Title: Test Suite for 'Future API' Backends
Description: Backends implementing the 'Future' API, as defined by the 'future' package, should use the tests provided by this package to validate that they meet the minimal requirements of the 'Future' API. The tests can be performed easily from within R or from outside of R from the command line making it easy to include them package tests and in Continuous Integration (CI) pipelines.
Author: Henrik Bengtsson [aut, cre, cph],
The R Consortium [fnd] grant in 2017)
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.tests versions 0.3.0 dated 2021-10-10 and 0.4.0 dated 2022-11-21
DESCRIPTION | 10 ++-- MD5 | 45 +++++++++++-------- NEWS.md | 75 ++++++++++++++++++++++--------- R/Test-class.R | 37 --------------- R/TestResult-class.R | 108 ---------------------------------------------- R/along_test_plans.R |only R/check.R | 6 +- R/check_plan.R | 8 +-- R/evaluate_expr.R | 30 +++++++++++- R/make_test.R |only R/run_test.R |only R/run_tests.R |only R/state.R | 21 ++++++++ R/test_plans.R | 54 ----------------------- build/vignette.rds |binary inst/CITATION | 54 +++++++++++------------ inst/WORDLIST | 1 inst/test-db/futureCall.R | 19 +++++--- inst/test-db/globalenv.R |only inst/test-db/globals.R |only inst/test-db/options.R |only man/along_test_plans.Rd | 2 man/check.Rd | 6 ++ man/check_plan.Rd | 5 +- man/make_test.Rd | 2 man/run_test.Rd | 2 man/run_tests.Rd | 2 27 files changed, 195 insertions(+), 292 deletions(-)
Title: Tools for DYRESM-CAEDYM Model Development: Calibration Assistant
and Post-Processing
Description: Tools for DYRESM-CAEDYM model development, including assisting with calibrating selected model parameters and visualising model output through time series plot, profile plot, contour plot, and scatter plot.
Author: Songyan Yu [aut, cre] ,
Christopher McBride [ctb],
Marieke Frassl [ctb]
Maintainer: Songyan Yu <sunny.yu@griffith.edu.au>
Diff between dycdtools versions 0.4.2 dated 2022-05-25 and 0.4.3 dated 2022-11-21
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 6 ++++++ R/Fun_Calib-assist.R | 4 ++++ R/Fun_Contour-plot_sim.R | 3 +++ R/Fun_Contour-plot_sim_obs.R | 3 +++ R/Fun_Profile-plot.R | 2 ++ R/Fun_Scatter-plot.R | 4 +++- R/Fun_TS-plot.R | 4 +++- README.md | 14 +++++++------- man/plot_cont.Rd | 4 ++++ man/plot_cont_comp.Rd | 4 ++++ man/plot_prof.Rd | 10 ++++++---- man/plot_scatter.Rd | 6 +++++- man/plot_ts.Rd | 8 ++++++-- 15 files changed, 74 insertions(+), 34 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between parameters versions 0.19.0 dated 2022-10-05 and 0.20.0 dated 2022-11-21
parameters-0.19.0/parameters/R/robust_estimation.R |only parameters-0.19.0/parameters/man/ci_robust.Rd |only parameters-0.19.0/parameters/man/p_value_robust.Rd |only parameters-0.19.0/parameters/man/standard_error_robust.Rd |only parameters-0.20.0/parameters/DESCRIPTION | 16 parameters-0.20.0/parameters/MD5 | 292 ++-- parameters-0.20.0/parameters/NAMESPACE | 17 parameters-0.20.0/parameters/NEWS.md | 58 parameters-0.20.0/parameters/R/1_model_parameters.R | 31 parameters-0.20.0/parameters/R/5_simulate_model.R | 8 parameters-0.20.0/parameters/R/compare_parameters.R | 45 parameters-0.20.0/parameters/R/display.R | 43 parameters-0.20.0/parameters/R/dof.R | 34 parameters-0.20.0/parameters/R/dof_ml1.R | 3 parameters-0.20.0/parameters/R/equivalence_test.R | 123 - parameters-0.20.0/parameters/R/extract_parameters.R | 16 parameters-0.20.0/parameters/R/extract_parameters_anova.R | 8 parameters-0.20.0/parameters/R/extract_random_variances.R | 14 parameters-0.20.0/parameters/R/format.R | 279 ++- parameters-0.20.0/parameters/R/format_p_adjust.R | 3 parameters-0.20.0/parameters/R/format_parameters.R | 51 parameters-0.20.0/parameters/R/methods_BayesFM.R | 4 parameters-0.20.0/parameters/R/methods_BayesFactor.R | 19 parameters-0.20.0/parameters/R/methods_DirichletReg.R | 2 parameters-0.20.0/parameters/R/methods_MCMCglmm.R | 2 parameters-0.20.0/parameters/R/methods_aod.R | 2 parameters-0.20.0/parameters/R/methods_aov.R | 4 parameters-0.20.0/parameters/R/methods_averaging.R | 2 parameters-0.20.0/parameters/R/methods_bamlss.R | 2 parameters-0.20.0/parameters/R/methods_bayesQR.R | 2 parameters-0.20.0/parameters/R/methods_betareg.R | 4 parameters-0.20.0/parameters/R/methods_bfsl.R | 2 parameters-0.20.0/parameters/R/methods_brglm2.R | 4 parameters-0.20.0/parameters/R/methods_brms.R | 2 parameters-0.20.0/parameters/R/methods_car.R | 2 parameters-0.20.0/parameters/R/methods_cgam.R | 2 parameters-0.20.0/parameters/R/methods_cplm.R | 7 parameters-0.20.0/parameters/R/methods_emmeans.R | 24 parameters-0.20.0/parameters/R/methods_fitdistr.R | 2 parameters-0.20.0/parameters/R/methods_gam.R | 2 parameters-0.20.0/parameters/R/methods_ggeffects.R | 2 parameters-0.20.0/parameters/R/methods_gjrm.R | 6 parameters-0.20.0/parameters/R/methods_glmm.R | 2 parameters-0.20.0/parameters/R/methods_glmmTMB.R | 11 parameters-0.20.0/parameters/R/methods_glmx.R | 4 parameters-0.20.0/parameters/R/methods_htest.R | 6 parameters-0.20.0/parameters/R/methods_ivfixed.R | 2 parameters-0.20.0/parameters/R/methods_lavaan.R | 2 parameters-0.20.0/parameters/R/methods_lme4.R | 7 parameters-0.20.0/parameters/R/methods_lmodel2.R | 2 parameters-0.20.0/parameters/R/methods_lqmm.R | 2 parameters-0.20.0/parameters/R/methods_marginaleffects.R | 10 parameters-0.20.0/parameters/R/methods_margins.R | 6 parameters-0.20.0/parameters/R/methods_mass.R | 2 parameters-0.20.0/parameters/R/methods_mediate.R | 2 parameters-0.20.0/parameters/R/methods_merTools.R | 2 parameters-0.20.0/parameters/R/methods_metafor.R | 2 parameters-0.20.0/parameters/R/methods_metaplus.R | 6 parameters-0.20.0/parameters/R/methods_mfx.R | 4 parameters-0.20.0/parameters/R/methods_mhurdle.R | 4 parameters-0.20.0/parameters/R/methods_mice.R | 2 parameters-0.20.0/parameters/R/methods_mixmod.R | 2 parameters-0.20.0/parameters/R/methods_mixor.R | 4 parameters-0.20.0/parameters/R/methods_mjoint.R | 2 parameters-0.20.0/parameters/R/methods_mlm.R | 6 parameters-0.20.0/parameters/R/methods_multcomp.R | 2 parameters-0.20.0/parameters/R/methods_mvord.R | 4 parameters-0.20.0/parameters/R/methods_ordinal.R | 4 parameters-0.20.0/parameters/R/methods_panelr.R | 2 parameters-0.20.0/parameters/R/methods_plm.R | 2 parameters-0.20.0/parameters/R/methods_posterior.R | 2 parameters-0.20.0/parameters/R/methods_pscl.R | 2 parameters-0.20.0/parameters/R/methods_psych.R | 1 parameters-0.20.0/parameters/R/methods_quantreg.R | 2 parameters-0.20.0/parameters/R/methods_rstan.R | 5 parameters-0.20.0/parameters/R/methods_rstanarm.R | 7 parameters-0.20.0/parameters/R/methods_selection.R | 4 parameters-0.20.0/parameters/R/methods_survey.R | 2 parameters-0.20.0/parameters/R/methods_systemfit.R | 2 parameters-0.20.0/parameters/R/methods_varest.R | 6 parameters-0.20.0/parameters/R/n_factors.R | 10 parameters-0.20.0/parameters/R/p_calibrate.R |only parameters-0.20.0/parameters/R/p_function.r |only parameters-0.20.0/parameters/R/p_value_betwithin.R | 16 parameters-0.20.0/parameters/R/p_value_kenward.R | 7 parameters-0.20.0/parameters/R/p_value_ml1.R | 17 parameters-0.20.0/parameters/R/p_value_satterthwaite.R | 6 parameters-0.20.0/parameters/R/parameters_type.R | 33 parameters-0.20.0/parameters/R/pool_parameters.R | 25 parameters-0.20.0/parameters/R/principal_components.R | 36 parameters-0.20.0/parameters/R/print.compare_parameters.R | 23 parameters-0.20.0/parameters/R/print.parameters_model.R | 76 - parameters-0.20.0/parameters/R/print_html.R | 142 +- parameters-0.20.0/parameters/R/print_md.R | 8 parameters-0.20.0/parameters/R/random_parameters.R | 37 parameters-0.20.0/parameters/R/reduce_parameters.R | 56 parameters-0.20.0/parameters/R/reshape_loadings.R | 4 parameters-0.20.0/parameters/R/simulate_parameters.R | 8 parameters-0.20.0/parameters/R/standardize_info.R | 21 parameters-0.20.0/parameters/R/standardize_parameters.R | 29 parameters-0.20.0/parameters/R/standardize_posteriors.R | 2 parameters-0.20.0/parameters/R/utils_cleaners.R | 23 parameters-0.20.0/parameters/R/utils_format.R | 244 ++- parameters-0.20.0/parameters/R/utils_model_parameters.R | 29 parameters-0.20.0/parameters/R/utils_pca_efa.R | 16 parameters-0.20.0/parameters/README.md | 84 - parameters-0.20.0/parameters/build/partial.rdb |binary parameters-0.20.0/parameters/build/vignette.rds |binary parameters-0.20.0/parameters/inst/doc/overview_of_vignettes.Rmd | 2 parameters-0.20.0/parameters/inst/doc/overview_of_vignettes.html | 4 parameters-0.20.0/parameters/man/compare_parameters.Rd | 62 parameters-0.20.0/parameters/man/degrees_of_freedom.Rd | 15 parameters-0.20.0/parameters/man/display.parameters_model.Rd | 77 + parameters-0.20.0/parameters/man/equivalence_test.lm.Rd | 47 parameters-0.20.0/parameters/man/figures/unconditional_interpretation.png |only parameters-0.20.0/parameters/man/get_scores.Rd | 13 parameters-0.20.0/parameters/man/model_parameters.Rd | 11 parameters-0.20.0/parameters/man/n_factors.Rd | 2 parameters-0.20.0/parameters/man/p_calibrate.Rd |only parameters-0.20.0/parameters/man/p_function.Rd |only parameters-0.20.0/parameters/man/p_value_betwithin.Rd | 10 parameters-0.20.0/parameters/man/p_value_kenward.Rd | 7 parameters-0.20.0/parameters/man/p_value_ml1.Rd | 9 parameters-0.20.0/parameters/man/p_value_satterthwaite.Rd | 6 parameters-0.20.0/parameters/man/principal_components.Rd | 26 parameters-0.20.0/parameters/man/print.parameters_model.Rd | 76 - 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Title: Bayesian Model Selection with Suspected Latent Grouping Factors
Description: Implements the Bayesian model selection method with suspected latent
grouping factor methodology of Metzger and Franck (2020),
<doi:10.1080/00401706.2020.1739561>. SLGF detects latent
heteroscedasticity or group-based regression effects based on the levels of a
user-specified categorical predictor.
Author: Thomas Metzger [aut, cre],
Christopher Franck [aut]
Maintainer: Thomas Metzger <metzger.181@osu.edu>
Diff between slgf versions 0.1.0 dated 2021-02-17 and 2.0.0 dated 2022-11-21
slgf-0.1.0/slgf/R/chips.R |only slgf-0.1.0/slgf/R/extract.hats.R |only slgf-0.1.0/slgf/R/groupings.R |only slgf-0.1.0/slgf/R/labeler.R |only slgf-0.1.0/slgf/R/locknut.R |only slgf-0.1.0/slgf/R/slgf.R |only slgf-0.1.0/slgf/R/utils.R |only slgf-0.1.0/slgf/build/vignette.rds |only slgf-0.1.0/slgf/data/chips.RData |only slgf-0.1.0/slgf/data/locknut.RData |only slgf-0.1.0/slgf/inst/doc |only slgf-0.1.0/slgf/man/chips.Rd |only slgf-0.1.0/slgf/man/column_centerer.Rd |only slgf-0.1.0/slgf/man/extract.hats.Rd |only slgf-0.1.0/slgf/man/groupings.Rd |only slgf-0.1.0/slgf/man/labeler.Rd |only slgf-0.1.0/slgf/man/locknut.Rd |only slgf-0.1.0/slgf/man/ms.slgf.Rd |only slgf-0.1.0/slgf/vignettes |only slgf-2.0.0/slgf/DESCRIPTION | 22 +++++---- slgf-2.0.0/slgf/MD5 | 64 ++++++++++++---------------- slgf-2.0.0/slgf/NAMESPACE | 6 -- slgf-2.0.0/slgf/R/bottles.R |only slgf-2.0.0/slgf/R/column_centerer.R | 20 -------- slgf-2.0.0/slgf/R/grouping_info.R |only slgf-2.0.0/slgf/R/level_parser.R |only slgf-2.0.0/slgf/R/lymphoma.R | 2 slgf-2.0.0/slgf/R/maketall.R | 1 slgf-2.0.0/slgf/R/marginal_calculator_hom.R |only slgf-2.0.0/slgf/R/model_builder.R |only slgf-2.0.0/slgf/R/ms_slgf.R |only slgf-2.0.0/slgf/R/prior_maker.R |only slgf-2.0.0/slgf/R/textile.R |only slgf-2.0.0/slgf/R/torque.R |only slgf-2.0.0/slgf/build/partial.rdb |binary slgf-2.0.0/slgf/data/bottles.RData |only slgf-2.0.0/slgf/data/lymphoma.RData |binary slgf-2.0.0/slgf/data/roadwear.RData |binary slgf-2.0.0/slgf/data/smell.RData |binary slgf-2.0.0/slgf/data/textile.RData |only slgf-2.0.0/slgf/data/torque.RData |only slgf-2.0.0/slgf/inst/REFERENCES.bib | 17 +++++-- slgf-2.0.0/slgf/man/bottles.Rd |only slgf-2.0.0/slgf/man/lymphoma.Rd | 2 slgf-2.0.0/slgf/man/maketall.Rd | 1 slgf-2.0.0/slgf/man/ms_slgf.Rd |only slgf-2.0.0/slgf/man/textile.Rd |only slgf-2.0.0/slgf/man/torque.Rd |only 48 files changed, 59 insertions(+), 76 deletions(-)
Title: Download and Display Map Tiles
Description: To create maps from tiles, 'maptiles' downloads, composes and
displays tiles from a large number of providers (e.g. 'OpenStreetMap',
'Stamen', 'Esri', 'CARTO', or 'Thunderforest').
Author: Timothee Giraud [cre, aut] ,
Diego Hernangomez [ctb] ,
Robert J. Hijmans [ctb] ,
Hugh A. Graham [ctb]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between maptiles versions 0.3.0 dated 2021-09-24 and 0.4.0 dated 2022-11-21
maptiles-0.3.0/maptiles/R/zzz.R |only maptiles-0.4.0/maptiles/DESCRIPTION | 8 - maptiles-0.4.0/maptiles/MD5 | 18 +-- maptiles-0.4.0/maptiles/NEWS.md | 9 + maptiles-0.4.0/maptiles/R/get_tiles.R | 31 ++++- maptiles-0.4.0/maptiles/R/plot_tiles.R | 4 maptiles-0.4.0/maptiles/README.md | 77 +++++++------- maptiles-0.4.0/maptiles/man/figures/README-example-1.png |binary maptiles-0.4.0/maptiles/man/figures/README-example2-1.png |binary maptiles-0.4.0/maptiles/man/figures/logo.png |only maptiles-0.4.0/maptiles/man/get_tiles.Rd | 12 +- 11 files changed, 96 insertions(+), 63 deletions(-)
Title: Web Interface to 'R' Functions
Description: Web front end for your 'R' functions producing plots or tables.
If you have a function or set of related functions, you can make them
available over the internet through a web browser. This is the same
motivation as the 'shiny' package, but note that the development of
'shinylight' is not in any way linked to that of 'shiny' (beyond the use of
the 'httpuv' package). You might prefer 'shinylight' to 'shiny' if you want
a lighter weight deployment with easier horizontal scaling, or if you want
to develop your front end yourself in JavaScript and HTML just using
a lightweight remote procedure call interface to your R code on the
server.
Author: Pieter Vermeesch [aut],
Tim Band [aut, cre]
Maintainer: Tim Band <t.band@ucl.ac.uk>
Diff between shinylight versions 1.1 dated 2022-11-18 and 1.1.1 dated 2022-11-21
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/shinylight.R | 25 +++++++++++++++++-------- 3 files changed, 23 insertions(+), 14 deletions(-)
Title: 'RStudio' Package Manager
Description: Enables binary package installations on Linux distributions.
Provides access to 'RStudio' public repositories at
<https://packagemanager.rstudio.com>, and transparent management of
system requirements without administrative privileges. Currently supported
distributions are 'CentOS' / 'RHEL' 7 and 8, and several 'RHEL' derivatives
('Rocky Linux' 8, 'AlmaLinux' 8, 'Oracle Linux' 7 and 8, 'Amazon Linux' 2),
'openSUSE' / 'SLES' 15.3, and 'Ubuntu' 18.04, 20.04 and 22.04.
Author: Inaki Ucar [aut, cph, cre] ,
R Core Team [aut, cph]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between rspm versions 0.2.2 dated 2022-09-15 and 0.2.3 dated 2022-11-21
rspm-0.2.2/rspm/R/centos.R |only rspm-0.2.2/rspm/R/centos_like.R |only rspm-0.2.2/rspm/R/opensuse.R |only rspm-0.2.2/rspm/R/opensuse_like.R |only rspm-0.2.2/rspm/R/ubuntu.R |only rspm-0.2.3/rspm/DESCRIPTION | 6 +++--- rspm-0.2.3/rspm/MD5 | 16 ++++++++-------- rspm-0.2.3/rspm/NEWS.md | 4 ++++ rspm-0.2.3/rspm/R/zzz_centos_base.R |only rspm-0.2.3/rspm/R/zzz_centos_like.R |only rspm-0.2.3/rspm/R/zzz_opensuse_base.R |only rspm-0.2.3/rspm/R/zzz_opensuse_like.R |only rspm-0.2.3/rspm/R/zzz_ubuntu_base.R |only rspm-0.2.3/rspm/README.md | 2 +- 14 files changed, 16 insertions(+), 12 deletions(-)
Title: Causal Inference and Prediction in Cohort-Based Analyses
Description: Numerous functions for cohort-based analyses, either for prediction or causal inference. For causal inference, it includes Inverse Probability Weighting and G-computation for marginal estimation of an exposure effect when confounders are expected. We deal with binary outcomes, times-to-events, competing events, and multi-state data. For multistate data, semi-Markov model with interval censoring may be considered, and we propose the possibility to consider the excess of mortality related to the disease compared to reference lifetime tables. For predictive studies, we propose a set of functions to estimate time-dependent receiver operating characteristic (ROC) curves with the possible consideration of right-censoring times-to-events or the presence of confounders. Finally, several functions are available to assess time-dependent ROC curves or survival curves from aggregated data.
Author: Yohann Foucher [aut, cre] ,
Florent Le Borgne [aut],
Arthur Chatton [aut],
Camille Sabathe [aut]
Maintainer: Yohann Foucher <Yohann.Foucher@univ-poitiers.fr>
Diff between RISCA versions 1.0.1 dated 2022-05-02 and 1.0.3 dated 2022-11-21
DESCRIPTION | 23 -- MD5 | 164 +++++++++---------- NAMESPACE | 2 R/gc.sl.binary.R | 89 ++++++++-- R/gc.sl.time.R | 2 R/hr.sl.time.R | 2 R/plot.sl.time.R | 28 ++- R/predict.sl.time.R | 2 R/roc.binary.R | 4 R/roc.net.R | 4 R/roc.summary.R | 4 R/roc.time.R | 3 R/sl.time.R | 25 +-- R/summary.sl.time.R | 9 - man/aft.gamma.Rd | 6 man/aft.ggamma.Rd | 6 man/aft.llogis.Rd | 6 man/aft.weibull.Rd | 6 man/auc.Rd | 65 +++---- man/cox.aic.Rd | 2 man/cox.all.Rd | 2 man/cox.en.Rd | 2 man/cox.lasso.Rd | 2 man/cox.ridge.Rd | 2 man/dataDIVAT1.Rd | 99 +++++------ man/dataDIVAT2.Rd | 76 ++++----- man/dataDIVAT3.Rd | 88 +++++----- man/dataDIVAT4.Rd | 11 + man/dataDIVAT5.Rd | 130 +++++++-------- man/expect.utility1.Rd | 156 +++++++++--------- man/expect.utility2.Rd | 170 ++++++++++---------- man/gc.logistic.Rd | 4 man/gc.sl.binary.Rd | 9 - man/gc.sl.time.Rd | 4 man/gc.survival.Rd | 4 man/hr.sl.time.Rd | 4 man/ipw.log.rank.Rd | 107 ++++++------ man/ipw.survival.Rd | 2 man/lines.rocrisca.Rd | 5 man/lrs.multistate.Rd | 145 ++++++++--------- man/markov.3states.Rd | 230 +++++++++++++-------------- man/markov.3states.rsadd.Rd | 2 man/markov.4states.Rd | 246 ++++++++++++++--------------- man/markov.4states.rsadd.Rd | 4 man/metric.Rd | 2 man/mixture.2states.Rd | 250 +++++++++++++++--------------- man/nnet.time.Rd | 2 man/ph.exponential.Rd | 6 man/ph.gompertz.Rd | 7 man/plot.rocrisca.Rd | 5 man/plot.sl.time.Rd | 25 +-- man/plot.survrisca.Rd | 3 man/port.Rd | 2 man/predict.cox.Rd | 2 man/predict.flexsurv.Rd | 9 - man/predict.mixture.2states.Rd | 198 +++++++++++------------ man/predict.nnet.time.Rd | 2 man/predict.rf.time.Rd | 2 man/predict.sl.time.Rd | 12 - man/rf.time.Rd | 2 man/rmst.Rd | 2 man/roc.binary.Rd | 14 - man/roc.net.Rd | 16 - man/roc.prognostic.aggregate.Rd | 4 man/roc.prognostic.individual.Rd | 4 man/roc.summary.Rd | 44 ++--- man/roc.time.Rd | 14 - man/semi.markov.3states.Rd | 232 ++++++++++++++-------------- man/semi.markov.3states.ic.Rd | 323 +++++++++++++++++++-------------------- man/semi.markov.3states.rsadd.Rd | 266 ++++++++++++++++---------------- man/semi.markov.4states.Rd | 256 +++++++++++++++--------------- man/semi.markov.4states.rsadd.Rd | 280 ++++++++++++++++----------------- man/sl.time.Rd | 20 +- man/summary.sl.time.Rd | 22 +- man/survival.mr.Rd | 4 man/survival.summary.Rd | 5 man/survival.summary.strata.Rd | 5 man/tune.cox.aic.Rd | 2 man/tune.cox.en.Rd | 2 man/tune.cox.lasso.Rd | 4 man/tune.cox.ridge.Rd | 3 man/tune.nnet.time.Rd | 4 man/tune.rf.time.Rd | 4 83 files changed, 2015 insertions(+), 2000 deletions(-)
Title: Estimating Regional Trends of a Prevalence from a DHS and
Similar Surveys
Description: Spatial estimation of a prevalence surface
or a relative risks surface, using data from a Demographic and Health
Survey (DHS) or an analog survey, see Larmarange et al. (2011)
<doi:10.4000/cybergeo.24606>.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph.larmarange@ird.fr>
Diff between prevR versions 4.0.0 dated 2022-05-11 and 4.0.1 dated 2022-11-21
DESCRIPTION | 8 MD5 | 16 - NEWS.md | 4 R/direct.label_prevR.r | 6 R/kde.prevR.r | 14 R/quick.prevR.r | 16 - build/vignette.rds |binary inst/doc/intro_prevR.html | 695 ++++++--------------------------------------- man/export-prevR-method.Rd | 4 9 files changed, 139 insertions(+), 624 deletions(-)
Title: Exact Floating-Point Arithmetic
Description: Provides a new type of numbers called the lazy numbers.
Arithmetic on lazy numbers is exact, contrary to ordinary
floating-point arithmetic. The lazy numbers are implemented in 'C++'
with the 'CGAL' library (<https://www.cgal.org/>).
Author: Stephane Laurent [aut, cre]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between lazyNumbers versions 1.2.0 dated 2022-11-21 and 1.2.1 dated 2022-11-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ src/lazyNumbers_types.h | 1 + tests/testthat/test-lazyMatrix.R | 31 +++++++++++++++++++++++++++++-- 5 files changed, 42 insertions(+), 9 deletions(-)
Title: Tools for Easy Use of 'e-Stat', 'RESAS' API, Etc
Description: Provides tools to use API such as 'e-Stat' (<https://www.e-stat.go.jp/>),
the portal site for Japanese government statistics, and
'RESAS' (Regional Economy and Society Analyzing System, <https://resas.go.jp>).
Author: Mizuki Uchida [aut, cre]
Maintainer: Mizuki Uchida <uchidamizuki@vivaldi.net>
Diff between jpstat versions 0.2.1 dated 2022-05-10 and 0.3.0 dated 2022-11-21
jpstat-0.2.1/jpstat/R/dplyr.R |only jpstat-0.2.1/jpstat/R/iretp.R |only jpstat-0.2.1/jpstat/R/japanstat.R |only jpstat-0.2.1/jpstat/man/iretp_trade.Rd |only jpstat-0.3.0/jpstat/DESCRIPTION | 25 - jpstat-0.3.0/jpstat/MD5 | 38 +- jpstat-0.3.0/jpstat/NAMESPACE | 27 +- jpstat-0.3.0/jpstat/NEWS.md | 23 + jpstat-0.3.0/jpstat/R/deprecated.R |only jpstat-0.3.0/jpstat/R/estat.R | 184 ++++++------- jpstat-0.3.0/jpstat/R/jpstat-package.R |only jpstat-0.3.0/jpstat/R/navigatr.R | 12 jpstat-0.3.0/jpstat/R/resas.R |only jpstat-0.3.0/jpstat/R/sysdata.rda |only jpstat-0.3.0/jpstat/R/utils.R | 64 +++- jpstat-0.3.0/jpstat/R/webland.R |only jpstat-0.3.0/jpstat/R/zzz.R |only jpstat-0.3.0/jpstat/README.md | 290 +++++++--------------- jpstat-0.3.0/jpstat/man/estat.Rd | 12 jpstat-0.3.0/jpstat/man/estat_table_info.Rd | 4 jpstat-0.3.0/jpstat/man/jpstat.Rd | 5 jpstat-0.3.0/jpstat/man/reexports.Rd | 11 jpstat-0.3.0/jpstat/man/resas.Rd |only jpstat-0.3.0/jpstat/man/webland.Rd |only jpstat-0.3.0/jpstat/tests/testthat/test-estat.R | 38 +- jpstat-0.3.0/jpstat/tests/testthat/test-resas.R |only jpstat-0.3.0/jpstat/tests/testthat/test-webland.R |only 27 files changed, 347 insertions(+), 386 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown" or "free") objects in R expressions
by code inspection using various strategies (ordered, liberal, or
conservative). The objective of this package is to make it as simple as
possible to identify global objects for the purpose of exporting them in
parallel, distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph],
Davis Vaughan [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.16.1 dated 2022-08-28 and 0.16.2 dated 2022-11-21
DESCRIPTION | 8 MD5 | 18 + NEWS.md | 7 R/call_find_globals_with_dotdotdot.R |only R/findGlobals.R | 343 ----------------------------------- R/find_globals_conservative.R |only R/find_globals_liberal.R |only R/find_globals_ordered.R |only R/globalsOf.R | 2 R/utils.R | 22 +- R/walkAST.R | 3 man/walkAST.Rd | 6 12 files changed, 40 insertions(+), 369 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Sebastian Funk [ctb],
Steven G. Johnson [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Eamon B. O'Dea [c [...truncated...]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 4.3 dated 2022-07-06 and 4.4 dated 2022-11-21
DESCRIPTION | 13 +- MD5 | 74 ++++++------ NAMESPACE | 1 R/abc.R | 8 - R/betabinom.R | 4 R/bsplines.R | 9 + R/builder.R | 25 ++-- R/coef.R | 2 R/cond_logLik.R | 3 R/csnippet.R | 16 +- R/distributions.R | 33 ++--- R/nlf.R | 2 R/pmcmc.R | 36 +++--- R/simulate.R | 2 R/time.R | 2 R/window.R | 2 R/wquant.R |only build/partial.rdb |binary data/LondonYorke.rda |binary data/bsflu.rda |binary data/ebolaWA2014.rda |binary data/ewcitmeas.rda |binary data/ewmeas.rda |binary inst/NEWS | 37 ++++++ inst/NEWS.Rd | 72 +++++++----- inst/doc/index.html | 303 ++++++++------------------------------------------- inst/include/pomp.h | 1 man/betabinom.Rd | 6 - man/bsplines.Rd | 7 - man/csnippet.Rd | 18 ++- man/distributions.Rd | 33 ++--- man/hitch.Rd | 7 - man/pomp.Rd | 7 - man/wquant.Rd |only src/bspline.c | 120 ++++++++++---------- src/init.c | 2 src/pomp.h | 1 src/pomp_decls.h | 3 src/vmeasure.c | 2 39 files changed, 380 insertions(+), 471 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 1.30.0 dated 2022-10-27 and 2.0.1 dated 2022-11-21
mlflow-1.30.0/mlflow/R/install.R |only mlflow-1.30.0/mlflow/man/install_mlflow.Rd |only mlflow-1.30.0/mlflow/man/mlflow_list_experiments.Rd |only mlflow-1.30.0/mlflow/man/mlflow_list_registered_models.Rd |only mlflow-1.30.0/mlflow/man/mlflow_list_run_infos.Rd |only mlflow-1.30.0/mlflow/man/mlflow_maybe_create_conda_env.Rd |only mlflow-1.30.0/mlflow/man/uninstall_mlflow.Rd |only mlflow-1.30.0/mlflow/tests/testthat/test-python-install.R |only mlflow-2.0.1/mlflow/DESCRIPTION | 31 +- mlflow-2.0.1/mlflow/MD5 | 73 +++--- mlflow-2.0.1/mlflow/NAMESPACE | 10 mlflow-2.0.1/mlflow/R/cli.R | 5 mlflow-2.0.1/mlflow/R/model-h2o.R | 8 mlflow-2.0.1/mlflow/R/model-keras.R | 9 mlflow-2.0.1/mlflow/R/model-registry.R | 19 + mlflow-2.0.1/mlflow/R/model-serve.R | 6 mlflow-2.0.1/mlflow/R/model-utils.R | 9 mlflow-2.0.1/mlflow/R/model-xgboost.R | 8 mlflow-2.0.1/mlflow/R/model.R | 46 ++-- mlflow-2.0.1/mlflow/R/project-run.R | 9 mlflow-2.0.1/mlflow/R/python.R | 42 +-- mlflow-2.0.1/mlflow/R/tracking-experiments.R | 26 -- mlflow-2.0.1/mlflow/R/tracking-runs.R | 29 -- mlflow-2.0.1/mlflow/R/tracking-server.R | 17 + mlflow-2.0.1/mlflow/R/tracking-ui.R | 1 mlflow-2.0.1/mlflow/README.md | 35 +-- mlflow-2.0.1/mlflow/man/mlflow_run.Rd | 7 mlflow-2.0.1/mlflow/man/mlflow_search_registered_models.Rd |only mlflow-2.0.1/mlflow/man/mlflow_server.Rd | 5 mlflow-2.0.1/mlflow/man/mlflow_ui.Rd | 1 mlflow-2.0.1/mlflow/tests/testthat.R | 2 mlflow-2.0.1/mlflow/tests/testthat/test-bypass-conda.R | 8 mlflow-2.0.1/mlflow/tests/testthat/test-client.R | 4 mlflow-2.0.1/mlflow/tests/testthat/test-model-h2o.R | 13 - mlflow-2.0.1/mlflow/tests/testthat/test-model-registry.R | 44 +++- mlflow-2.0.1/mlflow/tests/testthat/test-model-xgboost.R | 17 - mlflow-2.0.1/mlflow/tests/testthat/test-model.R | 22 +- mlflow-2.0.1/mlflow/tests/testthat/test-run.R | 4 mlflow-2.0.1/mlflow/tests/testthat/test-serve.R | 42 +-- mlflow-2.0.1/mlflow/tests/testthat/test-tracking-experiments.R | 110 ++++------ mlflow-2.0.1/mlflow/tests/testthat/test-tracking-runs.R | 19 - mlflow-2.0.1/mlflow/tests/testthat/test/crate.bin |binary 42 files changed, 318 insertions(+), 363 deletions(-)
Title: Prediction Intervals for Synthetic Control Methods with Multiple
Treated Units and Staggered Adoption
Description: Implementation of estimation and inference procedures for Synthetic Control methods using least square, lasso, ridge, or simplex-type constraints. Uncertainty is quantified with prediction intervals as developed in Cattaneo, Feng, and Titiunik (2021) <https://cattaneo.princeton.edu/papers/Cattaneo-Feng-Titiunik_2021_JASA.pdf>.
Author: Matias Cattaneo [aut],
Yingjie Feng [aut],
Filippo Palomba [aut, cre],
Rocio Titiunik [aut]
Maintainer: Filippo Palomba <fpalomba@princeton.edu>
Diff between scpi versions 2.0.0 dated 2022-10-10 and 2.0.1 dated 2022-11-21
DESCRIPTION | 8 +-- MD5 | 50 +++++++++++++---------- NAMESPACE | 4 + R/data.R | 2 R/scdata.R | 61 +++++++++++++++------------- R/scdataMulti.R | 65 ++++++++++++++++-------------- R/scdataMulti_methods.R |only R/scdata_methods.R |only R/scest.R | 77 +++++++++++++++++++----------------- R/scest_methods.R | 96 ++++++++++++++++++++++----------------------- R/scpi-package.R | 45 +++++++++++---------- R/scpi.R | 88 ++++++++++++++++++++++------------------- R/scplot.R | 10 ++-- R/scplotMulti.R | 8 ++- R/supporting_functions.R | 6 +- man/print.scdata.Rd |only man/print.scdataMulti.Rd |only man/print.scest.Rd | 8 +-- man/scdata.Rd | 29 ++++++++----- man/scdataMulti.Rd | 17 +++++-- man/scest.Rd | 29 +++++++------ man/scpi-package.Rd | 16 +++++-- man/scpi.Rd | 27 +++++++----- man/scpi_germany.Rd | 2 man/scplot.Rd | 10 ++-- man/scplotMulti.Rd | 8 ++- man/summary.scdata.Rd |only man/summary.scdataMulti.Rd |only man/summary.scest.Rd | 6 +- 29 files changed, 374 insertions(+), 298 deletions(-)
Title: The Maraca Plot: Visualization of Hierarchical Composite
Endpoints in Clinical Trials
Description: Library that supports visual interpretation of hierarchical composite
endpoints (HCEs). HCEs are complex constructs used as primary endpoints in
clinical trials, combining outcomes of different types into ordinal endpoints,
in which each patient contributes the most clinically important event (one and
only one) to the analysis.
Author: Martin Karpefors [aut],
Samvel B. Gasparyan [aut],
Stefano Borini [ctb, cre]
Maintainer: Stefano Borini <stefano.borini@astrazeneca.com>
Diff between maraca versions 0.3.10 dated 2022-10-05 and 0.4.0 dated 2022-11-21
DESCRIPTION | 12 ++-- MD5 | 21 +++---- NAMESPACE | 1 NEWS.md | 11 +++ R/aaa.R | 1 R/maraca.R | 150 ++++++++++++++++++++++++++++++++++++++------------- inst/doc/faq.html | 4 - inst/doc/maraca.R | 14 ++-- inst/doc/maraca.Rmd | 78 +++++++++++--------------- inst/doc/maraca.html | 59 +++++++++++--------- man/plot.hce.Rd |only vignettes/maraca.Rmd | 78 +++++++++++--------------- 12 files changed, 256 insertions(+), 173 deletions(-)
Title: Functions and Data for "Epidemics: Models and Data in R (2nd
Edition)"
Description: Functions, data sets and shiny apps for "Epidemics: Models and Data in R (2nd edition)" by Ottar N. Bjornstad (2022, ISBN: 978-3-031-12055-8) <https://link.springer.com/book/10.1007/978-3-319-97487-3>. The package contains functions to study the Susceptible-Exposed-Infected-Removed SEIR model, spatial and age-structured Susceptible-Infected-Removed SIR models; time-series SIR and chain-binomial stochastic models; catalytic disease models; coupled map lattice models of spatial transmission and network models for social spread of infection. The package is also an advanced quantitative companion to the 'Coursera' Epidemics Massive Online Open Course <https://www.coursera.org/learn/epidemics>.
Author: Ottar N. Bjornstad [aut, cre]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>
Diff between epimdr2 versions 1.0-7 dated 2022-09-14 and 1.0-8 dated 2022-11-21
CHANGES | 2 ++ DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NAMESPACE | 1 - R/shiny2.r | 14 ++++++++------ 5 files changed, 21 insertions(+), 18 deletions(-)
Title: Data Quality Reporting for Temporal Datasets
Description: Generate reports that enable quick visual review of
temporal shifts in record-level data. Time series plots showing aggregated
values are automatically created for each data field (column) depending on its
contents (e.g. min/max/mean values for numeric data, no. of distinct
values for categorical data), as well as overviews for missing values,
non-conformant values, and duplicated rows. The resulting reports are shareable
and can contribute to forming a transparent record of the entire analysis process.
It is designed with Electronic Health Records in mind, but can be used for
any type of record-level temporal data (i.e. tabular data where each row represents
a single "event", one column contains the "event date", and other columns
contain any associated values for the event).
Author: T. Phuong Quan [aut, cre] ,
Jack Cregan [ctb],
University of Oxford [cph],
National Institute for Health Research [fnd],
Brad Cannell [rev]
Maintainer: T. Phuong Quan <phuong.quan@ndm.ox.ac.uk>
Diff between daiquiri versions 1.0.1 dated 2022-11-11 and 1.0.2 dated 2022-11-21
DESCRIPTION | 6 +- MD5 | 20 +++---- NEWS.md | 8 ++- R/reports.R | 3 - README.md | 12 +++- inst/doc/daiquiri.R | 19 ------- inst/doc/daiquiri.Rmd | 20 ------- inst/doc/daiquiri.html | 111 +++++++++++++++++++++----------------------- inst/rmd/report_htmldoc.Rmd | 8 +-- man/report_data.Rd | 2 vignettes/daiquiri.Rmd | 20 ------- 11 files changed, 89 insertions(+), 140 deletions(-)
Title: Detection of Multiple Changes in Slope in Univariate Time-Series
Description: Detects multiple changes in slope using the CPOP dynamic programming approach of Fearnhead, Maidstone, and Letchford (2019) <doi:10.1080/10618600.2018.1512868>. This method finds the best continuous piecewise linear fit to data under a criterion that measures fit to data using the residual sum of squares, but penalizes complexity based on an L0 penalty on changes in slope.
Author: Daniel Grose [aut, cre],
Paul Fearnhead [aut]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between cpop versions 1.0.4 dated 2022-11-11 and 1.0.6 dated 2022-11-21
DESCRIPTION | 8 - MD5 | 40 ++++----- NEWS.md | 10 ++ R/cpop.R | 11 -- R/cpop.crops.R | 11 +- build/cpop.pdf |binary build/partial.rdb |binary inst/doc/cpop.ltx | 80 ++++++++---------- inst/doc/cpop.pdf |binary vignettes/cpop.ltx | 80 ++++++++---------- vignettes/figures/change_in_slope_examples_ggplot.pdf |binary vignettes/figures/cpop_CPU_ggplot.pdf |binary vignettes/figures/cpop_crops_example_ggplot.pdf |binary vignettes/figures/cpop_crops_ggplot.pdf |binary vignettes/figures/cpop_example1_ggplot.pdf |binary vignettes/figures/cpop_example_uneven_ggplot.pdf |binary vignettes/figures/cpop_minseg_ggplot.pdf |binary vignettes/figures/cpop_real_data_ggplot.pdf |binary vignettes/figures/cpop_uneven_examples_ggplot.pdf |binary vignettes/figures/simulate_example_ggplot.pdf |binary vignettes/refs.bib | 6 - 21 files changed, 119 insertions(+), 127 deletions(-)
Title: Spatiotemporal Arrays, Raster and Vector Data Cubes
Description: Reading, manipulating, writing and plotting
spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL'
bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Author: Edzer Pebesma [aut, cre] ,
Michael Sumner [ctb] ,
Etienne Racine [ctb],
Adriano Fantini [ctb],
David Blodgett [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between stars versions 0.5-6 dated 2022-07-21 and 0.6-0 dated 2022-11-21
stars-0.5-6/stars/man/read_mdim.Rd |only stars-0.6-0/stars/DESCRIPTION | 25 stars-0.6-0/stars/MD5 | 186 ++-- stars-0.6-0/stars/NAMESPACE | 6 stars-0.6-0/stars/NEWS.md | 30 stars-0.6-0/stars/R/aggregate.R | 30 stars-0.6-0/stars/R/dimensions.R | 78 + stars-0.6-0/stars/R/init.R | 4 stars-0.6-0/stars/R/intervals.R | 2 stars-0.6-0/stars/R/mdim.R |only stars-0.6-0/stars/R/ncproxy.R | 2 stars-0.6-0/stars/R/ops.R | 8 stars-0.6-0/stars/R/plot.R | 8 stars-0.6-0/stars/R/proxy.R | 69 + stars-0.6-0/stars/R/raster.R | 24 stars-0.6-0/stars/R/read.R | 129 -- stars-0.6-0/stars/R/sf.R | 11 stars-0.6-0/stars/R/stars.R | 162 ++- stars-0.6-0/stars/R/subset.R | 2 stars-0.6-0/stars/R/tidyverse.R | 31 stars-0.6-0/stars/R/write.R | 20 stars-0.6-0/stars/build/vignette.rds |binary stars-0.6-0/stars/inst/doc/stars1.R | 87 - stars-0.6-0/stars/inst/doc/stars1.Rmd | 5 stars-0.6-0/stars/inst/doc/stars1.html | 141 +-- stars-0.6-0/stars/inst/doc/stars2.R | 84 - stars-0.6-0/stars/inst/doc/stars2.Rmd | 10 stars-0.6-0/stars/inst/doc/stars2.html | 438 +++++---- stars-0.6-0/stars/inst/doc/stars3.R | 6 stars-0.6-0/stars/inst/doc/stars3.Rmd | 6 stars-0.6-0/stars/inst/doc/stars3.html | 83 - stars-0.6-0/stars/inst/doc/stars4.R | 49 - stars-0.6-0/stars/inst/doc/stars4.Rmd | 36 stars-0.6-0/stars/inst/doc/stars4.html | 192 +++- stars-0.6-0/stars/inst/doc/stars5.R | 7 stars-0.6-0/stars/inst/doc/stars5.Rmd | 7 stars-0.6-0/stars/inst/doc/stars5.html | 30 stars-0.6-0/stars/inst/doc/stars6.R | 14 stars-0.6-0/stars/inst/doc/stars6.Rmd | 14 stars-0.6-0/stars/inst/doc/stars6.html | 27 stars-0.6-0/stars/inst/doc/stars8.R | 2 stars-0.6-0/stars/inst/doc/stars8.Rmd | 2 stars-0.6-0/stars/inst/doc/stars8.html | 30 stars-0.6-0/stars/man/figures/README-plot3-1.png |binary stars-0.6-0/stars/man/geom_stars.Rd | 2 stars-0.6-0/stars/man/mdim.Rd |only stars-0.6-0/stars/man/plot.Rd | 7 stars-0.6-0/stars/man/print_stars.Rd |only stars-0.6-0/stars/man/read_stars.Rd | 5 stars-0.6-0/stars/man/redimension.Rd | 7 stars-0.6-0/stars/man/st_cells.Rd |only stars-0.6-0/stars/man/st_res.Rd |only stars-0.6-0/stars/man/write_stars.Rd | 9 stars-0.6-0/stars/tests/aggregate.Rout.save | 308 +++--- stars-0.6-0/stars/tests/align.Rout.save | 116 +- stars-0.6-0/stars/tests/area.R | 16 stars-0.6-0/stars/tests/area.Rout.save | 153 +-- stars-0.6-0/stars/tests/crop.Rout.save | 122 +- stars-0.6-0/stars/tests/curvilinear.R | 2 stars-0.6-0/stars/tests/curvilinear.Rout.save | 162 +-- stars-0.6-0/stars/tests/datasets.Rout.save | 105 +- stars-0.6-0/stars/tests/dimensions.Rout.save | 126 +- stars-0.6-0/stars/tests/ee.R |only stars-0.6-0/stars/tests/ee.Rout.save |only stars-0.6-0/stars/tests/extract.Rout.save | 298 +++--- stars-0.6-0/stars/tests/gridtypes.Rout.save | 670 +++++++------- stars-0.6-0/stars/tests/nc.Rout.save | 458 ++++----- stars-0.6-0/stars/tests/plot.Rout.save | 96 +- stars-0.6-0/stars/tests/predict.Rout.save | 190 ++-- stars-0.6-0/stars/tests/proxy.R | 12 stars-0.6-0/stars/tests/proxy.Rout.save | 662 +++++++------- stars-0.6-0/stars/tests/raster.Rout.save | 230 ++-- stars-0.6-0/stars/tests/rasterize.Rout.save | 216 ++-- stars-0.6-0/stars/tests/rectilinear.Rout.save | 158 +-- stars-0.6-0/stars/tests/redimension.R | 5 stars-0.6-0/stars/tests/redimension.Rout.save | 176 ++- stars-0.6-0/stars/tests/sf.Rout.save | 347 +++---- stars-0.6-0/stars/tests/sp.Rout.save | 166 +-- stars-0.6-0/stars/tests/spacetime.Rout.save | 674 +++++++------- stars-0.6-0/stars/tests/spatstat.Rout.save | 74 - stars-0.6-0/stars/tests/stars.R | 4 stars-0.6-0/stars/tests/stars.Rout.save | 924 +++++++++----------- stars-0.6-0/stars/tests/subset.Rout.save | 180 +-- stars-0.6-0/stars/tests/testthat.Rout.save | 63 - stars-0.6-0/stars/tests/testthat/test_ncdf.R | 1 stars-0.6-0/stars/tests/testthat/test_ncproxy.R | 1 stars-0.6-0/stars/tests/testthat/test_rectilinear.R | 1 stars-0.6-0/stars/tests/tidy.Rout.save | 146 +-- stars-0.6-0/stars/tests/transform.Rout.save | 181 ++- stars-0.6-0/stars/tests/warp.Rout.save | 118 +- stars-0.6-0/stars/tests/write.Rout.save | 102 +- stars-0.6-0/stars/vignettes/stars1.Rmd | 5 stars-0.6-0/stars/vignettes/stars2.Rmd | 10 stars-0.6-0/stars/vignettes/stars3.Rmd | 6 stars-0.6-0/stars/vignettes/stars4.Rmd | 36 stars-0.6-0/stars/vignettes/stars5.Rmd | 7 stars-0.6-0/stars/vignettes/stars6.Rmd | 14 stars-0.6-0/stars/vignettes/stars8.Rmd | 2 98 files changed, 4998 insertions(+), 4472 deletions(-)
Title: Render SVG Images into PDF, PNG, (Encapsulated) PostScript, or
Bitmap Arrays
Description: Renders vector-based svg images into high-quality custom-size
bitmap arrays using 'librsvg2'. The resulting bitmap can be written to
e.g. png, jpeg or webp format. In addition, the package can convert
images directly to various formats such as pdf or postscript.
Author: Jeroen Ooms [aut, cre] ,
Salim Brueggemann [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between rsvg versions 2.3.2 dated 2022-10-18 and 2.4.0 dated 2022-11-21
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 3 +++ build/vignette.rds |binary inst/doc/svg-css.html | 2 +- src/rsvg.c | 5 +++++ 6 files changed, 17 insertions(+), 9 deletions(-)
Title: Easy Computation of Functional Diversity Indices
Description: Computes six functional diversity indices. These are namely,
Functional Divergence (FDiv), Function Evenness (FEve), Functional Richness
(FRic), Functional Richness intersections (FRic_intersect), Functional
Dispersion (FDis), and Rao's entropy (Q) (reviewed in Villéger et al. 2008
<doi:10.1890/07-1206.1>). Provides efficient, modular, and parallel functions
to compute functional diversity indices
(preprint: <doi:10.32942/osf.io/dg7hw>).
Author: Matthias Grenie [aut, cre] ,
Hugo Gruson [aut]
Maintainer: Matthias Grenie <matthias.grenie@gmail.com>
Diff between fundiversity versions 1.0.0 dated 2022-08-25 and 1.1.1 dated 2022-11-21
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Title: R Integration for Edlib, the C/C++ Library for Exact Pairwise
Sequence Alignment using Edit (Levenshtein) Distance
Description: Bindings to edlib, a lightweight performant C/C++ library for exact pairwise sequence alignment using edit distance (Levenshtein distance). The algorithm computes the optimal alignment path, but also can be used to find only the start and/or end of the alignment path for convenience. Edlib was designed to be ultrafast and require little memory, with the capability to handle very large sequences. Three alignment methods are supported: global (Needleman-Wunsch), infix (Hybrid Wunsch), and prefix (Semi-Hybrid Wunsch). The original C/C++ library is described in "Edlib: a C/C++ library for fast, exact sequence alignment using edit distance", M. Šošić, M. Šikić, <doi:10.1093/bioinformatics/btw753>.
Author: Martin Sosić [aut],
Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between edlibR versions 1.0.0 dated 2022-01-12 and 1.0.1 dated 2022-11-21
DESCRIPTION | 6 MD5 | 12 - R/main.R | 92 ++++++------ README.md | 13 + inst/doc/edlibR_walkthrough.html | 288 ++++++++++++++++++++++++++------------- src/Makevars | 2 src/Makevars.win | 2 7 files changed, 267 insertions(+), 148 deletions(-)
Title: Penalised Maximum Likelihood for Survival Analysis Models
Description: Estimate the regression coefficients and the baseline hazard
of proportional hazard Cox models with left, right or interval censored survival data
using maximum penalised likelihood. A 'non-parametric' smooth estimate of the baseline hazard
function is provided.
Author: Dominique-Laurent Couturier, Jun Ma, Stephane Heritier, Maurizio Manuguerra.
Maintainer: Dominique-Laurent Couturier <dominique-laurent.couturier@cruk.cam.ac.uk>
Diff between survivalMPL versions 0.2-2 dated 2022-11-20 and 0.2-3 dated 2022-11-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 6 ++++++ man/bcos2.Rd | 2 +- 4 files changed, 13 insertions(+), 7 deletions(-)
Title: 10-Year Cardiovascular Disease Risk Calculator (QRISK3 2017)
Description: This function aims to calculate risk of developing cardiovascular disease of individual patients in next 10 years. The package was based on published risk prediction algorithm <https://qrisk.org/three/src.php>.
Author: Yan Li <bluefatterplaydota@gmail.com> [aut, cre, trl],
Matthew Sperrin [aut, ctb],
ClinRisk Ltd. [cph],
Tjeerd Pieter van Staa [aut, ths]
Maintainer: Yan Li <bluefatterplaydota@gmail.com>
Diff between QRISK3 versions 0.3.0 dated 2019-12-06 and 0.4.0 dated 2022-11-21
QRISK3-0.3.0/QRISK3/R/QRISK3-2017ver8.R |only QRISK3-0.3.0/QRISK3/README.md |only QRISK3-0.3.0/QRISK3/tests/testthat/testthat.R |only QRISK3-0.4.0/QRISK3/DESCRIPTION | 8 +- QRISK3-0.4.0/QRISK3/MD5 | 14 ++--- QRISK3-0.4.0/QRISK3/R/QRISK3-2017ver9.R |only QRISK3-0.4.0/QRISK3/man/QRISK3_2017.Rd | 2 QRISK3-0.4.0/QRISK3/man/QRISK3_2017_test.Rd | 4 + QRISK3-0.4.0/QRISK3/man/QRISK3_2019_test.Rd | 4 + QRISK3-0.4.0/QRISK3/tests/testthat/QRISK3-2017_testthat.R | 38 ++++++++++++++ 10 files changed, 55 insertions(+), 15 deletions(-)
Title: Inbreeding-Purging Estimation in Pedigreed Populations
Description: Inbreeding-purging analysis of pedigreed populations, including the computation of the inbreeding coefficient, partial, ancestral and purged inbreeding coefficients, and measures of the opportunity of purging related to the individual reduction of inbreeding load.
In addition, functions to calculate the effective population size and other parameters relevant to population genetics are included.
See López-Cortegano E. (2021) <doi:10.1093/bioinformatics/btab599>.
Author: Eugenio Lopez-Cortegano [aut, cre]
Maintainer: Eugenio Lopez-Cortegano <elcortegano@gmail.com>
Diff between purgeR versions 1.5 dated 2022-07-11 and 1.6 dated 2022-11-21
DESCRIPTION | 8 - MD5 | 46 ++++----- NEWS.md | 5 + R/Nancestors.R | 14 +- R/RcppExports.R | 3 R/check.R | 109 ++++++++++------------ R/clean.R | 6 - R/fitness.R | 22 ++-- R/generations.R | 4 R/maternal.R | 10 +- R/mating.R | 2 R/opurging.R | 2 R/partial.R | 41 ++++---- R/rename.R | 2 R/sort.R | 8 - build/vignette.rds |binary inst/doc/ip.R | 15 +++ inst/doc/ip.Rmd | 20 ++++ inst/doc/ip.html | 206 ++++++++++++++++++++++-------------------- inst/doc/purgeR-tutorial.html | 4 man/check_reference.Rd | 6 - man/search_ancestors.Rd | 4 src/populationSize.cpp | 16 +-- vignettes/ip.Rmd | 20 ++++ 24 files changed, 323 insertions(+), 250 deletions(-)
Title: Machine Learning Algorithms for Multivariate Time Series
Description: An implementation of several machine learning algorithms for
multivariate time series. The package includes functions allowing the
execution of clustering, classification or outlier detection methods,
among others. It also incorporates a collection of multivariate time
series datasets which can be used to analyse the performance of new
proposed algorithms. Some of these datasets are stored in GitHub data
packages 'ueadata1' to 'ueadata8'. To access these data packages, run
'install.packages(c('ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5', 'ueadata6', 'ueadata7', 'ueadata8'), repos='<https://anloor7.github.io/drat/>')'.
The installation takes a couple of minutes but we strongly encourage the
users to do it if they want to have available all datasets of mlmts.
Practitioners from a broad variety of fields could
benefit from the general framework provided by 'mlmts'.
Author: Angel Lopez-Oriona [aut, cre],
Jose A. Vilar [aut]
Maintainer: Angel Lopez-Oriona <oriona38@hotmail.com>
Diff between mlmts versions 1.0.1 dated 2022-04-19 and 1.1.0 dated 2022-11-21
DESCRIPTION | 19 - MD5 | 134 ++++++-- NAMESPACE | 3 R/ArticularlyWordRecognition.R |only R/CharacterTrajectories.R |only R/Cricket.R |only R/DuckDuckGeese_1.R |only R/DuckDuckGeese_2.R |only R/ERing.R | 50 +-- R/EigenWorms_1.R |only R/EigenWorms_2.R |only R/EthanolConcentration.R |only R/FingerMovements.R |only R/HandMovementDirection.R |only R/Handwriting.R |only R/Heartbeat.R |only R/JapaneseVowels.R |only R/LSST.R |only R/MotorImagery.R |only R/NATOPS.R |only R/PEMS_SF_1.R |only R/PEMS_SF_2.R |only R/Phoneme.R |only R/SelfRegulationSCP1.R |only R/SelfRegulationSCP2.R |only R/SpokenArabicDigits.R |only R/UWaveGestureLibrary.R |only R/auxiliary_forecasting_function.R |only R/auxiliary_mcc_function.R |only R/auxiliary_ppca_function.R |only R/dis_2dsvd.R | 13 R/dis_dtw_1.R | 5 R/dis_dtw_2.R | 5 R/dis_gcc.R | 6 R/dis_lpp.R | 14 R/dis_mcc.R |only R/dis_ppca.R |only R/dis_spectral.R | 5 R/dis_swmd.R | 14 R/mts_forecasting.R |only R/mts_plot.R | 125 ++++--- R/outlier_detection.R | 2 R/plot_2d_scaling.R | 7 R/vpca_clustering.R | 2 build/partial.rdb |binary data/ArticularlyWordRecognition.RData |only data/CharacterTrajectories.RData |only data/Cricket.RData |only data/DuckDuckGeese_1.RData |only data/DuckDuckGeese_2.RData |only data/ERing.RData |binary data/EigenWorms_1.RData |only data/EigenWorms_2.RData |only data/EthanolConcentration.RData |only data/FingerMovements.RData |only data/HandMovementDirection.RData |only data/Handwriting.RData |only data/Heartbeat.RData |only data/JapaneseVowels.RData |only data/LSST.RData |only data/MotorImagery.RData |only data/NATOPS.RData |only data/PEMS_SF_1.RData |only data/PEMS_SF_2.RData |only data/Phoneme.RData |only data/SelfRegulationSCP1.RData |only data/SelfRegulationSCP2.RData |only data/SpokenArabicDigits.RData |only data/UWaveGestureLibrary.RData |only inst/REFERENCES.bib | 560 +++++++++++++++++----------------- man/ArticularlyWordRecognition.Rd |only man/CharacterTrajectories.Rd |only man/Cricket.Rd |only man/DuckDuckGeese_1.Rd |only man/DuckDuckGeese_2.Rd |only man/ERing.Rd | 4 man/EigenWorms_1.Rd |only man/EigenWorms_2.Rd |only man/EthanolConcentration.Rd |only man/FingerMovements.Rd |only man/HandMovementDirection.Rd |only man/Handwriting.Rd |only man/Heartbeat.Rd |only man/JapaneseVowels.Rd |only man/LSST.Rd |only man/MotorImagery.Rd |only man/NATOPS.Rd |only man/PEMS_SF_1.Rd |only man/PEMS_SF_2.Rd |only man/Phoneme.Rd |only man/SelfRegulationSCP1.Rd |only man/SelfRegulationSCP2.Rd |only man/SpokenArabicDigits.Rd |only man/UWaveGestureLibrary.Rd |only man/dis_2dsvd.Rd | 13 man/dis_dtw_1.Rd | 5 man/dis_dtw_2.Rd | 5 man/dis_gcc.Rd | 6 man/dis_lpp.Rd | 14 man/dis_mcc.Rd |only man/dis_ppca.Rd |only man/dis_spectral.Rd | 5 man/dis_swmd.Rd | 14 man/mts_forecasting.Rd |only man/outlier_detection.Rd | 2 man/plot_2d_scaling.Rd | 2 man/vpca_clustering.Rd | 2 107 files changed, 602 insertions(+), 434 deletions(-)
Title: Lightweight Utilities for 'DIZ' R Package Development
Description: Lightweight utility functions used for the R package
development infrastructure inside the data integration centers ('DIZ')
to standardize and facilitate repetitive tasks such as setting up a
database connection or issuing notification messages and to avoid
redundancy.
Author: Jonathan M. Mang [aut, cre] ,
Lorenz A. Kapsner [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen, Germany [cph]
Maintainer: Jonathan M. Mang <jonathan.mang@uk-erlangen.de>
Diff between DIZtools versions 0.0.5 dated 2022-05-18 and 0.0.6 dated 2022-11-21
DESCRIPTION | 10 +++++----- MD5 | 27 +++++++++++++++++++-------- NAMESPACE | 3 +++ R/check_if_unique_rows.R | 2 -- R/feedback.R | 2 -- R/get_current_timestamp.R | 2 +- R/number_to_position.R |only R/paste2.R |only R/robust_round.R |only R/vgsub.R | 2 +- R/zzz.R |only man/number_to_position.Rd |only man/paste2.Rd |only man/robust_round.Rd |only man/vgsub.Rd | 2 +- tests/testthat/test-get_current_timestamp.R |only tests/testthat/test-lints.R | 2 +- tests/testthat/test-number_to_position.R |only tests/testthat/test-paste2.R |only tests/testthat/test-robust_round.R |only 20 files changed, 31 insertions(+), 21 deletions(-)
Title: Create 'Ascii' Screen Casts from R Scripts
Description: Record 'asciicast' screen casts from R scripts. Convert them
to animated SVG images, to be used in 'README' files, or blog posts.
Includes 'asciinema-player' as an 'HTML' widget, and an 'asciicast'
'knitr' engine, to embed 'ascii' screen casts in 'Rmarkdown' documents.
Author: Gabor Csardi [aut, cre],
Romain Francois [aut],
Mario Nebl [aut] ,
Marcin Kulik [aut]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between asciicast versions 2.2.0 dated 2022-10-26 and 2.2.1 dated 2022-11-21
asciicast-2.2.0/asciicast/tests/testthat/_snaps/html/html-truecolor.html |only asciicast-2.2.1/asciicast/DESCRIPTION | 6 asciicast-2.2.1/asciicast/MD5 | 19 - asciicast-2.2.1/asciicast/NAMESPACE | 1 asciicast-2.2.1/asciicast/NEWS.md | 10 asciicast-2.2.1/asciicast/R/errors.R | 147 +++++++--- asciicast-2.2.1/asciicast/R/test.R |only asciicast-2.2.1/asciicast/man/expect_snapshot_r_process.Rd |only asciicast-2.2.1/asciicast/src/rwin.c | 8 asciicast-2.2.1/asciicast/tests/testthat/_snaps/ascii |only asciicast-2.2.1/asciicast/tests/testthat/_snaps/test.md |only asciicast-2.2.1/asciicast/tests/testthat/_snaps/utf8 |only asciicast-2.2.1/asciicast/tests/testthat/test-html.R | 3 asciicast-2.2.1/asciicast/tests/testthat/test-test.R |only 14 files changed, 135 insertions(+), 59 deletions(-)
Title: Read and Write CSV on the Web (CSVW) Tables and Metadata
Description: Provide functions for reading and writing CSVW - i.e. CSV tables and JSON metadata.
The metadata helps interpret CSV by setting the types and variable names.
Author: Robin Gower
Maintainer: Robin Gower <csvwr@infonomics.ltd.uk>
Diff between csvwr versions 0.1.6 dated 2021-11-09 and 0.1.7 dated 2022-11-21
DESCRIPTION | 10 MD5 | 77 +++--- NAMESPACE | 1 NEWS.md | 11 R/csvwr.R | 89 +++++-- R/util.R | 5 README.md | 15 + build/vignette.rds |binary inst/doc/read-write-csvw.html | 423 ++++++++++++++++++++++++++-------- inst/extdata/computer-scientists.json | 2 man/add_dataframe.Rd | 7 man/base_url.Rd | 1 man/compact_json_ld.Rd | 1 man/csvwr.Rd | 11 man/default_schema.Rd | 4 man/find_existing_file.Rd | 1 man/find_metadata.Rd | 1 man/is_absolute_url.Rd | 1 man/is_non_core_annotation.Rd | 1 man/json_ld_to_json.Rd | 1 man/list_of_lists_to_df.Rd | 1 man/locate_metadata.Rd | 1 man/locate_table.Rd | 1 man/location_configuration.Rd | 1 man/normalise_property.Rd | 1 man/normalise_url.Rd | 1 man/override_defaults.Rd |only man/parse_columns.Rd | 1 man/parse_metadata.Rd | 1 man/render_cell.Rd | 1 man/resolve_url.Rd | 1 man/rlmap.Rd | 1 man/rmap.Rd | 1 man/set_uri_base.Rd | 1 man/table_to_list.Rd | 7 man/try_add_dataframe.Rd | 1 man/unlist1.Rd | 1 man/vec_depth.Rd | 1 tests/testthat/test-parsing.R | 30 ++ tests/testthat/test-util.R | 7 40 files changed, 552 insertions(+), 170 deletions(-)
Title: Deprecated 'classic' 'Rcpp' 'API'
Description: The 'RcppClassic' package provides a deprecated C++ library which
facilitates the integration of R and C++. New projects should use the new 'Rcpp'
'API' in the 'Rcpp' package.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by David Reiss,
and based on code written during 2005 and 2006 by Dominick Samperi
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppClassic versions 0.9.12 dated 2019-12-09 and 0.9.13 dated 2022-11-21
ChangeLog | 30 ++++++++++++++++++++++++++++++ DESCRIPTION | 10 ++++++---- MD5 | 12 ++++++------ README.md | 10 +++++----- build/vignette.rds |binary inst/doc/RcppClassic-intro.pdf |binary src/Makevars | 2 +- 7 files changed, 48 insertions(+), 16 deletions(-)
Title: Define and Work with Parameter Spaces for Complex Algorithms
Description: Define parameter spaces, constraints and
dependencies for arbitrary algorithms, to program on such spaces. Also
includes statistical designs and random samplers. Objects are
implemented as 'R6' classes.
Author: Michel Lang [cre, aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Xudong Sun [aut] ,
Martin Binder [aut],
Marc Becker [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between paradox versions 0.10.0 dated 2022-08-05 and 0.11.0 dated 2022-11-21
DESCRIPTION | 12 ++++----- MD5 | 20 +++++++++------- NAMESPACE | 1 NEWS.md | 5 ++++ R/ParamSet.R | 2 - R/generate_design_sobol.R |only README.md | 31 +++++++++---------------- man/generate_design_grid.Rd | 3 +- man/generate_design_lhs.Rd | 3 +- man/generate_design_random.Rd | 3 +- man/generate_design_sobol.Rd |only tests/testthat/test_generate_design.R | 41 +++++++++++++++++++++++++++++++++- 12 files changed, 82 insertions(+), 39 deletions(-)
Title: Calibration and Analysis of Radiocarbon Dates
Description: Enables the calibration and analysis of radiocarbon dates, often but not exclusively for the purposes of archaeological research. It includes functions not only for basic calibration, uncalibration, and plotting of one or more dates, but also a statistical framework for building demographic and related longitudinal inferences from aggregate radiocarbon date lists, including: Monte-Carlo simulation test (Timpson et al 2014 <doi:10.1016/j.jas.2014.08.011>), random mark permutation test (Crema et al 2016 <doi:10.1371/journal.pone.0154809>) and spatial permutation tests (Crema, Bevan, and Shennan 2017 <doi:10.1016/j.jas.2017.09.007>).
Author: Andrew Bevan [aut] ,
Enrico Crema [aut, cre] ,
R. Kyle Bocinsky [ctb],
Martin Hinz [ctb],
Philip Riris [ctb],
Fabio Silva [ctb]
Maintainer: Enrico Crema <enrico.crema@gmail.com>
Diff between rcarbon versions 1.4.4 dated 2022-07-21 and 1.5.0 dated 2022-11-21
rcarbon-1.4.4/rcarbon/man/SPpermTest-deprecated.Rd |only rcarbon-1.4.4/rcarbon/man/spweights.Rd |only rcarbon-1.5.0/rcarbon/DESCRIPTION | 10 rcarbon-1.5.0/rcarbon/MD5 | 32 rcarbon-1.5.0/rcarbon/NAMESPACE | 6 rcarbon-1.5.0/rcarbon/R/package-rcarbon.R | 2 rcarbon-1.5.0/rcarbon/R/plots.R | 138 +- rcarbon-1.5.0/rcarbon/R/tests.R | 160 +- rcarbon-1.5.0/rcarbon/R/utilities.R | 83 - rcarbon-1.5.0/rcarbon/build/vignette.rds |binary rcarbon-1.5.0/rcarbon/inst/doc/rcarbon.Rmd | 59 rcarbon-1.5.0/rcarbon/inst/doc/rcarbon.html | 1283 +++++++++++++-------- rcarbon-1.5.0/rcarbon/man/modelTest.Rd | 4 rcarbon-1.5.0/rcarbon/man/plot.spatialTest.Rd | 4 rcarbon-1.5.0/rcarbon/man/rcarbon-deprecated.Rd | 26 rcarbon-1.5.0/rcarbon/man/rcarbon.Rd | 2 rcarbon-1.5.0/rcarbon/man/sptest.Rd | 63 - rcarbon-1.5.0/rcarbon/vignettes/rcarbon.Rmd | 59 18 files changed, 1118 insertions(+), 813 deletions(-)
Title: A Cartographic Tool to Chart Spatial Microbial Interaction
Networks
Description: Most existing approaches for network reconstruction can only infer an overall network
and, also, fail to capture a complete set of network properties. To address these issues,
a new model has been developed, which converts static data into their 'dynamic' form.
'idopNetwork' is an 'R' interface to this model, it can inferring informative, dynamic,
omnidirectional and personalized networks. For more information on functional
clustering part, see Kim et al. (2008) <doi:10.1534/genetics.108.093690>,
Wang et al. (2011) <doi:10.1093/bib/bbr032>. For more information on our model,
see Chen et al. (2019) <doi:10.1038/s41540-019-0116-1>, and Cao et al. (2022)
<doi:10.1080/19490976.2022.2106103>.
Author: Ang Dong
Maintainer: Ang Dong <fantasys05227@gmail.com>
Diff between idopNetwork versions 0.1.0 dated 2022-11-09 and 0.1.1 dated 2022-11-21
idopNetwork-0.1.0/idopNetwork/R/idol_variable.R |only idopNetwork-0.1.0/idopNetwork/man/GB.Rd |only idopNetwork-0.1.1/idopNetwork/DESCRIPTION | 6 idopNetwork-0.1.1/idopNetwork/MD5 | 62 idopNetwork-0.1.1/idopNetwork/NAMESPACE | 7 idopNetwork-0.1.1/idopNetwork/R/base.R | 8 idopNetwork-0.1.1/idopNetwork/R/bi_functional_clustering.R | 87 idopNetwork-0.1.1/idopNetwork/R/data.R | 5 idopNetwork-0.1.1/idopNetwork/R/functional_clustering.R | 55 idopNetwork-0.1.1/idopNetwork/R/network_reconstruction.R | 65 idopNetwork-0.1.1/idopNetwork/R/ode_solving.R | 282 ++ idopNetwork-0.1.1/idopNetwork/R/power_equation_fitting.R | 123 + idopNetwork-0.1.1/idopNetwork/R/sysdata.rda |binary idopNetwork-0.1.1/idopNetwork/R/variable_selection.R | 2 idopNetwork-0.1.1/idopNetwork/data/mustard_microbe.rda |binary idopNetwork-0.1.1/idopNetwork/inst/doc/idopNetwork_vignette.R | 82 idopNetwork-0.1.1/idopNetwork/inst/doc/idopNetwork_vignette.Rmd | 101 - idopNetwork-0.1.1/idopNetwork/inst/doc/idopNetwork_vignette.html | 962 +++++----- idopNetwork-0.1.1/idopNetwork/man/bifun_clu.Rd | 2 idopNetwork-0.1.1/idopNetwork/man/bifun_clu_convert.Rd | 6 idopNetwork-0.1.1/idopNetwork/man/bifun_clu_plot.Rd | 18 idopNetwork-0.1.1/idopNetwork/man/bipower_equation_plot.Rd |only idopNetwork-0.1.1/idopNetwork/man/biqdODE_plot_all.Rd |only idopNetwork-0.1.1/idopNetwork/man/biqdODE_plot_base.Rd |only idopNetwork-0.1.1/idopNetwork/man/fun_clu_BIC.Rd | 4 idopNetwork-0.1.1/idopNetwork/man/fun_clu_plot.Rd | 6 idopNetwork-0.1.1/idopNetwork/man/mustard_microbe.Rd | 5 idopNetwork-0.1.1/idopNetwork/man/network_maxeffect.Rd |only idopNetwork-0.1.1/idopNetwork/man/network_plot.Rd | 6 idopNetwork-0.1.1/idopNetwork/man/normalization.Rd |only idopNetwork-0.1.1/idopNetwork/man/power_equation_all.Rd | 2 idopNetwork-0.1.1/idopNetwork/man/power_equation_plot.Rd | 2 idopNetwork-0.1.1/idopNetwork/man/qdODE_plot_all.Rd | 16 idopNetwork-0.1.1/idopNetwork/man/qdODE_plot_base.Rd | 9 idopNetwork-0.1.1/idopNetwork/man/qdODEplot_convert.Rd |only idopNetwork-0.1.1/idopNetwork/vignettes/idopNetwork_vignette.Rmd | 101 - 36 files changed, 1304 insertions(+), 720 deletions(-)
Title: Tools for Working with Geohashes
Description: Tools for working with Gustavo Niemeyer's geohash coordinate system, including API for interacting with other common R GIS libraries.
Author: Michael Chirico [aut, cre],
Dmitry Shkolnik [ctb]
Maintainer: Michael Chirico <MichaelChirico4@gmail.com>
Diff between geohashTools versions 0.3.1 dated 2020-05-26 and 0.3.2 dated 2022-11-21
DESCRIPTION | 11 + MD5 | 17 +- NEWS.md | 10 + R/gis_tools.R | 3 README.md | 275 ++++++++++++++++++---------------------- build |only inst |only src/init.c | 13 + tests/testthat/test-gis-tools.R | 10 + vignettes |only 10 files changed, 174 insertions(+), 165 deletions(-)
Title: Secure in-Browser Storage for 'Shiny' Inputs and Variables
Description: Store persistent and synchronized data from 'Shiny' inputs within the browser in a secure format. Refresh 'Shiny' applications and preserve user-inputs over multiple sessions. A database-like storage format is implemented using 'Dexie.js' <https://dexie.org>, a minimal wrapper for 'IndexedDB'. Transfer browser link parameters to 'Shiny' input or output values.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between shinyStorePlus versions 0.7 dated 2022-11-03 and 0.8 dated 2022-11-21
shinyStorePlus-0.7/shinyStorePlus/inst/example/server.R |only shinyStorePlus-0.7/shinyStorePlus/inst/example/ui.R |only shinyStorePlus-0.8/shinyStorePlus/DESCRIPTION | 10 +- shinyStorePlus-0.8/shinyStorePlus/MD5 | 34 ++++++---- shinyStorePlus-0.8/shinyStorePlus/NAMESPACE | 1 shinyStorePlus-0.8/shinyStorePlus/NEWS.md | 10 ++ shinyStorePlus-0.8/shinyStorePlus/R/locationParms.R |only shinyStorePlus-0.8/shinyStorePlus/R/seeex.R | 10 ++ shinyStorePlus-0.8/shinyStorePlus/R/shinyStorePlus-package.R |only shinyStorePlus-0.8/shinyStorePlus/README.md | 2 shinyStorePlus-0.8/shinyStorePlus/build/vignette.rds |binary shinyStorePlus-0.8/shinyStorePlus/inst/doc/introduction_to_shinystoreplus.html | 4 - shinyStorePlus-0.8/shinyStorePlus/inst/doc/shinystoreplus_v08.R |only shinyStorePlus-0.8/shinyStorePlus/inst/doc/shinystoreplus_v08.Rmd |only shinyStorePlus-0.8/shinyStorePlus/inst/doc/shinystoreplus_v08.html |only shinyStorePlus-0.8/shinyStorePlus/inst/doc/using_shinystoreplus.html | 4 - shinyStorePlus-0.8/shinyStorePlus/inst/example/browserLinkToInput |only shinyStorePlus-0.8/shinyStorePlus/inst/example/storeInputs |only shinyStorePlus-0.8/shinyStorePlus/inst/scripts/shinystoreplus.js | 4 - shinyStorePlus-0.8/shinyStorePlus/man/link2input.Rd |only shinyStorePlus-0.8/shinyStorePlus/man/seeexample.Rd | 6 + shinyStorePlus-0.8/shinyStorePlus/man/shinyStorePlus-package.Rd |only shinyStorePlus-0.8/shinyStorePlus/vignettes/shinystoreplus_v08.Rmd |only 23 files changed, 56 insertions(+), 29 deletions(-)
More information about shinyStorePlus at CRAN
Permanent link
Title: E-Value in the Omics Data Association Studies
Description: In the omics data association studies, it is common to conduct the p-value corrections to control the false significance. Among those p-value correction methods, E-value is recently studied based on V. Vovk and R. Wang (2021) <doi:10.1214/20-AOS2020>. This package provides e-value calculation for several types of omics data association studies. Currently, four data formats are supported: BiSeq, MDRfinder, methylKit and metilene data. The relevant references are listed below: Katja Hebestreit and Hans-Ulrich Klein (2022) <doi:10.18129/B9.bioc.BiSeq>; Altuna Akalin et.al (2012) <doi:10.18129/B9.bioc.methylKit>.
Author: Yifan Yang [aut, cre, cph],
Xiaoqing Pan [aut],
Haoyuan Liu [aut]
Maintainer: Yifan Yang <yfyang.86@hotmail.com>
Diff between metevalue versions 0.1.10 dated 2022-10-28 and 0.1.13 dated 2022-11-21
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/evalue_data_chk.R | 8 ++++---- R/evalue_main.R | 11 +++++------ build/partial.rdb |binary data/demo_biseq_DMR.rda |binary data/demo_methylkit_met_all.rda |binary data/demo_methylkit_methyrate.rda |binary tests/testthat/test-evalue_main.R | 8 +++----- 9 files changed, 24 insertions(+), 27 deletions(-)
Title: Miscellaneous Functions for 'ggplot2'
Description: Useful functions and utilities for 'ggplot' object (e.g., geometric layers, themes, and utilities to edit the object).
Author: Guangchuang Yu [aut, cre, cph]
,
Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggfun versions 0.0.8 dated 2022-11-07 and 0.0.9 dated 2022-11-21
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NAMESPACE | 1 + NEWS.md | 4 ++++ R/theme.R | 19 +++++++++++++++++++ inst/doc/ggfun.html | 6 +++--- man/theme_noxaxis.Rd |only 7 files changed, 38 insertions(+), 13 deletions(-)
Title: Filtering of Flow Cytometry Samples
Description: Filtering, also known as gating, of flow cytometry samples using
the curvHDR method, which is described in Naumann, U., Luta, G. and
Wand, M.P. (2010) <DOI:10.1186/1471-2105-11-44>.
Author: Matt Wand [aut, cre],
George Luta [aut],
Ulrike Naumann [aut],
Mathew W. McLean [ctb],
Dai Feng [ctb],
Luke Tierney [ctb],
Florian Hahne [ctb]
Maintainer: Matt Wand <matt.wand@uts.edu.au>
Diff between curvHDR versions 1.2-1 dated 2019-01-09 and 1.2-1.1 dated 2022-11-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/manual.pdf |binary src/inpolygon.c | 2 +- 5 files changed, 8 insertions(+), 8 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-17 1.1.7
2010-04-28 1.1.6
2010-04-27 1.1.5
2008-04-04 1.1.4
2005-08-07 1.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-01 0.2
2020-11-02 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-13 2.1.4
2018-03-15 2.1.3
2017-02-17 2.1.2
2017-02-09 2.1.1
2017-02-06 2.1
2016-06-16 2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-30 1.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-10 1.0.0
2022-05-05 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-09 6.0.1
2020-02-04 6.0.0
2019-11-26 5.0.1
2019-11-21 5.0.0
2019-04-08 4.0.3
2019-04-06 4.0.2
2019-03-11 4.0.1
2019-03-08 4.0.0
2018-11-05 3.0.1
2018-11-01 3.0.0
2018-09-24 2.0.3
2018-08-19 2.0.2
2018-08-13 2.0.1
2018-08-05 2.0.0
2018-07-28 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-28 1.0-6.1
2013-06-12 1.0-6
2012-12-16 1.0-5
2012-03-28 1.0-4
2008-10-19 1.0-3
2008-08-18 1.0-2
2008-07-14 1.0-1
2008-01-07 0.97-1
2007-11-23 0.96
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-15 1.13.2
2019-01-28 1.13.1
2015-10-19 1.13.0
2014-12-11 1.12.1
2014-12-02 1.12.0
2014-01-25 1.11.0
2013-09-30 1.10.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-10 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-21 0.69
2022-02-25 0.68
2018-05-23 0.67
2017-09-22 0.65
2015-06-16 0.62
2014-07-22 0.54
2014-03-19 0.50
2012-12-14 0.45
2012-03-20 0.43
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-07 1.16.1
2020-03-10 1.15.7
2020-03-06 1.15.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-10 0.3-0
2020-02-12 0.2-1
2020-02-01 0.2-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-09 0.1.3