyPovertyR-2.1.0/FuzzyPovertyR/R/Not_exp_fun.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/DESCRIPTION | 12 FuzzyPovertyR-3.0.0/FuzzyPovertyR/MD5 | 98 FuzzyPovertyR-3.0.0/FuzzyPovertyR/NAMESPACE | 2 FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/FuzzyPoverty_class.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/HCR.R | 73 FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/eq_predicate.R | 156 FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fm_FL.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fm_ZBM.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fm_belhadj2011.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fm_belhadj2015.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fm_chakravarty.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fm_construct.R | 380 FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fm_cz.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fm_equate.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fm_mu.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fm_objective.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fm_tfr.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fm_var.R | 499 - FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fm_verma.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fm_verma2.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fs_construct.R | 209 FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fs_construct_all.R | 109 FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fs_equate.R | 129 FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fs_fuzzyScaleItem.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fs_modified_sum.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fs_mu.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fs_objective.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fs_order.R | 119 FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fs_plot.R | 213 FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fs_summary.R | 94 FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fs_transform.R | 84 FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fs_var.R | 393 - FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fs_wb.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/fs_weight.R | 127 FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/plot_method.R | 300 FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/summary_method.R | 115 FuzzyPovertyR-3.0.0/FuzzyPovertyR/R/weighted_quantile.R |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/build/vignette.rds |binary FuzzyPovertyR-3.0.0/FuzzyPovertyR/inst/WORDLIST | 141 FuzzyPovertyR-3.0.0/FuzzyPovertyR/inst/doc/FuzzyPovertyR.R | 384 FuzzyPovertyR-3.0.0/FuzzyPovertyR/inst/doc/FuzzyPovertyR.Rmd | 1196 +-- FuzzyPovertyR-3.0.0/FuzzyPovertyR/inst/doc/FuzzyPovertyR.html | 3896 ++++------ FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/FuzzyPoverty.Rd |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/FuzzySupplementary.Rd |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/eq_predicate.Rd | 7 FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/eusilc.Rd | 60 FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/fm_construct.Rd | 108 FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/fm_mu.Rd |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/fm_objective.Rd |only FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/fm_var.Rd | 38 FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/fs_construct.Rd | 10 FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/fs_construct_all.Rd | 14 FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/fs_equate.Rd | 10 FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/fs_order.Rd | 2 FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/fs_transform.Rd | 8 FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/fs_var.Rd | 41 FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/fs_weight.Rd | 6 FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/plot.FuzzyMonetary.Rd | 4 FuzzyPovertyR-3.0.0/FuzzyPovertyR/man/summary.FuzzyMonetary.Rd | 5 FuzzyPovertyR-3.0.0/FuzzyPovertyR/vignettes/FuzzyPovertyR.Rmd | 1196 +-- FuzzyPovertyR-3.0.0/FuzzyPovertyR/vignettes/bib.bib | 684 - 62 files changed, 5501 insertions(+), 5421 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph],
William K. Morris [aut, cre]
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.9.7 dated 2024-07-23 and 0.9.8 dated 2024-08-19
DESCRIPTION | 8 MD5 | 116 ++-- NEWS.md | 15 R/api_get.R | 30 - R/caching.R | 26 R/filters.R | 4 R/finbif-package.R | 6 R/finbif_clear_cache.R | 6 R/finbif_collections.R | 6 R/finbif_informal_groups.R | 10 R/finbif_metadata.R | 40 - R/finbif_occurrence.R | 71 +- R/finbif_occurrence_load.R | 60 +- R/finbif_records.R | 62 +- R/finbif_update_cache.R | 6 R/sysdata.R | 220 ++++--- R/to_dwc.R | 8 R/utils.R | 48 - R/zzz.R | 2 README.md | 2 inst/NEWS.Rd | 18 inst/doc/finbif.Rmd | 10 inst/doc/v02_occurrence_data.Rmd | 4 inst/doc/v04_metadata.Rmd | 2 man/caching.Rd | 30 - man/filters.Rd | 4 man/finbif-package.Rd | 6 man/finbif_clear_cache.Rd | 2 man/finbif_collections.Rd | 2 man/finbif_informal_groups.Rd | 7 man/finbif_metadata.Rd | 10 man/finbif_occurrence.Rd | 7 man/finbif_occurrence_load.Rd | 7 man/finbif_update_cache.Rd | 2 tests/fixtures/finbif_cache_db_timeout.yml | 86 +-- tests/fixtures/finbif_cache_file_timeout.yml | 92 +-- tests/fixtures/finbif_cache_timeout.yml | 86 +-- tests/fixtures/finbif_check_taxa.yml | 18 tests/fixtures/finbif_collections.yml | 146 ++--- tests/fixtures/finbif_informal_groups.yml | 6 tests/fixtures/finbif_last_mod1.yml | 8 tests/fixtures/finbif_last_mod2.yml | 8 tests/fixtures/finbif_last_mod3.yml | 8 tests/fixtures/finbif_metadata.yml | 424 +++++++-------- tests/fixtures/finbif_occurrence.yml | 663 ++++++++++++------------ tests/fixtures/finbif_occurrence_aggregate.yml | 75 +- tests/fixtures/finbif_occurrence_api_error.yml | 6 tests/fixtures/finbif_occurrence_dates.yml | 97 +-- tests/fixtures/finbif_occurrence_load.yml | 302 +++++----- tests/fixtures/finbif_occurrence_print.yml | 24 tests/fixtures/finbif_taxa.yml | 20 tests/testthat/_snaps/caching.md | 93 +-- tests/testthat/_snaps/finbif_collections.md | 14 tests/testthat/_snaps/finbif_occurrence.md | 78 +- tests/testthat/_snaps/finbif_occurrence_load.md | 60 +- tests/testthat/helper.R | 2 vignettes/finbif.Rmd | 10 vignettes/v02_occurrence_data.Rmd | 4 vignettes/v04_metadata.Rmd | 2 59 files changed, 1705 insertions(+), 1484 deletions(-)
Title: Variable Length Markov Chains ('VLMC') Models
Description: Functions, Classes & Methods for estimation, prediction, and
simulation (bootstrap) of Variable Length Markov Chain ('VLMC') Models.
Author: Martin Maechler [aut, cre]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between VLMC versions 1.4-3-1 dated 2019-04-29 and 1.4-4 dated 2024-08-19
ChangeLog | 12 +++++++++++- DESCRIPTION | 17 +++++++++++------ MD5 | 18 +++++++++--------- man/OZrain.Rd | 5 +++-- man/bnrf1.Rd | 7 ++++--- man/draw.vlmc.Rd | 4 ++-- src/drawvlmc.c | 2 +- src/init.c | 4 ++-- src/util.c | 18 +++++++++--------- src/vlmc.h | 9 +++++---- 10 files changed, 57 insertions(+), 39 deletions(-)
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
some of which were ported from S-plus in the 1990s.
For graphics, have pretty (Log-scale) axes eaxis(), an enhanced Tukey-Anscombe
plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()',
pretty arrows, etc.
For robustness, have a robust F test and robust range().
For system support, notably on Linux, provides 'Sys.*()' functions with
more access to system and CPU information.
Finally, miscellaneous utilities such as simple efficient prime numbers,
integer codes, Duplicated(), toLatex.numeric() and is.whole().
Author: Martin Maechler [aut, cre] ,
Werner Stahel [ctb] , f.robftest, last,
p.scales, p.dnorm),
Andreas Ruckstuhl [ctb] , p.profileTraces,
p.res.2x),
Christian Keller [ctb] , p.tachoPlot),
Kjetil Halvorsen [ctb] , ecdf.ksCI),
Alain Hauser [ctb] , is.whole,
[...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.1-18 dated 2024-04-25 and 1.1-19 dated 2024-08-19
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- R/prettylab.R | 6 +++++- build/partial.rdb |binary inst/NEWS.Rd | 14 ++++++++++++++ man/pretty10exp.Rd | 27 +++++++++++++++++++++++++++ 6 files changed, 58 insertions(+), 13 deletions(-)
Title: Regression Models for Ordinal Data
Description: Implementation of cumulative link (mixed) models also known
as ordered regression models, proportional odds models, proportional
hazards models for grouped survival times and ordered logit/probit/...
models. Estimation is via maximum likelihood and mixed models are fitted
with the Laplace approximation and adaptive Gauss-Hermite quadrature.
Multiple random effect terms are allowed and they may be nested, crossed or
partially nested/crossed. Restrictions of symmetry and equidistance can be
imposed on the thresholds (cut-points/intercepts). Standard model
methods are available (summary, anova, drop-methods, step,
confint, predict etc.) in addition to profile methods and slice
methods for visualizing the likelihood function and checking
convergence.
Author: Rune Haubo Bojesen Christensen [aut, cre]
Maintainer: Rune Haubo Bojesen Christensen <rune.haubo@gmail.com>
Diff between ordinal versions 2023.12-4 dated 2023-12-04 and 2023.12-4.1 dated 2024-08-19
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ build/vignette.rds |binary data/income.rda |binary data/soup.rda |binary data/wine.rda |binary inst/CITATION | 2 +- inst/doc/clm_article.pdf |binary inst/doc/clmm2_tutorial.pdf |binary man/addtermOld.Rd | 2 +- man/clm.Rd | 4 ++-- man/clm.control.Rd | 2 +- man/ordinal-package.Rd | 2 +- 13 files changed, 21 insertions(+), 21 deletions(-)
Title: Generalized Autoregressive Score Models
Description: Simulate, estimate and forecast using univariate and multivariate GAS models
as described in Ardia et al. (2019) <doi:10.18637/jss.v088.i06>.
Author: Leopoldo Catania [aut, cre] ,
David Ardia [ctb] ,
Kris Boudt [ctb]
Maintainer: Leopoldo Catania <leopoldo.catania@econ.au.dk>
Diff between GAS versions 0.3.4 dated 2022-02-04 and 0.3.4.1 dated 2024-08-19
DESCRIPTION | 14 +++++++------- MD5 | 20 ++++++++++---------- build/partial.rdb |binary data/Goals.rda |binary data/StockIndices.rda |binary data/cpichg.rda |binary data/dji30ret.rda |binary data/sp500ret.rda |binary data/sp500rv.rda |binary data/tqdata.rda |binary data/usunp.rda |binary 11 files changed, 17 insertions(+), 17 deletions(-)
Title: Rmetrics - Markets and Basic Statistics
Description: Provides a collection of functions to
explore and to investigate basic properties of financial returns
and related quantities.
The covered fields include techniques of explorative data analysis
and the investigation of distributional properties, including
parameter estimation and hypothesis testing. Even more there are
several utility functions for data handling and management.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Martin Maechler [ctb] ,
CRAN Team [ctb],
Georgi N. Boshnakov [cre, aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between fBasics versions 4032.96 dated 2023-11-03 and 4041.97 dated 2024-08-19
DESCRIPTION | 6 - MD5 | 140 +++++++++++++++++++++--------------------- NAMESPACE | 2 NEWS.md | 10 ++- R/test-normalityTest.R | 6 - data/Capitalization.rda |binary data/DowJones30.csv.gz |binary data/HedgeFund.rda |binary data/PensionFund.csv.gz |binary data/SWXLP.csv.gz |binary data/cars2.csv.gz |binary data/msft.dat.rda |binary data/nyse.csv.gz |binary data/swissEconomy.rda |binary data/usdthb.csv.gz |binary inst/pkgdown.yml | 17 ++--- man/00fBasics-package.Rd | 15 +++- man/data-examples.Rd | 6 - man/dist-DistributionFits.Rd | 28 ++++---- man/dist-ghFit.Rd | 49 ++------------ man/dist-ghtFit.Rd | 38 +---------- man/dist-gldFit.Rd | 58 +++-------------- man/dist-hypFit.Rd | 55 ++-------------- man/dist-nigFit.Rd | 64 ++++++------------- man/dist-sghFit.Rd | 52 +++------------ man/dist-snigFit.Rd | 47 ++------------ man/fDISTFIT-class.Rd | 24 ++++--- man/fHTEST-class.Rd | 3 man/matrix-colVec.Rd | 8 -- man/matrix-hilbert.Rd | 4 - man/matrix-inv.Rd | 12 +-- man/matrix-kron.Rd | 11 +-- man/matrix-norm.Rd | 6 - man/matrix-pascal.Rd | 12 +-- man/matrix-posDefinite.Rd | 5 - man/matrix-rk.Rd | 8 +- man/matrix-tr.Rd | 7 -- man/matrix-triang.Rd | 8 +- man/matrix-vech.Rd | 8 +- man/plot-acfPlot.Rd | 17 ++--- man/plot-boxPlot.Rd | 13 +-- man/plot-histPlot.Rd | 16 ++-- man/plot-qqPlot.Rd | 22 ++---- man/plot-returnSeriesGUI.Rd | 2 man/plot-scalinglawPlot.Rd | 22 ++---- man/plot-seriesPlot.Rd | 117 +++++++++++++++++++---------------- man/stats-basicStats.Rd | 8 -- man/stats-interpLinear.Rd | 25 +++---- man/stats-maxdd.Rd | 110 ++++++++++++++++----------------- man/stats-rowStats.Rd | 11 +-- man/stats-sampleLMoments.Rd | 26 +++---- man/stats-sampleRobMoments.Rd | 8 -- man/test-correlationTest.Rd | 19 ++--- man/test-ks2Test.Rd | 11 --- man/test-locationTest.Rd | 19 +---- man/test-normalityTests.Rd | 27 +++----- man/test-scaleTest.Rd | 15 +--- man/test-varianceTest.Rd | 47 ++++++-------- man/utils-Heaviside.Rd | 25 ++----- man/utils-characterTable.Rd | 1 man/utils-colIds.Rd | 19 ++--- man/utils-colorPalette.Rd | 3 man/utils-colorTable.Rd | 10 +-- man/utils-decor.Rd | 2 man/utils-getS4.Rd | 54 ++++++++-------- man/utils-interactivePlot.Rd | 87 +++++++++++++------------- man/utils-listFunctions.Rd | 6 - man/utils-printControl.Rd | 12 +-- man/utils-randLCG.Rd | 12 +-- man/utils-symbolTable.Rd | 2 man/volatility.Rd | 2 71 files changed, 598 insertions(+), 881 deletions(-)
Title: FastICA Algorithms to Perform ICA and Projection Pursuit
Description: Implementation of FastICA algorithm to perform Independent
Component Analysis (ICA) and Projection Pursuit.
Author: J L Marchini [aut],
C Heaton [aut],
Brian Ripley [aut, cre]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between fastICA versions 1.2-4 dated 2023-11-27 and 1.2-5 dated 2024-08-19
DESCRIPTION | 19 +++-- MD5 | 4 - src/ica.c | 208 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 119 insertions(+), 112 deletions(-)
Title: Client for the Microsoft's 'Cognitive Services Text to Speech
REST' API
Description: Convert text into synthesized speech and get a list of supported voices for a region.
Microsoft's 'Cognitive Services Text to Speech REST' API <https://learn.microsoft.com/en-us/azure/cognitive-services/speech-service/rest-text-to-speech?tabs=streaming>
supports neural text to speech voices, which support specific languages and dialects that are identified by locale.
Author: Howard Baek [aut, cre, cph] ,
John Muschelli [aut]
Maintainer: Howard Baek <howardbaek.fh@gmail.com>
Diff between conrad versions 1.0.0 dated 2023-07-03 and 1.0.0.1 dated 2024-08-19
DESCRIPTION | 13 ++++++------- MD5 | 4 ++-- data/region.rda |binary 3 files changed, 8 insertions(+), 9 deletions(-)
Title: Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM,
PBS/Torque)
Description: Evaluate arbitrary function calls using workers on HPC schedulers
in single line of code. All processing is done on the network without
accessing the file system. Remote schedulers are supported via SSH.
Author: Michael Schubert [aut, cre, cph]
,
ZeroMQ authors [aut, cph]
Maintainer: Michael Schubert <mschu.dev@gmail.com>
Diff between clustermq versions 0.9.4 dated 2024-03-04 and 0.9.5 dated 2024-08-19
DESCRIPTION | 8 - MD5 | 46 +++--- NEWS.md | 5 R/Q.r | 8 - R/foreach.r | 9 - R/qsys_lsf.r | 3 R/qsys_sge.r | 3 R/qsys_slurm.r | 3 R/qsys_ssh.r | 4 R/util.r | 2 build/vignette.rds |binary configure | 5 inst/doc/faq.Rmd | 28 ++- inst/doc/faq.html | 22 +- inst/doc/technicaldocs.html | 2 inst/doc/userguide.R | 40 +++-- inst/doc/userguide.Rmd | 64 ++++++-- inst/doc/userguide.html | 332 +++++++++++++++++++++++++------------------- man/Q.Rd | 8 - man/Q_rows.Rd | 8 - man/host.Rd | 2 src/util/test_libzmq.c | 8 - vignettes/faq.Rmd | 28 ++- vignettes/userguide.Rmd | 64 ++++++-- 24 files changed, 433 insertions(+), 269 deletions(-)
More information about WeatherSentiment at CRAN
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More information about tidychangepoint at CRAN
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Title: Sparse Arrays and Multivariate Polynomials
Description: Sparse arrays interpreted as multivariate polynomials.
Uses 'disordR' discipline (Hankin, 2022,
<doi:10.48550/ARXIV.2210.03856>). To cite the package in
publications please use Hankin (2022) <doi:10.48550/ARXIV.2210.10848>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between spray versions 1.0-25 dated 2024-02-12 and 1.0-26 dated 2024-08-19
spray-1.0-25/spray/build/spray.pdf |only spray-1.0-25/spray/build/stage23.rdb |only spray-1.0-26/spray/DESCRIPTION | 13 ++- spray-1.0-26/spray/MD5 | 43 ++++++------- spray-1.0-26/spray/NAMESPACE | 7 +- spray-1.0-26/spray/NEWS.md | 8 ++ spray-1.0-26/spray/R/RcppExports.R | 4 + spray-1.0-26/spray/R/spray.R | 89 ++++++++++++++++----------- spray-1.0-26/spray/R/spray_ops.R | 15 +++- spray-1.0-26/spray/README.md | 48 ++++++-------- spray-1.0-26/spray/build/vignette.rds |binary spray-1.0-26/spray/inst/doc/spray.pdf |binary spray-1.0-26/spray/man/Ops.spray.Rd | 8 ++ spray-1.0-26/spray/man/deriv.Rd | 6 - spray-1.0-26/spray/man/ooom.Rd | 6 - spray-1.0-26/spray/man/pmax.Rd | 10 +-- spray-1.0-26/spray/man/print.Rd | 14 +++- spray-1.0-26/spray/man/rspray.Rd | 8 +- spray-1.0-26/spray/man/spray.Rd | 8 ++ spray-1.0-26/spray/man/spray_cpp.Rd | 1 spray-1.0-26/spray/src/RcppExports.cpp | 14 ++++ spray-1.0-26/spray/src/spray_ops.cpp | 40 +++++++++++- spray-1.0-26/spray/tests/testthat/test_aab.R | 13 +++ spray-1.0-26/spray/tests/testthat/test_aac.R |only 24 files changed, 244 insertions(+), 111 deletions(-)
Title: Compare Human Performance to Sampling Algorithms
Description: Understand human performance from the perspective of sampling, both looking at how people generate samples and how people use the samples they have generated. A longer overview and other resources can be found at <https://sampling.warwick.ac.uk>.
Author: Lucas Castillo [aut, cre, cph]
,
Yun-Xiao Li [aut, cph] ,
Adam N Sanborn [aut, cph] ,
European Research Council [fnd]
Maintainer: Lucas Castillo <lucas.castillo-marti@warwick.ac.uk>
Diff between samplr versions 1.0.0 dated 2024-08-01 and 1.0.1 dated 2024-08-19
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 5 +++-- R/Z_identities.R | 2 +- R/samplers.R | 2 +- build/partial.rdb |binary inst/doc/custom-density-functions.html | 16 ++++++++-------- inst/doc/time-comparisons.html | 24 ++++++++++++------------ 8 files changed, 35 insertions(+), 34 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-25 0.4.0
2024-06-19 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-03 1.2.5
2023-11-02 1.2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-12 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-24 1.1.0
2021-03-03 0.2.2
2021-02-26 0.2.1
2021-02-19 0.2.0
2020-11-20 0.1.2
2020-11-09 0.1.0
Title: Relationship-Based Mixed-Effects Models
Description: Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the
'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between lme4breeding versions 1.0.30 dated 2024-07-30 and 1.0.31 dated 2024-08-19
DESCRIPTION | 8 MD5 | 70 +-- NAMESPACE | 2 R/funs.R | 11 R/utils.R | 53 +- build/vignette.rds |binary data/DT_augment.RData |binary data/DT_btdata.RData |binary data/DT_cornhybrids.RData |binary data/DT_cpdata.RData |binary data/DT_example.RData |binary data/DT_expdesigns.RData |binary data/DT_fulldiallel.RData |binary data/DT_gryphon.RData |binary data/DT_h2.RData |binary data/DT_halfdiallel.RData |binary data/DT_ige.RData |binary data/DT_legendre.RData |binary data/DT_mohring.RData |binary data/DT_polyploid.RData |binary data/DT_rice.RData |binary data/DT_sleepstudy.RData |binary data/DT_technow.RData |binary data/DT_wheat.RData |binary data/DT_yatesoats.RData |binary inst/doc/lmebreed.gxe.R | 109 +++-- inst/doc/lmebreed.gxe.Rmd | 110 +++-- inst/doc/lmebreed.qg.R | 39 + inst/doc/lmebreed.qg.Rmd | 40 +- man/impute.Rd | 3 man/lme4breeding-package.Rd | 2 man/rrm.Rd | 2 vignettes/lmebreed.gxe.Rmd | 110 +++-- vignettes/lmebreed.gxe.html | 368 +++++++++--------- vignettes/lmebreed.qg.Rmd | 40 +- vignettes/lmebreed.qg.html | 877 +++++++++++++++++++++----------------------- 36 files changed, 950 insertions(+), 894 deletions(-)
Title: Copula Graphical Models for Heterogeneous Mixed Data
Description: A multi-core R package that allows for the statistical modeling of multi-group multivariate mixed data using Gaussian graphical models. Combining the Gaussian copula framework with the fused graphical lasso penalty, the 'heteromixgm' package can handle a wide variety of datasets found in various sciences. The package also includes an option to perform model selection using the AIC, BIC and EBIC information criteria, a function that plots partial correlation graphs based on the selected precision matrices, as well as simulate mixed heterogeneous data for exploratory or simulation purposes and one multi-group multivariate mixed agricultural dataset pertaining to maize yields. The package implements the methodological developments found in Hermes et al. (2024) <doi:10.1080/10618600.2023.2289545>.
Author: Sjoerd Hermes [aut, cre],
Joost van Heerwaarden [ctb],
Pariya Behrouzi [ctb]
Maintainer: Sjoerd Hermes <sjoerd.hermes@wur.nl>
Diff between heteromixgm versions 2.0.1 dated 2024-08-01 and 2.0.2 dated 2024-08-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NAMESPACE | 1 + 3 files changed, 6 insertions(+), 5 deletions(-)
Title: Available Light Within the Water Column and on the Seafloor of
Arctic Fjords
Description: Satellite data collected between 2003 and 2022,
in conjunction with gridded bathymetric data (50-150 m resolution),
are used to estimate the irradiance reaching the bottom of a series of representative EU Arctic fjords.
An Earth System Science Data (ESSD) manuscript, Schlegel et al. (2024),
provides a detailed explanation of the methodology.
Author: Bernard Gentili [aut],
Jean-Pierre Gattuso [aut] ,
Robert W. Schlegel [aut, cre]
Maintainer: Robert W. Schlegel <robwschlegel@gmail.com>
Diff between FjordLight versions 1.0.0 dated 2024-07-30 and 1.0.1 dated 2024-08-19
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/fl_DownloadFjord.R | 9 ++++++--- inst/doc/fl_example.html | 42 +++++++++++++++++++++--------------------- tests/testthat/Rplots.pdf |binary 6 files changed, 40 insertions(+), 33 deletions(-)
Title: Adaptive Optimal Two-Stage Designs
Description: Optimize one or two-arm, two-stage designs for clinical trials with
respect to several implemented objective criteria or custom objectives.
Optimization under uncertainty and conditional (given stage-one outcome)
constraints are supported.
See Pilz et al. (2019) <doi:10.1002/sim.8291> and
Kunzmann et al. (2021) <doi:10.18637/jss.v098.i09> for details.
Author: Kevin Kunzmann [aut, cph] ,
Maximilian Pilz [aut, cre] ,
Jan Meis [aut] ,
Nico Bruder [aut]
Maintainer: Maximilian Pilz <maximilian.pilz@itwm.fraunhofer.de>
Diff between adoptr versions 1.0.1 dated 2024-06-07 and 1.1.0 dated 2024-08-19
DESCRIPTION | 22 - MD5 | 118 +++-- NAMESPACE | 23 + NEWS.md | 178 ++++---- R/BinomialDistribution.R | 18 R/ChiSquaredDistribution.R |only R/CompositeScore.R | 1 R/ConditionalSampleSize.R | 5 R/ContinuousPrior.R | 2 R/FDistribution.R |only R/GroupSequentialDesign.R | 131 +++++- R/OneStageDesign.R | 179 ++++++-- R/Scores.R | 5 R/Survival.R |only R/TwoStageDesign.R | 164 ++++++- R/adoptr.R | 7 R/minimize.R | 566 +++++++++++++++++++++++++-- README.md | 6 build/vignette.rds |binary inst/doc/adoptr.R | 2 inst/doc/adoptr.Rmd | 2 inst/doc/adoptr.html | 22 - inst/doc/adoptr_jss.Rmd | 4 inst/doc/adoptr_jss.html | 8 inst/doc/composite-scores.Rmd | 4 inst/doc/composite-scores.html | 12 inst/doc/conditional-scores.html | 4 inst/doc/defining-new-scores.html | 2 inst/doc/other-endpoints.R |only inst/doc/other-endpoints.Rmd |only inst/doc/other-endpoints.html |only man/ANOVA-class.Rd |only man/ChiSquaredDataDistribution-class.Rd |only man/ConditionalSampleSize-class.Rd | 4 man/GroupSequentialDesign-class.Rd | 30 + man/GroupSequentialDesignSurvival-class.Rd |only man/NestedModels-class.Rd |only man/OneStageDesign-class.Rd | 25 - man/OneStageDesignSurvival-class.Rd |only man/Pearson2xK-class.Rd |only man/Scores.Rd | 1 man/SurvivalDataDistribution-class.Rd |only man/SurvivalDesign.Rd |only man/TwoStageDesign-class.Rd | 14 man/TwoStageDesignSurvival-class.Rd |only man/ZSquared-class.Rd |only man/adoptr.Rd | 7 man/bounds.Rd | 16 man/condition.Rd | 16 man/cumulative_distribution_function.Rd | 20 man/expectation.Rd | 16 man/get_initial_design.Rd | 51 ++ man/minimize.Rd | 8 man/n.Rd | 10 man/posterior.Rd | 14 man/predictive_cdf.Rd | 14 man/predictive_pdf.Rd | 14 man/probability_density_function.Rd | 20 tests/testthat/test_ANOVA.R |only tests/testthat/test_BinomialDistribution.R | 2 tests/testthat/test_ChiSquaredDistribution.R |only tests/testthat/test_GroupSequentialDesign.R | 88 ++++ tests/testthat/test_OneStageDesign.R | 75 +++ tests/testthat/test_Survival.R |only tests/testthat/test_TwoStageDesign.R | 122 +++++ tests/testthat/test_minimize.R | 291 ++++++++++++- vignettes/adoptr.Rmd | 2 vignettes/adoptr_jss.Rmd | 4 vignettes/composite-scores.Rmd | 4 vignettes/other-endpoints.Rmd |only 70 files changed, 1913 insertions(+), 440 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-29 0.5
2021-11-24 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-17 1.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-25 0.3.1
2022-05-12 0.3.0
2020-03-23 0.2.0
2019-02-18 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-18 0.5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-29 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-18 0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-09 2.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-30 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-20 1.1
2021-10-08 1.0
2020-04-28 0.98.30
2019-11-16 0.98.24
2019-02-19 0.98.6
2018-10-08 0.98.5.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-31 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-10 1.0.4
Title: Interface to the National 'Phenology' Network 'API'
Description: Programmatic interface to the
Web Service methods provided by the National 'Phenology' Network
(<https://usanpn.org/>), which includes data on various life history
events that occur at specific times.
Author: Jeff Switzer [aut, cre],
Scott Chamberlain [aut],
Lee Marsh [aut],
Kevin Wong [aut],
David LeBauer [ctb],
Eric R Scott [ctb]
Maintainer: Jeff Switzer <jeff@usanpn.org>
Diff between rnpn versions 1.2.8.0 dated 2024-02-08 and 1.2.9.0 dated 2024-08-19
rnpn-1.2.8.0/rnpn/inst/doc/VI_geospatial.R |only rnpn-1.2.9.0/rnpn/DESCRIPTION | 6 - rnpn-1.2.9.0/rnpn/MD5 | 31 +++--- rnpn-1.2.9.0/rnpn/NEWS.md | 7 + rnpn-1.2.9.0/rnpn/build/vignette.rds |binary rnpn-1.2.9.0/rnpn/inst/doc/III_individual_phenometrics.html | 2 rnpn-1.2.9.0/rnpn/inst/doc/II_status_intensity.html | 2 rnpn-1.2.9.0/rnpn/inst/doc/IV_site_phenometrics.html | 2 rnpn-1.2.9.0/rnpn/inst/doc/I_introduction.html | 2 rnpn-1.2.9.0/rnpn/inst/doc/VIII_data_cleaning.html | 2 rnpn-1.2.9.0/rnpn/inst/doc/VII_combine_raster_point.html | 2 rnpn-1.2.9.0/rnpn/inst/doc/VI_geospatial.Rmd | 61 +++++++----- rnpn-1.2.9.0/rnpn/inst/doc/VI_geospatial.html | 2 rnpn-1.2.9.0/rnpn/inst/doc/V_magnitude_phenometrics.html | 2 rnpn-1.2.9.0/rnpn/vignettes/VI_geospatial.Rmd | 61 +++++++----- rnpn-1.2.9.0/rnpn/vignettes/VI_geospatial.Rmd.orig |only rnpn-1.2.9.0/rnpn/vignettes/figures/unnamed-chunk-13-1.png |only rnpn-1.2.9.0/rnpn/vignettes/figures/unnamed-chunk-14-1.png |only rnpn-1.2.9.0/rnpn/vignettes/figures/unnamed-chunk-9-1.png |only 19 files changed, 111 insertions(+), 71 deletions(-)
Title: Raster-Based Spatial Stratification Algorithms
Description: Algorithms for the spatial stratification of landscapes, sampling and modeling of
spatially-varying phenomena. These algorithms offer a simple framework for the stratification
of geographic space based on raster layers representing landscape factors and/or factor scales.
The stratification process follows a hierarchical approach, which is based on first level units
(i.e., classification units) and second-level units (i.e., stratification units). Nonparametric
techniques allow to measure the correspondence between the geographic space and the landscape
configuration represented by the units. These correspondence metrics are useful to define
sampling schemes and to model the spatial variability of environmental phenomena. The
theoretical background of the algorithms and code examples are presented in Fuentes et al. (2022).
<doi:10.32614/RJ-2022-036>.
Author: Bryan A. Fuentes [aut, cre] ,
Minerva J. Dorantes [aut] ,
John R. Tipton [aut],
Robert J. Hijmans [ctb] ,
Andrew G. Brown [ctb]
Maintainer: Bryan A. Fuentes <bryandrep@gmail.com>
Diff between rassta versions 1.0.5 dated 2022-08-30 and 1.0.6 dated 2024-08-19
DESCRIPTION | 17 +- MD5 | 24 +-- NEWS.md | 9 + README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 9 - inst/doc/classunits.html | 278 ++++++++++++++++++----------------- inst/doc/modeling.html | 272 +++++++++++++++++------------------ inst/doc/sampling.html | 364 +++++++++++++++++++++++------------------------ inst/doc/signature.html | 238 +++++++++++++++--------------- inst/doc/similarity.html | 230 +++++++++++++++-------------- inst/doc/stratunits.html | 240 +++++++++++++++--------------- 13 files changed, 865 insertions(+), 822 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 10.8.2 dated 2024-05-12 and 10.9 dated 2024-08-19
DESCRIPTION | 12 +- MD5 | 52 ++++++------ NAMESPACE | 1 R/ARMA.R | 2 R/Binary_ANOVA.R | 2 R/Boost.R | 5 - R/Copula.R | 2 R/Dependence.R | 19 ++-- R/Internal_Functions.R | 81 ++++++++++++------- R/NNS_Distance.R | 13 +-- R/Partial_Moments.R | 2 R/Partition_Map.R | 4 R/Regression.R | 6 - R/gvload.R | 1 README.md | 11 -- inst/doc/NNSvignette_Classification.html | 2 inst/doc/NNSvignette_Clustering_and_Regression.html | 2 inst/doc/NNSvignette_Comparing_Distributions.html | 2 inst/doc/NNSvignette_Correlation_and_Dependence.html | 8 - inst/doc/NNSvignette_Forecasting.html | 2 inst/doc/NNSvignette_Partial_Moments.html | 2 inst/doc/NNSvignette_Sampling.html | 2 man/NNS.ARMA.Rd | 2 man/NNS.copula.Rd | 2 man/NNS.part.Rd | 4 man/NNS.reg.Rd | 6 - src/partial_moments.cpp | 2 27 files changed, 135 insertions(+), 114 deletions(-)
Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is
a socket library implementing 'Scalability Protocols', a reliable,
high-performance standard for common communications patterns including
publish/subscribe, request/reply and service discovery, over in-process,
IPC, TCP, WebSocket and secure TLS transports. As its own threaded
concurrency framework, provides a toolkit for asynchronous programming and
distributed computing, with intuitive 'aio' objects which resolve
automatically upon completion of asynchronous operations, and
synchronisation primitives allowing R to wait upon events signalled by
concurrent threads.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph],
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between nanonext versions 1.2.0 dated 2024-08-17 and 1.2.1 dated 2024-08-19
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NEWS.md | 6 ++++++ R/sendrecv.R | 2 +- R/utils.R | 1 + man/next_config.Rd | 1 + man/reply.Rd | 2 +- man/request.Rd | 2 +- man/send.Rd | 2 +- man/send_aio.Rd | 2 +- src/core.c | 14 ++++++++------ src/init.c | 2 +- src/utils.c | 3 --- tests/tests.R | 1 - 14 files changed, 38 insertions(+), 32 deletions(-)
Title: A Framework for Robust Shiny Applications
Description: An opinionated framework for building a production-ready
'Shiny' application. This package contains a series of tools for
building a robust 'Shiny' application from start to finish.
Author: Colin Fay [cre, aut] ,
Vincent Guyader [aut] ,
Sebastien Rochette [aut] ,
Cervan Girard [aut] ,
Novica Nakov [ctb],
David Granjon [ctb],
Arthur Breant [ctb],
Antoine Languillaume [ctb],
Ilya Zarubin [ctb],
ThinkR [cph]
Maintainer: Colin Fay <contact@colinfay.me>
Diff between golem versions 0.4.1 dated 2023-06-05 and 0.5.0 dated 2024-08-19
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Title: A Bayesian No-Effect- Concentration (NEC) Algorithm
Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>), 'NSEC' (see Fisher and Fox (2023)<doi:10.1002/etc.5610>), and 'N(S)EC (see Fisher et al. 2023<doi:10.1002/ieam.4809>). A full description of this package can be found in Fisher 'et al.' (2024)<doi:10.18637/jss.v110.i05>. This package expands and supersedes an original version implemented in 'R2jags' (see Su and Yajima (2020)<https://CRAN.R-project.org/package=R2jags>; Fisher et al. (2020)<doi:10.5281/ZENODO.3966864>).
Author: Rebecca Fisher [aut, cre] ,
Diego R. Barneche [aut] ,
Gerard F. Ricardo [aut] ,
David R. Fox [aut]
Maintainer: Rebecca Fisher <r.fisher@aims.gov.au>
Diff between bayesnec versions 2.1.2.0 dated 2024-03-28 and 2.1.3.0 dated 2024-08-19
DESCRIPTION | 18 +++++++++--------- MD5 | 41 +++++++++++++++++++++-------------------- NEWS.md | 8 ++++++++ R/bayesmanecfit-class.R | 4 ++++ R/bayesnec-package.R | 21 ++++++++++++++++----- R/bayesnecfit-class.R | 4 ++++ R/bnec.R | 4 ++++ R/check_priors.R | 12 +++++++----- R/manecsummary-class.R | 4 ++++ R/necsummary-class.R | 4 ++++ R/pull_brmsfit.R | 4 ++-- README.md | 2 +- inst/CITATION |only man/bayesmanecfit-class.Rd | 4 ++++ man/bayesnec-package.Rd | 19 +++++++++++++++---- man/bayesnecfit-class.Rd | 4 ++++ man/bnec.Rd | 4 ++++ man/check_priors.Rd | 6 +++++- man/manecsummary-class.Rd | 4 ++++ man/necsummary-class.Rd | 4 ++++ man/pull_brmsfit.Rd | 6 +++--- man/step.Rd | 44 ++++++++++++++++++++++---------------------- 22 files changed, 149 insertions(+), 72 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
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2022-11-28 3.0.1
2022-10-11 3.0.0
2019-04-22 2.5.7
2019-01-11 2.5.6
2018-08-09 2.5.5
2018-07-05 2.5.4
2018-05-21 2.5.3
2018-03-12 2.5.2
2018-01-24 2.5.1
2017-12-15 2.5.0
2017-11-20 2.4.7
2017-08-18 2.4.6
2017-03-01 2.4.5
2017-01-20 2.4.0
2017-01-06 2.3.5
2016-10-27 2.3.2
2016-10-12 2.3.1
2016-10-03 2.3.0
2016-09-26 2.2.0
2016-09-08 2.0.10
2016-08-17 2.0.9
2016-03-10 2.0.8
2016-03-02 2.0.7
2016-02-21 2.0.6
2016-02-14 2.0.5
2016-01-28 2.0.4
2016-01-20 2.0.3
2015-12-03 2.0.2
2015-09-22 2.0.1
2015-07-08 2.0.0
2015-05-06 1.1.0
2015-02-13 1.0
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