Title: Vectorised Probability Distributions
Description: Vectorised distribution objects with tools for manipulating,
visualising, and using probability distributions. Designed to allow model
prediction outputs to return distributions rather than their parameters,
allowing users to directly interact with predictive distributions in a
data-oriented workflow. In addition to providing generic replacements for
p/d/q/r functions, other useful statistics can be computed including means,
variances, intervals, and highest density regions.
Author: Mitchell O'Hara-Wild [aut, cre]
,
Matthew Kay [aut] ,
Alex Hayes [aut] ,
Rob Hyndman [aut] ,
Earo Wang [ctb] ,
Vencislav Popov [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between distributional versions 0.4.0 dated 2024-02-07 and 0.5.0 dated 2024-09-17
distributional-0.4.0/distributional/tests/testthat/test-dist_categorical.R |only distributional-0.4.0/distributional/tests/testthat/test-dist_lognormal.R |only distributional-0.5.0/distributional/DESCRIPTION | 28 ++ distributional-0.5.0/distributional/MD5 | 66 ++++--- distributional-0.5.0/distributional/NAMESPACE | 46 ++++ distributional-0.5.0/distributional/NEWS.md | 40 ++++ distributional-0.5.0/distributional/R/default.R | 39 +++- distributional-0.5.0/distributional/R/dist_categorical.R | 7 distributional-0.5.0/distributional/R/dist_gev.R |only distributional-0.5.0/distributional/R/dist_gh.R |only distributional-0.5.0/distributional/R/dist_gk.R |only distributional-0.5.0/distributional/R/dist_gpd.R |only distributional-0.5.0/distributional/R/dist_missing.R | 6 distributional-0.5.0/distributional/R/dist_multivariate_normal.R | 26 +- distributional-0.5.0/distributional/R/dist_percentile.R | 38 +++- distributional-0.5.0/distributional/R/dist_sample.R | 69 ++++--- distributional-0.5.0/distributional/R/distribution.R | 37 +++ distributional-0.5.0/distributional/R/mixture.R | 76 +++++--- distributional-0.5.0/distributional/R/support.R | 27 +- distributional-0.5.0/distributional/R/transformed.R | 57 +++++- distributional-0.5.0/distributional/R/utils.R | 5 distributional-0.5.0/distributional/README.md | 28 +- distributional-0.5.0/distributional/man/dist_gev.Rd |only distributional-0.5.0/distributional/man/dist_gh.Rd |only distributional-0.5.0/distributional/man/dist_gk.Rd |only distributional-0.5.0/distributional/man/dist_gpd.Rd |only distributional-0.5.0/distributional/man/dist_multivariate_normal.Rd | 6 distributional-0.5.0/distributional/man/dist_sample.Rd | 6 distributional-0.5.0/distributional/man/distributional-package.Rd | 2 distributional-0.5.0/distributional/man/figures/README-plot-1.png |binary distributional-0.5.0/distributional/man/new_support_region.Rd | 4 distributional-0.5.0/distributional/tests/testthat/test-apply.R | 13 - distributional-0.5.0/distributional/tests/testthat/test-dist-categorical.R |only distributional-0.5.0/distributional/tests/testthat/test-dist-gh.R |only distributional-0.5.0/distributional/tests/testthat/test-dist-gk.R |only distributional-0.5.0/distributional/tests/testthat/test-dist-lognormal.R |only distributional-0.5.0/distributional/tests/testthat/test-dist-missing.R |only distributional-0.5.0/distributional/tests/testthat/test-dist-multivariate-normal.R | 9 distributional-0.5.0/distributional/tests/testthat/test-mixture.R | 83 +++++++- distributional-0.5.0/distributional/tests/testthat/test-support.R |only distributional-0.5.0/distributional/tests/testthat/test-transformations.R | 94 +++++++++- distributional-0.5.0/distributional/tests/testthat/test_gev.R |only distributional-0.5.0/distributional/tests/testthat/test_gpd.R |only 43 files changed, 638 insertions(+), 174 deletions(-)
More information about distributional at CRAN
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Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, single step (<doi:10.1534/g3.119.400728>), univariate and multivariate (<doi:10.1186/s12711-022-00730-w>),
with optional kernel term and sampling techniques (<doi:10.1186/s12859-017-1582-3>).
Author: Alencar Xavier [aut, cre] ,
William Muir [aut],
David Habier [aut],
Kyle Kocak [aut],
Shizhong Xu [aut],
Katy Rainey [aut]
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 2.2.9 dated 2024-05-20 and 2.2.10 dated 2024-09-17
DESCRIPTION | 8 ++-- MD5 | 17 +++++----- R/RcppExports.R | 8 +++- R/mix.R | 6 +-- demo/multivariates.R | 30 ++++++++--------- man/bWGR.Rd | 4 +- man/mvr.Rd | 18 ++++++---- src/RcppEigen20230423.cpp | 77 ++++++++++++++++++++++++++++++++-------------- src/RcppExports.cpp | 23 +++++++++++-- src/RegisteringDynamic.c |only 10 files changed, 122 insertions(+), 69 deletions(-)
Title: Feature Extraction and Statistics for Time Series
Description: Provides a collection of features, decomposition methods,
statistical summaries and graphics functions for the analysing tidy time
series data. The package name 'feasts' is an acronym comprising of its key
features: Feature Extraction And Statistics for Time Series.
Author: Mitchell O'Hara-Wild [aut, cre],
Rob Hyndman [aut],
Earo Wang [aut],
Di Cook [ctb],
Thiyanga Talagala [ctb] ,
Leanne Chhay [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between feasts versions 0.3.2 dated 2024-03-15 and 0.4.0 dated 2024-09-17
DESCRIPTION | 8 ++--- MD5 | 31 ++++++++++++---------- NAMESPACE | 4 ++ NEWS.md | 17 ++++++++++++ R/features.R | 45 +++++++++++++++++++++++++++++++++ R/graphics.R | 45 +++++++++++++++++++++++++++++---- README.md | 44 +++++++++++++++++--------------- build/vignette.rds |binary inst/doc/feasts.html | 2 - man/ACF.Rd | 2 - man/cointegration_johansen.Rd |only man/cointegration_phillips_ouliaris.Rd |only man/gg_irf.Rd |only man/gg_lag.Rd | 9 +++++- man/gg_season.Rd | 9 +++++- man/gg_subseries.Rd | 9 +++++- tests/testthat/Rplots.pdf |binary tests/testthat/test-graphics.R | 8 ++--- 18 files changed, 181 insertions(+), 52 deletions(-)
Title: Data Supporting the 'VGAM' Package
Description: Mainly data sets to accompany the VGAM package and
the book "Vector Generalized Linear and
Additive Models: With an Implementation in R" (Yee, 2015)
<DOI:10.1007/978-1-4939-2818-7>.
These are used to illustrate vector generalized
linear and additive models (VGLMs/VGAMs), and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column
Interaction Models, and constrained and unconstrained ordination
models in ecology). This package now contains some
old VGAM family functions which have been replaced by newer
ones (often because they are now special cases).
Author: Thomas Yee [aut, cre, cph] ,
James Gray [dtc]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAMdata versions 1.1-9 dated 2023-09-18 and 1.1-12 dated 2024-09-17
DESCRIPTION | 8 +- MD5 | 176 +++++++++++++++++++++++--------------------- NAMESPACE | 23 +++++ NEWS | 13 +++ R/family.fishing.R | 2 R/family.laplace.R |only R/family.vd1.R | 2 R/family.vd2.R | 125 +------------------------------ data/SardiniaHotels.rda |binary data/airbnb.ac.rda |binary data/bb.de.rda |binary data/bd.us.rda |binary data/belcap.rda |binary data/covid19.nz.rda |binary data/crashf.au.rda |binary data/crim.nz.rda |only data/crime.us.rda |binary data/ecb06it.rda |binary data/ecb14it.rda |binary data/exam1.rda |binary data/fibre15.rda |binary data/fibre1dot5.rda |binary data/flamingo.rda |binary data/gala.rda |binary data/hued.rda |binary data/huie.rda |binary data/huse.rda |binary data/mbflood.rda |binary data/oly12.rda |binary data/pirates1.rda |binary data/pirates2.rda |binary data/prison.us.rda |binary data/profs.nz.rda |binary data/rainfall.rda |binary data/rar.df.rda |binary data/rugby.rda |binary data/rugby.ties.rda |binary data/smqP.rda |binary data/students.tw.rda |binary data/trapO.rda |binary data/tube10.rda |binary data/ugss.rda |binary data/vtinpat.rda |binary data/wffc.indiv.rda |binary data/wffc.nc.rda |binary data/wffc.rda |binary data/wffc.teams.rda |binary data/xs.nz.rda |binary demo/binom2.or.R | 30 ++++--- demo/cqo.R | 71 +++++++++-------- demo/distributions.R | 8 +- demo/lmsqreg.R | 31 ++++--- demo/vgam.R | 20 ++--- demo/zipoisson.R | 33 ++++---- man/SardiniaHotels.Rd | 7 + man/alaplace3.Rd |only man/alaplaceUC.Rd |only man/bellUC.Rd | 2 man/bellff.Rd | 14 +-- man/bigamma.mckay.Rd | 10 +- man/crim.nz.Rd |only man/exam1.Rd | 159 ++++++++++++++++++++------------------- man/genpoisson.Rd | 4 - man/laplace.Rd |only man/laplaceUC.Rd |only man/loglaplace.Rd |only man/notdocumentedyet.Rd | 26 +++++- man/oalog.Rd | 28 +++---- man/oalogUC.Rd | 2 man/oapospoisson.Rd | 24 +++--- man/oazeta.Rd | 28 +++---- man/oazetaUC.Rd | 2 man/oilog.Rd | 22 ++--- man/oilogUC.Rd | 14 +-- man/oiposbinomUC.Rd | 10 +- man/oiposbinomial.Rd | 44 +++++------ man/oipospoisUC.Rd | 14 +-- man/oipospoisson.Rd | 28 +++---- man/oizeta.Rd | 28 +++---- man/oizetaUC.Rd | 8 +- man/oizipf.Rd | 22 ++--- man/oizipfUC.Rd | 12 +-- man/otlog.Rd | 24 +++--- man/otlogUC.Rd | 16 ++-- man/otpospoisUC.Rd | 14 +-- man/otpospoisson.Rd | 20 ++--- man/otzeta.Rd | 30 +++---- man/otzetaUC.Rd | 14 +-- man/posbinomUC.Rd | 4 - man/posnegbinUC.Rd | 4 - man/prison.us.Rd | 191 ++++++++++++++++++++++++------------------------ man/smqP.Rd | 5 - man/triangle.Rd |only man/triangleUC.Rd |only 94 files changed, 673 insertions(+), 699 deletions(-)
Title: Marginal Structural Models with Latent Class Growth Analysis of
Treatment Trajectories
Description: Implements marginal structural models combined with a latent class growth analysis framework for assessing the causal effect of treatment trajectories. Based on the approach described in "Marginal Structural Models with Latent Class Growth Analysis of Treatment Trajectories" Diop, A., Sirois, C., Guertin, J.R., Schnitzer, M.E., Candas, B., Cossette, B., Poirier, P., Brophy, J., Mésidor, M., Blais, C. and Hamel, D., (2023) <doi:10.1177/09622802231202384>.
Author: Awa Diop [aut, cre],
Denis Talbot [aut]
Maintainer: Awa Diop <awa.diop.2@ulaval.ca>
Diff between trajmsm versions 0.1.1 dated 2024-09-08 and 0.1.2 dated 2024-09-16
DESCRIPTION | 9 - MD5 | 16 +-- R/pltmle.R | 230 +++++++++++++++++++++++++------------------------- R/trajhrmsm_pltmle.R | 13 +- R/trajmsm_ipw.R | 2 R/trajmsm_pltmle.R | 9 + man/pltmle.Rd | 9 + man/trajmsm_ipw.Rd | 2 man/trajmsm_pltmle.Rd | 10 +- 9 files changed, 158 insertions(+), 142 deletions(-)
Title: Likelihood Based Inference
Description: Maximum likelihood estimation and likelihood ratio test are essential for modern statistics. This package supports in calculating likelihood based inference.
Reference: Pawitan Y. (2001, ISBN:0-19-850765-8).
Author: Kyun-Seop Bae [aut, cre, cph]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between LBI versions 0.1.3 dated 2024-08-18 and 0.1.4 dated 2024-09-16
LBI-0.1.3/LBI/inst/doc/LBI_0.1.3.pdf |only LBI-0.1.4/LBI/DESCRIPTION | 6 +++--- LBI-0.1.4/LBI/MD5 | 10 +++++----- LBI-0.1.4/LBI/R/LInorm.R | 14 +++++++------- LBI-0.1.4/LBI/inst/NEWS.Rd | 6 ++++++ LBI-0.1.4/LBI/inst/doc/LBI_0.1.4.pdf |only LBI-0.1.4/LBI/man/LInorm.Rd | 8 ++++---- 7 files changed, 25 insertions(+), 19 deletions(-)
Title: Bayesian Variable Selection and Model Averaging using Bayesian
Adaptive Sampling
Description: Package for Bayesian Variable Selection and Model Averaging
in linear models and generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
mixture of g-priors from Liang et al (2008)
<DOI:10.1198/016214507000001337>
for linear models or mixtures of g-priors from Li and Clyde
(2019) <DOI:10.1080/01621459.2018.1469992> in generalized linear models.
Other model selection criteria include AIC, BIC and Empirical Bayes
estimates of g. Sampling probabilities may be updated based on the sampled
models using sampling w/out replacement or an efficient MCMC algorithm which
samples models using a tree structure of the model space
as an efficient hash table. See Clyde, Ghosh and Littman (2010)
<DOI:10.1198/jcgs.2010.09049> for details on the sampling algorithms.
Uniform prior [...truncated...]
Author: Merlise Clyde [aut, cre, cph] ,
Michael Littman [ctb],
Joyee Ghosh [ctb],
Yingbo Li [ctb],
Betsy Bersson [ctb],
Don van de Bergh [ctb],
Quanli Wang [ctb]
Maintainer: Merlise Clyde <clyde@duke.edu>
Diff between BAS versions 1.7.1 dated 2023-12-06 and 1.7.2 dated 2024-09-16
DESCRIPTION | 13 - MD5 | 131 +++++++++-------- NEWS.md | 11 + R/BAS-package.R | 8 - R/bas_glm.R | 60 -------- R/bas_lm.R | 127 +++++++++++------ R/plot.R | 12 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/BAS-vignette.html | 136 +++++++++--------- man/BAS.Rd | 6 man/CCH.Rd | 2 man/EB.local.Rd | 2 man/IC.prior.Rd | 2 man/Jeffreys.Rd | 2 man/TG.Rd | 2 man/bas.lm.Rd | 22 ++ man/beta.binomial.Rd | 2 man/beta.prime.Rd | 2 man/coef.Rd | 2 man/confint.coef.Rd | 2 man/confint.pred.Rd | 2 man/diagnostics.Rd | 2 man/fitted.Rd | 4 man/force.heredity.bas.Rd | 2 man/g.prior.Rd | 2 man/image.bas.Rd | 2 man/intrinsic.Rd | 2 man/plot.confint.Rd | 2 man/robust.Rd | 2 man/summary.Rd | 2 man/tCCH.Rd | 2 man/testBF.prior.Rd | 2 man/tr.beta.binomial.Rd | 2 man/tr.poisson.Rd | 2 man/tr.power.prior.Rd | 2 man/uniform.Rd | 2 man/update.Rd | 2 man/variable.names.pred.bas.Rd | 6 src/E_ZS.c | 4 src/MH-funs.c |only src/ZS_approx_null_np.c | 4 src/amcmc-funs.c |only src/bas.h | 19 ++ src/bayesreg.c | 6 src/cch.c | 4 src/dch1up.f |only src/family.c | 13 + src/glm_mcmc.c | 64 ++++++-- src/glm_mcmcbas.c | 81 ++++++++--- src/glm_sampleworep.c | 60 ++++++-- src/hg_approx_null_np.c | 5 src/hypergeometric1F1.c | 2 src/init.c | 2 src/lm_amcmc.c |only src/lm_deterministic.c | 2 src/lm_mcmc.c | 63 ++++++-- src/lm_mcmcbas.c | 60 ++++++-- src/lm_sampleworep.c | 57 +++++-- src/mem.c | 2 src/model_probabilities.c | 34 ++++ src/tree_structures.c | 257 +++++++++++++---------------------- tests/testthat/Rplots.pdf |binary tests/testthat/test-amcmc.R |only tests/testthat/test-bas-glm.R | 53 ++++++- tests/testthat/test-bas-lm-lowrank.R | 3 tests/testthat/test-bas-lm.R | 27 ++- tests/testthat/test-family.R |only tests/testthat/test-logit-BIC-coef.R |only tests/testthat/test-plot.R | 4 70 files changed, 857 insertions(+), 555 deletions(-)
Title: Causal Inference using Bayesian Additive Regression Trees
Description: Contains a variety of methods to generate typical causal inference estimates using Bayesian Additive Regression Trees (BART) as the underlying regression model (Hill (2012) <doi:10.1198/jcgs.2010.08162>).
Author: Vincent Dorie [aut, cre] ,
Jennifer Hill [aut]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between bartCause versions 1.0-8 dated 2024-05-01 and 1.0-9 dated 2024-09-16
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/bartc.R | 4 ++-- R/responseFit.R | 4 +++- R/summary.R | 2 +- build/partial.rdb |binary man/bartc.Rd | 12 ++++++------ man/plot.Rd | 2 +- tests/testthat/test-09-binary.R | 5 +++-- 9 files changed, 28 insertions(+), 25 deletions(-)
Title: Financial Time Series Objects (Rmetrics)
Description: 'S4' classes and various tools for financial time series:
Basic functions such as scaling and sorting, subsetting,
mathematical operations and statistical functions.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Martin Maechler [ctb] ,
Georgi N. Boshnakov [cre, aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between timeSeries versions 4032.109 dated 2024-01-14 and 4041.110 dated 2024-09-16
DESCRIPTION | 6 MD5 | 18 NAMESPACE | 32 NEWS.md | 7 R/methods-as.R | 24 build/vignette.rds |binary inst/doc/timeSeriesPlot.R | 1438 ++++++++++++++++++++--------------------- inst/doc/timeSeriesPlot.pdf |binary inst/doc/timeSeriesRefCard.pdf |binary inst/pkgdown.yml | 2 10 files changed, 769 insertions(+), 758 deletions(-)
Title: Helper Functions for Working with 'REDCap' Data
Description: Helper functions for processing 'REDCap' data in R. 'REDCap' is a
web-enabled application for building and managing surveys and databases
developed at Vanderbilt University.
Author: Raymond Balise [aut, cre] ,
Gabriel Odom [aut] ,
Anna Calderon [aut] ,
Layla Bouzoubaa [aut] ,
Wayne DeFreitas [aut] ,
Lauren Nahodyl [ctb] ,
Kyle Grealis [aut]
Maintainer: Raymond Balise <balise@miami.edu>
Diff between tidyREDCap versions 1.1.1 dated 2023-05-29 and 1.1.2 dated 2024-09-16
DESCRIPTION | 8 +- MD5 | 44 ++++++------- NEWS.md | 15 ++++ R/drop_labels.R | 1 R/import_instruments.R | 11 ++- R/make_choose_all_table.R | 12 ++- R/make_instrument_auto.R | 2 build/vignette.rds |binary inst/doc/dropLabels.R | 2 inst/doc/dropLabels.html | 28 ++++---- inst/doc/import_instruments.R | 2 inst/doc/import_instruments.html | 28 ++++---- inst/doc/makeBinaryWord.R | 2 inst/doc/makeBinaryWord.html | 102 +++++++++++++++---------------- inst/doc/makeChooseAllTable.R | 2 inst/doc/makeChooseAllTable.html | 86 +++++++++++++------------- inst/doc/makeChooseOneTable.R | 2 inst/doc/makeChooseOneTable.html | 68 ++++++++++---------- inst/doc/makeInstrument.R | 2 inst/doc/makeInstrument.html | 48 +++++++------- inst/doc/useAPI.R | 2 inst/doc/useAPI.html | 56 ++++++++--------- tests/testthat/test-import_instruments.R | 15 +++- 23 files changed, 286 insertions(+), 252 deletions(-)
Title: Stochastic Blockmodels
Description: A collection of tools and functions to adjust a variety of stochastic blockmodels (SBM).
Supports at the moment Simple, Bipartite, 'Multipartite' and Multiplex SBM (undirected or directed with Bernoulli, Poisson or Gaussian emission laws on the edges, and possibly covariate for Simple and Bipartite SBM). See Léger (2016) <doi:10.48550/arXiv.1602.07587>, 'Barbillon et al.' (2020) <doi:10.1111/rssa.12193> and 'Bar-Hen et al.' (2020) <doi:10.48550/arXiv.1807.10138>.
Author: Julien Chiquet [aut, cre] ,
Sophie Donnet [aut] ,
grossBM team [ctb],
Pierre Barbillon [aut]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between sbm versions 0.4.6 dated 2024-01-31 and 0.4.7 dated 2024-09-16
sbm-0.4.6/sbm/tests/spelling.Rout.save |only sbm-0.4.7/sbm/DESCRIPTION | 13 sbm-0.4.7/sbm/MD5 | 33 +- sbm-0.4.7/sbm/NEWS.md | 6 sbm-0.4.7/sbm/R/R6Class-BipartiteSBM_fit.R | 87 +++--- sbm-0.4.7/sbm/R/estimate.R | 6 sbm-0.4.7/sbm/README.md | 5 sbm-0.4.7/sbm/build/partial.rdb |binary sbm-0.4.7/sbm/build/vignette.rds |binary sbm-0.4.7/sbm/inst/WORDLIST | 2 sbm-0.4.7/sbm/inst/doc/Multipartite_EcologicalNetwork.html | 19 - sbm-0.4.7/sbm/inst/doc/MultiplexNetwork_principle.html | 23 - sbm-0.4.7/sbm/inst/doc/Multiplex_allianceNwar_case_study.html | 36 +- sbm-0.4.7/sbm/inst/doc/SBM_fungus_tree_network.html | 77 ++--- sbm-0.4.7/sbm/man/estimateSimpleSBM.Rd | 6 sbm-0.4.7/sbm/man/sbm-package.Rd | 2 sbm-0.4.7/sbm/tests/testthat/Rplots.pdf |binary sbm-0.4.7/sbm/tests/testthat/test-BipartiteSBM_fit.R | 141 ++++------ 18 files changed, 228 insertions(+), 228 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 0.2.22 dated 2024-08-19 and 0.2.23 dated 2024-09-16
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/doc/json_rpc_server.pdf |binary 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Pediatric Blood Pressure
Description: Data and utilities for estimating pediatric blood pressure
percentiles by sex, age, and optionally height (stature) as described in
Martin et.al. (2022) <doi:10.1001/jamanetworkopen.2022.36918>.
Blood pressure percentiles for children under one year of age come from Gemelli
et.al. (1990) <doi:10.1007/BF02171556>. Estimates of blood pressure
percentiles for children at least one year of age are informed by
data from the National Heart, Lung, and Blood Institute (NHLBI) and the
Centers for Disease Control and Prevention (CDC)
<doi:10.1542/peds.2009-2107C> or from Lo et.al. (2013)
<doi:10.1542/peds.2012-1292>. The flowchart for selecting the informing
data source comes from Martin et.al. (2022)
<doi:10.1542/hpeds.2021-005998>.
Author: Peter DeWitt [aut, cre] ,
Blake Martin [ctb] ,
David Albers [ctb] ,
Tell Bennett [ctb]
Maintainer: Peter DeWitt <peter.dewitt@cuanschutz.edu>
Diff between pedbp versions 2.0.0 dated 2024-04-23 and 2.0.1 dated 2024-09-16
DESCRIPTION | 13 ++++++----- MD5 | 36 +++++++++++++++---------------- NEWS.md | 7 ++++++ README.md | 30 +++++++++++++------------- build/partial.rdb |binary build/vignette.rds |binary data/bp_parameters.rda |binary inst/doc/bp-distributions.R | 2 - inst/doc/bp-distributions.Rmd | 2 - inst/shinyapps/pedbp/server.R | 18 +++++++++------ inst/shinyapps/pedbp/ui.R | 8 +++--- tests/test-bp-by-source.R | 2 - tests/test-bp_chart.R | 20 ++++++++--------- tests/test-bp_distributions.R | 12 +++++----- tests/test-cppBP.R | 34 ++++++++++++++--------------- tests/test-cppPGSF.R | 47 +++++++++++++++++++---------------------- tests/test-est_norm.R | 18 +++++++-------- tests/test-gs_chart.R | 6 ++--- vignettes/bp-distributions.Rmd | 2 - 19 files changed, 133 insertions(+), 124 deletions(-)
Title: PEDALFAST Data
Description: Data files and documentation for PEDiatric vALidation oF vAriableS
in TBI (PEDALFAST). The data was used in "Functional Status Scale in
Children With Traumatic Brain Injury: A Prospective Cohort Study" by Bennett,
Dixon, et al (2016) <doi:10.1097/PCC.0000000000000934>.
Author: Peter DeWitt [aut, cre] ,
Tell Bennett [aut]
Maintainer: Peter DeWitt <peter.dewitt@cuanschutz.edu>
Diff between pedalfast.data versions 1.0.1 dated 2023-11-10 and 1.0.2 dated 2024-09-16
DESCRIPTION | 16 MD5 | 26 NEWS.md | 4 build/vignette.rds |binary data/pedalfast.rda |binary data/pedalfast_metadata.rda |binary inst/doc/datasets.R | 310 +++- inst/doc/datasets.Rmd | 475 +++++- inst/doc/datasets.html | 3051 ++++++++++++++++++++++++++++---------------- inst/doc/fss.R | 24 inst/doc/fss.Rmd | 36 inst/doc/fss.html | 814 +++++------ vignettes/datasets.Rmd | 475 +++++- vignettes/fss.Rmd | 36 14 files changed, 3378 insertions(+), 1889 deletions(-)
More information about pedalfast.data at CRAN
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Title: Statistical Inference for Unsupervised Learning
Description: Test for association between the observed data and their estimated latent variables. The jackstraw package provides a resampling strategy and testing scheme to estimate statistical significance of association between the observed data and their latent variables. Depending on the data type and the analysis aim, the latent variables may be estimated by principal component analysis (PCA), factor analysis (FA), K-means clustering, and related unsupervised learning algorithms. The jackstraw methods learn over-fitting characteristics inherent in this circular analysis, where the observed data are used to estimate the latent variables and used again to test against that estimated latent variables. When latent variables are estimated by PCA, the jackstraw enables statistical testing for association between observed variables and latent variables, as estimated by low-dimensional principal components (PCs). This essentially leads to identifying variables that are significantly associated with PC [...truncated...]
Author: Neo Christopher Chung [aut, cre]
,
John D. Storey [aut] ,
Wei Hao [aut],
Alejandro Ochoa [aut]
Maintainer: Neo Christopher Chung <nchchung@gmail.com>
Diff between jackstraw versions 1.3.15 dated 2024-08-30 and 1.3.17 dated 2024-09-16
DESCRIPTION | 12 MD5 | 52 +- NEWS.md | 18 R/empPvals.R | 25 - R/find_k.R | 2 R/jackstraw_MiniBatchKmeans.R | 12 R/jackstraw_alstructure.R | 19 R/jackstraw_cluster.R | 46 +- R/jackstraw_irlba.R | 14 R/jackstraw_kmeans.R | 12 R/jackstraw_kmeanspp.R | 10 R/jackstraw_lfa.R | 29 + R/jackstraw_pam.R | 16 R/jackstraw_pca.R | 16 R/jackstraw_rpca.R | 12 R/jackstraw_subspace.R | 44 +- R/likelihood.R | 12 R/pip.R | 12 README.md | 20 - man/efron_Rsq.Rd | 2 man/jackstraw_alstructure.Rd | 1 man/jackstraw_lfa.Rd | 18 man/jackstraw_pca.Rd | 2 man/permutationPA.Rd | 2 man/pip.Rd | 3 man/pseudo_Rsq.Rd | 2 tests/testthat/test-jackstraw.R | 762 ++++++++++++++++++++-------------------- 27 files changed, 642 insertions(+), 533 deletions(-)
Title: Interface to 'LMDB'
Description: Key-value store, implemented as a wrapper around 'LMDB';
the "lightning memory-mapped database" <https://www.symas.com/lmdb>.
'LMDB' is a transactional key value store that uses a memory map
for efficient access. This package wraps the entire 'LMDB'
interface (except duplicated keys), and provides objects for
transactions and cursors.
Author: Rich FitzJohn [aut, cre],
Howard Chu [aut, cph],
Symas Corporation [cph],
Martin Hedenfalk [aut, cph],
The OpenLDAP Foundation [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between thor versions 1.1.5 dated 2023-11-29 and 1.1.6 dated 2024-09-16
DESCRIPTION | 6 - MD5 | 10 +- build/vignette.rds |binary inst/doc/thor.html | 8 +- src/thor.c | 190 ++++++++++++++++++++++++++--------------------------- src/util.c | 40 +++++------ 6 files changed, 127 insertions(+), 127 deletions(-)
Title: Value Added in Exports and Other Input-Output Table Analysis
Tools
Description: Analysis of trade in value added with international
input-output tables. Includes commands for easy data extraction,
matrix manipulation, decomposition of value added in gross exports and
calculation of value added indicators, with full geographical and
sector customization. Decomposition methods include Borin and Mancini
(2023) <doi:10.1080/09535314.2022.2153221>, Miroudot and Ye (2021)
<doi:10.1080/09535314.2020.1730308>, Wang et al. (2013)
<https://econpapers.repec.org/paper/nbrnberwo/19677.htm> and Koopman
et al. (2014) <doi:10.1257/aer.104.2.459>.
Author: Enrique Feas [aut, cre]
Maintainer: Enrique Feas <efeas@runbox.com>
Diff between exvatools versions 0.8.0 dated 2024-04-05 and 0.9.0 dated 2024-09-16
DESCRIPTION | 8 +-- MD5 | 36 ++++++------- NEWS.md | 11 ++++ R/extract_figaro.R | 55 +++++++++++++++++++- R/extract_mrio.R | 125 +++++++++++++++++++++++++++++++++------------- R/get_exvadec_bkdown.R | 22 ++++++-- R/make_exvadec.R | 27 +++++++--- R/make_exvadec_bm_src.R | 128 ++++++++++++++++++++++++++++++++++++++++-------- R/make_wio.R | 40 +++++++++------ R/matrix_extract.R | 83 ++++++++++++++++++------------- R/sysdata.rda |binary R/utils-validators.R | 16 +++--- build/vignette.rds |binary inst/doc/exvatools.R | 2 inst/doc/exvatools.Rmd | 2 inst/doc/exvatools.html | 15 ++--- man/make_exvadec.Rd | 22 ++++++-- man/make_wio.Rd | 34 +++++++----- vignettes/exvatools.Rmd | 2 19 files changed, 450 insertions(+), 178 deletions(-)
Title: Probabilistic Knowledge Structures
Description: Fitting and testing probabilistic knowledge structures,
especially the basic local independence model (BLIM, Doignon & Flamagne,
1999) and the simple learning model (SLM), using the minimum discrepancy
maximum likelihood (MDML) method (Heller & Wickelmaier, 2013
<doi:10.1016/j.endm.2013.05.145>).
Author: Florian Wickelmaier [aut, cre],
Juergen Heller [aut],
Julian Mollenhauer [aut],
Pasquale Anselmi [ctb],
Debora de Chiusole [ctb],
Andrea Brancaccio [ctb],
Luca Stefanutti [ctb]
Maintainer: Florian Wickelmaier <wickelmaier@web.de>
Diff between pks versions 0.6-0 dated 2023-07-07 and 0.6-1 dated 2024-09-16
ChangeLog | 4 + DESCRIPTION | 12 ++--- MD5 | 22 +++++----- build/partial.rdb |binary build/vignette.rds |binary data/DoignonFalmagne7.rda |binary data/Taagepera.rda |binary data/endm.rda |binary inst/doc/EstimationStepByStep.Rnw | 80 +++++++++++++++++++------------------ inst/doc/EstimationStepByStep.pdf |binary man/schoolarithm.Rd | 2 vignettes/EstimationStepByStep.Rnw | 80 +++++++++++++++++++------------------ 12 files changed, 106 insertions(+), 94 deletions(-)
Title: Probability Distributions as S3 Objects
Description: Tools to create and manipulate probability distributions
using S3. Generics pdf(), cdf(), quantile(), and random() provide
replacements for base R's d/p/q/r style functions. Functions and
arguments have been named carefully to minimize confusion for students
in intro stats courses. The documentation for each distribution
contains detailed mathematical notes.
Author: Alex Hayes [aut, cre] ,
Ralph Moller-Trane [aut],
Emil Hvitfeldt [ctb] ,
Daniel Jordan [aut],
Paul Northrop [aut],
Moritz N. Lang [aut] ,
Achim Zeileis [aut] ,
Bruna Wundervald [ctb],
Alessandro Gasparini [ctb]
Maintainer: Alex Hayes <alexpghayes@gmail.com>
Diff between distributions3 versions 0.2.1 dated 2022-09-07 and 0.2.2 dated 2024-09-16
distributions3-0.2.1/distributions3/R/distributions_package.R |only distributions3-0.2.2/distributions3/DESCRIPTION | 14 distributions3-0.2.2/distributions3/MD5 | 255 ++--- distributions3-0.2.2/distributions3/NAMESPACE | 22 distributions3-0.2.2/distributions3/NEWS.md | 39 distributions3-0.2.2/distributions3/R/Bernoulli.R | 12 distributions3-0.2.2/distributions3/R/Beta.R | 12 distributions3-0.2.2/distributions3/R/Binomial.R | 12 distributions3-0.2.2/distributions3/R/Categorical.R | 6 distributions3-0.2.2/distributions3/R/Cauchy.R | 12 distributions3-0.2.2/distributions3/R/ChiSquare.R | 12 distributions3-0.2.2/distributions3/R/Erlang.R | 6 distributions3-0.2.2/distributions3/R/Exponential.R | 18 distributions3-0.2.2/distributions3/R/FisherF.R | 10 distributions3-0.2.2/distributions3/R/Frechet.R | 8 distributions3-0.2.2/distributions3/R/Gamma.R | 12 distributions3-0.2.2/distributions3/R/GeneralisedExtremeValue.R | 8 distributions3-0.2.2/distributions3/R/GeneralisedPareto.R | 8 distributions3-0.2.2/distributions3/R/Geometric.R | 8 distributions3-0.2.2/distributions3/R/Gumbel.R | 8 distributions3-0.2.2/distributions3/R/HurdleNegativeBinomial.R | 18 distributions3-0.2.2/distributions3/R/HurdlePoisson.R | 18 distributions3-0.2.2/distributions3/R/HyperGeometric.R | 8 distributions3-0.2.2/distributions3/R/LogNormal.R | 8 distributions3-0.2.2/distributions3/R/Logistic.R | 8 distributions3-0.2.2/distributions3/R/Multinomial.R | 6 distributions3-0.2.2/distributions3/R/NegativeBinomial.R | 18 distributions3-0.2.2/distributions3/R/Normal.R | 8 distributions3-0.2.2/distributions3/R/Poisson.R | 14 distributions3-0.2.2/distributions3/R/PoissonBinomial.R |only distributions3-0.2.2/distributions3/R/ReversedWeibull.R | 8 distributions3-0.2.2/distributions3/R/StudentsT.R | 10 distributions3-0.2.2/distributions3/R/Tukey.R | 8 distributions3-0.2.2/distributions3/R/Uniform.R | 8 distributions3-0.2.2/distributions3/R/Weibull.R | 10 distributions3-0.2.2/distributions3/R/ZINegativeBinomial.R | 14 distributions3-0.2.2/distributions3/R/ZIPoisson.R | 14 distributions3-0.2.2/distributions3/R/ZTNegativeBinomial.R | 17 distributions3-0.2.2/distributions3/R/ZTPoisson.R | 17 distributions3-0.2.2/distributions3/R/distributions3-package.R |only distributions3-0.2.2/distributions3/R/methods.R | 43 distributions3-0.2.2/distributions3/R/plot.R | 8 distributions3-0.2.2/distributions3/R/prodist.R | 62 - distributions3-0.2.2/distributions3/R/simulate.default.R |only distributions3-0.2.2/distributions3/R/tibble-vctrs.R |only distributions3-0.2.2/distributions3/R/utils.R | 17 distributions3-0.2.2/distributions3/README.md | 34 distributions3-0.2.2/distributions3/build/partial.rdb |binary distributions3-0.2.2/distributions3/build/vignette.rds |binary distributions3-0.2.2/distributions3/inst/doc/intro-to-hypothesis-testing.R | 6 distributions3-0.2.2/distributions3/inst/doc/intro-to-hypothesis-testing.html | 16 distributions3-0.2.2/distributions3/inst/doc/one-sample-sign-tests.R | 2 distributions3-0.2.2/distributions3/inst/doc/one-sample-sign-tests.html | 233 ++-- distributions3-0.2.2/distributions3/inst/doc/one-sample-t-confidence-interval.R | 6 distributions3-0.2.2/distributions3/inst/doc/one-sample-t-confidence-interval.html | 199 ++-- distributions3-0.2.2/distributions3/inst/doc/one-sample-t-test.R | 2 distributions3-0.2.2/distributions3/inst/doc/one-sample-t-test.html | 261 ++--- distributions3-0.2.2/distributions3/inst/doc/one-sample-z-confidence-interval.R | 6 distributions3-0.2.2/distributions3/inst/doc/one-sample-z-confidence-interval.html | 151 +-- distributions3-0.2.2/distributions3/inst/doc/one-sample-z-test-for-proportion.R | 2 distributions3-0.2.2/distributions3/inst/doc/one-sample-z-test-for-proportion.html | 155 +-- distributions3-0.2.2/distributions3/inst/doc/one-sample-z-test.R | 2 distributions3-0.2.2/distributions3/inst/doc/one-sample-z-test.html | 179 +-- distributions3-0.2.2/distributions3/inst/doc/paired-tests.R | 2 distributions3-0.2.2/distributions3/inst/doc/paired-tests.html | 125 +- distributions3-0.2.2/distributions3/inst/doc/poisson.R | 6 distributions3-0.2.2/distributions3/inst/doc/poisson.html | 474 ++++------ distributions3-0.2.2/distributions3/inst/doc/two-sample-z-test.R | 6 distributions3-0.2.2/distributions3/inst/doc/two-sample-z-test.html | 223 ++-- distributions3-0.2.2/distributions3/man/Bernoulli.Rd | 1 distributions3-0.2.2/distributions3/man/Binomial.Rd | 1 distributions3-0.2.2/distributions3/man/Categorical.Rd | 1 distributions3-0.2.2/distributions3/man/Exponential.Rd | 6 distributions3-0.2.2/distributions3/man/Geometric.Rd | 1 distributions3-0.2.2/distributions3/man/HurdleNegativeBinomial.Rd | 5 distributions3-0.2.2/distributions3/man/HurdlePoisson.Rd | 5 distributions3-0.2.2/distributions3/man/HyperGeometric.Rd | 1 distributions3-0.2.2/distributions3/man/Multinomial.Rd | 1 distributions3-0.2.2/distributions3/man/NegativeBinomial.Rd | 1 distributions3-0.2.2/distributions3/man/Poisson.Rd | 1 distributions3-0.2.2/distributions3/man/PoissonBinomial.Rd |only distributions3-0.2.2/distributions3/man/ZINegativeBinomial.Rd | 1 distributions3-0.2.2/distributions3/man/ZIPoisson.Rd | 1 distributions3-0.2.2/distributions3/man/ZTNegativeBinomial.Rd | 1 distributions3-0.2.2/distributions3/man/ZTPoisson.Rd | 1 distributions3-0.2.2/distributions3/man/apply_dpqr.Rd | 2 distributions3-0.2.2/distributions3/man/cdf.PoissonBinomial.Rd |only distributions3-0.2.2/distributions3/man/distributions3-package.Rd | 2 distributions3-0.2.2/distributions3/man/geom_auc.Rd | 90 + distributions3-0.2.2/distributions3/man/pdf.PoissonBinomial.Rd |only distributions3-0.2.2/distributions3/man/prodist.Rd | 3 distributions3-0.2.2/distributions3/man/quantile.PoissonBinomial.Rd |only distributions3-0.2.2/distributions3/man/random.PoissonBinomial.Rd |only distributions3-0.2.2/distributions3/man/random.Rd | 5 distributions3-0.2.2/distributions3/man/simulate.default.Rd |only distributions3-0.2.2/distributions3/man/support.PoissonBinomial.Rd |only distributions3-0.2.2/distributions3/man/vec_proxy.distribution.Rd |only distributions3-0.2.2/distributions3/tests/testthat/test-Bernoulli.R | 4 distributions3-0.2.2/distributions3/tests/testthat/test-Beta.R | 4 distributions3-0.2.2/distributions3/tests/testthat/test-Binomial.R | 10 distributions3-0.2.2/distributions3/tests/testthat/test-Categorical.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-Cauchy.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-ChiSquare.R | 2 distributions3-0.2.2/distributions3/tests/testthat/test-Erlang.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-Exponential.R | 8 distributions3-0.2.2/distributions3/tests/testthat/test-FisherF.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-Frechet.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-Gamma.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-GeneralisedExtremeValue.R | 10 distributions3-0.2.2/distributions3/tests/testthat/test-GeneralisedPareto.R | 10 distributions3-0.2.2/distributions3/tests/testthat/test-Geometric.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-Gumbel.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-HurdleNegativeBinomial.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-HurdlePoisson.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-HyperGeometric.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-LogNormal.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-Logistic.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-Multinomial.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-NegativeBinomial.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-Normal.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-Poisson.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-PoissonBinomial.R |only distributions3-0.2.2/distributions3/tests/testthat/test-RevWeibull.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-StudentsT.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-Tukey.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-Uniform.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-Weibull.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-ZINegativeBinomial.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-ZIPoisson.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-ZTNegativeBinomial.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-ZTPoisson.R | 6 distributions3-0.2.2/distributions3/tests/testthat/test-methods.R | 2 distributions3-0.2.2/distributions3/tests/testthat/test-plot.R | 2 distributions3-0.2.2/distributions3/tests/testthat/test-prodist.R | 2 distributions3-0.2.2/distributions3/tests/testthat/test-simulate.R |only distributions3-0.2.2/distributions3/tests/testthat/test-utils.R | 18 136 files changed, 1688 insertions(+), 1584 deletions(-)
More information about distributions3 at CRAN
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Title: Model BIC Posterior Probability
Description: Fits the neighboring models of a fitted
structural equation model and assesses the model
uncertainty of the fitted model based on BIC posterior
probabilities, using the method presented in
Wu, Cheung, and Leung (2020)
<doi:10.1080/00273171.2019.1574546>.
Author: Shu Fai Cheung [aut, cre] ,
Huiping Wu [aut],
Shing On Leung [aut] ,
Ivan Jacob Agaloos Pesigan [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between modelbpp versions 0.1.3 dated 2024-02-20 and 0.1.5 dated 2024-09-16
modelbpp-0.1.3/modelbpp/vignettes/ExportedItems.bib |only modelbpp-0.1.3/modelbpp/vignettes/graph1_no_cov-1.png |only modelbpp-0.1.5/modelbpp/DESCRIPTION | 10 modelbpp-0.1.5/modelbpp/MD5 | 171 modelbpp-0.1.5/modelbpp/NAMESPACE | 43 modelbpp-0.1.5/modelbpp/NEWS.md | 353 modelbpp-0.1.5/modelbpp/R/c_partables.R | 474 - modelbpp-0.1.5/modelbpp/R/check_sem_out.R | 34 modelbpp-0.1.5/modelbpp/R/data.R | 294 modelbpp-0.1.5/modelbpp/R/fit_many.R | 828 +- modelbpp-0.1.5/modelbpp/R/get_add.R | 637 - modelbpp-0.1.5/modelbpp/R/get_drop.R | 440 - modelbpp-0.1.5/modelbpp/R/helpers1.R | 600 - modelbpp-0.1.5/modelbpp/R/helpers2_for_model_check.R | 252 modelbpp-0.1.5/modelbpp/R/helpers3_for_model_graph.R | 1146 +- modelbpp-0.1.5/modelbpp/R/helpers4_for_model_graph.R | 454 - modelbpp-0.1.5/modelbpp/R/helpers_print.R | 142 modelbpp-0.1.5/modelbpp/R/measurement_invariance.R |only modelbpp-0.1.5/modelbpp/R/min_bpp.R | 156 modelbpp-0.1.5/modelbpp/R/model_graph.R | 894 +- modelbpp-0.1.5/modelbpp/R/model_set.R | 1155 +-- modelbpp-0.1.5/modelbpp/R/modelbpp-package.R | 16 modelbpp-0.1.5/modelbpp/R/partables_helpers.R | 622 - modelbpp-0.1.5/modelbpp/R/print.model_set.R | 682 - modelbpp-0.1.5/modelbpp/R/print.partables.R | 142 modelbpp-0.1.5/modelbpp/R/print.sem_outs.R | 140 modelbpp-0.1.5/modelbpp/R/z_test_helpers.R | 106 modelbpp-0.1.5/modelbpp/README.md | 106 modelbpp-0.1.5/modelbpp/build/partial.rdb |binary modelbpp-0.1.5/modelbpp/build/vignette.rds |binary modelbpp-0.1.5/modelbpp/inst/doc/modelbpp.R | 12 modelbpp-0.1.5/modelbpp/inst/doc/modelbpp.Rmd | 745 - modelbpp-0.1.5/modelbpp/inst/doc/modelbpp.html | 550 - modelbpp-0.1.5/modelbpp/inst/tinytest/test_check_equivalent.R | 86 modelbpp-0.1.5/modelbpp/inst/tinytest/test_check_sem_out.R | 58 modelbpp-0.1.5/modelbpp/inst/tinytest/test_feedback_and_xy_cov.R |only modelbpp-0.1.5/modelbpp/inst/tinytest/test_fit_many.R | 142 modelbpp-0.1.5/modelbpp/inst/tinytest/test_fit_many_mg.R |only modelbpp-0.1.5/modelbpp/inst/tinytest/test_get_add.R | 136 modelbpp-0.1.5/modelbpp/inst/tinytest/test_get_add_p06.R | 80 modelbpp-0.1.5/modelbpp/inst/tinytest/test_get_add_sem.R | 118 modelbpp-0.1.5/modelbpp/inst/tinytest/test_get_drop.R | 132 modelbpp-0.1.5/modelbpp/inst/tinytest/test_get_drop_sem.R | 76 modelbpp-0.1.5/modelbpp/inst/tinytest/test_get_mi.R |only modelbpp-0.1.5/modelbpp/inst/tinytest/test_invalid_input.R | 42 modelbpp-0.1.5/modelbpp/inst/tinytest/test_model_graph_user.R | 120 modelbpp-0.1.5/modelbpp/inst/tinytest/test_model_graph_user2.R | 160 modelbpp-0.1.5/modelbpp/inst/tinytest/test_model_set.R | 300 modelbpp-0.1.5/modelbpp/inst/tinytest/test_model_set_models_mixed.R | 326 modelbpp-0.1.5/modelbpp/inst/tinytest/test_model_set_more_models.R | 102 modelbpp-0.1.5/modelbpp/inst/tinytest/test_model_set_target_bpp.R | 84 modelbpp-0.1.5/modelbpp/inst/tinytest/test_model_set_update_bpp.R | 68 modelbpp-0.1.5/modelbpp/inst/tinytest/test_model_set_user_models.R | 108 modelbpp-0.1.5/modelbpp/inst/tinytest/test_model_set_user_priors.R | 82 modelbpp-0.1.5/modelbpp/inst/tinytest/test_net.R | 254 modelbpp-0.1.5/modelbpp/inst/tinytest/test_net_eq.R |only modelbpp-0.1.5/modelbpp/inst/tinytest/test_no_convergence.R | 36 modelbpp-0.1.5/modelbpp/inst/tinytest/test_partables_combine.R | 196 modelbpp-0.1.5/modelbpp/inst/tinytest/test_partables_helpers.R | 150 modelbpp-0.1.5/modelbpp/inst/tinytest/test_plot_model_est.R | 162 modelbpp-0.1.5/modelbpp/inst/tinytest/test_post_check_failed.R | 36 modelbpp-0.1.5/modelbpp/inst/tinytest/test_syntax_to_add_list.R | 50 modelbpp-0.1.5/modelbpp/inst/tinytest/test_syntax_to_id.R | 62 modelbpp-0.1.5/modelbpp/man/dat_cfa.Rd | 74 modelbpp-0.1.5/modelbpp/man/dat_path_model.Rd | 66 modelbpp-0.1.5/modelbpp/man/dat_path_model_p06.Rd | 74 modelbpp-0.1.5/modelbpp/man/dat_sem.Rd | 60 modelbpp-0.1.5/modelbpp/man/dat_serial_4.Rd | 66 modelbpp-0.1.5/modelbpp/man/dat_serial_4_weak.Rd | 66 modelbpp-0.1.5/modelbpp/man/fit_many.Rd | 276 modelbpp-0.1.5/modelbpp/man/get_add.Rd | 295 modelbpp-0.1.5/modelbpp/man/get_drop.Rd | 240 modelbpp-0.1.5/modelbpp/man/manipulate_partables.Rd | 272 modelbpp-0.1.5/modelbpp/man/measurement_invariance_models.Rd |only modelbpp-0.1.5/modelbpp/man/min_prior.Rd | 154 modelbpp-0.1.5/modelbpp/man/model_graph.Rd | 626 - modelbpp-0.1.5/modelbpp/man/model_set.Rd | 708 - modelbpp-0.1.5/modelbpp/man/modelbpp-package.Rd | 72 modelbpp-0.1.5/modelbpp/man/partables_helpers.Rd | 268 modelbpp-0.1.5/modelbpp/man/plot.model_graph.Rd | 126 modelbpp-0.1.5/modelbpp/man/print.model_set.Rd | 241 modelbpp-0.1.5/modelbpp/man/print.partables.Rd | 114 modelbpp-0.1.5/modelbpp/man/print.sem_outs.Rd | 108 modelbpp-0.1.5/modelbpp/tests/tinytest.R | 10 modelbpp-0.1.5/modelbpp/vignettes/apa.csl | 3832 +++++----- modelbpp-0.1.5/modelbpp/vignettes/graph1-1.png |binary modelbpp-0.1.5/modelbpp/vignettes/graph1_df2-1.png |binary modelbpp-0.1.5/modelbpp/vignettes/modelbpp.Rmd | 745 - modelbpp-0.1.5/modelbpp/vignettes/out1_no_m1_x-1.png |only modelbpp-0.1.5/modelbpp/vignettes/out1_prior-1.png |binary modelbpp-0.1.5/modelbpp/vignettes/references.bib | 40 91 files changed, 11720 insertions(+), 11183 deletions(-)
Title: Multivariate Normal Mixture Models and Mixtures of Generalized
Linear Mixed Models Including Model Based Clustering
Description: Contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models. The package is primarily related to the publications Komárek (2009, Comp. Stat. and Data Anal.) <doi:10.1016/j.csda.2009.05.006> and Komárek and Komárková (2014, J. of Stat. Soft.) <doi:10.18637/jss.v059.i12>. It also implements methods published in Komárek and Komárková (2013, Ann. of Appl. Stat.) <doi:10.1214/12-AOAS580>, Hughes, Komárek, Bonnett, Czanner, García-Fiñana (2017, Stat. in Med.) <doi:10.1002/sim.7397>, Jaspers, Komárek, Aerts (2018, Biom. J.) <doi:10.1002/bimj.201600253> and Hughes, Komárek, Czanner, García-Fiñana (2018, Stat. Meth. in Med. Res) <doi:10.1177/0962280216674496>.
Author: Arnost Komarek [aut, cre]
Maintainer: Arnost Komarek <arnost.komarek@mff.cuni.cz>
Diff between mixAK versions 5.7 dated 2023-12-14 and 5.8 dated 2024-09-16
DESCRIPTION | 10 MD5 | 206 +++++------ NEWS | 5 build/partial.rdb |binary data/Acidity.rda |binary data/Enzyme.rda |binary data/Galaxy.rda |binary inst/CITATION | 2 src/AK_LAPACK.cpp | 57 +-- src/AK_LAPACK.h | 2 src/Dist_MVN.cpp | 7 src/Dist_MVN.h | 3 src/Dist_MVT.cpp | 5 src/Dist_MVT.h | 1 src/Dist_TMVN.cpp | 20 - src/Dist_TMVN.h | 1 src/Dist_TNorm.cpp | 2 src/Dist_TNorm.h | 1 src/Dist_Wishart.cpp | 9 src/Dist_Wishart.h | 1 src/Dist_mixMVN.cpp | 5 src/Dist_mixMVN.h | 1 src/GLMM_Deviance.cpp | 21 - src/GLMM_Deviance.h | 1 src/GLMM_Deviance2.cpp | 21 - src/GLMM_Deviance2.h | 1 src/GLMM_MCMC.cpp | 416 +++++++++++------------ src/GLMM_MCMC.h | 2 src/GLMM_NMixRelabel.cpp | 294 ++++++++-------- src/GLMM_NMixRelabel.h | 2 src/GLMM_PED.cpp | 510 ++++++++++++++--------------- src/GLMM_PED.h | 2 src/GLMM_dY_meanY.cpp | 4 src/GLMM_dY_meanY.h | 1 src/GLMM_eta_fixed_random2eta_meanY.cpp | 2 src/GLMM_eta_fixed_random2eta_meanY.h | 1 src/GLMM_linear_predictors.cpp | 4 src/GLMM_linear_predictors.h | 1 src/GLMM_longitDA.cpp | 108 +++--- src/GLMM_longitDA.h | 2 src/GLMM_longitDA2.cpp | 206 +++++------ src/GLMM_longitDA2.h | 2 src/GLMM_longitPred_nmix_gauss.cpp | 4 src/GLMM_longitPred_nmix_gauss.h | 1 src/GLMM_newData.cpp | 4 src/GLMM_newData.h | 1 src/GLMM_updateFixEf.cpp | 6 src/GLMM_updateFixEf.h | 1 src/GLMM_updateRanEf.cpp | 10 src/GLMM_updateRanEf.h | 1 src/GLMM_updateRanEf_QR.cpp | 2 src/GLMM_updateRanEf_QR.h | 1 src/MCMC_Moments_NormalApprox.cpp | 2 src/MCMC_Moments_NormalApprox.h | 1 src/MCMC_Moments_NormalApprox_QR.cpp | 4 src/MCMC_Moments_NormalApprox_QR.h | 1 src/MCMC_loglik_Zwork1_stres.cpp | 22 - src/MCMC_loglik_Zwork1_stres.h | 1 src/Misc_generatePermutations.cpp | 2 src/Misc_generatePermutations.h | 1 src/NMix_ChainsDerived.cpp | 2 src/NMix_ChainsDerived.h | 1 src/NMix_Deviance.cpp | 4 src/NMix_Deviance.h | 1 src/NMix_MCMC.cpp | 218 ++++++------ src/NMix_MCMC.h | 2 src/NMix_NMixRelabel.cpp | 120 +++--- src/NMix_NMixRelabel.h | 2 src/NMix_PED.cpp | 4 src/NMix_PED.h | 1 src/NMix_PredCDFMarg.cpp | 2 src/NMix_PredCDFMarg.h | 1 src/NMix_PredCondDensCDFMarg.cpp | 18 - src/NMix_PredCondDensCDFMarg.h | 2 src/NMix_PredCondDensJoint2.cpp | 8 src/NMix_PredCondDensJoint2.h | 1 src/NMix_PredDA.cpp | 52 +- src/NMix_PredDA.h | 1 src/NMix_PredDensJoint2.cpp | 6 src/NMix_PredDensJoint2.h | 1 src/NMix_PredDensMarg.cpp | 2 src/NMix_PredDensMarg.h | 1 src/NMix_RJMCMC_logJacLambdaVSigma.cpp | 4 src/NMix_RJMCMC_logJacLambdaVSigma.h | 1 src/NMix_RJMCMC_logJac_part3.cpp | 2 src/NMix_RJMCMC_logJac_part3.h | 1 src/NMix_RJMCMCbirth.cpp | 4 src/NMix_RJMCMCbirth.h | 1 src/NMix_RJMCMCcombine.cpp | 18 - src/NMix_RJMCMCcombine.h | 1 src/NMix_RJMCMCsplit.cpp | 22 - src/NMix_RJMCMCsplit.h | 1 src/NMix_Utils.cpp | 12 src/NMix_Utils.h | 1 src/NMix_fullCondMean_WeightsMeansVars.cpp | 4 src/NMix_fullCondMean_WeightsMeansVars.h | 1 src/NMix_updateMeansVars.cpp | 22 - src/NMix_updateMeansVars.h | 1 src/Rand_RotationMatrix.cpp | 4 src/Rand_RotationMatrix.h | 1 src/Stat_BLA.cpp | 2 src/Stat_BLA.h | 1 src/Stat_Quantile.cpp | 14 src/Stat_Quantile.h | 2 104 files changed, 1322 insertions(+), 1252 deletions(-)
Title: Comprehensive Single-Cell Annotation and Transcriptomic Analysis
Toolkit
Description: Provides a comprehensive toolkit for single-cell annotation with the 'CellMarker2.0' database (see Xia Li, Peng Wang, Yunpeng Zhang (2023) <doi: 10.1093/nar/gkac947>). Streamlines biological label assignment in single-cell RNA-seq data and facilitates transcriptomic analysis, including preparation of TCGA<https://portal.gdc.cancer.gov/> and GEO<https://www.ncbi.nlm.nih.gov/geo/> datasets, differential expression analysis and visualization of enrichment analysis results. Additional utility functions support various bioinformatics workflows. See Wei Cui (2024) <doi: 10.1101/2024.09.14.609619> for more details.
Author: Wei Cui [aut, cre, cph]
Maintainer: Wei Cui <m2c.w@outlook.com>
Diff between easybio versions 1.0.1 dated 2024-09-08 and 1.1.0 dated 2024-09-16
easybio-1.0.1/easybio/data/CHOL.DEGs.rda |only easybio-1.0.1/easybio/man/CHOL.DEGs.Rd |only easybio-1.1.0/easybio/DESCRIPTION | 10 easybio-1.1.0/easybio/MD5 | 71 +- easybio-1.1.0/easybio/NEWS.md | 26 easybio-1.1.0/easybio/R/Artist.R | 153 ++++- easybio-1.1.0/easybio/R/easybio-package.R | 2 easybio-1.1.0/easybio/R/limma.R | 6 easybio-1.1.0/easybio/R/ora.R | 5 easybio-1.1.0/easybio/R/prepare.R | 48 + easybio-1.1.0/easybio/R/sc.R | 18 easybio-1.1.0/easybio/R/uniprot.R | 2 easybio-1.1.0/easybio/README.md | 35 + easybio-1.1.0/easybio/data/CHOL_DEGs.rda |only easybio-1.1.0/easybio/inst/CITATION |only easybio-1.1.0/easybio/inst/doc/example-bulk-rna-seq-workflow.R | 60 +- easybio-1.1.0/easybio/inst/doc/example-bulk-rna-seq-workflow.Rmd | 285 +++++----- easybio-1.1.0/easybio/inst/doc/example-bulk-rna-seq-workflow.html | 191 +++--- easybio-1.1.0/easybio/inst/doc/example-single-cell-annotation.R | 2 easybio-1.1.0/easybio/inst/doc/example-single-cell-annotation.Rmd | 196 +++--- easybio-1.1.0/easybio/inst/doc/example-single-cell-annotation.html | 2 easybio-1.1.0/easybio/inst/example-bulk-rna-seq.R |only easybio-1.1.0/easybio/man/Artist.Rd | 210 ++++++- easybio-1.1.0/easybio/man/CHOL_DEGs.Rd |only easybio-1.1.0/easybio/man/dprocess_dgeList.Rd | 54 - easybio-1.1.0/easybio/man/pbmc.markers.Rd | 20 easybio-1.1.0/easybio/man/plotMarkerDistribution.Rd | 42 - easybio-1.1.0/easybio/man/plotPossibleCell.Rd | 40 - easybio-1.1.0/easybio/man/plotRank.Rd | 38 - easybio-1.1.0/easybio/man/prepare_geo.Rd | 64 -- easybio-1.1.0/easybio/man/prepare_tcga.Rd | 36 - easybio-1.1.0/easybio/man/theme_publication.Rd | 58 +- easybio-1.1.0/easybio/man/tuneParameters.Rd | 46 - easybio-1.1.0/easybio/man/uniprot_id_map.Rd | 52 - easybio-1.1.0/easybio/tests/testthat.R | 24 easybio-1.1.0/easybio/tests/testthat/test-finsert.R | 52 - easybio-1.1.0/easybio/vignettes/example-bulk-rna-seq-workflow.Rmd | 285 +++++----- easybio-1.1.0/easybio/vignettes/example-single-cell-annotation.Rmd | 196 +++--- easybio-1.1.0/easybio/vignettes/limmaFilter.png |only easybio-1.1.0/easybio/vignettes/limmaNorm.png |only easybio-1.1.0/easybio/vignettes/ora.png |only 41 files changed, 1449 insertions(+), 880 deletions(-)
Title: Innovative Complex Split Procedures in Random Forests Through
Candidate Split Sampling
Description: Implementations of three diversity forest (DF) (Hornung, 2022,
<doi:10.1007/s42979-021-00920-1>) variants.
The DF algorithm is a split-finding approach that allows complex split procedures to
be realized in random forest variants.
The three DF variants implemented are:
1. interaction forests (IFs) (Hornung & Boulesteix, 2022, <doi:10.1016/j.csda.2022.107460>):
Model quantitative and qualitative interaction effects using bivariable splitting.
Come with the Effect Importance Measure (EIM), which can be used to identify variable
pairs that have well-interpretable quantitative and qualitative interaction effects
with high predictive relevance.
2. multi forests (MuFs) (Hornung & Hapfelmeier, 2024, <doi:10.48550/arXiv.2409.08925>):
Model multi-class outcomes using multi-way and binary splitting. Come with two
variable importance measures (VIMs): The multi-class VIM measures the degree to which
the variables are specifically associated with one or more outcome classe [...truncated...]
Author: Roman Hornung [aut, cre],
Marvin N. Wright [ctb, cph]
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between diversityForest versions 0.4.0 dated 2023-03-08 and 0.5.0 dated 2024-09-16
diversityForest-0.4.0/diversityForest/NEWS |only diversityForest-0.4.0/diversityForest/inst/NEWS.Rd |only diversityForest-0.5.0/diversityForest/DESCRIPTION | 61 diversityForest-0.5.0/diversityForest/MD5 | 103 diversityForest-0.5.0/diversityForest/NAMESPACE | 29 diversityForest-0.5.0/diversityForest/NEWS.md |only diversityForest-0.5.0/diversityForest/R/RcppExports.R | 4 diversityForest-0.5.0/diversityForest/R/ctg.R |only diversityForest-0.5.0/diversityForest/R/diversityForest-package.R | 33 diversityForest-0.5.0/diversityForest/R/divfor.R | 3 diversityForest-0.5.0/diversityForest/R/hars.R |only diversityForest-0.5.0/diversityForest/R/interactionfor.R | 8 diversityForest-0.5.0/diversityForest/R/multifor.R |only diversityForest-0.5.0/diversityForest/R/plot.multifor.R |only diversityForest-0.5.0/diversityForest/R/plotMcl.R |only diversityForest-0.5.0/diversityForest/R/plotVar.R |only diversityForest-0.5.0/diversityForest/R/predict.divfor.R | 4 diversityForest-0.5.0/diversityForest/R/predict.interactionfor.R | 4 diversityForest-0.5.0/diversityForest/R/predict.multifor.R |only diversityForest-0.5.0/diversityForest/R/predictions.R | 32 diversityForest-0.5.0/diversityForest/R/print.R | 364 +- diversityForest-0.5.0/diversityForest/R/timepoints.R | 2 diversityForest-0.5.0/diversityForest/R/zoo.R | 4 diversityForest-0.5.0/diversityForest/build/partial.rdb |binary diversityForest-0.5.0/diversityForest/data/ctg.rda |only diversityForest-0.5.0/diversityForest/data/hars.rda |only diversityForest-0.5.0/diversityForest/man/ctg.Rd |only diversityForest-0.5.0/diversityForest/man/diversityForest-package.Rd | 33 diversityForest-0.5.0/diversityForest/man/hars.Rd |only diversityForest-0.5.0/diversityForest/man/interactionfor.Rd | 2 diversityForest-0.5.0/diversityForest/man/multifor.Rd |only diversityForest-0.5.0/diversityForest/man/plot.multifor.Rd |only diversityForest-0.5.0/diversityForest/man/plotMcl.Rd |only diversityForest-0.5.0/diversityForest/man/plotVar.Rd |only diversityForest-0.5.0/diversityForest/man/predict.multifor.Rd |only diversityForest-0.5.0/diversityForest/man/predictions.divfor.Rd |only diversityForest-0.5.0/diversityForest/man/predictions.divfor.prediction.Rd |only diversityForest-0.5.0/diversityForest/man/zoo.Rd | 4 diversityForest-0.5.0/diversityForest/src/Data.cpp | 39 diversityForest-0.5.0/diversityForest/src/Data.h | 1 diversityForest-0.5.0/diversityForest/src/Forest.cpp | 436 -- diversityForest-0.5.0/diversityForest/src/Forest.h | 29 diversityForest-0.5.0/diversityForest/src/ForestClassification.cpp | 269 - diversityForest-0.5.0/diversityForest/src/ForestClassification.h | 65 diversityForest-0.5.0/diversityForest/src/ForestProbability.cpp | 246 - diversityForest-0.5.0/diversityForest/src/ForestProbability.h | 59 diversityForest-0.5.0/diversityForest/src/ForestRegression.cpp | 102 diversityForest-0.5.0/diversityForest/src/ForestRegression.h | 4 diversityForest-0.5.0/diversityForest/src/ForestSurvival.cpp | 145 diversityForest-0.5.0/diversityForest/src/ForestSurvival.h | 4 diversityForest-0.5.0/diversityForest/src/Hungarian.cpp |only diversityForest-0.5.0/diversityForest/src/Hungarian.h |only diversityForest-0.5.0/diversityForest/src/RcppExports.cpp | 9 diversityForest-0.5.0/diversityForest/src/Tree.cpp | 160 diversityForest-0.5.0/diversityForest/src/Tree.h | 12 diversityForest-0.5.0/diversityForest/src/TreeClassification.cpp | 1653 +++++++++- diversityForest-0.5.0/diversityForest/src/TreeClassification.h | 60 diversityForest-0.5.0/diversityForest/src/TreeProbability.cpp | 1649 +++++++++ diversityForest-0.5.0/diversityForest/src/TreeProbability.h | 56 diversityForest-0.5.0/diversityForest/src/TreeRegression.cpp | 5 diversityForest-0.5.0/diversityForest/src/divforCpp.cpp | 362 +- diversityForest-0.5.0/diversityForest/src/globals.h | 5 diversityForest-0.5.0/diversityForest/src/utility.cpp | 27 diversityForest-0.5.0/diversityForest/src/utility.h | 9 64 files changed, 4670 insertions(+), 1426 deletions(-)
More information about diversityForest at CRAN
Permanent link
Title: Phase I/II CRM Based Drug Combination Design
Description: Implements the adaptive designs for integrated phase I/II trials of drug combinations via continual reassessment method (CRM) to evaluate toxicity and efficacy simultaneously for each enrolled patient cohort based on Bayesian inference. It supports patients assignment guidance in a single trial using current enrolled data, as well as conducting extensive simulation studies to evaluate operating characteristics before the trial starts. It includes various link functions such as empiric, one-parameter logistic, two-parameter logistic, and hyperbolic tangent, as well as considering multiple prior distributions of the parameters like normal distribution, gamma distribution and exponential distribution to accommodate diverse clinical scenarios. Method using Bayesian framework with empiric link function is described in: Wages and Conaway (2014) <doi:10.1002/sim.6097>.
Author: Junying Wang [cre, aut],
Song Wu [aut],
Jie Yang [aut]
Maintainer: Junying Wang <junying.wang@stonybrook.edu>
Diff between crm12Comb versions 0.1.6 dated 2024-06-07 and 0.1.7 dated 2024-09-16
crm12Comb-0.1.6/crm12Comb/data/examples_results.rda |only crm12Comb-0.1.7/crm12Comb/DESCRIPTION | 6 +- crm12Comb-0.1.7/crm12Comb/MD5 | 26 +++++----- crm12Comb-0.1.7/crm12Comb/R/Bayesian_likelihood.R | 6 +- crm12Comb-0.1.7/crm12Comb/R/est.R | 6 +- crm12Comb-0.1.7/crm12Comb/R/get_orders.R | 2 crm12Comb-0.1.7/crm12Comb/build/partial.rdb |binary crm12Comb-0.1.7/crm12Comb/build/vignette.rds |binary crm12Comb-0.1.7/crm12Comb/data/examples_results.RData |only crm12Comb-0.1.7/crm12Comb/inst/doc/crm12Comb.R | 4 - crm12Comb-0.1.7/crm12Comb/inst/doc/crm12Comb.Rmd | 6 +- crm12Comb-0.1.7/crm12Comb/inst/doc/crm12Comb.html | 36 +++++++-------- crm12Comb-0.1.7/crm12Comb/man/doseComb_to_mat.Rd | 2 crm12Comb-0.1.7/crm12Comb/man/tanh_ExpPriorLikelihood.Rd | 2 crm12Comb-0.1.7/crm12Comb/vignettes/crm12Comb.Rmd | 6 +- 15 files changed, 51 insertions(+), 51 deletions(-)
Title: Analysis of Variance and Other Important Complementary Analyses
Description: Perform analysis of variance and other important complementary
analyses. The functions are easy to use. Performs analysis in various
designs, with balanced and unbalanced data.
Author: Emmanuel Arnhold [aut, cre]
Maintainer: Emmanuel Arnhold <emmanuelarnhold@yahoo.com.br>
Diff between easyanova versions 10.0 dated 2023-10-19 and 11.0 dated 2024-09-16
DESCRIPTION | 14 +- MD5 | 30 +++- NAMESPACE | 27 +++- R/box.plot.R |only R/ea1.R | 247 ++++++++++++++++++++++++++++++---------- R/ea2.R | 290 ++++++++++++++++++++++++++++++++++------------- R/ic.R |only R/ic.plot.R |only R/m.plot.R |only R/means.plot.R |only R/means.plotfat.R |only R/p.plot.R |only R/tab.R |only man/box.plot.Rd |only man/ea1.Rd | 94 +++++++++++---- man/ea2.Rd | 8 + man/easyanova-package.Rd | 4 man/ic.Rd |only man/ic.plot.Rd |only man/m.plot.Rd |only man/means.plot.Rd |only man/means.plotfat.Rd |only man/p.plot.Rd |only man/tab.Rd |only 24 files changed, 529 insertions(+), 185 deletions(-)
Title: Calculate Distance Measures for a Given List of Data Frames with
Factors
Description: It provides functions that calculate Mahalanobis distance, Euclidean distance, Manhattan distance and Chebyshev distance between each pair of species in a list of data frames. These metrics are fundamental in various fields, such as cluster analysis, classification, and other applications of machine learning and data mining, where assessing similarity or dissimilarity between data is crucial. The package is designed to be flexible and easily integrated into data analysis workflows, providing reliable tools for evaluating distances in multidimensional contexts.
Author: Flavio Gioia [aut, cre]
Maintainer: Flavio Gioia <flaviogioia.fg@gmail.com>
Diff between cmahalanobis versions 0.3.0 dated 2024-05-20 and 0.4.0 dated 2024-09-16
cmahalanobis-0.3.0/cmahalanobis/build |only cmahalanobis-0.3.0/cmahalanobis/inst/doc |only cmahalanobis-0.3.0/cmahalanobis/vignettes |only cmahalanobis-0.4.0/cmahalanobis/DESCRIPTION | 17 cmahalanobis-0.4.0/cmahalanobis/MD5 | 34 cmahalanobis-0.4.0/cmahalanobis/NAMESPACE | 12 cmahalanobis-0.4.0/cmahalanobis/R/cmahalanobis.R | 1088 +++++++-- cmahalanobis-0.4.0/cmahalanobis/R/zzz.R |only cmahalanobis-0.4.0/cmahalanobis/inst/rmarkdown |only cmahalanobis-0.4.0/cmahalanobis/man/cchebyshev.Rd | 70 cmahalanobis-0.4.0/cmahalanobis/man/ceuclide.Rd | 73 cmahalanobis-0.4.0/cmahalanobis/man/cmahalanobis.Rd | 55 cmahalanobis-0.4.0/cmahalanobis/man/cmanhattan.Rd | 72 cmahalanobis-0.4.0/cmahalanobis/man/generate_report_cchebyshev.Rd |only cmahalanobis-0.4.0/cmahalanobis/man/generate_report_ceuclide.Rd |only cmahalanobis-0.4.0/cmahalanobis/man/generate_report_cmahalanobis.Rd |only cmahalanobis-0.4.0/cmahalanobis/man/generate_report_cmanhattan.Rd |only cmahalanobis-0.4.0/cmahalanobis/man/pvaluesccheb.Rd |only cmahalanobis-0.4.0/cmahalanobis/man/pvaluesceucl.Rd |only cmahalanobis-0.4.0/cmahalanobis/man/pvaluescmaha.Rd |only cmahalanobis-0.4.0/cmahalanobis/man/pvaluescmanh.Rd |only cmahalanobis-0.4.0/cmahalanobis/tests/testthat/cmahalanobis.R | 1091 +++++++--- 22 files changed, 1786 insertions(+), 726 deletions(-)
Title: Nanosecond-Resolution Time Support for R
Description: Full 64-bit resolution date and time functionality with
nanosecond granularity is provided, with easy transition to and from
the standard 'POSIXct' type. Three additional classes offer interval,
period and duration functionality for nanosecond-resolution timestamps.
Author: Dirk Eddelbuettel [aut, cre] ,
Leonardo Silvestri [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between nanotime versions 0.3.9 dated 2024-06-21 and 0.3.10 dated 2024-09-16
nanotime-0.3.10/nanotime/ChangeLog | 31 + nanotime-0.3.10/nanotime/DESCRIPTION | 18 nanotime-0.3.10/nanotime/MD5 | 27 nanotime-0.3.10/nanotime/NAMESPACE | 2 nanotime-0.3.10/nanotime/R/nanoival.R | 2 nanotime-0.3.10/nanotime/R/nanotime.R | 11 nanotime-0.3.10/nanotime/demo/00Index | 1 nanotime-0.3.10/nanotime/inst/NEWS.Rd | 10 nanotime-0.3.10/nanotime/inst/doc/nanotime-introduction.pdf |binary nanotime-0.3.10/nanotime/inst/tinytest/test_nanoival.R | 59 - nanotime-0.3.10/nanotime/inst/tinytest/test_nanoperiod.R | 371 +++++------- nanotime-0.3.10/nanotime/inst/tinytest/test_nanotime.R | 362 +++++------ nanotime-0.3.10/nanotime/inst/tinytest/test_zoo.R | 4 nanotime-0.3.10/nanotime/man/nanotime.Rd | 1 nanotime-0.3.9/nanotime/demo/ggplot2Example.R |only 15 files changed, 458 insertions(+), 441 deletions(-)
Title: Bayesian Network Meta-Analysis of Individual and Aggregate Data
Description: Network meta-analysis and network meta-regression models for
aggregate data, individual patient data, and mixtures of both individual
and aggregate data using multilevel network meta-regression as described by
Phillippo et al. (2020) <doi:10.1111/rssa.12579>. Models are estimated in a
Bayesian framework using 'Stan'.
Author: David M. Phillippo [aut, cre]
Maintainer: David M. Phillippo <david.phillippo@bristol.ac.uk>
Diff between multinma versions 0.7.1 dated 2024-06-11 and 0.7.2 dated 2024-09-16
DESCRIPTION | 8 +++--- MD5 | 50 +++++++++++++++++++++--------------------- NEWS.md | 14 +++++++++++ R/integration.R | 2 - R/marginal_effects.R | 2 - R/nma.R | 41 ++++++++++++++++++++++++++-------- R/nma_data-class.R | 23 +++++++++++-------- R/nma_nodesplit-class.R | 2 - R/nma_summary-class.R | 11 +++++---- R/nodesplit_summary-class.R | 18 ++++++++------- R/predict.R | 11 ++++++++- R/stan_nma-class.R | 4 +-- README.md | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 - man/add_integration.Rd | 2 - man/as.array.stan_nma.Rd | 2 - man/graph_conversion.Rd | 5 ++-- man/nma.Rd | 13 ++++++---- man/plot.nma_data.Rd | 18 +++++++++------ man/plot.nma_summary.Rd | 11 +++++---- man/plot.nodesplit_summary.Rd | 18 ++++++++------- man/print.nma_nodesplit_df.Rd | 2 - man/print.stan_nma.Rd | 2 - tests/testthat/test-nma.R | 41 ++++++++++++++++++++++++++++++++++ 26 files changed, 204 insertions(+), 100 deletions(-)
Title: Bayesian Survival Regression with Flexible Error and Random
Effects Distributions
Description: Contains Bayesian implementations of the Mixed-Effects Accelerated Failure Time (MEAFT) models
for censored data. Those can be not only right-censored but also interval-censored,
doubly-interval-censored or misclassified interval-censored. The methods implemented in the package
have been published in Komárek and Lesaffre (2006, Stat. Modelling) <doi:10.1191/1471082X06st107oa>,
Komárek, Lesaffre and Legrand (2007, Stat. in Medicine) <doi:10.1002/sim.3083>, Komárek and Lesaffre (2007, Stat. Sinica) <https://www3.stat.sinica.edu.tw/statistica/oldpdf/A17n27.pdf>, Komárek and Lesaffre (2008, JASA) <doi:10.1198/016214507000000563>,
García-Zattera, Jara and Komárek (2016, Biometrics) <doi:10.1111/biom.12424>.
Author: Arnost Komarek [aut, cre]
Maintainer: Arnost Komarek <arnost.komarek@mff.cuni.cz>
Diff between bayesSurv versions 3.7 dated 2023-12-18 and 3.8 dated 2024-09-16
CHANGES | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- inst/CITATION | 12 ++++-------- inst/doc/ex-cgd.R | 2 +- inst/doc/ex-tandmobCS.R | 2 +- inst/doc/ex-tandmobMixture.R | 2 +- inst/doc/ex-tandmobPA.R | 2 +- src/arms.cpp | 18 ++++++++++-------- src/arms.h | 2 ++ 10 files changed, 37 insertions(+), 33 deletions(-)
Title: Expected Value of Information
Description: Methods to calculate the expected value of information from a decision-analytic model. This includes the expected value of perfect information (EVPI), partial perfect information (EVPPI) and sample information (EVSI), and the expected net benefit of sampling (ENBS). A range of alternative computational methods are provided under the same user interface. See Heath et al. (2024) <doi:10.1201/9781003156109>, Jackson et al. (2022) <doi:10.1146/annurev-statistics-040120-010730>.
Author: Christopher Jackson [aut, cre],
Anna Heath [aut],
Gianluca Baio [ctb] ,
Mark Strong [ctb] ,
Kofi Placid Adragni [ctb] ,
Andrew Raim [ctb]
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between voi versions 1.0.2 dated 2023-11-27 and 1.0.3 dated 2024-09-16
DESCRIPTION | 12 +++--- MD5 | 48 +++++++++++++-------------- NEWS.md | 9 +++++ R/check_regression.R | 11 +++--- R/evppi.R | 10 ++++- R/evppi_mc.R | 2 + R/evppi_npreg.R | 2 + R/evsi.R | 5 ++ R/model.R | 4 ++ R/voi-package.R | 5 +- build/vignette.rds |binary inst/Chemotherapy_Book/06_figs/CEAC.pdf |binary inst/Chemotherapy_Book/06_figs/CEAF.pdf |binary inst/doc/plots.html | 8 ++-- inst/doc/voi.R | 14 ++++---- inst/doc/voi.Rmd | 8 +--- inst/doc/voi.html | 55 ++++++++++++++------------------ man/check_regression.Rd | 6 +-- man/evppi.Rd | 8 +++- man/evppivar.Rd | 2 - man/evsi.Rd | 2 + man/voi-package.Rd | 28 ++++++++++++++++ tests/testthat/test_evsi.R | 10 +++++ tests/testthat/test_heemod.R | 7 +--- vignettes/voi.Rmd | 8 +--- 25 files changed, 161 insertions(+), 103 deletions(-)
Title: Computation of Optimal Transport Plans and Wasserstein Distances
Description: Solve optimal transport problems. Compute Wasserstein distances (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p distances), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, (weighted) point patterns, and mass vectors.
Author: Dominic Schuhmacher [aut, cre],
Bjoern Baehre [aut] ,
Nicolas Bonneel [aut] ,
Carsten Gottschlich [aut] ,
Valentin Hartmann [aut] ,
Florian Heinemann [aut] ,
Bernhard Schmitzer [aut] ,
Joern Schrieber [aut] ,
Timo Wilm [ctb]
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>
Diff between transport versions 0.15-2 dated 2024-05-09 and 0.15-4 dated 2024-09-16
DESCRIPTION | 11 ++- MD5 | 36 ++++++------- NEWS | 27 ++++++++- R/RcppExports.R | 4 - R/fundament.R | 9 ++- R/unbalanced_wpp.R | 3 - build/partial.rdb |binary src/OT_SparseSimplex/sparsebasicfeasible.c | 40 +++++++------- src/OT_SparseSimplex/sparsesimplex.c | 64 +++++++++++------------ src/RcppExports.cpp | 7 +- src/aha.c | 80 ++++++++++++++--------------- src/network_simplex_simple.h | 9 ++- src/networksimplex.cpp | 11 ++- src/power_diagram.h | 6 +- src/revsimplex.c | 20 +++---- src/shortsimplex.c | 24 ++++---- src/transport_init.c | 4 - tests/testthat/_data |only tests/testthat/test-main.R | 58 --------------------- tests/testthat/test-unbalanced_wpp.R |only 20 files changed, 197 insertions(+), 216 deletions(-)
Title: Testing in Conditional Likelihood Context
Description: An implementation of hypothesis testing in an extended Rasch modeling framework,
including sample size planning procedures and power computations. Provides 4 statistical tests,
i.e., gradient test (GR), likelihood ratio test (LR), Rao score or Lagrange multiplier test (RS),
and Wald test, for testing a number of hypotheses referring to the Rasch model (RM), linear
logistic test model (LLTM), rating scale model (RSM), and partial credit model (PCM). Three
types of functions for power and sample size computations are provided. Firstly, functions to
compute the sample size given a user-specified (predetermined) deviation from the hypothesis
to be tested, the level alpha, and the power of the test. Secondly, functions to evaluate the
power of the tests given a user-specified (predetermined) deviation from the hypothesis to be
tested, the level alpha of the test, and the sample size. Thirdly, functions to evaluate the
so-called post hoc power of the tests. This is the power of the tests giv [...truncated...]
Author: Clemens Draxler [aut, cre],
Andreas Kurz [aut]
Maintainer: Clemens Draxler <clemens.draxler@umit-tirol.at>
Diff between tcl versions 0.2.0 dated 2023-05-02 and 0.2.1 dated 2024-09-16
DESCRIPTION | 10 ++++---- MD5 | 56 ++++++++++++++++++++++----------------------- R/discr_test.R | 4 +-- R/invar_test.R | 28 +++++++++++----------- R/post_hocChange.R | 16 ++++++------ R/post_hocPCM.R | 26 ++++++++++---------- R/post_hocRM.R | 28 +++++++++++----------- R/powerChange.R | 25 +++++++++++--------- R/powerPCM.R | 45 +++++++++++++++++++----------------- R/powerRM.R | 38 ++++++++++++++++-------------- R/sa_sizeChange.R | 27 ++++++++++++--------- R/sa_sizePCM.R | 37 ++++++++++++++++------------- R/sa_sizeRM.R | 33 ++++++++++++++------------ build/vignette.rds |binary inst/doc/tcl-vignette.R | 2 - inst/doc/tcl-vignette.Rmd | 2 - inst/doc/tcl-vignette.html | 4 +-- man/discr_test.Rd | 4 +-- man/invar_test.Rd | 2 - man/post_hocChange.Rd | 8 +++--- man/post_hocPCM.Rd | 8 +++--- man/post_hocRM.Rd | 8 +++--- man/powerChange.Rd | 8 +++--- man/powerPCM.Rd | 23 ++++++++---------- man/powerRM.Rd | 16 ++++++------ man/sa_sizeChange.Rd | 12 ++++----- man/sa_sizePCM.Rd | 14 +++++------ man/sa_sizeRM.Rd | 10 ++++---- vignettes/tcl-vignette.Rmd | 2 - 29 files changed, 257 insertions(+), 239 deletions(-)
Title: Search Algorithms and Loss Functions for Bayesian Clustering
Description: The SALSO algorithm is an efficient randomized greedy search method to find a point estimate for a random partition based on a loss function and posterior Monte Carlo samples. The algorithm is implemented for many loss functions, including the Binder loss and a generalization of the variation of information loss, both of which allow for unequal weights on the two types of clustering mistakes. Efficient implementations are also provided for Monte Carlo estimation of the posterior expected loss of a given clustering estimate. See Dahl, Johnson, Müller (2022) <doi:10.1080/10618600.2022.2069779>.
Author: David B. Dahl [aut, cre] ,
Devin J. Johnson [aut] ,
Peter Mueller [aut],
Alex Crichton [ctb] ,
Brendan Zabarauskas [ctb] ,
David B. Dahl [ctb] ,
David Tolnay [ctb] ,
Jim Turner [ctb] ,
Josh Stone [ctb] ,
R. Janis Goldschmidt [ctb] ,
Sean McArthur [ctb [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.3.41 dated 2024-09-06 and 0.3.42 dated 2024-09-16
DESCRIPTION | 8 ++-- MD5 | 22 +++++------ NAMESPACE | 1 NEWS | 4 ++ R/psm.R | 4 +- build/partial.rdb |binary inst/cargo.log | 9 ++-- man/psm.Rd | 3 + src/rust/Cargo.lock | 97 +++++++++++++++++++++++++++++++------------------ src/rust/Cargo.toml | 6 ++- src/rust/src/lib.rs | 3 + src/rust/vendor.tar.gz |binary 12 files changed, 98 insertions(+), 59 deletions(-)
Title: Diet Estimated Trophic Levels
Description: Estimates fractional trophic level from quantitative and qualitative diet data and calculates electivity indices in R. Borstein (2020) <doi:10.1007/s10750-020-04417-5>.
Author: Samuel R. Borstein [aut, cre]
Maintainer: Samuel R. Borstein <sam@borstein.com>
Diff between dietr versions 1.1.4 dated 2023-02-25 and 1.1.5-1 dated 2024-09-16
dietr-1.1.4/dietr/inst/doc/dietr-vignette.pdf |only dietr-1.1.5-1/dietr/DESCRIPTION | 22 +++-- dietr-1.1.5-1/dietr/MD5 | 35 +++++---- dietr-1.1.5-1/dietr/NEWS.md | 7 - dietr-1.1.5-1/dietr/R/ConvertFishbaseDiet.R | 10 +- dietr-1.1.5-1/dietr/R/pkgname.R | 4 - dietr-1.1.5-1/dietr/build/vignette.rds |binary dietr-1.1.5-1/dietr/inst/doc/dietr-vignette.R | 38 +++++----- dietr-1.1.5-1/dietr/inst/doc/dietr-vignette.Rmd | 4 - dietr-1.1.5-1/dietr/inst/doc/dietr-vignette.html |only dietr-1.1.5-1/dietr/man/dietr.Rd | 3 dietr-1.1.5-1/dietr/vignettes/dietr-vignette.Rmd | 4 - dietr-1.1.5-1/dietr/vignettes/dietr-vignette_files/figure-html |only dietr-1.1.5-1/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-18-1.pdf |binary dietr-1.1.5-1/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-19-1.pdf |binary dietr-1.1.5-1/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-19-2.pdf |binary dietr-1.1.5-1/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-19-3.pdf |binary dietr-1.1.5-1/dietr/vignettes/dietr-vignette_files/figure-latex/unnamed-chunk-19-4.pdf |binary 18 files changed, 67 insertions(+), 60 deletions(-)
Title: Provides 'box' Compatibility for 'languageserver'
Description: A 'box' compatible custom language parser for the 'languageserver' package to provide
completion and signature hints in code editors.
Author: Ricardo Rodrigo Basa [aut, cre],
Pavel Demin [aut],
Jakub Nowicki [aut],
Appsilon Sp. z o.o. [cph]
Maintainer: Ricardo Rodrigo Basa <opensource+rodrigo@appsilon.com>
Diff between box.lsp versions 0.1.1 dated 2024-09-10 and 0.1.2 dated 2024-09-16
DESCRIPTION | 12 +++++++----- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/box_lsp.R | 7 ++++++- README.md | 30 ++++++++++++++++++++++++++++-- 5 files changed, 49 insertions(+), 12 deletions(-)
Title: Visualizing Categorical Data
Description: Visualization techniques, data sets, summary and inference
procedures aimed particularly at categorical data. Special
emphasis is given to highly extensible grid graphics. The
package was package was originally inspired by the book
"Visualizing Categorical Data" by Michael Friendly and is
now the main support package for a new book,
"Discrete Data Analysis with R" by Michael Friendly and
David Meyer (2015).
Author: David Meyer [aut, cre] ,
Achim Zeileis [aut] ,
Kurt Hornik [aut] ,
Florian Gerber [ctb],
Michael Friendly [aut]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between vcd versions 1.4-12 dated 2023-12-29 and 1.4-13 dated 2024-09-16
DESCRIPTION | 6 ++--- MD5 | 48 ++++++++++++++++++++--------------------- build/partial.rdb |binary build/vignette.rds |binary data/Butterfly.rda |binary data/Employment.rda |binary data/Federalist.rda |binary data/HorseKicks.rda |binary data/Hospital.rda |binary data/Lifeboats.rda |binary data/MSPatients.rda |binary data/PreSex.rda |binary data/RepVict.rda |binary data/Rochdale.rda |binary data/Saxony.rda |binary data/Suicide.rda |binary data/UKSoccer.rda |binary data/WeldonDice.rda |binary data/WomenQueue.rda |binary inst/NEWS.Rd | 4 +++ inst/doc/residual-shadings.pdf |binary inst/doc/strucplot.pdf |binary man/Bundestag2005.Rd | 4 +-- man/agreementplot.Rd | 2 - man/plot.loglm.Rd | 4 +-- 25 files changed, 36 insertions(+), 32 deletions(-)
Title: Estimation, Simulation and Visualization of Hierarchical
Archimedean Copulae (HAC)
Description: Package provides the estimation of the structure and the parameters, sampling methods and structural plots of Hierarchical Archimedean Copulae (HAC).
Author: Ostap Okhrin [aut],
Alexander Ristig [aut],
Gong Chen [cre]
Maintainer: Gong Chen <gong.chen1@tu-dresden.de>
Diff between HAC versions 1.1-0 dated 2022-03-14 and 1.1-1 dated 2024-09-16
DESCRIPTION | 25 +++ MD5 | 20 +-- R/constructor.r | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 inst/doc/HAC.R | 334 ++++++++++++++++++++++++++--------------------------- inst/doc/HAC.Rnw | 2 inst/doc/HAC.pdf |binary man/hac.Rd | 2 vignettes/HAC.Rnw | 2 11 files changed, 203 insertions(+), 190 deletions(-)
Title: Censored Regression with Conditional Heteroscedasticity
Description: Different approaches to censored or truncated regression with
conditional heteroscedasticity are provided. First, continuous
distributions can be used for the (right and/or left censored or truncated)
response with separate linear predictors for the mean and variance.
Second, cumulative link models for ordinal data
(obtained by interval-censoring continuous data) can be employed for
heteroscedastic extended logistic regression (HXLR). In the latter type of
models, the intercepts depend on the thresholds that define the intervals.
Infrastructure for working with censored or truncated normal, logistic,
and Student-t distributions, i.e., d/p/q/r functions and distributions3
objects.
Author: Achim Zeileis [aut, cre] ,
Jakob W. Messner [aut] ,
Reto Stauffer [aut] ,
Ioannis Kosmidis [ctb] ,
Georg J. Mayr [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between crch versions 1.2-0 dated 2024-08-22 and 1.2-1 dated 2024-09-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 9 +++++++++ man/CensoredStudentsT.Rd | 2 ++ man/TruncatedStudentsT.Rd | 2 ++ tests/Examples/crch-Ex.Rout.save | 14 ++++---------- 6 files changed, 26 insertions(+), 19 deletions(-)
Title: Bayesian Dynamic Borrowing with Flexible Baseline Hazard
Function
Description: Allows Bayesian borrowing from a historical dataset for time-to-
event data. A flexible baseline hazard function is achieved via a piecewise
exponential likelihood with time varying split points and smoothing prior on the
historic baseline hazards. The method is described in Scott and Lewin (2024)
<doi:10.48550/arXiv.2401.06082>, and the software paper is in Axillus et al.
(2024) <doi:10.48550/arXiv.2408.04327>.
Author: Darren Scott [aut, cre],
Sophia Axillus [aut]
Maintainer: Darren Scott <darren.scott@astrazeneca.com>
Diff between BayesFBHborrow versions 2.0.1 dated 2024-06-24 and 2.0.2 dated 2024-09-16
DESCRIPTION | 9 +-- MD5 | 20 +++---- R/GibbsMH.R | 112 ++++++++++++++++++++++++------------------ R/beta_updates.R | 2 R/run_mcmc.R | 45 ++++++++-------- man/BayesFBHborrow.Rd | 21 +++---- man/BayesFBHborrow.WBorrow.Rd | 18 +++--- man/GibbsMH.NoBorrow.Rd | 6 +- man/GibbsMH.Rd | 11 ++-- man/GibbsMH.WBorrow.Rd | 11 ++-- man/dot-beta_MH_RW.Rd | 2 11 files changed, 139 insertions(+), 118 deletions(-)
More information about BayesFBHborrow at CRAN
Permanent link
Title: The Composer of Plots
Description: The 'ggplot2' package provides a strong API for sequentially
building up a plot, but does not concern itself with composition of multiple
plots. 'patchwork' is a package that expands the API to allow for
arbitrarily complex composition of plots by, among others, providing
mathematical operators for combining multiple plots. Other packages that try
to address this need (but with a different approach) are 'gridExtra' and
'cowplot'.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between patchwork versions 1.2.0 dated 2024-01-08 and 1.3.0 dated 2024-09-16
patchwork-1.2.0/patchwork/tests/testthat/_snaps/collect_axes |only patchwork-1.2.0/patchwork/tests/testthat/test-collect_axes.R |only patchwork-1.3.0/patchwork/DESCRIPTION | 12 patchwork-1.3.0/patchwork/MD5 | 129 +-- patchwork-1.3.0/patchwork/NAMESPACE | 16 patchwork-1.3.0/patchwork/NEWS.md | 61 + patchwork-1.3.0/patchwork/R/aaa.R | 2 patchwork-1.3.0/patchwork/R/add_plot.R | 37 - patchwork-1.3.0/patchwork/R/arithmetic.R | 3 patchwork-1.3.0/patchwork/R/collect_axes.R | 82 +- patchwork-1.3.0/patchwork/R/free.R | 73 +- patchwork-1.3.0/patchwork/R/guides.R | 86 +- patchwork-1.3.0/patchwork/R/inset_element.R | 6 patchwork-1.3.0/patchwork/R/merge.R |only patchwork-1.3.0/patchwork/R/plot_annotation.R | 30 patchwork-1.3.0/patchwork/R/plot_layout.R | 39 - patchwork-1.3.0/patchwork/R/plot_patchwork.R | 359 ++++++++-- patchwork-1.3.0/patchwork/R/wrap_elements.R | 12 patchwork-1.3.0/patchwork/R/wrap_ggplot_grob.R | 18 patchwork-1.3.0/patchwork/R/wrap_plots.R | 6 patchwork-1.3.0/patchwork/R/wrap_table.R |only patchwork-1.3.0/patchwork/R/zzz.R | 26 patchwork-1.3.0/patchwork/build/vignette.rds |binary patchwork-1.3.0/patchwork/inst/doc/patchwork.html | 20 patchwork-1.3.0/patchwork/man/free.Rd | 53 + patchwork-1.3.0/patchwork/man/inset_element.Rd | 2 patchwork-1.3.0/patchwork/man/plot_annotation.Rd | 19 patchwork-1.3.0/patchwork/man/plot_arithmetic.Rd | 3 patchwork-1.3.0/patchwork/man/plot_layout.Rd | 21 patchwork-1.3.0/patchwork/man/wrap_elements.Rd | 4 patchwork-1.3.0/patchwork/man/wrap_plots.Rd | 16 patchwork-1.3.0/patchwork/man/wrap_table.Rd |only patchwork-1.3.0/patchwork/tests/testthat/_snaps/arithmetic/add-ggplot-elements-p1-p2-theme-bw.svg | 22 patchwork-1.3.0/patchwork/tests/testthat/_snaps/arithmetic/add-patchwork-to-plot-p1-p2-p3.svg | 40 - patchwork-1.3.0/patchwork/tests/testthat/_snaps/arithmetic/adding-to-all-on-level-patchwork-theme-bw.svg | 80 +- patchwork-1.3.0/patchwork/tests/testthat/_snaps/arithmetic/adding-to-all-subplots-patchwork-theme-bw.svg | 78 +- patchwork-1.3.0/patchwork/tests/testthat/_snaps/arithmetic/adding-to-patchwork-p1-p2-p3.svg | 60 - patchwork-1.3.0/patchwork/tests/testthat/_snaps/arithmetic/complex-composition-p1-p2-p3-p4.svg | 80 +- patchwork-1.3.0/patchwork/tests/testthat/_snaps/arithmetic/nest-left-hand-side-p1-p2-p3.svg | 58 - patchwork-1.3.0/patchwork/tests/testthat/_snaps/arithmetic/nest-right-hand-side-p1-p2-p3.svg | 40 - patchwork-1.3.0/patchwork/tests/testthat/_snaps/arithmetic/pack-4-plots-p1-p2-p3-p4.svg | 78 +- patchwork-1.3.0/patchwork/tests/testthat/_snaps/arithmetic/stack-3-plots-p1-p2-p3.svg | 58 - patchwork-1.3.0/patchwork/tests/testthat/_snaps/arithmetic/standard-addition-p1-p2-p3.svg | 60 - patchwork-1.3.0/patchwork/tests/testthat/_snaps/collect |only patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/basic-inset-works.svg | 18 patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/far-dimensions-can-be-set-with-units.svg | 42 - patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/far-legend-justification.svg | 20 patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/far-optimise-space-by-default-1.svg | 78 +- patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/far-optimise-space-by-default-2.svg | 60 - patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/far-optimise-space-by-default-3.svg | 78 +- patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/far-space-optimisation-can-be-turned-off.svg | 62 - patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/free-can-be-nested.svg |only patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/free-can-be-stacked-and-nested.svg |only patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/free-label-works.svg |only patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/free-panel-works-on-one-side.svg |only patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/free-panel-works.svg |only patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/free-space-works.svg |only patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/grobs-can-be-inset.svg | 18 patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/insets-can-be-changed.svg | 18 patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/other-alignments-work.svg | 18 patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/patchworks-can-be-inset.svg | 64 + patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/setting-heights-as-units.svg | 82 +- patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/setting-heights.svg | 80 +- patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/setting-ncol.svg | 78 +- patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/setting-nrow.svg | 80 +- patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/setting-widths-as-units.svg | 78 +- patchwork-1.3.0/patchwork/tests/testthat/_snaps/layout/setting-widths.svg | 80 +- patchwork-1.3.0/patchwork/tests/testthat/test-collect.R |only patchwork-1.3.0/patchwork/tests/testthat/test-layout.R | 30 69 files changed, 1708 insertions(+), 1065 deletions(-)
Title: Fitting Hidden Markov Models to Financial Data
Description: Fitting (hierarchical) hidden Markov models to financial data
via maximum likelihood estimation. See Oelschläger, L. and Adam, T.
"Detecting Bearish and Bullish Markets in Financial Time Series Using
Hierarchical Hidden Markov Models" (2021, Statistical Modelling)
<doi:10.1177/1471082X211034048> for a reference on the method. A user guide
is provided by the accompanying software paper "fHMM: Hidden Markov Models
for Financial Time Series in R", Oelschläger, L., Adam, T., and Michels, R.
(2024, Journal of Statistical Software) <doi:10.18637/jss.v109.i09>.
Author: Lennart Oelschlaeger [aut, cre]
,
Timo Adam [aut] ,
Rouven Michels [aut]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between fHMM versions 1.4.0 dated 2024-08-26 and 1.4.1 dated 2024-09-16
DESCRIPTION | 11 MD5 | 263 NAMESPACE | 231 NEWS.md | 264 R/RcppExports.R | 22 R/compare_models.R | 152 R/compute_T_star.R | 174 R/compute_ci.R | 122 R/compute_residuals.R | 238 R/data_and_models.R | 612 R/decode_states.R | 350 R/download_data.R | 273 R/fHMM-package.R | 5 R/fHMM_colors.R | 152 R/fHMM_controls.R | 1846 +- R/fHMM_data.R | 432 R/fHMM_events.R | 116 R/fHMM_likelihood.R | 478 R/fHMM_model.R | 898 - R/fHMM_parameters.R | 2192 +- R/fHMM_sdds.R | 320 R/fit_model.R | 500 R/get_initial_values.R | 652 R/helpers.R | 108 R/parameter_labels.R | 132 R/plot.R | 1536 +- R/read_data.R | 462 R/reorder_states.R | 264 R/simulate_hmm.R | 416 README.md | 626 build/partial.rdb |binary build/vignette.rds |binary inst/doc/fHMM.R | 14 inst/doc/fHMM.Rmd | 108 inst/doc/fHMM.html | 934 - inst/doc/v01_model_definition.R | 14 inst/doc/v01_model_definition.Rmd | 104 inst/doc/v01_model_definition.html | 866 - inst/doc/v02_controls.R | 86 inst/doc/v02_controls.Rmd | 176 inst/doc/v02_controls.html | 1002 - inst/doc/v03_data_management.R | 88 inst/doc/v03_data_management.Rmd | 184 inst/doc/v03_data_management.html | 922 - inst/doc/v04_model_estimation.R | 82 inst/doc/v04_model_estimation.Rmd | 252 inst/doc/v04_model_estimation.html | 1136 - inst/doc/v05_state_decoding_and_prediction.R | 52 inst/doc/v05_state_decoding_and_prediction.Rmd | 148 inst/doc/v05_state_decoding_and_prediction.html | 948 - inst/doc/v06_model_checking.R | 46 inst/doc/v06_model_checking.Rmd | 132 inst/doc/v06_model_checking.html | 920 - inst/doc/v07_model_selection.R | 32 inst/doc/v07_model_selection.Rmd | 108 inst/doc/v07_model_selection.html | 914 - inst/extdata/dax.csv |18024 ++++++++++++------------ man/compare_models.Rd | 60 man/compute_T_star.Rd | 58 man/compute_ci.Rd | 54 man/compute_residuals.Rd | 48 man/dax.Rd | 70 man/dax_model_2n.Rd | 82 man/dax_model_3t.Rd | 92 man/dax_vw_model.Rd | 94 man/decode_states.Rd | 138 man/download_data.Rd | 134 man/fHMM-package.Rd | 62 man/fHMM_colors.Rd | 80 man/fHMM_data.Rd | 140 man/fHMM_events.Rd | 82 man/fHMM_model.Rd | 178 man/fHMM_parameters.Rd | 324 man/fHMM_sdds.Rd | 126 man/find_closest_year.Rd | 2 man/fit_model.Rd | 338 man/get_initial_values.Rd | 98 man/list_to_vector.Rd |only man/ll_hmm.Rd | 256 man/nLL_hhmm.Rd | 44 man/nLL_hmm.Rd | 44 man/parameter_labels.Rd | 40 man/parameter_transformations.Rd | 458 man/plot.fHMM_data.Rd | 70 man/plot.fHMM_model.Rd | 118 man/plot_ll.Rd | 46 man/plot_pr.Rd | 40 man/plot_sdds.Rd | 52 man/plot_ts.Rd | 86 man/prepare_data.Rd | 60 man/read_data.Rd | 58 man/reorder_states.Rd | 96 man/set_controls.Rd | 652 man/sim_model_2gamma.Rd | 78 man/simulate_hmm.Rd | 270 man/simulate_observations.Rd | 82 man/spx.Rd | 72 man/unemp.Rd | 54 man/unemp_spx_model_3_2.Rd | 86 man/vw.Rd | 70 tests/testthat.R | 8 tests/testthat/test-compare_models.R | 40 tests/testthat/test-compute_T_star.R | 84 tests/testthat/test-compute_ci.R | 26 tests/testthat/test-compute_residuals.R | 46 tests/testthat/test-data_and_models.R | 88 tests/testthat/test-decode_states.R | 60 tests/testthat/test-download_data.R | 146 tests/testthat/test-fHMM_colors.R | 70 tests/testthat/test-fHMM_controls.R | 1260 - tests/testthat/test-fHMM_data.R | 120 tests/testthat/test-fHMM_events.R | 56 tests/testthat/test-fHMM_likelihood.R | 66 tests/testthat/test-fHMM_model.R | 96 tests/testthat/test-fHMM_parameters.R | 426 tests/testthat/test-fHMM_sdds.R | 214 tests/testthat/test-fit_model.R | 178 tests/testthat/test-get_initial_values.R | 118 tests/testthat/test-helpers.R | 81 tests/testthat/test-parameter_labels.R | 68 tests/testthat/test-plot.R | 232 tests/testthat/test-read_data.R | 42 tests/testthat/test-reorder_states.R | 12 tests/testthat/test-simulate_hmm.R | 100 vignettes/fHMM.Rmd | 108 vignettes/ref.bib | 662 vignettes/v01_model_definition.Rmd | 104 vignettes/v02_controls.Rmd | 176 vignettes/v03_data_management.Rmd | 184 vignettes/v04_model_estimation.Rmd | 252 vignettes/v05_state_decoding_and_prediction.Rmd | 148 vignettes/v06_model_checking.Rmd | 132 vignettes/v07_model_selection.Rmd | 108 133 files changed, 25919 insertions(+), 25823 deletions(-)
Title: Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
Description: Functions for latent class analysis, short time Fourier
transform, fuzzy clustering, support vector machines,
shortest path computation, bagged clustering, naive Bayes
classifier, generalized k-nearest neighbour ...
Author: David Meyer [aut, cre] ,
Evgenia Dimitriadou [aut, cph],
Kurt Hornik [aut] ,
Andreas Weingessel [aut],
Friedrich Leisch [aut],
Chih-Chung Chang [ctb, cph] ,
Chih-Chen Lin [ctb, cph]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between e1071 versions 1.7-14 dated 2023-12-06 and 1.7-16 dated 2024-09-16
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- R/sparse.R | 2 +- build/vignette.rds |binary inst/NEWS.Rd | 11 +++++++++++ inst/doc/svmdoc.R | 4 ++-- inst/doc/svmdoc.Rnw | 8 ++++---- inst/doc/svmdoc.pdf |binary inst/doc/svminternals.Rnw | 1 + inst/doc/svminternals.pdf |binary man/matchControls.Rd | 4 ++-- src/svm.cpp | 2 +- vignettes/svmdoc.Rnw | 8 ++++---- vignettes/svminternals.Rnw | 1 + 14 files changed, 43 insertions(+), 30 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-04 0.1.4
2017-10-08 0.1.3
2017-02-11 0.1.2
2017-02-05 0.1.1
2017-01-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-05 0.3.0
2017-04-30 0.2.0
2017-02-12 0.1.0
Title: Bayesian Vector Heterogeneous Autoregressive Modeling
Description: Tools to model and forecast multivariate time series
including Bayesian Vector heterogeneous autoregressive (VHAR) model
by Kim & Baek (2023) (<doi:10.1080/00949655.2023.2281644>).
'bvhar' can model Vector Autoregressive (VAR), VHAR, Bayesian VAR (BVAR), and Bayesian VHAR (BVHAR) models.
Author: Young Geun Kim [aut, cre, cph]
,
Changryong Baek [ctb]
Maintainer: Young Geun Kim <ygeunkimstat@gmail.com>
Diff between bvhar versions 2.0.1 dated 2024-03-01 and 2.1.0 dated 2024-09-16
bvhar-2.0.1/bvhar/R/bvar-hierarchical.R |only bvhar-2.0.1/bvhar/R/doc-models.R |only bvhar-2.0.1/bvhar/data/oxfordman_rk.rda |only bvhar-2.0.1/bvhar/data/oxfordman_rv.rda |only bvhar-2.0.1/bvhar/inst/doc/empirical-bayes.R |only bvhar-2.0.1/bvhar/inst/doc/empirical-bayes.Rmd |only bvhar-2.0.1/bvhar/inst/doc/empirical-bayes.html |only bvhar-2.0.1/bvhar/man/AIC.varlse.Rd |only bvhar-2.0.1/bvhar/man/BIC.varlse.Rd |only bvhar-2.0.1/bvhar/man/FPE.varlse.Rd |only bvhar-2.0.1/bvhar/man/HQ.varlse.Rd |only bvhar-2.0.1/bvhar/man/analyze_ir.Rd |only bvhar-2.0.1/bvhar/man/bvar_adding_dummy.Rd |only bvhar-2.0.1/bvhar/man/bvar_niwhm.Rd |only bvhar-2.0.1/bvhar/man/bvar_predictive_density.Rd |only bvhar-2.0.1/bvhar/man/coef.varlse.Rd |only bvhar-2.0.1/bvhar/man/figures/README-predfig-1.png |only bvhar-2.0.1/bvhar/man/fitted.varlse.Rd |only bvhar-2.0.1/bvhar/man/horseshoe_bvar_algo.Rd |only bvhar-2.0.1/bvhar/man/is.stable.varlse.Rd |only bvhar-2.0.1/bvhar/man/is.varlse.Rd |only bvhar-2.0.1/bvhar/man/logLik.varlse.Rd |only bvhar-2.0.1/bvhar/man/lpl.Rd |only bvhar-2.0.1/bvhar/man/oxfordman.Rd |only bvhar-2.0.1/bvhar/man/predict.varlse.Rd |only bvhar-2.0.1/bvhar/man/residuals.varlse.Rd |only bvhar-2.0.1/bvhar/man/set_sv.Rd |only bvhar-2.0.1/bvhar/man/split_coef.Rd |only bvhar-2.0.1/bvhar/man/ssvs_bvar_algo.Rd |only bvhar-2.0.1/bvhar/man/ssvs_bvhar_algo.Rd |only bvhar-2.0.1/bvhar/man/stableroot.varlse.Rd |only bvhar-2.0.1/bvhar/man/summary.ssvsmod.Rd |only bvhar-2.0.1/bvhar/man/ts_forecasting_cv.Rd |only bvhar-2.0.1/bvhar/man/var_design_formulation.Rd |only bvhar-2.0.1/bvhar/man/var_vec_formulation.Rd |only bvhar-2.0.1/bvhar/src/forecast-var.cpp |only bvhar-2.0.1/bvhar/src/forecast-vhar.cpp |only bvhar-2.0.1/bvhar/tests/testthat/test-bvar-sv.R |only bvhar-2.0.1/bvhar/tests/testthat/test-bvhar-sv.R |only bvhar-2.0.1/bvhar/vignettes/empirical-bayes.Rmd |only bvhar-2.1.0/bvhar/DESCRIPTION | 15 bvhar-2.1.0/bvhar/MD5 | 420 ++-- bvhar-2.1.0/bvhar/NAMESPACE | 64 bvhar-2.1.0/bvhar/NEWS.md | 74 bvhar-2.1.0/bvhar/R/RcppExports.R | 1176 ++++++++---- bvhar-2.1.0/bvhar/R/bvar-flat.R | 177 + bvhar-2.1.0/bvhar/R/bvar-horseshoe.R | 92 bvhar-2.1.0/bvhar/R/bvar-minnesota.R | 375 +++ bvhar-2.1.0/bvhar/R/bvar-ssvs.R | 106 - bvhar-2.1.0/bvhar/R/bvar-sv.R | 150 + bvhar-2.1.0/bvhar/R/bvhar-horseshoe.R | 88 bvhar-2.1.0/bvhar/R/bvhar-minnesota.R | 445 ++++ bvhar-2.1.0/bvhar/R/bvhar-package.R | 10 bvhar-2.1.0/bvhar/R/bvhar-ssvs.R | 106 - bvhar-2.1.0/bvhar/R/bvhar-sv.R | 156 + bvhar-2.1.0/bvhar/R/criteria.R | 203 -- bvhar-2.1.0/bvhar/R/data.R | 97 - bvhar-2.1.0/bvhar/R/forecast.R | 608 +++++- bvhar-2.1.0/bvhar/R/generate-process.R | 85 bvhar-2.1.0/bvhar/R/globals.R | 1 bvhar-2.1.0/bvhar/R/hyperparam.R | 440 +++- bvhar-2.1.0/bvhar/R/irf.R | 32 bvhar-2.1.0/bvhar/R/member.R | 112 - bvhar-2.1.0/bvhar/R/misc-r.R | 56 bvhar-2.1.0/bvhar/R/plot-spillover.R |only bvhar-2.1.0/bvhar/R/plot.R | 32 bvhar-2.1.0/bvhar/R/print-bvarflat.R | 2 bvhar-2.1.0/bvhar/R/print-bvarmn.R | 61 bvhar-2.1.0/bvhar/R/print-bvharmn.R | 61 bvhar-2.1.0/bvhar/R/print-bvharsp.R | 125 + bvhar-2.1.0/bvhar/R/print-bvharspec.R | 129 + bvhar-2.1.0/bvhar/R/print-forecast.R | 4 bvhar-2.1.0/bvhar/R/print-irf.R | 4 bvhar-2.1.0/bvhar/R/print-spillover.R |only bvhar-2.1.0/bvhar/R/print-summarymniw.R | 6 bvhar-2.1.0/bvhar/R/print-varlse.R | 2 bvhar-2.1.0/bvhar/R/simulate-param.R | 56 bvhar-2.1.0/bvhar/R/spillover.R |only bvhar-2.1.0/bvhar/R/stable-process.R | 73 bvhar-2.1.0/bvhar/R/summary-bayes.R | 257 +- bvhar-2.1.0/bvhar/R/summary-forecast.R | 1237 ++++++++++++- bvhar-2.1.0/bvhar/R/summary-sparse.R | 109 - bvhar-2.1.0/bvhar/R/summary-varlse.R | 2 bvhar-2.1.0/bvhar/R/summary-vharlse.R | 6 bvhar-2.1.0/bvhar/R/tuning.R | 25 bvhar-2.1.0/bvhar/R/var-bayes.R |only bvhar-2.1.0/bvhar/R/varlse.R | 39 bvhar-2.1.0/bvhar/R/vhar-bayes.R |only bvhar-2.1.0/bvhar/R/vharlse.R | 35 bvhar-2.1.0/bvhar/README.md | 79 bvhar-2.1.0/bvhar/build/partial.rdb |binary bvhar-2.1.0/bvhar/build/vignette.rds |binary bvhar-2.1.0/bvhar/inst/CITATION | 10 bvhar-2.1.0/bvhar/inst/doc/bvhar.R | 15 bvhar-2.1.0/bvhar/inst/doc/bvhar.Rmd | 32 bvhar-2.1.0/bvhar/inst/doc/bvhar.html | 354 +-- bvhar-2.1.0/bvhar/inst/doc/forecasting.R | 2 bvhar-2.1.0/bvhar/inst/doc/forecasting.Rmd | 2 bvhar-2.1.0/bvhar/inst/doc/forecasting.html | 140 - bvhar-2.1.0/bvhar/inst/doc/linking.Rmd | 12 bvhar-2.1.0/bvhar/inst/doc/linking.html | 21 bvhar-2.1.0/bvhar/inst/doc/minnesota.R | 6 bvhar-2.1.0/bvhar/inst/doc/minnesota.Rmd | 11 bvhar-2.1.0/bvhar/inst/doc/minnesota.html | 189 +- bvhar-2.1.0/bvhar/inst/doc/shrinkage.R | 22 bvhar-2.1.0/bvhar/inst/doc/shrinkage.Rmd | 65 bvhar-2.1.0/bvhar/inst/doc/shrinkage.html | 273 +- bvhar-2.1.0/bvhar/inst/doc/stochastic-volatility.R |only bvhar-2.1.0/bvhar/inst/doc/stochastic-volatility.Rmd |only bvhar-2.1.0/bvhar/inst/doc/stochastic-volatility.html |only bvhar-2.1.0/bvhar/inst/include/bvharcommon.h | 78 bvhar-2.1.0/bvhar/inst/include/bvhardesign.h | 8 bvhar-2.1.0/bvhar/inst/include/bvhardraw.h | 782 +++++++- bvhar-2.1.0/bvhar/inst/include/bvharinterrupt.h | 2 bvhar-2.1.0/bvhar/inst/include/bvharprogress.h | 16 bvhar-2.1.0/bvhar/inst/include/bvharsim.h | 504 ++++- bvhar-2.1.0/bvhar/inst/include/bvharstructural.h |only bvhar-2.1.0/bvhar/inst/include/commondefs.h |only bvhar-2.1.0/bvhar/inst/include/mcmchs.h | 72 bvhar-2.1.0/bvhar/inst/include/mcmcreg.h |only bvhar-2.1.0/bvhar/inst/include/mcmcssvs.h | 6 bvhar-2.1.0/bvhar/inst/include/mcmcsv.h | 1310 ++++++++++--- bvhar-2.1.0/bvhar/inst/include/minnesota.h | 423 ++++ bvhar-2.1.0/bvhar/inst/include/minnforecaster.h |only bvhar-2.1.0/bvhar/inst/include/minnspillover.h |only bvhar-2.1.0/bvhar/inst/include/ols.h | 104 - bvhar-2.1.0/bvhar/inst/include/olsforecaster.h |only bvhar-2.1.0/bvhar/inst/include/olsspillover.h |only bvhar-2.1.0/bvhar/inst/include/regforecaster.h |only bvhar-2.1.0/bvhar/inst/include/regspillover.h |only bvhar-2.1.0/bvhar/inst/include/svforecaster.h |only bvhar-2.1.0/bvhar/inst/include/svspillover.h |only bvhar-2.1.0/bvhar/man/FPE.Rd | 22 bvhar-2.1.0/bvhar/man/HQ.Rd | 41 bvhar-2.1.0/bvhar/man/VARtoVMA.Rd | 2 bvhar-2.1.0/bvhar/man/VHARtoVMA.Rd | 2 bvhar-2.1.0/bvhar/man/autoplot.bvhardynsp.Rd |only bvhar-2.1.0/bvhar/man/autoplot.bvharirf.Rd | 4 bvhar-2.1.0/bvhar/man/autoplot.bvharsp.Rd | 4 bvhar-2.1.0/bvhar/man/autoplot.normaliw.Rd | 2 bvhar-2.1.0/bvhar/man/autoplot.predbvhar.Rd | 4 bvhar-2.1.0/bvhar/man/autoplot.summary.bvharsp.Rd | 2 bvhar-2.1.0/bvhar/man/autoplot.summary.normaliw.Rd | 4 bvhar-2.1.0/bvhar/man/bound_bvhar.Rd | 5 bvhar-2.1.0/bvhar/man/bvar_flat.Rd | 46 bvhar-2.1.0/bvhar/man/bvar_horseshoe.Rd | 28 bvhar-2.1.0/bvhar/man/bvar_minnesota.Rd | 77 bvhar-2.1.0/bvhar/man/bvar_ssvs.Rd | 38 bvhar-2.1.0/bvhar/man/bvar_sv.Rd | 34 bvhar-2.1.0/bvhar/man/bvhar-package.Rd | 12 bvhar-2.1.0/bvhar/man/bvhar_horseshoe.Rd | 27 bvhar-2.1.0/bvhar/man/bvhar_minnesota.Rd | 79 bvhar-2.1.0/bvhar/man/bvhar_ssvs.Rd | 34 bvhar-2.1.0/bvhar/man/bvhar_sv.Rd | 34 bvhar-2.1.0/bvhar/man/choose_bayes.Rd | 2 bvhar-2.1.0/bvhar/man/choose_bvar.Rd | 9 bvhar-2.1.0/bvhar/man/choose_ssvs.Rd | 10 bvhar-2.1.0/bvhar/man/coef.Rd |only bvhar-2.1.0/bvhar/man/compute_logml.Rd | 4 bvhar-2.1.0/bvhar/man/conf_fdr.Rd | 2 bvhar-2.1.0/bvhar/man/conf_fnr.Rd | 2 bvhar-2.1.0/bvhar/man/conf_prec.Rd | 2 bvhar-2.1.0/bvhar/man/conf_recall.Rd | 2 bvhar-2.1.0/bvhar/man/confusion.Rd | 2 bvhar-2.1.0/bvhar/man/dynamic_spillover.Rd |only bvhar-2.1.0/bvhar/man/financial_history_appendix.Rd | 10 bvhar-2.1.0/bvhar/man/fitted.Rd |only bvhar-2.1.0/bvhar/man/forecast_expand.Rd | 48 bvhar-2.1.0/bvhar/man/forecast_roll.Rd | 54 bvhar-2.1.0/bvhar/man/fromse.Rd | 2 bvhar-2.1.0/bvhar/man/geom_eval.Rd | 2 bvhar-2.1.0/bvhar/man/gg_loss.Rd | 4 bvhar-2.1.0/bvhar/man/init_ssvs.Rd | 15 bvhar-2.1.0/bvhar/man/irf.Rd |only bvhar-2.1.0/bvhar/man/is.stable.Rd | 31 bvhar-2.1.0/bvhar/man/mae.Rd | 2 bvhar-2.1.0/bvhar/man/mape.Rd | 2 bvhar-2.1.0/bvhar/man/mase.Rd | 2 bvhar-2.1.0/bvhar/man/mrae.Rd | 2 bvhar-2.1.0/bvhar/man/mse.Rd | 2 bvhar-2.1.0/bvhar/man/predict.Rd |only bvhar-2.1.0/bvhar/man/relmae.Rd | 2 bvhar-2.1.0/bvhar/man/residuals.Rd |only bvhar-2.1.0/bvhar/man/rmafe.Rd | 2 bvhar-2.1.0/bvhar/man/rmape.Rd | 2 bvhar-2.1.0/bvhar/man/rmase.Rd | 2 bvhar-2.1.0/bvhar/man/rmsfe.Rd | 2 bvhar-2.1.0/bvhar/man/set_bvar.Rd | 9 bvhar-2.1.0/bvhar/man/set_dl.Rd |only bvhar-2.1.0/bvhar/man/set_horseshoe.Rd | 19 bvhar-2.1.0/bvhar/man/set_intercept.Rd | 5 bvhar-2.1.0/bvhar/man/set_lambda.Rd | 9 bvhar-2.1.0/bvhar/man/set_ldlt.Rd |only bvhar-2.1.0/bvhar/man/set_ng.Rd |only bvhar-2.1.0/bvhar/man/set_ssvs.Rd | 59 bvhar-2.1.0/bvhar/man/sim_gig.Rd |only bvhar-2.1.0/bvhar/man/sim_horseshoe_var.Rd | 4 bvhar-2.1.0/bvhar/man/sim_matgaussian.Rd | 4 bvhar-2.1.0/bvhar/man/sim_mncoef.Rd | 3 bvhar-2.1.0/bvhar/man/sim_mniw.Rd | 10 bvhar-2.1.0/bvhar/man/sim_mnormal.Rd | 4 bvhar-2.1.0/bvhar/man/sim_mnvhar_coef.Rd | 3 bvhar-2.1.0/bvhar/man/sim_mvt.Rd | 4 bvhar-2.1.0/bvhar/man/sim_ssvs_var.Rd | 10 bvhar-2.1.0/bvhar/man/sim_var.Rd | 8 bvhar-2.1.0/bvhar/man/sim_vhar.Rd | 8 bvhar-2.1.0/bvhar/man/spillover.Rd |only bvhar-2.1.0/bvhar/man/stableroot.Rd | 29 bvhar-2.1.0/bvhar/man/summary.bvharsp.Rd |only bvhar-2.1.0/bvhar/man/summary.normaliw.Rd | 19 bvhar-2.1.0/bvhar/man/summary.varlse.Rd | 2 bvhar-2.1.0/bvhar/man/summary.vharlse.Rd | 6 bvhar-2.1.0/bvhar/man/var_bayes.Rd |only bvhar-2.1.0/bvhar/man/var_lm.Rd | 106 - bvhar-2.1.0/bvhar/man/vhar_bayes.Rd |only bvhar-2.1.0/bvhar/man/vhar_lm.Rd | 47 bvhar-2.1.0/bvhar/src/Makevars | 4 bvhar-2.1.0/bvhar/src/Makevars.ucrt |only bvhar-2.1.0/bvhar/src/Makevars.win | 4 bvhar-2.1.0/bvhar/src/RcppExports.cpp | 1410 +++++++++++---- bvhar-2.1.0/bvhar/src/bvharsim.cpp | 139 - bvhar-2.1.0/bvhar/src/bvharstructural.cpp |only bvhar-2.1.0/bvhar/src/estimate-bvar.cpp | 352 +++ bvhar-2.1.0/bvhar/src/estimate-hierarchical.cpp | 68 bvhar-2.1.0/bvhar/src/estimate-horseshoe.cpp | 5 bvhar-2.1.0/bvhar/src/estimate-ssvs.cpp | 2 bvhar-2.1.0/bvhar/src/estimate-sur.cpp |only bvhar-2.1.0/bvhar/src/estimate-sv.cpp | 75 bvhar-2.1.0/bvhar/src/estimate-var.cpp | 125 - bvhar-2.1.0/bvhar/src/estimate-vhar.cpp | 130 - bvhar-2.1.0/bvhar/src/forecast-bvar.cpp | 507 ----- bvhar-2.1.0/bvhar/src/forecast-bvhar.cpp | 412 ---- bvhar-2.1.0/bvhar/src/forecast-ldlt.cpp |only bvhar-2.1.0/bvhar/src/forecast-minn.cpp |only bvhar-2.1.0/bvhar/src/forecast-ols.cpp |only bvhar-2.1.0/bvhar/src/forecast-sv.cpp |only bvhar-2.1.0/bvhar/src/simulate-data.cpp | 4 bvhar-2.1.0/bvhar/src/spillover-ldlt.cpp |only bvhar-2.1.0/bvhar/src/spillover-minn.cpp |only bvhar-2.1.0/bvhar/src/spillover-ols.cpp |only bvhar-2.1.0/bvhar/src/spillover-sv.cpp |only bvhar-2.1.0/bvhar/src/tuning-models.cpp | 78 bvhar-2.1.0/bvhar/tests/testthat/test-bvar-flat.R | 2 bvhar-2.1.0/bvhar/tests/testthat/test-bvar-minnesota.R | 6 bvhar-2.1.0/bvhar/tests/testthat/test-bvhar-minnesota.R | 12 bvhar-2.1.0/bvhar/tests/testthat/test-criteria.R | 2 bvhar-2.1.0/bvhar/tests/testthat/test-generate-process.R |only bvhar-2.1.0/bvhar/tests/testthat/test-spillover.R |only bvhar-2.1.0/bvhar/tests/testthat/test-var-bayes.R |only bvhar-2.1.0/bvhar/tests/testthat/test-vhar-bayes.R |only bvhar-2.1.0/bvhar/vignettes/bvhar.Rmd | 32 bvhar-2.1.0/bvhar/vignettes/forecasting.Rmd | 2 bvhar-2.1.0/bvhar/vignettes/linking.Rmd | 12 bvhar-2.1.0/bvhar/vignettes/minnesota.Rmd | 11 bvhar-2.1.0/bvhar/vignettes/shrinkage.Rmd | 65 bvhar-2.1.0/bvhar/vignettes/stochastic-volatility.Rmd |only 256 files changed, 11157 insertions(+), 5283 deletions(-)
Title: Multiblock Data Fusion in Statistics and Machine Learning
Description: Functions and datasets to support Smilde, Næs and Liland (2021, ISBN: 978-1-119-60096-1)
"Multiblock Data Fusion in Statistics and Machine Learning - Applications in the Natural and Life Sciences".
This implements and imports a large collection of methods for multiblock data analysis with common interfaces, result- and plotting
functions, several real data sets and six vignettes covering a range different applications.
Author: Kristian Hovde Liland [aut, cre]
,
Solve Saeboe [ctb],
Stefan Schrunner [rev]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between multiblock versions 0.8.8.1 dated 2024-03-11 and 0.8.8.2 dated 2024-09-16
DESCRIPTION | 10 +- MD5 | 37 +++++---- NAMESPACE | 4 + NEWS | 5 + R/asca.R | 4 - R/asca_plots.R | 5 + R/mbpls_results.R |only R/multiblock_plots.R | 5 + R/popls.R | 2 R/supervised.R | 4 - R/utilities.R | 1 build/vignette.rds |binary inst/doc/vignette_A_data.html | 130 ++++++++++++++++------------------ inst/doc/vignette_B_basic.html | 2 inst/doc/vignette_C_unsupervised.html | 2 inst/doc/vignette_D_asca.html | 2 inst/doc/vignette_E_supervised.html | 64 ++++++++-------- inst/doc/vignette_F_complex.html | 2 man/mvrVal.Rd |only man/popls.Rd | 2 man/predict.mbpls.Rd |only 21 files changed, 149 insertions(+), 132 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-06-07 0.8.2
Title: Tidy Verbs for Fast Data Manipulation
Description: A toolkit of tidy data manipulation verbs with 'data.table' as the backend.
Combining the merits of syntax elegance from 'dplyr' and computing performance from 'data.table',
'tidyfst' intends to provide users with state-of-the-art data manipulation tools with least pain.
This package is an extension of 'data.table'. While enjoying a tidy syntax,
it also wraps combinations of efficient functions to facilitate frequently-used data operations.
Author: Tian-Yuan Huang [aut, cre]
Maintainer: Tian-Yuan Huang <huang.tian-yuan@qq.com>
Diff between tidyfst versions 1.8.0 dated 2024-08-30 and 1.8.1 dated 2024-09-16
DESCRIPTION | 6 +- MD5 | 16 +++-- NAMESPACE | 1 R/bind_rows_dt.R |only R/col_max.R | 58 ++++++++++++++------- inst/doc/benchmark.html | 32 +++++------ inst/doc/chinese_tutorial.html | 16 ++--- inst/doc/english_tutorial.html | 110 +++++++++++++++++++++-------------------- man/bind_rows_dt.Rd |only man/col_max.Rd | 10 ++- 10 files changed, 144 insertions(+), 105 deletions(-)
Title: Analysis of Spatial Stratified Heterogeneity
Description: Analyzing spatial factors and exploring spatial associations based on the concept of spatial
stratified heterogeneity, and also takes into account local spatial dependencies, spatial
interpretability, potential spatial interactions, and robust spatial stratification. Additionally,
it supports geographical detector models established in academic literature.
Author: Wenbo Lv [aut, cre, cph] ,
Yangyang Lei [aut] ,
Yongze Song [aut] ,
Wufan Zhao [aut] ,
Jianwu Yan [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between gdverse versions 1.0.0 dated 2024-09-09 and 1.0-1 dated 2024-09-15
gdverse-1.0-1/gdverse/DESCRIPTION | 15 gdverse-1.0-1/gdverse/MD5 | 147 +- gdverse-1.0-1/gdverse/NEWS.md | 89 - gdverse-1.0-1/gdverse/R/discretization.R | 7 gdverse-1.0-1/gdverse/R/gd.R | 3 gdverse-1.0-1/gdverse/R/geodetector.R | 1176 +++++++++--------- gdverse-1.0-1/gdverse/R/gozh.R | 3 gdverse-1.0-1/gdverse/R/idsa.R | 49 gdverse-1.0-1/gdverse/R/lesh.R | 3 gdverse-1.0-1/gdverse/R/loess.R | 194 +- gdverse-1.0-1/gdverse/R/opgd.R | 10 gdverse-1.0-1/gdverse/R/pid_idsa.R | 12 gdverse-1.0-1/gdverse/R/psd_pseudop.R | 55 gdverse-1.0-1/gdverse/R/psd_spade.R | 70 - gdverse-1.0-1/gdverse/R/rgd.R | 3 gdverse-1.0-1/gdverse/R/rid.R | 5 gdverse-1.0-1/gdverse/R/robustdisc.R | 108 - gdverse-1.0-1/gdverse/R/rpartdisc.R | 62 gdverse-1.0-1/gdverse/R/sesu_gozh.R | 350 ++--- gdverse-1.0-1/gdverse/R/sesu_opgd.R | 368 ++--- gdverse-1.0-1/gdverse/R/spade.R | 85 - gdverse-1.0-1/gdverse/R/spd_lesh.R | 366 ++--- gdverse-1.0-1/gdverse/R/srsgd.R | 507 +++---- gdverse-1.0-1/gdverse/R/utils_helper.R | 358 ++--- gdverse-1.0-1/gdverse/R/zzz.R | 8 gdverse-1.0-1/gdverse/README.md | 3 gdverse-1.0-1/gdverse/build/vignette.rds |binary gdverse-1.0-1/gdverse/inst/doc/gd.Rmd |only gdverse-1.0-1/gdverse/inst/doc/gd.html |only gdverse-1.0-1/gdverse/inst/doc/idsa.Rmd |only gdverse-1.0-1/gdverse/inst/doc/idsa.html |only gdverse-1.0-1/gdverse/inst/doc/opgd.Rmd |only gdverse-1.0-1/gdverse/inst/doc/opgd.html |only gdverse-1.0-1/gdverse/inst/doc/rgdrid.Rmd |only gdverse-1.0-1/gdverse/inst/doc/rgdrid.html |only gdverse-1.0-1/gdverse/inst/doc/sesu.Rmd |only gdverse-1.0-1/gdverse/inst/doc/sesu.html |only gdverse-1.0-1/gdverse/inst/doc/shegd.Rmd |only gdverse-1.0-1/gdverse/inst/doc/shegd.html |only gdverse-1.0-1/gdverse/inst/doc/spade.Rmd |only gdverse-1.0-1/gdverse/inst/doc/spade.html |only gdverse-1.0-1/gdverse/man/cpsd_disc.Rd | 10 gdverse-1.0-1/gdverse/man/figures/gd/gd_all-1.png |binary gdverse-1.0-1/gdverse/man/figures/gd/rd-1.png |binary gdverse-1.0-1/gdverse/man/figures/spade/XianSUHII.png |only gdverse-1.0-1/gdverse/man/gd.Rd | 2 gdverse-1.0-1/gdverse/man/gd_bestunidisc.Rd | 5 gdverse-1.0-1/gdverse/man/geodetector.Rd | 134 +- gdverse-1.0-1/gdverse/man/gozh.Rd | 2 gdverse-1.0-1/gdverse/man/idsa.Rd | 20 gdverse-1.0-1/gdverse/man/lesh.Rd | 2 gdverse-1.0-1/gdverse/man/opgd.Rd | 11 gdverse-1.0-1/gdverse/man/plot.gd_result.Rd | 44 gdverse-1.0-1/gdverse/man/print.gd_result.Rd | 44 gdverse-1.0-1/gdverse/man/psmd_pseudop.Rd | 33 gdverse-1.0-1/gdverse/man/psmd_spade.Rd | 28 gdverse-1.0-1/gdverse/man/rgd.Rd | 2 gdverse-1.0-1/gdverse/man/rid.Rd | 2 gdverse-1.0-1/gdverse/man/spade.Rd | 35 gdverse-1.0-1/gdverse/vignettes/gd.Rmd |only gdverse-1.0-1/gdverse/vignettes/gd.Rmd.orig |only gdverse-1.0-1/gdverse/vignettes/idsa.Rmd |only gdverse-1.0-1/gdverse/vignettes/idsa.Rmd.orig |only gdverse-1.0-1/gdverse/vignettes/opgd.Rmd |only gdverse-1.0-1/gdverse/vignettes/opgd.Rmd.orig |only gdverse-1.0-1/gdverse/vignettes/precompile.R | 28 gdverse-1.0-1/gdverse/vignettes/rgdrid.Rmd |only gdverse-1.0-1/gdverse/vignettes/rgdrid.Rmd.orig |only gdverse-1.0-1/gdverse/vignettes/sesu.Rmd |only gdverse-1.0-1/gdverse/vignettes/sesu.Rmd.orig |only gdverse-1.0-1/gdverse/vignettes/shegd.Rmd |only gdverse-1.0-1/gdverse/vignettes/shegd.Rmd.orig |only gdverse-1.0-1/gdverse/vignettes/spade.Rmd |only gdverse-1.0-1/gdverse/vignettes/spade.Rmd.orig |only gdverse-1.0.0/gdverse/inst/doc/GD.Rmd |only gdverse-1.0.0/gdverse/inst/doc/GD.html |only gdverse-1.0.0/gdverse/inst/doc/IDSA.Rmd |only gdverse-1.0.0/gdverse/inst/doc/IDSA.html |only gdverse-1.0.0/gdverse/inst/doc/OPGD.Rmd |only gdverse-1.0.0/gdverse/inst/doc/OPGD.html |only gdverse-1.0.0/gdverse/inst/doc/RGDRID.Rmd |only gdverse-1.0.0/gdverse/inst/doc/RGDRID.html |only gdverse-1.0.0/gdverse/inst/doc/SESU.Rmd |only gdverse-1.0.0/gdverse/inst/doc/SESU.html |only gdverse-1.0.0/gdverse/inst/doc/SHEGD.Rmd |only gdverse-1.0.0/gdverse/inst/doc/SHEGD.html |only gdverse-1.0.0/gdverse/inst/doc/SPADE.Rmd |only gdverse-1.0.0/gdverse/inst/doc/SPADE.html |only gdverse-1.0.0/gdverse/inst/python/__pycache__ |only gdverse-1.0.0/gdverse/man/figures/spade/studyarea.png |only gdverse-1.0.0/gdverse/vignettes/GD.Rmd |only gdverse-1.0.0/gdverse/vignettes/GD.Rmd.orig |only gdverse-1.0.0/gdverse/vignettes/IDSA.Rmd |only gdverse-1.0.0/gdverse/vignettes/IDSA.Rmd.orig |only gdverse-1.0.0/gdverse/vignettes/OPGD.Rmd |only gdverse-1.0.0/gdverse/vignettes/OPGD.Rmd.orig |only gdverse-1.0.0/gdverse/vignettes/RGDRID.Rmd |only gdverse-1.0.0/gdverse/vignettes/RGDRID.Rmd.orig |only gdverse-1.0.0/gdverse/vignettes/SESU.Rmd |only gdverse-1.0.0/gdverse/vignettes/SESU.Rmd.orig |only gdverse-1.0.0/gdverse/vignettes/SHEGD.Rmd |only gdverse-1.0.0/gdverse/vignettes/SHEGD.Rmd.orig |only gdverse-1.0.0/gdverse/vignettes/SPADE.Rmd |only gdverse-1.0.0/gdverse/vignettes/SPADE.Rmd.orig |only 104 files changed, 2173 insertions(+), 2285 deletions(-)
Title: Hierarchical Partitioning of Marginal R2 for Generalized
Mixed-Effect Models
Description: Conducts hierarchical partitioning to calculate individual contributions of each predictor (fixed effects) towards marginal R2 for generalized linear mixed-effect model (including lm, glm and glmm) based on output of r.squaredGLMM() in 'MuMIn', applying the algorithm of Lai J.,Zou Y., Zhang S.,Zhang X.,Mao L.(2022)glmm.hp: an R package for computing individual effect of predictors in generalized linear mixed models.Journal of Plant Ecology,15(6)1302-1307<doi:10.1093/jpe/rtac096>.
Author: Jiangshan Lai [aut, cre] ,
Kim Nimon [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between glmm.hp versions 0.1-4 dated 2024-08-24 and 0.1-5 dated 2024-09-15
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/glmm.hp.r | 17 ++++++++++++++++- 3 files changed, 23 insertions(+), 8 deletions(-)
Title: Time-Ordered and Time-Aggregated Network Analyses
Description: Approaches for incorporating time into network analysis. Methods include: construction of time-ordered networks (temporal graphs); shortest-time and shortest-path-length analyses; resource spread calculations; data resampling and rarefaction for null model construction; reduction to time-aggregated networks with variable window sizes; application of common descriptive statistics to these networks; vector clock latencies; and plotting functionalities. The package supports <doi:10.1371/journal.pone.0020298>.
Author: Benjamin Wong Blonder [aut, cre]
Maintainer: Benjamin Wong Blonder <benjamin.blonder@berkeley.edu>
Diff between timeordered versions 1.0.0 dated 2023-08-20 and 1.0.1 dated 2024-09-15
DESCRIPTION | 18 ++++++++++-------- MD5 | 34 +++++++++++++++++----------------- R/generatelatencies.R | 2 +- R/generatetonetwork.R | 2 +- man/applynetworkfunction.Rd | 2 +- man/generatelatencies.Rd | 2 +- man/generatenetworkslices.Rd | 2 +- man/generatetimeaggregatednetwork.Rd | 2 +- man/generatetonetwork.Rd | 2 +- man/plotnetworkslices.Rd | 2 +- man/plottanet.Rd | 2 +- man/plottonet.Rd | 2 +- man/randomizeidentities.Rd | 2 +- man/randomizetimes.Rd | 2 +- man/shortesthoppath.Rd | 2 +- man/shortesttimepath.Rd | 2 +- man/spreadanalysis.Rd | 2 +- man/transformspreadbyindividual.Rd | 2 +- 18 files changed, 43 insertions(+), 41 deletions(-)
Title: 'Rcpp' Bindings to 'FastAD' Auto-Differentiation
Description: The header-only 'C++' template library 'FastAD' for automatic
differentiation <https://github.com/JamesYang007/FastAD> is provided by
this package, along with a few illustrative examples that can all be called
from R.
Author: Dirk Eddelbuettel [aut, cre] ,
James Yang [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppFastAD versions 0.0.2 dated 2023-03-06 and 0.0.3 dated 2024-09-15
ChangeLog | 16 ++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- README.md | 10 ++++++++-- build/partial.rdb |binary inst/NEWS.Rd | 11 ++++++++++- src/Makevars | 2 +- src/Makevars.win | 2 +- 8 files changed, 47 insertions(+), 16 deletions(-)
Title: Generalized Latent Markov Models
Description: Latent Markov models for longitudinal continuous and categorical data. See Bartolucci, Pandolfi, Pennoni (2017)<doi:10.18637/jss.v081.i04>.
Author: Francesco Bartolucci [aut, cre],
Silvia Pandolfi [aut],
Fulvia Pennoni [aut],
Alessio Farcomeni [ctb],
Alessio Serafini [ctb]
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between LMest versions 3.2.1 dated 2024-09-09 and 3.2.2 dated 2024-09-15
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/lmbasic.R | 3 +-- R/lmcovmanifest.cont.R | 4 +++- R/lmestCont.R | 4 +++- R/lmestSearch.R | 8 ++++---- data/data_heart_sim.rda |binary inst/doc/vignetteLMest.html | 8 ++++---- man/data_heart_sim.Rd | 4 ++-- 9 files changed, 29 insertions(+), 26 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ctb],
Paola Sebastiani [ctb],
Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.75 dated 2024-06-17 and 2.0.76 dated 2024-09-15
DESCRIPTION | 14 +- MD5 | 44 +++--- NEWS | 7 + R/epi.2by2.R | 20 ++ R/epi.ccc.R | 7 - build/vignette.rds |binary inst/doc/epiR_descriptive.R | 28 ++-- inst/doc/epiR_descriptive.Rmd | 43 +++--- inst/doc/epiR_descriptive.html | 113 ++++++++-------- inst/doc/epiR_measures_of_association.R | 29 ++-- inst/doc/epiR_measures_of_association.Rmd | 75 +++++----- inst/doc/epiR_measures_of_association.html | 201 +++++++++++++++-------------- inst/doc/epiR_sample_size.Rmd | 8 - inst/doc/epiR_sample_size.html | 40 ++--- inst/doc/epiR_surveillance.R | 20 ++ inst/doc/epiR_surveillance.Rmd | 38 +++-- inst/doc/epiR_surveillance.html | 116 ++++++++-------- vignettes/epiR_descriptive.Rmd | 43 +++--- vignettes/epiR_descriptive.bib | 10 + vignettes/epiR_measures_of_association.Rmd | 75 +++++----- vignettes/epiR_sample_size.Rmd | 8 - vignettes/epiR_surveillance.Rmd | 38 +++-- vignettes/epiR_surveillance.bib | 2 23 files changed, 536 insertions(+), 443 deletions(-)
Title: Robust Covariance Matrix Estimators
Description: Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic
robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC)
covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC)
covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators);
clustered covariances (one-way and multi-way); panel and panel-corrected covariances;
outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are
applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted
to other classes through S3 methods. Details can be found in Zeileis et al. (2020) <doi:10.18637/jss.v095.i01>,
Zeileis (2004) <doi:10.18637/jss.v011.i10> and Zeileis (2006) <doi:10.18637/jss.v016.i09>.
Author: Achim Zeileis [aut, cre] ,
Thomas Lumley [aut] ,
Nathaniel Graham [ctb] ,
Susanne Koell [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between sandwich versions 3.1-0 dated 2023-12-11 and 3.1-1 dated 2024-09-15
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 14 ++++++++++++++ R/bread.R | 2 +- R/vcovCL.R | 4 ++-- R/vcovHC.R | 22 ++++++++++++++-------- R/vcovPL.R | 13 ++++++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/sandwich-CL.pdf |binary inst/doc/sandwich-OOP.pdf |binary inst/doc/sandwich.pdf |binary man/vcovCL.Rd | 4 ++-- tests/Examples/sandwich-Ex.Rout.save | 8 ++++---- vignettes/sandwich-CL.Rout.save | 10 +++++----- 15 files changed, 70 insertions(+), 43 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 0.3.4 dated 2024-09-06 and 0.3.5 dated 2024-09-15
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/locuszoomr.R | 15 ++++++++------- inst/doc/locuszoomr.Rmd | 9 +++++---- inst/doc/locuszoomr.html | 13 ++++--------- vignettes/locuszoomr.Rmd | 9 +++++---- vignettes/recomb.png |only 9 files changed, 37 insertions(+), 34 deletions(-)
More information about spectralAnomaly at CRAN
Permanent link
More information about PytrendsLongitudinalR at CRAN
Permanent link
Title: Partial Least Squares and Principal Component Regression
Description: Multivariate regression methods
Partial Least Squares Regression (PLSR), Principal Component
Regression (PCR) and Canonical Powered Partial Least Squares (CPPLS).
Author: Kristian Hovde Liland [aut, cre],
Bjoern-Helge Mevik [aut],
Ron Wehrens [aut],
Paul Hiemstra [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between pls versions 2.8-4 dated 2024-08-01 and 2.8-5 dated 2024-09-15
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/plots.R | 2 +- inst/NEWS.Rd | 8 ++++++++ inst/doc/pls-manual.pdf |binary 5 files changed, 18 insertions(+), 10 deletions(-)
More information about CohortGenerator at CRAN
Permanent link
Title: Minimization Methods for Ill-Conditioned Problems
Description: Implementation of methods for minimizing ill-conditioned problems. Currently only includes regularized (quasi-)newton optimization (Kanzow and Steck et al. (2023), <doi:10.1007/s12532-023-00238-4>).
Author: Bert van der Veen [aut, cre]
Maintainer: Bert van der Veen <bert_van_der_veen@hotmail.com>
Diff between minic versions 1.0 dated 2024-06-24 and 1.0.1 dated 2024-09-15
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NEWS.md |only R/RcppExports.R | 4 ++-- R/print.rnewton.R | 2 +- R/rnewton.R | 12 +++++++----- man/rnewton.Rd | 7 ++++--- src/RcppExports.cpp | 9 +++++---- src/minic.cpp | 15 +++++++++++++-- 9 files changed, 44 insertions(+), 28 deletions(-)
More information about lavaan.printer at CRAN
Permanent link
Title: Using CF-Compliant Calendars with Climate Projection Data
Description: Support for all calendars as specified in the Climate and Forecast
(CF) Metadata Conventions for climate and forecasting data. The CF Metadata
Conventions is widely used for distributing files with climate observations
or projections, including the Coupled Model Intercomparison Project (CMIP)
data used by climate change scientists and the Intergovernmental Panel on
Climate Change (IPCC). This package specifically allows the user to work
with any of the CF-compliant calendars (many of which are not compliant with
POSIXt). The CF time coordinate is formally defined in the CF Metadata
Conventions document available at <https://cfconventions.org/Data/cf-conventions/cf-conventions-1.11/cf-conventions.html#time-coordinate>.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between CFtime versions 1.4.0 dated 2024-06-05 and 1.4.1 dated 2024-09-15
DESCRIPTION | 8 MD5 | 24 +- NEWS.md | 12 + R/CFformat.R | 12 - R/CFparse.R | 2 R/CFtime.R | 33 ++- TODO | 8 build/vignette.rds |binary inst/doc/CFtime.html | 332 +++++++++++++++++++-------------------- inst/doc/Processing.html | 220 ++++++++++++------------- man/indexOf-ANY-CFtime-method.Rd | 12 - man/slab.Rd | 5 tests/testthat/test-CFbounds.R | 2 13 files changed, 352 insertions(+), 318 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
Posit Software, PBC [cph, fnd],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.52 dated 2024-07-18 and 0.53 dated 2024-09-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/latex.R | 4 +++- tests/test-cran/test-latex.R | 1 + 4 files changed, 10 insertions(+), 7 deletions(-)
Title: Mixture of Multiple Highly Variable Feature Selection Methods
Description: Highly variable gene selection methods, including popular public available methods, and also the mixture of multiple highly variable gene selection methods, <https://github.com/RuzhangZhao/mixhvg>. Reference: <doi:10.1101/2024.08.25.608519>.
Author: Ruzhang Zhao [aut, cre] ,
Hongkai Ji [aut]
Maintainer: Ruzhang Zhao <ruzhangzhao@gmail.com>
Diff between mixhvg versions 0.2.1 dated 2024-09-01 and 1.0.1 dated 2024-09-15
mixhvg-0.2.1/mixhvg/README.md |only mixhvg-1.0.1/mixhvg/DESCRIPTION | 6 +-- mixhvg-1.0.1/mixhvg/MD5 | 12 ++++-- mixhvg-1.0.1/mixhvg/R/FindVariableFeaturesMix.R | 46 +++++++++++++++++++++--- mixhvg-1.0.1/mixhvg/man/figures |only 5 files changed, 54 insertions(+), 10 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington', 'Ludwig' and Omnivariant Generalised Least-Squares ('OGLS') approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Th-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isoch [...truncated...]
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 6.2 dated 2024-05-04 and 6.3 dated 2024-09-15
DESCRIPTION | 10 +-- MD5 | 36 ++++++------ R/bayes.R | 9 +-- R/ci.R | 5 + R/commonPb.R | 2 R/concordia.R | 14 ++-- R/discordia.R | 3 - R/diseq.R | 21 +++++++ R/errorellipse.R | 22 +++++-- R/flipper.R | 11 ++- R/isochron.R | 23 +++++++ R/kde.R | 164 +++++++++++++++++++++++++++---------------------------- R/ludwig.R | 14 ++-- R/radialplot.R | 9 --- R/toolbox.R | 6 -- man/Pb0corr.Rd | 2 man/concordia.Rd | 8 +- man/isochron.Rd | 7 +- man/kde.Rd | 2 19 files changed, 204 insertions(+), 164 deletions(-)
Title: Custom 'xaringan' CSS Themes
Description: Create beautifully color-coordinated and customized themes
for your 'xaringan' slides, without writing any CSS. Complete your
slide theme with 'ggplot2' themes that match the font and colors used
in your slides. Customized styles can be created directly in your
slides' 'R Markdown' source file or in a separate external script.
Author: Garrick Aden-Buie [aut, cre]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between xaringanthemer versions 0.4.2 dated 2022-08-20 and 0.4.3 dated 2024-09-15
xaringanthemer-0.4.2/xaringanthemer/inst/rmarkdown/templates/xaringanthemer/skeleton/xaringan-themer.css |only xaringanthemer-0.4.2/xaringanthemer/tests/manual |only xaringanthemer-0.4.3/xaringanthemer/DESCRIPTION | 8 xaringanthemer-0.4.3/xaringanthemer/MD5 | 79 +- xaringanthemer-0.4.3/xaringanthemer/NAMESPACE | 2 xaringanthemer-0.4.3/xaringanthemer/NEWS.md | 44 - xaringanthemer-0.4.3/xaringanthemer/R/ggplot2.R | 1 xaringanthemer-0.4.3/xaringanthemer/R/style_extra_css.R | 2 xaringanthemer-0.4.3/xaringanthemer/R/style_font_default.R | 3 xaringanthemer-0.4.3/xaringanthemer/R/utils.R | 3 xaringanthemer-0.4.3/xaringanthemer/R/xaringanthemer-package.R | 56 - xaringanthemer-0.4.3/xaringanthemer/README.md | 4 xaringanthemer-0.4.3/xaringanthemer/build/vignette.rds |binary xaringanthemer-0.4.3/xaringanthemer/inst/doc/ggplot2-themes.R | 14 xaringanthemer-0.4.3/xaringanthemer/inst/doc/ggplot2-themes.Rmd | 14 xaringanthemer-0.4.3/xaringanthemer/inst/doc/ggplot2-themes.html | 321 ++++----- xaringanthemer-0.4.3/xaringanthemer/inst/doc/template-variables.html | 26 xaringanthemer-0.4.3/xaringanthemer/inst/doc/xaringanthemer.R | 2 xaringanthemer-0.4.3/xaringanthemer/inst/doc/xaringanthemer.html | 326 +++++----- xaringanthemer-0.4.3/xaringanthemer/man/fragments/_thanks.Rmd | 6 xaringanthemer-0.4.3/xaringanthemer/man/style_duo.Rd | 8 xaringanthemer-0.4.3/xaringanthemer/man/style_duo_accent.Rd | 8 xaringanthemer-0.4.3/xaringanthemer/man/style_duo_accent_inverse.Rd | 8 xaringanthemer-0.4.3/xaringanthemer/man/style_mono_accent.Rd | 4 xaringanthemer-0.4.3/xaringanthemer/man/style_mono_accent_inverse.Rd | 4 xaringanthemer-0.4.3/xaringanthemer/man/style_mono_dark.Rd | 8 xaringanthemer-0.4.3/xaringanthemer/man/style_mono_light.Rd | 8 xaringanthemer-0.4.3/xaringanthemer/man/style_solarized_dark.Rd | 6 xaringanthemer-0.4.3/xaringanthemer/man/style_solarized_light.Rd | 6 xaringanthemer-0.4.3/xaringanthemer/man/style_xaringan.Rd | 6 xaringanthemer-0.4.3/xaringanthemer/man/theme_xaringan_base.Rd | 4 xaringanthemer-0.4.3/xaringanthemer/man/theme_xaringan_inverse.Rd | 4 xaringanthemer-0.4.3/xaringanthemer/man/theme_xaringan_set_defaults.Rd | 4 xaringanthemer-0.4.3/xaringanthemer/tests/testthat/_snaps/utils.md | 17 xaringanthemer-0.4.3/xaringanthemer/tests/testthat/test-ggplot2.R | 2 xaringanthemer-0.4.3/xaringanthemer/tests/testthat/test-helpers.R | 1 xaringanthemer-0.4.3/xaringanthemer/tests/testthat/test-style_xaringan.R | 1 xaringanthemer-0.4.3/xaringanthemer/tests/testthat/test-themes.R | 1 xaringanthemer-0.4.3/xaringanthemer/vignettes/ggplot2-themes.Rmd | 14 39 files changed, 504 insertions(+), 521 deletions(-)
More information about xaringanthemer at CRAN
Permanent link
Title: Explanation Groves
Description: Compute surrogate explanation groves for predictive machine learning models and analyze complexity vs. explanatory power of an explanation according to Szepannek, G. and von Holt, B. (2023) <doi:10.1007/s41237-023-00205-2>.
Author: Gero Szepannek [aut, cre]
Maintainer: Gero Szepannek <gero.szepannek@web.de>
Diff between xgrove versions 0.1-11 dated 2024-08-23 and 0.1-12 dated 2024-09-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 2 ++ R/xgrove.R | 5 +++++ 4 files changed, 14 insertions(+), 7 deletions(-)
Title: Tidy Data and 'Geoms' for Bayesian Models
Description: Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models
('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided
to help extract tidy data frames of draws from Bayesian models and that generate point
summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for
common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus
densities), and fit curves with multiple, arbitrary uncertainty bands.
Author: Matthew Kay [aut, cre],
Timothy Mastny [ctb]
Maintainer: Matthew Kay <mjskay@northwestern.edu>
Diff between tidybayes versions 3.0.6 dated 2023-08-12 and 3.0.7 dated 2024-09-15
DESCRIPTION | 18 MD5 | 270 NAMESPACE | 961 - NEWS.md | 517 R/add_draws.R | 198 R/compare_levels.R | 442 R/compose_data.R | 770 R/density_bins.R | 194 R/deprecated.R | 2164 +- R/emmeans_comparison.R | 162 R/epred_draws.R | 164 R/epred_rvars.R | 156 R/flip_aes.R | 101 R/gather_draws.R | 75 R/gather_emmeans_draws.R | 276 R/gather_pairs.R | 290 R/gather_rvars.R | 90 R/gather_variables.R | 204 R/get_variables.R | 106 R/ggdist-curve_interval.R | 6 R/ggdist-cut_cdf_qi.R | 6 R/ggdist-stat_pointinterval.R | 14 R/linpred_draws.R | 216 R/linpred_rvars.R | 156 R/nest_rvars.R | 175 R/predict_curve.R | 258 R/predicted_draws.R | 800 - R/predicted_rvars.R | 512 R/recover_types.R | 364 R/residual_draws.R | 128 R/sample_draws.R | 132 R/spread_draws.R | 1399 - R/spread_rvars.R | 564 R/summarise_draws.R | 152 R/testthat.R | 39 R/tidy_draws.R | 584 R/tidybayes-models.R | 158 R/tidybayes-package.R | 73 R/ungather_draws.R | 146 R/unspread_draws.R | 230 R/util.R | 358 R/x_at_y.R | 174 build/partial.rdb |binary build/vignette.rds |binary inst/doc/tidy-brms.R | 1228 - inst/doc/tidy-brms.Rmd | 1892 +- inst/doc/tidy-brms.html | 5674 +++---- inst/doc/tidy-posterior.R | 926 - inst/doc/tidy-posterior.Rmd | 1632 +- inst/doc/tidy-posterior.html | 2834 +-- inst/doc/tidy-rstanarm.R | 710 inst/doc/tidy-rstanarm.Rmd | 1278 - inst/doc/tidy-rstanarm.html | 5162 +++--- inst/doc/tidybayes-residuals.R | 892 - inst/doc/tidybayes-residuals.Rmd | 1440 - inst/doc/tidybayes-residuals.html | 2294 +- inst/doc/tidybayes.R | 764 inst/doc/tidybayes.Rmd | 1594 +- inst/doc/tidybayes.html | 7967 ++++------ man/add_draws.Rd | 146 man/add_predicted_draws.Rd | 870 - man/add_predicted_rvars.Rd | 752 man/compare_levels.Rd | 274 man/compose_data.Rd | 212 man/density_bins.Rd | 166 man/emmeans_comparison.Rd | 138 man/gather_emmeans_draws.Rd | 194 man/gather_pairs.Rd | 232 man/nest_rvars.Rd | 120 man/predict_curve.Rd | 202 man/recover_types.Rd | 262 man/reexports.Rd | 288 man/sample_draws.Rd | 122 man/spread_draws.Rd | 526 man/spread_rvars.Rd | 308 man/summarise_draws.grouped_df.Rd | 160 man/tidy_draws.Rd | 210 man/tidybayes-deprecated.Rd | 522 man/tidybayes-models.Rd | 152 man/tidybayes-package.Rd | 86 man/unspread_draws.Rd | 169 tests/testthat/_snaps/test.geom_dotsinterval/stat-dotsh-with-a-group-with-1-dot.svg | 198 tests/testthat/_snaps/test.geom_dotsinterval/vanilla-geom-dotsh.svg | 182 tests/testthat/_snaps/test.geom_interval/grouped-intervals-h-stat.svg | 146 tests/testthat/_snaps/test.geom_interval/grouped-intervals-h.svg | 144 tests/testthat/_snaps/test.geom_pointinterval/grouped-pointintervals-h-stat.svg | 134 tests/testthat/_snaps/test.geom_pointinterval/grouped-pointintervals-h.svg | 178 tests/testthat/_snaps/test.stat_dist_slabinterval/ccdfintervalh-using-args.svg | 118 tests/testthat/_snaps/test.stat_dist_slabinterval/horizontal-half-eye-using-args.svg | 118 tests/testthat/_snaps/test.stat_eye/one-parameter-horizontal-eye-mode-hdi.svg | 116 tests/testthat/_snaps/test.stat_eye/one-parameter-horizontal-eye.svg | 116 tests/testthat/_snaps/test.stat_eye/one-parameter-horizontal-half-eye.svg | 116 tests/testthat/_snaps/test.stat_eye/one-parameter-vertical-eye.svg | 116 tests/testthat/_snaps/test.stat_eye/one-parameter-vertical-halfeye.svg | 116 tests/testthat/_snaps/test.stat_eye/two-parameter-factor-horizontal-eye-fill.svg | 130 tests/testthat/_snaps/test.stat_eye/two-parameter-factor-horizontal-half-eye.svg | 114 tests/testthat/test.add_draws.R | 118 tests/testthat/test.as_constructor.R | 90 tests/testthat/test.combine_chains.R | 76 tests/testthat/test.compare_levels.R | 532 tests/testthat/test.compose_data.R | 264 tests/testthat/test.emmeans_comparison.R | 52 tests/testthat/test.epred_draws.R | 766 tests/testthat/test.epred_rvars.R | 454 tests/testthat/test.gather_draws.R | 114 tests/testthat/test.gather_emmeans_draws.R | 158 tests/testthat/test.gather_pairs.R | 110 tests/testthat/test.gather_rvars.R | 176 tests/testthat/test.gather_variables.R | 86 tests/testthat/test.geom_dotsinterval.R | 60 tests/testthat/test.geom_interval.R | 72 tests/testthat/test.geom_pointinterval.R | 70 tests/testthat/test.get_variables.R | 70 tests/testthat/test.linpred_draws.R | 460 tests/testthat/test.linpred_rvars.R | 256 tests/testthat/test.nest_rvars.R | 221 tests/testthat/test.point_interval.R | 58 tests/testthat/test.predicted_draws.R | 466 tests/testthat/test.predicted_rvars.R | 292 tests/testthat/test.residual_draws.R | 128 tests/testthat/test.sample_draws.R | 46 tests/testthat/test.spread_draws.R | 1063 - tests/testthat/test.spread_rvars.R | 376 tests/testthat/test.stat_dist_slabinterval.R | 64 tests/testthat/test.stat_eye.R | 114 tests/testthat/test.summarise_draws.R | 44 tests/testthat/test.tidy_draws.R | 453 tests/testthat/test.ungather_draws.R | 184 tests/testthat/test.unspread_draws.R | 146 tests/testthat/test.util.R | 64 tests/testthat/test.x_at_y.R | 130 vignettes/tidy-brms.Rmd | 1892 +- vignettes/tidy-posterior.Rmd | 1632 +- vignettes/tidy-rstanarm.Rmd | 1278 - vignettes/tidybayes-residuals.Rmd | 1440 - vignettes/tidybayes.Rmd | 1594 +- 136 files changed, 37031 insertions(+), 36880 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-16 0.1.0
Title: Test Functions for Simulation Experiments and Evaluating
Optimization and Emulation Algorithms
Description: Test functions are often used to test computer code.
They are used in optimization to test algorithms and in
metamodeling to evaluate model predictions. This package provides
test functions that can be used for any purpose.
Author: Collin Erickson [aut, cre]
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between TestFunctions versions 0.2.1 dated 2024-01-21 and 0.2.2 dated 2024-09-15
DESCRIPTION | 18 ++++++----- MD5 | 19 ++++++----- NAMESPACE | 4 ++ NEWS.md | 7 ++++ R/add_zoom.R | 2 + R/derivatives.R | 1 R/funcprofile.R | 28 +++++++++++------ R/random_lhs.R |only R/subtractlm.R | 3 + build/vignette.rds |binary inst/doc/AnIntroductiontoTestFunctions.html | 45 ++++++++++++++-------------- 11 files changed, 80 insertions(+), 47 deletions(-)
Title: Spatial Data Science Complementary Features
Description: Wrapping and supplementing commonly used functions in the R ecosystem related
to spatial data science, while serving as a basis for other packages maintained
by Wenbo Lv.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between sdsfun versions 0.1.1 dated 2024-09-08 and 0.2.0 dated 2024-09-15
DESCRIPTION | 6 MD5 | 17 - NAMESPACE | 1 NEWS.md | 4 R/sf_helpers.R | 38 +++ R/spdep_helpers.R | 2 R/spwt.R | 444 ++++++++++++++++++------------------ man/sf_distance_matrix.Rd |only man/spdep_distance_swm.Rd | 2 tests/testthat/test-spdep_helpers.R | 134 +++++----- 10 files changed, 346 insertions(+), 302 deletions(-)
Title: Vector Representing a Random Variable
Description: Random vectors, called rvecs. An rvec holds
multiple draws, but tries to behave like a standard
R vector, including working well in data frames. Rvecs are
useful for working with output from a simulation or
a Bayesian analysis.
Author: John Bryant [aut, cre],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between rvec versions 0.0.6 dated 2023-11-08 and 0.0.7 dated 2024-09-15
rvec-0.0.6/rvec/R/is.numeric.R |only rvec-0.0.6/rvec/tests/testthat/test-is.numeric.R |only rvec-0.0.7/rvec/DESCRIPTION | 8 rvec-0.0.7/rvec/MD5 | 63 - rvec-0.0.7/rvec/NAMESPACE | 11 rvec-0.0.7/rvec/NEWS.md | 24 rvec-0.0.7/rvec/R/check-functions.R | 106 +- rvec-0.0.7/rvec/R/constructors.R | 457 ++++++---- rvec-0.0.7/rvec/R/distributions.R | 508 ++++++------ rvec-0.0.7/rvec/R/draws.R | 189 +++- rvec-0.0.7/rvec/R/extract_draw.R |only rvec-0.0.7/rvec/R/format.R | 2 rvec-0.0.7/rvec/R/rvec-package.R | 92 +- rvec-0.0.7/rvec/R/util.R | 11 rvec-0.0.7/rvec/R/vec_math.R | 89 +- rvec-0.0.7/rvec/README.md | 2 rvec-0.0.7/rvec/build/vignette.rds |binary rvec-0.0.7/rvec/inst/doc/vig1_overview.html | 758 +++++++++--------- rvec-0.0.7/rvec/man/draws_all.Rd | 4 rvec-0.0.7/rvec/man/draws_ci.Rd | 14 rvec-0.0.7/rvec/man/draws_fun.Rd | 2 rvec-0.0.7/rvec/man/draws_median.Rd | 4 rvec-0.0.7/rvec/man/draws_min.Rd |only rvec-0.0.7/rvec/man/draws_quantile.Rd | 4 rvec-0.0.7/rvec/man/dweibull_rvec.Rd | 2 rvec-0.0.7/rvec/man/extract_draw.Rd |only rvec-0.0.7/rvec/man/new_rvec.Rd |only rvec-0.0.7/rvec/man/rvec-package.Rd | 92 +- rvec-0.0.7/rvec/man/rvec.Rd | 27 rvec-0.0.7/rvec/tests/testthat/test-check-functions.R | 46 - rvec-0.0.7/rvec/tests/testthat/test-constructors.R | 134 ++- rvec-0.0.7/rvec/tests/testthat/test-distributions.R | 50 - rvec-0.0.7/rvec/tests/testthat/test-draws.R | 106 ++ rvec-0.0.7/rvec/tests/testthat/test-extract_draw.R |only rvec-0.0.7/rvec/tests/testthat/test-format.R | 2 rvec-0.0.7/rvec/tests/testthat/test-util.R | 7 36 files changed, 1703 insertions(+), 1111 deletions(-)
Title: Geographically Optimal Similarity
Description: Understanding spatial association is essential for spatial
statistical inference, including factor exploration and spatial prediction.
Geographically optimal similarity (GOS) model is an effective method
for spatial prediction, as described in Yongze Song (2022)
<doi:10.1007/s11004-022-10036-8>. GOS was developed based on
the geographical similarity principle, as described in Axing Zhu (2018)
<doi:10.1080/19475683.2018.1534890>. GOS has advantages in
more accurate spatial prediction using fewer samples and
critically reduced prediction uncertainty.
Author: Yongze Song [aut, cph] ,
Wenbo Lv [aut, cre]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between geosimilarity versions 3.2 dated 2024-09-08 and 3.3 dated 2024-09-14
geosimilarity-3.2/geosimilarity/inst/doc/GOS.Rmd |only geosimilarity-3.2/geosimilarity/inst/doc/GOS.html |only geosimilarity-3.2/geosimilarity/vignettes/GOS.Rmd |only geosimilarity-3.2/geosimilarity/vignettes/GOS.Rmd.orig |only geosimilarity-3.3/geosimilarity/DESCRIPTION | 10 +-- geosimilarity-3.3/geosimilarity/MD5 | 26 +++++----- geosimilarity-3.3/geosimilarity/NEWS.md | 7 ++ geosimilarity-3.3/geosimilarity/R/gos.R | 8 +-- geosimilarity-3.3/geosimilarity/R/gos_bestkappa.R | 2 geosimilarity-3.3/geosimilarity/R/utils.R | 7 +- geosimilarity-3.3/geosimilarity/R/zzz.R | 2 geosimilarity-3.3/geosimilarity/build/vignette.rds |binary geosimilarity-3.3/geosimilarity/inst/doc/geosimilarity.Rmd |only geosimilarity-3.3/geosimilarity/inst/doc/geosimilarity.html |only geosimilarity-3.3/geosimilarity/man/pipe.Rd | 3 + geosimilarity-3.3/geosimilarity/vignettes/geosimilarity.Rmd |only geosimilarity-3.3/geosimilarity/vignettes/geosimilarity.Rmd.orig |only geosimilarity-3.3/geosimilarity/vignettes/precompile.R | 4 - 18 files changed, 40 insertions(+), 29 deletions(-)
Title: Spacekime Analytics, Time Complexity and Inferential Uncertainty
Description: Provide the core functionality to transform longitudinal data to
complex-time (kime) data using analytic and numerical techniques, visualize the original
time-series and reconstructed kime-surfaces, perform model based (e.g., tensor-linear regression)
and model-free classification and clustering methods in the book Dinov, ID and Velev, MV. (2021)
"Data Science: Time Complexity, Inferential Uncertainty, and Spacekime Analytics", De Gruyter STEM Series,
ISBN 978-3-11-069780-3. <https://www.degruyter.com/view/title/576646>.
The package includes 18 core functions which can be separated into three groups.
1) draw longitudinal data, such as Functional magnetic resonance imaging(fMRI) time-series, and forecast or transform the time-series data.
2) simulate real-valued time-series data, e.g., fMRI time-courses, detect the activated areas,
report the corresponding p-values, and visualize the p-values in the 3D brain space.
3) Laplace transform and kimesurface reconstructions of the fMRI d [...truncated...]
Author: Yongkai Qiu [aut],
Zhe Yin [aut],
Jinwen Cao [aut],
Yupeng Zhang [aut],
Yuyao Liu [aut],
Rongqian Zhang [aut],
Yueyang Shen [aut, cre],
Rouben Rostamian [ctb],
Ranjan Maitra [ctb],
Daniel Rowe [ctb],
Daniel Adrian [ctb] ,
Yunjie Guo [aut],
Ivo Dinov [...truncated...]
Maintainer: Yueyang Shen <petersyy@umich.edu>
Diff between TCIU versions 1.2.6 dated 2024-05-17 and 1.2.7 dated 2024-09-14
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/doc/tciu-LT-kimesurface.html | 16 ++++++++-------- inst/doc/tciu-fMRI-analytics.html | 32 ++++++++++++++++---------------- src/array.h | 5 +++-- src/spatial.c | 22 +++++++++++----------- 6 files changed, 46 insertions(+), 45 deletions(-)
Title: Probabilistic Regression Trees
Description: Probabilistic Regression Trees (PRTree). Functions for fitting and predicting PRTree models with some adaptations to handle missing values. The main calculations are performed in 'FORTRAN', resulting in highly efficient algorithms.
This package's implementation is based on the PRTree methodology described in Alkhoury, S.; Devijver, E.; Clausel, M.; Tami, M.; Gaussier, E.; Oppenheim, G. (2020) - "Smooth And Consistent Probabilistic Regression Trees" <https://proceedings.neurips.cc/paper_files/paper/2020/file/8289889263db4a40463e3f358bb7c7a1-Paper.pdf>.
Author: Alisson Silva Neimaier [aut, cre]
,
Taiane Schaedler Prass [aut, ths]
Maintainer: Alisson Silva Neimaier <alissonneimaier@hotmail.com>
Diff between PRTree versions 0.1.0 dated 2024-01-16 and 0.1.1 dated 2024-09-14
DESCRIPTION | 10 +++++----- MD5 | 5 +++-- inst |only src/base.f90 | 20 +++++++++++++++----- 4 files changed, 23 insertions(+), 12 deletions(-)
Title: Estimation of Entropy and Related Quantities
Description: Contains methods for the estimation of Shannon's entropy, variants of Renyi's entropy, mutual information, Kullback-Leibler divergence, and generalized Simpson's indices. The estimators used have a bias that decays exponentially fast.
Author: Lijuan Cao [aut],
Michael Grabchak [aut, cre]
Maintainer: Michael Grabchak <mgrabcha@charlotte.edu>
Diff between EntropyEstimation versions 1.2 dated 2015-01-04 and 1.2.1 dated 2024-09-14
DESCRIPTION | 21 +++++++++--- MD5 | 9 +++-- NAMESPACE | 7 +++- man/EntropyEstimation-package.Rd | 6 +-- src/EntropEst.c | 65 +++++++++++++++++++-------------------- src/init.c |only 6 files changed, 61 insertions(+), 47 deletions(-)
More information about EntropyEstimation at CRAN
Permanent link
Title: A Collection of Useful Functions by John
Description: A set of general functions that I have used in various
projects and other R packages. Miscellaneous operations on data
frames, matrices and vectors, ROC and PR statistics.
Author: John Zobolas [aut, cph, cre]
Maintainer: John Zobolas <bblodfon@gmail.com>
Diff between usefun versions 0.5.0 dated 2023-09-17 and 0.5.2 dated 2024-09-14
DESCRIPTION | 26 ++-- MD5 | 33 +++-- NAMESPACE | 7 + NEWS.md | 8 + R/bibentries.R | 28 +++- R/intersection_powerset.R |only R/operations.R | 8 - R/pr.R | 164 +++++++++++++++++++++++++--- R/roc.R | 11 - R/usefun.R | 2 README.md | 2 man/get_roc_stats.Rd | 7 - man/get_ternary_class_id.Rd | 6 - man/powerset_icounts.Rd |only man/pr.boot.Rd |only man/pr.test.Rd | 16 +- man/usefun.Rd | 3 tests/testthat/helper.R |only tests/testthat/test-intersection_powerset.R |only tests/testthat/test-pr.R | 11 + 20 files changed, 249 insertions(+), 83 deletions(-)
Title: Forest Mensuration and Management
Description: Processing forest inventory data with methods such as simple random sampling, stratified random sampling and systematic sampling. There are also functions for yield and growth predictions and model fitting, linear and nonlinear grouped data fitting, and statistical tests. References: Kershaw Jr., Ducey, Beers and Husch (2016). <doi:10.1002/9781118902028>.
Author: Sollano Rabelo Braga [aut, cre, cph],
Marcio Leles Romarco de Oliveira [aut],
Eric Bastos Gorgens [aut]
Maintainer: Sollano Rabelo Braga <sollanorb@gmail.com>
Diff between forestmangr versions 0.9.6 dated 2023-11-23 and 0.9.7 dated 2024-09-14
forestmangr-0.9.6/forestmangr/R/graybill_f.R |only forestmangr-0.9.6/forestmangr/man/graybill_f.Rd |only forestmangr-0.9.7/forestmangr/DESCRIPTION | 10 forestmangr-0.9.7/forestmangr/MD5 | 112 - forestmangr-0.9.7/forestmangr/NEWS.md | 3 forestmangr-0.9.7/forestmangr/R/Graybill_F.R |only forestmangr-0.9.7/forestmangr/R/exfm10.R | 2 forestmangr-0.9.7/forestmangr/R/exfm13.R | 2 forestmangr-0.9.7/forestmangr/R/exfm15.R | 2 forestmangr-0.9.7/forestmangr/R/exfm18.R | 4 forestmangr-0.9.7/forestmangr/R/exfm19.R | 2 forestmangr-0.9.7/forestmangr/R/exfm20.R | 2 forestmangr-0.9.7/forestmangr/R/exfm21.R | 2 forestmangr-0.9.7/forestmangr/R/exfm6.R | 4 forestmangr-0.9.7/forestmangr/R/exfm7.R | 2 forestmangr-0.9.7/forestmangr/R/exfm8.R | 2 forestmangr-0.9.7/forestmangr/R/exfm9.R | 2 forestmangr-0.9.7/forestmangr/build/vignette.rds |binary forestmangr-0.9.7/forestmangr/inst/doc/eq_group_fit_en.html | 258 +-- forestmangr-0.9.7/forestmangr/inst/doc/eq_group_fit_ptbr.html | 258 +-- forestmangr-0.9.7/forestmangr/inst/doc/invent_vol_plot_en.html | 264 +-- forestmangr-0.9.7/forestmangr/inst/doc/invent_vol_plot_ptbr.html | 264 +-- forestmangr-0.9.7/forestmangr/inst/doc/phyto_ana_en.html | 336 ++-- forestmangr-0.9.7/forestmangr/inst/doc/phyto_ana_ptbr.html | 336 ++-- forestmangr-0.9.7/forestmangr/inst/doc/sampling_en.html | 826 +++++----- forestmangr-0.9.7/forestmangr/inst/doc/sampling_ptbr.html | 652 +++---- forestmangr-0.9.7/forestmangr/inst/doc/volume_est_en.html | 184 +- forestmangr-0.9.7/forestmangr/inst/doc/volume_est_ptbr.html | 184 +- forestmangr-0.9.7/forestmangr/inst/doc/yield_growth_en.html | 134 - forestmangr-0.9.7/forestmangr/inst/doc/yield_growth_ptbr.html | 134 - forestmangr-0.9.7/forestmangr/man/Graybill_F.Rd |only forestmangr-0.9.7/forestmangr/man/avg_tree_curve.Rd | 126 - forestmangr-0.9.7/forestmangr/man/check_names.Rd | 70 forestmangr-0.9.7/forestmangr/man/exfm10.Rd | 2 forestmangr-0.9.7/forestmangr/man/exfm11.Rd | 54 forestmangr-0.9.7/forestmangr/man/exfm12.Rd | 58 forestmangr-0.9.7/forestmangr/man/exfm13.Rd | 2 forestmangr-0.9.7/forestmangr/man/exfm14.Rd | 50 forestmangr-0.9.7/forestmangr/man/exfm15.Rd | 2 forestmangr-0.9.7/forestmangr/man/exfm16.Rd | 56 forestmangr-0.9.7/forestmangr/man/exfm17.Rd | 58 forestmangr-0.9.7/forestmangr/man/exfm18.Rd | 4 forestmangr-0.9.7/forestmangr/man/exfm19.Rd | 2 forestmangr-0.9.7/forestmangr/man/exfm20.Rd | 2 forestmangr-0.9.7/forestmangr/man/exfm21.Rd | 2 forestmangr-0.9.7/forestmangr/man/exfm22.Rd | 48 forestmangr-0.9.7/forestmangr/man/exfm4.Rd | 54 forestmangr-0.9.7/forestmangr/man/exfm6.Rd | 4 forestmangr-0.9.7/forestmangr/man/exfm7.Rd | 2 forestmangr-0.9.7/forestmangr/man/exfm8.Rd | 2 forestmangr-0.9.7/forestmangr/man/exfm9.Rd | 2 forestmangr-0.9.7/forestmangr/man/lm_resid_group.Rd | 150 - forestmangr-0.9.7/forestmangr/man/na_to_0.Rd | 66 forestmangr-0.9.7/forestmangr/man/npv_irr.Rd | 124 - forestmangr-0.9.7/forestmangr/man/outliersiqr.Rd | 46 forestmangr-0.9.7/forestmangr/man/pipe.Rd | 22 forestmangr-0.9.7/forestmangr/man/pow.Rd | 86 - forestmangr-0.9.7/forestmangr/man/rm_empty_col.Rd | 72 forestmangr-0.9.7/forestmangr/man/round_df.Rd | 82 59 files changed, 2616 insertions(+), 2613 deletions(-)
Title: Robust Bayesian Variable Selection via Expectation-Maximization
Description: Variable selection methods have been extensively developed for analyzing highdimensional omics data within both the frequentist and Bayesian frameworks. This package provides implementations of the spike-and-slab quantile (group) LASSO which have been developed along the line of Bayesian hierarchical models but deeply rooted in frequentist regularization methods by utilizing Expectation–Maximization (EM) algorithm. The spike-and-slab quantile LASSO can handle data irregularity in terms of skewness and outliers in response variables, compared to its non-robust alternative, the spike-and-slab LASSO, which has also been implemented in the package. In addition, procedures for fitting the spike-and-slab quantile group LASSO and its non-robust counterpart have been implemented in the form of quantile/least-square varying coefficient mixed effect models for high-dimensional longitudinal data. The core module of this package is developed in 'C++'.
Author: Yuwen Liu [aut, cre],
Cen Wu [aut]
Maintainer: Yuwen Liu <yuwenliu9@gmail.com>
Diff between emBayes versions 0.1.5 dated 2024-03-29 and 0.1.6 dated 2024-09-14
DESCRIPTION | 14 ++-- MD5 | 26 ++++---- R/RcppExports.R | 16 +++++ R/cv.emBayes.R | 52 +++++++++++++++-- R/emBayes-package.R | 7 +- R/emBayes.R | 137 +++++++++++++++++++++++++++++++++++++++++++--- man/cv.emBayes.Rd | 11 +++ man/emBayes-package.Rd | 7 +- man/emBayes.Rd | 38 ++++++++++--- src/EM.cpp | 143 +++++++++++++++++++++++++++++++++++++++++++++++++ src/EM.h | 2 src/RcppExports.cpp | 129 ++++++++++++++++++++++++++++++++++++++++++++ src/Utilities.cpp | 92 +++++++++++++++++++++++++++++++ src/Utilities.h | 2 14 files changed, 625 insertions(+), 51 deletions(-)
Title: Wrapper Functions Around 'Charles Schwab Individual Trader API'
Description: For those wishing to interact with the 'Charles Schwab Individual Trader API' (<https://developer.schwab.com/products/trader-api--individual>) with R in a simplified manner, this package offers wrapper functions around authentication and the available API calls to streamline the process.
Author: Nick Bultman [aut, cre, cph]
Maintainer: Nick Bultman <njbultman74@gmail.com>
Diff between charlesschwabapi versions 1.0.2 dated 2024-07-17 and 1.0.3 dated 2024-09-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/get_authentication_tokens.R | 2 +- README.md | 11 ++++++++++- 4 files changed, 17 insertions(+), 8 deletions(-)
More information about charlesschwabapi at CRAN
Permanent link
Title: Accesses Brazilian Public Security Data from SINESP Since 2015
Description: Allows access to data from the Brazilian Public Security Information System (SINESP) by state and municipality. <https://www.gov.br/mj/pt-br/assuntos/sua-seguranca/seguranca-publica/sinesp-1>.
Author: Giovanni Vargette [aut, cre] ,
Igor Laltuf [aut] ,
Marcelo Justus [aut]
Maintainer: Giovanni Vargette <g216978@dac.unicamp.br>
Diff between BrazilCrime versions 0.2 dated 2024-06-21 and 0.2.1 dated 2024-09-14
DESCRIPTION | 20 +++--- MD5 | 11 ++- R/get_sinesp_data.R | 11 ++- README.md | 110 ++++++++++++++++++++++++++++++++-- man/figures/grafico.png |only man/figures/mapa.png |only tests/testthat/test-get_sinesp_data.R | 61 +++++++++--------- tests/testthat/testthat-problems.rds |only 8 files changed, 161 insertions(+), 52 deletions(-)
Title: Create and Evaluate Stopping Rules for Safety Monitoring
Description: Provides functions for creating, displaying, and evaluating stopping rules for safety monitoring in clinical studies. Implements stopping rule methods described in Goldman (1987) <doi:10.1016/0197-2456(87)90153-X>; Geller et al. (2003, ISBN:9781135524388); Ivanova, Qaqish, and Schell (2005) <doi:10.1111/j.1541-0420.2005.00311.x>; Chen and Chaloner (2006) <doi:10.1002/sim.2429>; and Kulldorff et al. (2011) <doi:10.1080/07474946.2011.539924>.
Author: Michael J. Martens [aut, cre],
Qinghua Lian [aut],
Brent R. Logan [ctb]
Maintainer: Michael J. Martens <mmartens@mcw.edu>
Diff between stoppingrule versions 0.4.0 dated 2024-03-17 and 0.5.0 dated 2024-09-14
DESCRIPTION | 14 ++++++++++---- MD5 | 22 +++++++++++----------- R/calc.bnd.surv.R | 23 ++++++++++++++--------- R/calc.rule.bin.R | 2 +- R/calc.rule.surv.R | 17 +++++++++++------ R/findconst.surv.R | 15 ++++++++++++--- R/table.rule.bin.R | 11 ++++++----- R/table.rule.surv.R | 2 +- man/calc.bnd.surv.Rd | 8 ++++++-- man/calc.rule.bin.Rd | 2 +- man/calc.rule.surv.Rd | 6 +++++- man/findconst.surv.Rd | 6 +++++- 12 files changed, 83 insertions(+), 45 deletions(-)
Title: Create, and Refine Data Nuggets
Description: Creating, and refining data nuggets.
Data nuggets reduce a large dataset into a small collection of nuggets of
data, each containing a center (location), weight (importance), and scale
(variability) parameter. Data nugget centers are created by choosing
observations in the dataset which are as equally spaced apart as possible.
Data nugget weights are created by counting the number observations
closest to a given data nugget center. We then say the data nugget
'contains' these observations and the data nugget center is recalculated
as the mean of these observations. Data nugget scales are created by
calculating the trace of the covariance matrix of the observations
contained within a data nugget divided by the dimension of the dataset.
Data nuggets are refined by 'splitting' data nuggets which have scales or
shapes (defined as the ratio of the two largest eigenvalues of the
covariance matrix of the observations contained within the data nugget)
Reference paper: [1] Beavers, T. E., Cheng [...truncated...]
Author: Yajie Duan [cre, ctb],
Traymon Beavers [aut],
Javier Cabrera [aut],
Ge Cheng [aut],
Kunting Qi [aut],
Mariusz Lubomirski [aut]
Maintainer: Yajie Duan <yajieritaduan@gmail.com>
Diff between datanugget versions 1.3.0 dated 2024-07-29 and 1.3.1 dated 2024-09-14
DESCRIPTION | 8 MD5 | 4 R/refineDN.R | 4809 +++++++++++++++++++++++++++++------------------------------ 3 files changed, 2412 insertions(+), 2409 deletions(-)
Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files
containing spectral data from spectrometers and their associated software,
output from daylight simulation models in common use, and some spectral
data repositories. As well as functions for exchange of spectral data with
other R packages. Part of the 'r4photobiology' suite,
Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb] ,
Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyInOut versions 0.4.27 dated 2023-07-20 and 0.4.28-1 dated 2024-09-14
DESCRIPTION | 15 MD5 | 129 NAMESPACE | 4 NEWS.md | 93 R/color-wrappers.r | 12 R/on-load.r | 3 R/read-cid-spectravue-csv.r | 4 R/read-cie-csv.r |only R/read-fmi-cum.R | 16 R/read-licor-prn.r | 4 R/read-oojaz-file.r | 2 R/read-oopi-file.r | 2 R/read-ooss-file.r | 2 R/read-tuv-file.r | 696 README.md | 49 build/partial.rdb |binary build/vignette.rds |binary inst/doc/user-guide.R | 54 inst/doc/user-guide.Rmd | 50 inst/doc/user-guide.html | 840 - inst/extdata/2013-05-01.hel |16890 ++++++++++++------------ inst/extdata/2014-08-21_cum.hel | 1028 - inst/extdata/2014-08-22_cum.hel | 1028 - inst/extdata/CIE_illum_C.csv |only inst/extdata/CIE_illum_C.csv_metadata.json |only inst/extdata/CIE_sle_photopic.csv |only inst/extdata/CIE_sle_photopic.csv_metadata.json |only inst/extdata/FReDflowerID_157.csv | 802 - inst/extdata/qtuv-00.htm |only inst/extdata/reflectance.jaz | 4134 ++--- inst/extdata/spectrum-seq0.pi | 4108 ++--- inst/extdata/spectrum.JazIrrad | 8240 +++++------ inst/extdata/spectrum.jaz | 4134 ++--- inst/extdata/spectrum.pi | 4108 ++--- inst/extdata/uvspec-multi.dat | 6110 ++++---- inst/extdata/yoctopuce-data.csv | 1412 +- man/as.colorSpec.Rd | 164 man/colorSpec2mspct.Rd | 218 man/hyperSpec2mspct.Rd | 160 man/photobiologyInOut-package.Rd | 118 man/qtuv_clouds.Rd |only man/qtuv_s.e.irrad.Rd |only man/read_ASTER_txt.Rd | 146 man/read_CIE_csv.Rd |only man/read_FReD_csv.Rd | 128 man/read_avaspec_csv.Rd | 148 man/read_cid_spectravue_csv.Rd | 4 man/read_csi_dat.Rd | 116 man/read_fmi2mspct.Rd | 166 man/read_fmi_cum.Rd | 180 man/read_foreign2mspct.Rd | 88 man/read_li180_txt.Rd | 204 man/read_licor_prn.Rd | 204 man/read_macam_dta.Rd | 124 man/read_oo_jazirrad.Rd | 212 man/read_oo_pidata.Rd | 164 man/read_oo_ssirrad.Rd | 150 man/read_qtuv_txt.Rd | 111 man/read_tuv_usrout.Rd | 130 man/read_uvspec_disort.Rd | 126 man/read_uvspec_disort_vesa.Rd | 114 man/read_wasatch_csv.Rd | 266 man/read_yoctopuce_csv.Rd | 152 man/rspec2mspct.Rd | 158 man/spct_CCT.Rd | 108 man/spct_CRI.Rd | 92 man/spct_SSI.Rd | 100 tests/testthat/test-licor.R | 74 tests/testthat/test-tuv.R | 124 vignettes/user-guide.Rmd | 50 70 files changed, 29607 insertions(+), 28661 deletions(-)
More information about photobiologyInOut at CRAN
Permanent link
Title: SHAP Visualizations
Description: Visualizations for SHAP (SHapley Additive exPlanations), such
as waterfall plots, force plots, various types of importance plots,
dependence plots, and interaction plots. These plots act on a
'shapviz' object created from a matrix of SHAP values and a
corresponding feature dataset. Wrappers for the R packages 'xgboost',
'lightgbm', 'fastshap', 'shapr', 'h2o', 'treeshap', 'DALEX', and
'kernelshap' are added for convenience. By separating visualization
and computation, it is possible to display factor variables in graphs,
even if the SHAP values are calculated by a model that requires
numerical features. The plots are inspired by those provided by the
'shap' package in Python, but there is no dependency on it.
Author: Michael Mayer [aut, cre],
Adrian Stando [ctb]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between shapviz versions 0.9.4 dated 2024-08-20 and 0.9.5 dated 2024-09-14
shapviz-0.9.4/shapviz/man/figures/README-dep.png |only shapviz-0.9.4/shapviz/man/figures/VIGNETTE-dep.png |only shapviz-0.9.5/shapviz/DESCRIPTION | 6 shapviz-0.9.5/shapviz/MD5 | 59 - shapviz-0.9.5/shapviz/NEWS.md | 12 shapviz-0.9.5/shapviz/R/sv_force.R | 2 shapviz-0.9.5/shapviz/R/sv_waterfall.R | 2 shapviz-0.9.5/shapviz/README.md | 56 - shapviz-0.9.5/shapviz/build/vignette.rds |binary shapviz-0.9.5/shapviz/inst/doc/basic_use.R | 29 shapviz-0.9.5/shapviz/inst/doc/basic_use.Rmd | 48 - shapviz-0.9.5/shapviz/inst/doc/basic_use.html | 98 +- shapviz-0.9.5/shapviz/inst/doc/geographic.R | 68 - shapviz-0.9.5/shapviz/inst/doc/geographic.Rmd | 70 - shapviz-0.9.5/shapviz/inst/doc/geographic.html | 138 +-- shapviz-0.9.5/shapviz/inst/doc/multiple_output.html | 8 shapviz-0.9.5/shapviz/inst/doc/tidymodels.Rmd |only shapviz-0.9.5/shapviz/inst/doc/tidymodels.html |only shapviz-0.9.5/shapviz/man/figures/README-bee.svg |only shapviz-0.9.5/shapviz/man/figures/README-dep.svg |only shapviz-0.9.5/shapviz/man/figures/README-force.svg | 381 +--------- shapviz-0.9.5/shapviz/man/figures/README-imp.svg | 360 +-------- shapviz-0.9.5/shapviz/man/figures/README-waterfall.svg | 373 +-------- shapviz-0.9.5/shapviz/man/figures/VIGNETTE-dep-ranger.png |binary shapviz-0.9.5/shapviz/man/figures/VIGNETTE-tidy-class-lgb-dep.png |only shapviz-0.9.5/shapviz/man/figures/VIGNETTE-tidy-class-lgb-imp.png |only shapviz-0.9.5/shapviz/man/figures/VIGNETTE-tidy-class-normal-dep1.png |only shapviz-0.9.5/shapviz/man/figures/VIGNETTE-tidy-class-normal-dep2.png |only shapviz-0.9.5/shapviz/man/figures/VIGNETTE-tidy-class-normal-imp.png |only shapviz-0.9.5/shapviz/man/figures/VIGNETTE-tidy-class-xgb-dep.png |only shapviz-0.9.5/shapviz/man/figures/VIGNETTE-tidy-class-xgb-imp.png |only shapviz-0.9.5/shapviz/man/figures/VIGNETTE-tidy-lgb-dep.png |only shapviz-0.9.5/shapviz/man/figures/VIGNETTE-tidy-lgb-imp.png |only shapviz-0.9.5/shapviz/man/figures/VIGNETTE-tidy-rf-dep.png |only shapviz-0.9.5/shapviz/man/figures/VIGNETTE-tidy-rf-imp.png |only shapviz-0.9.5/shapviz/man/figures/VIGNETTE-tidy-xgb-dep.png |only shapviz-0.9.5/shapviz/man/figures/VIGNETTE-tidy-xgb-imp.png |only shapviz-0.9.5/shapviz/man/figures/VIGNETTE-tidy-xgb-inter.png |only shapviz-0.9.5/shapviz/vignettes/basic_use.Rmd | 48 - shapviz-0.9.5/shapviz/vignettes/geographic.Rmd | 70 - shapviz-0.9.5/shapviz/vignettes/tidymodels.Rmd |only 41 files changed, 571 insertions(+), 1257 deletions(-)
Title: Genotypic Variance Components
Description: Functionalities to compute model based genetic components i.e. genotypic variance, phenotypic variance and heritability for given traits of different genotypes from replicated data using methodology explained by Burton, G. W. & Devane, E. H. (1953) (<doi:10.2134/agronj1953.00021962004500100005x>) and Allard, R.W. (2010, ISBN:8126524154).
Author: Muhammad Yaseen [aut, cre],
Sami Ullah [aut, ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between gvcR versions 0.1.0 dated 2018-02-20 and 0.3.0 dated 2024-09-14
gvcR-0.1.0/gvcR/R/gvc_gvar.R |only gvcR-0.1.0/gvcR/R/gvc_herit.R |only gvcR-0.1.0/gvcR/R/gvc_pvar.R |only gvcR-0.1.0/gvcR/man/gvc_gvar.Rd |only gvcR-0.1.0/gvcR/man/gvc_herit.Rd |only gvcR-0.1.0/gvcR/man/gvc_pvar.Rd |only gvcR-0.3.0/gvcR/DESCRIPTION | 20 ++++--- gvcR-0.3.0/gvcR/MD5 | 17 ++---- gvcR-0.3.0/gvcR/NAMESPACE | 8 +- gvcR-0.3.0/gvcR/NEWS.md | 6 ++ gvcR-0.3.0/gvcR/R/gvc.R |only gvcR-0.3.0/gvcR/README.md | 107 +++++++++++++++++++++++++++++++++++---- gvcR-0.3.0/gvcR/inst |only gvcR-0.3.0/gvcR/man/gvc.Rd |only 14 files changed, 127 insertions(+), 31 deletions(-)
Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data).
(MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>,
HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>,
RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>,
JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>,
MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>,
JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>,
DAVIES, D.L., BOULDIN, D.W. (1979) &l [...truncated...]
Author: Marek Walesiak [aut] ,
Andrzej Dudek [aut, cre]
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Diff between clusterSim versions 0.51-4 dated 2024-06-26 and 0.51-5 dated 2024-09-14
clusterSim-0.51-4/clusterSim/INDEX |only clusterSim-0.51-5/clusterSim/DESCRIPTION | 8 +-- clusterSim-0.51-5/clusterSim/MD5 | 27 ++++++------- clusterSim-0.51-5/clusterSim/build/partial.rdb |binary clusterSim-0.51-5/clusterSim/data/data_binary.rda |binary clusterSim-0.51-5/clusterSim/data/data_interval.rda |binary clusterSim-0.51-5/clusterSim/data/data_mixed.rda |binary clusterSim-0.51-5/clusterSim/data/data_nominal.rda |binary clusterSim-0.51-5/clusterSim/data/data_ordinal.rda |binary clusterSim-0.51-5/clusterSim/data/data_ratio.rda |binary clusterSim-0.51-5/clusterSim/man/HINoV.Symbolic.rd | 2 clusterSim-0.51-5/clusterSim/man/cluster.Gen.rd | 4 - clusterSim-0.51-5/clusterSim/man/data.Normalization.rd | 2 clusterSim-0.51-5/clusterSim/man/interval_normalization.rd | 4 - clusterSim-0.51-5/clusterSim/man/speccl.rd | 3 - 15 files changed, 25 insertions(+), 25 deletions(-)
Title: Mappable Vector Library for Handling Large Datasets
Description: Mappable vector library provides convenient way to access large datasets. Use all of your data at once, with few limits. Memory mapped data can be shared between multiple R processes. Access speed depends on storage medium, so solid state drive is recommended, preferably with PCI Express (or M.2 nvme) interface or a fast network file system. The data is memory mapped into R and then accessed using usual R list and array subscription operators. Convenience functions are provided for merging, grouping and indexing large vectors and data.frames. The layout of underlying MVL files is optimized for large datasets. The vectors are stored to guarantee alignment for vector intrinsics after memory map. The package is built on top of libMVL, which can be used as a standalone C library. libMVL has simple C API making it easy to interchange datasets with outside programs. Large MVL datasets are distributed via Academic Torrents <https://academictorrents.com/collection/mvl-datasets>.
Author: Vladimir Dergachev [aut, cre]
Maintainer: Vladimir Dergachev <support@altumrete.com>
Diff between RMVL versions 1.1.0.0 dated 2024-05-08 and 1.1.0.1 dated 2024-09-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/RlibMVL.c | 20 ++++++++++---------- src/libMVL.c | 2 ++ 4 files changed, 18 insertions(+), 16 deletions(-)
Title: React Helpers
Description: Make it easy to use 'React' in R with 'htmlwidget' scaffolds,
helper dependency functions, an embedded 'Babel' 'transpiler',
and examples.
Author: Facebook Inc [aut, cph] ,
Michel Weststrate [aut, cph] ,
Kent Russell [aut, cre] ,
Alan Dipert [aut] ,
Greg Lin [aut]
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between reactR versions 0.6.0 dated 2024-06-26 and 0.6.1 dated 2024-09-14
reactR-0.6.0/reactR/inst/www/react-tools/react-tools.umd.cjs |only reactR-0.6.1/reactR/DESCRIPTION | 19 +++++++---- reactR-0.6.1/reactR/MD5 | 14 ++++---- reactR-0.6.1/reactR/NEWS.md | 4 ++ reactR-0.6.1/reactR/R/dependencies.R | 2 - reactR-0.6.1/reactR/inst/doc/intro_htmlwidgets.html | 4 +- reactR-0.6.1/reactR/inst/doc/intro_inputs.html | 4 +- reactR-0.6.1/reactR/inst/doc/intro_reactR.html | 6 +-- reactR-0.6.1/reactR/inst/www/react-tools/react-tools.js |only 9 files changed, 32 insertions(+), 21 deletions(-)
Title: Inference for Phase-Type Distributions
Description: Functions to perform Bayesian inference on absorption time data for
Phase-type distributions. The methods of Bladt et al (2003)
<doi:10.1080/03461230110106435> and Aslett (2012)
<https://www.louisaslett.com/PhD_Thesis.pdf> are provided.
Author: Louis Aslett [aut, cre],
Wally Gilks [ctb]
Maintainer: Louis Aslett <louis.aslett@durham.ac.uk>
Diff between PhaseType versions 0.2.1 dated 2023-04-07 and 0.3.0 dated 2024-09-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 6 ++++++ README.md | 21 ++++++++++++--------- src/utility.c | 4 ++-- 5 files changed, 27 insertions(+), 18 deletions(-)
Title: EZ-to-Use Biplots
Description: Provides users with an EZ-to-use platform for representing data
with biplots. Currently principal component analysis (PCA), canonical variate
analysis (CVA) and simple correspondence analysis (CA) biplots are included.
This is accompanied by various formatting
options for the samples and axes. Alpha-bags and concentration ellipses
are included for visual enhancements and interpretation. For an extensive
discussion on the topic, see Gower, J.C., Lubbe, S. and le Roux, N.J.
(2011, ISBN: 978-0-470-01255-0) Understanding Biplots. Wiley: Chichester.
Author: Sugnet Lubbe [aut, cre, cph] ,
Niel le Roux [aut] ,
Johane Nienkemper-Swanepoel [aut]
,
Raeesa Ganey [aut] ,
Ruan Buys [aut] ,
Zoe-Mae Adams [aut] ,
Peter Manefeldt [aut]
Maintainer: Sugnet Lubbe <muvisu@sun.ac.za>
Diff between biplotEZ versions 2.0 dated 2024-07-08 and 2.1 dated 2024-09-14
biplotEZ-2.0/biplotEZ/man/plot3D.Rd |only biplotEZ-2.1/biplotEZ/DESCRIPTION | 13 biplotEZ-2.1/biplotEZ/MD5 | 80 biplotEZ-2.1/biplotEZ/NAMESPACE | 3 biplotEZ-2.1/biplotEZ/R/CA.R | 2 biplotEZ-2.1/biplotEZ/R/CVA.R | 147 biplotEZ-2.1/biplotEZ/R/MDS.R | 3 biplotEZ-2.1/biplotEZ/R/PCA.R | 8 biplotEZ-2.1/biplotEZ/R/aesthetics.R | 437 - biplotEZ-2.1/biplotEZ/R/biplot.R | 23 biplotEZ-2.1/biplotEZ/R/calibrate_axes.R |only biplotEZ-2.1/biplotEZ/R/clouds.R | 4 biplotEZ-2.1/biplotEZ/R/more_biplots.R | 2 biplotEZ-2.1/biplotEZ/R/plot2D.R | 175 biplotEZ-2.1/biplotEZ/R/plotting.R | 86 biplotEZ-2.1/biplotEZ/R/utility.R | 3 biplotEZ-2.1/biplotEZ/inst/doc/Biplots_in_1D.html | 8 biplotEZ-2.1/biplotEZ/inst/doc/Biplots_in_3D.html | 54 biplotEZ-2.1/biplotEZ/inst/doc/CA_in_biplotEZ.Rmd | 1 biplotEZ-2.1/biplotEZ/inst/doc/CA_in_biplotEZ.html | 8 biplotEZ-2.1/biplotEZ/inst/doc/Class_separation.Rmd | 5 biplotEZ-2.1/biplotEZ/inst/doc/Class_separation.html | 4072 -------------- biplotEZ-2.1/biplotEZ/inst/doc/MDS.html | 650 -- biplotEZ-2.1/biplotEZ/inst/doc/biplotEZ.Rmd | 5 biplotEZ-2.1/biplotEZ/inst/doc/biplotEZ.html | 70 biplotEZ-2.1/biplotEZ/inst/doc/biplotEZ_enhancements.html | 12 biplotEZ-2.1/biplotEZ/man/AoD.Rd | 6 biplotEZ-2.1/biplotEZ/man/AoD.biplot.Rd | 6 biplotEZ-2.1/biplotEZ/man/CA.Rd | 3 biplotEZ-2.1/biplotEZ/man/CLPs.Rd |only biplotEZ-2.1/biplotEZ/man/CVA.Rd | 3 biplotEZ-2.1/biplotEZ/man/PCA.Rd | 6 biplotEZ-2.1/biplotEZ/man/axes.Rd | 113 biplotEZ-2.1/biplotEZ/man/axes_coordinates.Rd |only biplotEZ-2.1/biplotEZ/man/means.Rd | 52 biplotEZ-2.1/biplotEZ/man/newaxes.Rd | 61 biplotEZ-2.1/biplotEZ/man/newsamples.Rd | 60 biplotEZ-2.1/biplotEZ/man/plot.biplot.Rd | 26 biplotEZ-2.1/biplotEZ/man/samples.Rd | 83 biplotEZ-2.1/biplotEZ/vignettes/CA_in_biplotEZ.Rmd | 1 biplotEZ-2.1/biplotEZ/vignettes/Class_separation.Rmd | 5 biplotEZ-2.1/biplotEZ/vignettes/biplotEZ.Rmd | 5 biplotEZ-2.1/biplotEZ/vignettes/references.bib | 2 43 files changed, 985 insertions(+), 5318 deletions(-)
Title: Workflow for Open Reproducible Code in Science
Description: Create reproducible and transparent research projects in 'R'.
This package is based on the Workflow for Open
Reproducible Code in Science (WORCS), a step-by-step procedure based on best
practices for
Open Science. It includes an 'RStudio' project template, several
convenience functions, and all dependencies required to make your project
reproducible and transparent. WORCS is explained in the tutorial paper
by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2021).
<doi:10.3233/DS-210031>.
Author: Caspar J. Van Lissa [aut, cre]
,
Aaron Peikert [aut] ,
Andreas M. Brandmaier [aut]
Maintainer: Caspar J. Van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between worcs versions 0.1.14 dated 2023-10-25 and 0.1.15 dated 2024-09-14
DESCRIPTION | 15 +- MD5 | 63 +++++--- NAMESPACE | 1 R/check_installation.R | 4 R/save_load.R | 14 - R/targets.R |only R/update_worcs_package.R |only R/worcs_badge.R | 4 R/worcs_project.R | 132 ++++++++++++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/citation.R | 4 inst/doc/citation.Rmd | 2 inst/doc/citation.html | 13 - inst/doc/endpoints.R | 2 inst/doc/endpoints.html | 2 inst/doc/git_cloud.R | 2 inst/doc/reproduce.R | 2 inst/doc/setup-docker.R | 4 inst/doc/setup-docker.html | 2 inst/doc/setup.R | 2 inst/doc/synthetic_data.R |only inst/doc/synthetic_data.Rmd |only inst/doc/synthetic_data.html |only inst/doc/workflow.R | 4 inst/doc/workflow.Rmd | 2 inst/doc/workflow.html | 6 inst/rstudio/templates/project/resources/_targets.rmd |only inst/rstudio/templates/project/worcs.dcf | 11 + man/add_targets.Rd |only man/figures |only man/worcs_project.Rd | 4 tests/testthat/helper_usethis.R |only tests/testthat/test-checksum_markdown.R | 4 tests/testthat/test-targets.R |only vignettes/citation.Rmd | 2 vignettes/synthetic_data.Rmd |only vignettes/workflow.Rmd | 2 38 files changed, 201 insertions(+), 102 deletions(-)
Title: An Interface to IMF (International Monetary Fund) Data JSON API
Description: A straightforward interface for accessing the IMF
(International Monetary Fund) data JSON API,
available at <https://data.imf.org/>. This package offers direct access to
the primary API endpoints: Dataflow, DataStructure, and CompactData.
And, it provides an intuitive interface for exploring available
dimensions and attributes, as well as querying individual time-series datasets.
Additionally, the package implements a rate limit on API calls to reduce the
chances of exceeding service limits (limited to 10 calls every 5 seconds)
and encountering response errors.
Author: Pedro Baltazar [aut, cre]
Maintainer: Pedro Baltazar <pedrobtz@gmail.com>
Diff between imf.data versions 0.1.6 dated 2024-07-16 and 0.1.7 dated 2024-09-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/database.R | 25 ++++++++++++++++++------- R/methods.R | 5 ++++- 5 files changed, 38 insertions(+), 16 deletions(-)
Title: Machine Learning Time Series Forecasting
Description: Compute static, onestep and multistep time series forecasts for machine learning models.
Author: Ho Tsung-wu [aut, cre]
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between iForecast versions 1.0.7 dated 2023-07-01 and 1.0.8 dated 2024-09-14
iForecast-1.0.7/iForecast/R/ttsLSTM.R |only iForecast-1.0.8/iForecast/DESCRIPTION | 18 ++- iForecast-1.0.8/iForecast/MD5 | 22 ++-- iForecast-1.0.8/iForecast/NAMESPACE | 5 - iForecast-1.0.8/iForecast/R/deprecate.R |only iForecast-1.0.8/iForecast/R/ttsAutoML.R | 8 + iForecast-1.0.8/iForecast/R/ttsCaret.R | 2 iForecast-1.0.8/iForecast/R/ttsPredict.R | 44 ++++----- iForecast-1.0.8/iForecast/man/iForecast.Rd | 18 +-- iForecast-1.0.8/iForecast/man/tts.autoML.Rd |only iForecast-1.0.8/iForecast/man/tts.caret.Rd |only iForecast-1.0.8/iForecast/man/ttsAutoML.Rd | 91 +----------------- iForecast-1.0.8/iForecast/man/ttsCaret.Rd | 135 +--------------------------- iForecast-1.0.8/iForecast/man/ttsLSTM.Rd | 113 ----------------------- 14 files changed, 78 insertions(+), 378 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-10 1.0-1
Title: Bayesian Cure Rate Modeling for Time-to-Event Data
Description: A fully Bayesian approach in order to estimate a general family of cure rate models under the presence of covariates, see Papastamoulis and Milienos (2024) <doi:10.1007/s11749-024-00942-w>. The promotion time can be modelled (a) parametrically using typical distributional assumptions for time to event data (including the Weibull, Exponential, Gompertz, log-Logistic distributions), or (b) semiparametrically using finite mixtures of distributions. In both cases, user-defined families of distributions are allowed under some specific requirements. Posterior inference is carried out by constructing a Metropolis-coupled Markov chain Monte Carlo (MCMC) sampler, which combines Gibbs sampling for the latent cure indicators and Metropolis-Hastings steps with Langevin diffusion dynamics for parameter updates. The main MCMC algorithm is embedded within a parallel tempering scheme by considering heated versions of the target posterior distribution.
Author: Panagiotis Papastamoulis [aut, cre]
,
Fotios Milienos [aut]
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Diff between bayesCureRateModel versions 1.1 dated 2024-07-24 and 1.2 dated 2024-09-14
DESCRIPTION | 14 MD5 | 29 NAMESPACE | 7 R/bayesian_cure_rate_model.R | 1181 ++++++++++++++++++++++++++++++++++---- build/partial.rdb |binary data/marriage_dataset.RData |binary data/sim_mix_data.RData |only inst |only man/bayesCureRateModel-package.Rd | 20 man/compute_fdr_tpr.Rd |only man/cure_rate_MC3.Rd | 64 +- man/cure_rate_mcmc.Rd | 9 man/log_user_mixture.Rd |only man/marriage_dataset.Rd | 6 man/plot.bayesCureModel.Rd | 45 - man/predict.bayesCureModel.Rd |only man/residuals.bayesCureModel.Rd |only man/sim_mix_data.Rd |only man/summary.bayesCureModel.Rd | 34 - 19 files changed, 1222 insertions(+), 187 deletions(-)
More information about bayesCureRateModel at CRAN
Permanent link
Title: Multiple Indicator Cluster Survey (MICS) 2017-18 Data for
Punjab, Pakistan
Description: Provides data set and function for exploration of Multiple Indicator Cluster Survey (MICS) 2017-18 data for Punjab, Pakistan. The results of the present survey are critically important for the purposes of SDG monitoring, as the survey produces information on 32 global SDG indicators. The data was collected from 53,840 households selected at the second stage with systematic random sampling out of a sample of 2,692 clusters selected using Probability Proportional to size sampling. Six questionnaires were used in the survey: (1) a household questionnaire to collect basic demographic information on all de jure household members (usual residents), the household, and the dwelling; (2) a water quality testing questionnaire administered in three households in each cluster of the sample; (3) a questionnaire for individual women administered in each household to all women age 15-49 years; (4) a questionnaire for individual men administered in every second household to all men age 15-49 years; (5 [...truncated...]
Author: Muhammad Yaseen [aut, cre]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between PakPMICS2018 versions 1.0.0 dated 2020-01-25 and 1.1.0 dated 2024-09-13
DESCRIPTION | 19 ++++++++--------- MD5 | 42 +++++++++++++++++++------------------- NEWS.md | 6 +++++ R/PakPMICS2018bh.R | 4 +-- R/PakPMICS2018ch.R | 4 +-- R/PakPMICS2018fs.R | 4 +-- R/PakPMICS2018hh.R | 4 +-- R/PakPMICS2018hl.R | 4 +-- R/PakPMICS2018mm.R | 4 +-- R/PakPMICS2018mn.R | 4 +-- R/PakPMICS2018wm.R | 4 +-- README.md | 55 +++++++++++++++++++------------------------------- build/vignette.rds |binary inst/CITATION | 43 +++++++-------------------------------- man/PakPMICS2018bh.Rd | 10 +++++---- man/PakPMICS2018ch.Rd | 10 +++++---- man/PakPMICS2018fs.Rd | 10 +++++---- man/PakPMICS2018hh.Rd | 10 +++++---- man/PakPMICS2018hl.Rd | 10 +++++---- man/PakPMICS2018mm.Rd | 10 +++++---- man/PakPMICS2018mn.Rd | 10 +++++---- man/PakPMICS2018wm.Rd | 10 +++++---- 22 files changed, 129 insertions(+), 148 deletions(-)
Title: Demographic Analysis and Data Manipulation
Description: Perform tasks commonly encountered when
preparing and analysing demographic data.
Some functions are intended for end users, and
others for developers. Includes functions for
working with life tables.
Author: John Bryant [aut, cre],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between poputils versions 0.3.1 dated 2024-06-12 and 0.3.3 dated 2024-09-13
DESCRIPTION | 8 MD5 | 58 ++-- NAMESPACE | 4 NEWS.md | 44 +++ R/age.R | 201 ++++++++------- R/check-functions.R | 370 ++++++++++++++++++---------- R/cpp11.R | 4 R/lifetab.R | 300 +++++++++++++++-------- R/logit.R | 12 R/poputils-package.R | 39 +-- R/rr3.R |only R/to_matrix.R | 147 ++++------- R/trim_01.R |only README.md | 46 ++- build/vignette.rds |binary inst/doc/poputils.R | 6 inst/doc/poputils.Rmd | 10 inst/doc/poputils.html | 196 ++++++++------- man/check_n.Rd |only man/lifetab.Rd | 12 man/poputils-package.Rd | 40 +-- man/q0_to_m0.Rd |only man/rr3.Rd |only man/trim_01.Rd |only src/cpp11.cpp | 8 src/lifetab.cpp | 29 ++ tests/testthat/test-age.R | 37 ++ tests/testthat/test-check-functions.R | 122 ++++++++- tests/testthat/test-lifetab-src.R | 440 ++++++++++++---------------------- tests/testthat/test-lifetab.R | 193 +++++++++++++- tests/testthat/test-rr3.R |only tests/testthat/test-to_matrix.R | 16 - tests/testthat/test-trim_01.R |only vignettes/poputils.Rmd | 10 34 files changed, 1447 insertions(+), 905 deletions(-)
Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
Description: Raman and (FT)IR spectral analysis tool for plastic particles and
other environmental samples (Cowger et al. 2021,
<doi:10.1021/acs.analchem.1c00123>). With read_any(), Open Specy provides a
single function for reading individual, batch, or map spectral data files
like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies
processing spectra, including smoothing, baseline correction,
range restriction and flattening, intensity conversions, wavenumber
alignment, and min-max normalization. Spectra can be identified in batch
using an onboard reference library (Cowger et al. 2020,
<doi:10.1177/0003702820929064>) using match_spec(). A Shiny app is available
via run_app() or online at <https://openanalysis.org/openspecy/>.
Author: Win Cowger [cre, aut, dtc] ,
Zacharias Steinmetz [aut] ,
Nick Leong [aut] ,
Andrea Faltynkova [aut, dtc] ,
Hannah Sherrod [aut] ,
Andrew B Gray [ctb] ,
Hannah Hapich [ctb] ,
Jennifer Lynch [ctb, dtc] ,
Hannah De Frond [ctb, dtc] ,
Keenan Munno [ctb, [...truncated...]
Maintainer: Win Cowger <wincowger@gmail.com>
Diff between OpenSpecy versions 1.1.0 dated 2024-06-13 and 1.2.0 dated 2024-09-13
OpenSpecy-1.1.0/OpenSpecy/R/share_spec.R |only OpenSpecy-1.1.0/OpenSpecy/man/share_spec.Rd |only OpenSpecy-1.1.0/OpenSpecy/tests/testthat/test-share_spec.R |only OpenSpecy-1.1.0/OpenSpecy/tests/testthat/test-workflows.R |only OpenSpecy-1.2.0/OpenSpecy/DESCRIPTION | 15 OpenSpecy-1.2.0/OpenSpecy/MD5 | 217 OpenSpecy-1.2.0/OpenSpecy/NAMESPACE | 414 OpenSpecy-1.2.0/OpenSpecy/NEWS.md | 464 OpenSpecy-1.2.0/OpenSpecy/R/OpenSpecy-package.R | 86 OpenSpecy-1.2.0/OpenSpecy/R/adj_intens.R | 152 OpenSpecy-1.2.0/OpenSpecy/R/adj_range.R | 242 OpenSpecy-1.2.0/OpenSpecy/R/adj_wave.R | 86 OpenSpecy-1.2.0/OpenSpecy/R/as_OpenSpecy.R | 792 - OpenSpecy-1.2.0/OpenSpecy/R/conform_spec.R | 226 OpenSpecy-1.2.0/OpenSpecy/R/data_norm.R | 218 OpenSpecy-1.2.0/OpenSpecy/R/def_features.R | 612 OpenSpecy-1.2.0/OpenSpecy/R/gen_OpenSpecy.R | 256 OpenSpecy-1.2.0/OpenSpecy/R/human_ts.R | 54 OpenSpecy-1.2.0/OpenSpecy/R/interactive_plots.R | 660 - OpenSpecy-1.2.0/OpenSpecy/R/io_spec.R | 320 OpenSpecy-1.2.0/OpenSpecy/R/make_rel.R | 114 OpenSpecy-1.2.0/OpenSpecy/R/manage_lib.R | 534 OpenSpecy-1.2.0/OpenSpecy/R/manage_na.R | 214 OpenSpecy-1.2.0/OpenSpecy/R/manage_spec.R | 422 OpenSpecy-1.2.0/OpenSpecy/R/match_spec.R | 1050 - OpenSpecy-1.2.0/OpenSpecy/R/process_spec.R | 274 OpenSpecy-1.2.0/OpenSpecy/R/raman_hdpe.R | 66 OpenSpecy-1.2.0/OpenSpecy/R/read_envi.R | 348 OpenSpecy-1.2.0/OpenSpecy/R/read_ext.R | 698 - OpenSpecy-1.2.0/OpenSpecy/R/read_multi.R | 209 OpenSpecy-1.2.0/OpenSpecy/R/read_opus.R | 374 OpenSpecy-1.2.0/OpenSpecy/R/read_opus_raw.R | 2054 +-- OpenSpecy-1.2.0/OpenSpecy/R/run_app.R | 112 OpenSpecy-1.2.0/OpenSpecy/R/sig_noise.R | 284 OpenSpecy-1.2.0/OpenSpecy/R/smooth_intens.R | 362 OpenSpecy-1.2.0/OpenSpecy/R/spec_res.R | 90 OpenSpecy-1.2.0/OpenSpecy/R/split_spec.R | 104 OpenSpecy-1.2.0/OpenSpecy/R/subtr_baseline.R | 300 OpenSpecy-1.2.0/OpenSpecy/R/test_lib.R | 38 OpenSpecy-1.2.0/OpenSpecy/R/zzz.R | 14 OpenSpecy-1.2.0/OpenSpecy/README.md | 214 OpenSpecy-1.2.0/OpenSpecy/build/partial.rdb |binary OpenSpecy-1.2.0/OpenSpecy/build/vignette.rds |binary OpenSpecy-1.2.0/OpenSpecy/inst/doc/sop.R | 644 - OpenSpecy-1.2.0/OpenSpecy/inst/doc/sop.Rmd | 1624 +- OpenSpecy-1.2.0/OpenSpecy/inst/doc/sop.html | 6425 +++++----- OpenSpecy-1.2.0/OpenSpecy/inst/extdata/fitr_nitrocellulose.jdx | 2050 +-- OpenSpecy-1.2.0/OpenSpecy/inst/extdata/raman_hdpe.csv | 1930 +-- OpenSpecy-1.2.0/OpenSpecy/inst/extdata/raman_hdpe.json | 2 OpenSpecy-1.2.0/OpenSpecy/inst/extdata/raman_hdpe.yml | 3882 +++--- OpenSpecy-1.2.0/OpenSpecy/inst/extdata/raman_hdpe_os.csv | 4 OpenSpecy-1.2.0/OpenSpecy/man/adj_intens.Rd | 118 OpenSpecy-1.2.0/OpenSpecy/man/adj_range.Rd | 140 OpenSpecy-1.2.0/OpenSpecy/man/as_OpenSpecy.Rd | 414 OpenSpecy-1.2.0/OpenSpecy/man/conform_spec.Rd | 112 OpenSpecy-1.2.0/OpenSpecy/man/data_norm.Rd | 154 OpenSpecy-1.2.0/OpenSpecy/man/def_features.Rd | 232 OpenSpecy-1.2.0/OpenSpecy/man/gen_OpenSpecy.Rd | 146 OpenSpecy-1.2.0/OpenSpecy/man/human_ts.Rd | 60 OpenSpecy-1.2.0/OpenSpecy/man/interactive_plots.Rd | 292 OpenSpecy-1.2.0/OpenSpecy/man/io_spec.Rd | 171 OpenSpecy-1.2.0/OpenSpecy/man/make_rel.Rd | 98 OpenSpecy-1.2.0/OpenSpecy/man/manage_lib.Rd | 388 OpenSpecy-1.2.0/OpenSpecy/man/manage_na.Rd | 116 OpenSpecy-1.2.0/OpenSpecy/man/manage_spec.Rd | 166 OpenSpecy-1.2.0/OpenSpecy/man/match_spec.Rd | 410 OpenSpecy-1.2.0/OpenSpecy/man/process_spec.Rd | 236 OpenSpecy-1.2.0/OpenSpecy/man/raman_hdpe.Rd | 70 OpenSpecy-1.2.0/OpenSpecy/man/read_envi.Rd | 144 OpenSpecy-1.2.0/OpenSpecy/man/read_ext.Rd | 308 OpenSpecy-1.2.0/OpenSpecy/man/read_multi.Rd | 102 OpenSpecy-1.2.0/OpenSpecy/man/read_opus.Rd | 178 OpenSpecy-1.2.0/OpenSpecy/man/read_opus_raw.Rd | 158 OpenSpecy-1.2.0/OpenSpecy/man/run_app.Rd | 88 OpenSpecy-1.2.0/OpenSpecy/man/sig_noise.Rd | 196 OpenSpecy-1.2.0/OpenSpecy/man/smooth_intens.Rd | 208 OpenSpecy-1.2.0/OpenSpecy/man/spec_res.Rd | 82 OpenSpecy-1.2.0/OpenSpecy/man/split_spec.Rd | 80 OpenSpecy-1.2.0/OpenSpecy/man/subtr_baseline.Rd | 156 OpenSpecy-1.2.0/OpenSpecy/man/test_lib.Rd | 42 OpenSpecy-1.2.0/OpenSpecy/tests/logging/test-logging.R | 12 OpenSpecy-1.2.0/OpenSpecy/tests/testthat.R | 14 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/Rplots.pdf |only OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-adj_intens.R | 58 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-adj_range.R | 130 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-adj_wave.R | 34 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-as_OpenSpecy.R | 228 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-conform_spec.R | 148 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-data_norm.R | 38 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-def_features.R | 452 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-gen_OpenSpecy.R | 64 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-human_ts.R | 12 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-interactive_plots.R | 69 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-io_spec.R | 197 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-make_rel.R | 42 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-manage_lib.R | 126 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-manage_na.R | 82 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-manage_spec.R | 144 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-match_spec.R | 625 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-process_spec.R | 70 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-read_envi.R | 61 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-read_ext.R | 231 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-read_multi.R | 40 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-read_opus.R | 86 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-run_app.R | 22 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-sig_noise.R | 124 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-smooth_intens.R | 82 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-spec_res.R | 10 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-split_spec.R | 22 OpenSpecy-1.2.0/OpenSpecy/tests/testthat/test-subtr_baseline.R | 64 OpenSpecy-1.2.0/OpenSpecy/tests/validation/test-augmented.R | 260 OpenSpecy-1.2.0/OpenSpecy/vignettes/sop.Rmd | 1624 +- 112 files changed, 19747 insertions(+), 19739 deletions(-)
Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then
performing them and processing the results. 'httr2' is a modern
re-imagining of 'httr' that uses a pipe-based interface and solves
more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
Maximilian Girlich [ctb]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between httr2 versions 1.0.3 dated 2024-08-21 and 1.0.4 dated 2024-09-13
DESCRIPTION | 9 - MD5 | 202 ++++++++++++------------ NAMESPACE | 6 NEWS.md | 13 + R/content-type.R | 2 R/curl.R | 2 R/iterate.R | 5 R/multi-req.R | 6 R/oauth-client.R | 2 R/oauth-flow-auth-code.R | 5 R/oauth-flow-client-credentials.R | 3 R/oauth-flow-device.R | 3 R/oauth-flow-jwt.R | 3 R/oauth-flow-password.R | 3 R/oauth-flow-refresh.R | 3 R/req-body.R | 64 ++++--- R/req-cache.R | 43 +++-- R/req-cookies.R | 57 +++++- R/req-perform-connection.R |only R/req-perform-stream.R | 41 ---- R/req-perform.R | 30 ++- R/req-promise.R | 2 R/req-retries.R | 46 +++-- R/req-throttle.R | 2 R/req.R | 13 + R/resp-body.R | 36 +++- R/resp-headers.R | 4 R/resp-stream.R |only R/resp.R | 10 - R/secret.R | 6 R/sequential.R | 4 R/test.R | 2 R/url.R | 8 R/utils.R | 47 +++++ README.md | 9 - inst/doc/httr2.R | 3 inst/doc/httr2.Rmd | 3 inst/doc/httr2.html | 38 ++-- man/multi_req_perform.Rd | 4 man/oauth_client_req_auth.Rd | 2 man/oauth_token_cached.Rd | 2 man/req_auth_basic.Rd | 2 man/req_auth_bearer_token.Rd | 2 man/req_body.Rd | 2 man/req_cache.Rd | 9 - man/req_cookie_preserve.Rd | 46 ++++- man/req_dry_run.Rd | 2 man/req_error.Rd | 2 man/req_method.Rd | 2 man/req_oauth.Rd | 2 man/req_oauth_auth_code.Rd | 7 man/req_oauth_bearer_jwt.Rd | 5 man/req_oauth_client_credentials.Rd | 5 man/req_oauth_device.Rd | 7 man/req_oauth_password.Rd | 7 man/req_oauth_refresh.Rd | 5 man/req_perform.Rd | 2 man/req_perform_connection.Rd |only man/req_perform_iterative.Rd | 5 man/req_perform_parallel.Rd | 4 man/req_perform_promise.Rd | 4 man/req_perform_sequential.Rd | 4 man/req_perform_stream.Rd | 2 man/req_proxy.Rd | 2 man/req_retry.Rd | 29 ++- man/req_template.Rd | 2 man/req_throttle.Rd | 2 man/req_timeout.Rd | 2 man/req_url.Rd | 2 man/req_user_agent.Rd | 2 man/req_verbose.Rd | 2 man/request.Rd | 16 + man/resp_body_raw.Rd | 2 man/resp_check_content_type.Rd | 2 man/resp_content_type.Rd | 2 man/resp_date.Rd | 2 man/resp_headers.Rd | 2 man/resp_link_url.Rd | 2 man/resp_raw.Rd | 2 man/resp_retry_after.Rd | 2 man/resp_status.Rd | 2 man/resp_stream_raw.Rd |only man/resp_url.Rd | 2 man/secrets.Rd | 6 tests/testthat/_snaps/req-body.md | 9 + tests/testthat/_snaps/req-perform-connection.md |only tests/testthat/_snaps/req-retries.md | 18 ++ tests/testthat/_snaps/resp-stream.md |only tests/testthat/_snaps/resp.md | 7 tests/testthat/_snaps/utils.md | 6 tests/testthat/helper-webfakes.R |only tests/testthat/helper.R |only tests/testthat/test-curl.R | 7 tests/testthat/test-oauth-flow-auth-code.R | 14 - tests/testthat/test-req-body.R | 16 + tests/testthat/test-req-cache.R | 4 tests/testthat/test-req-cookies.R | 18 ++ tests/testthat/test-req-perform-connection.R |only tests/testthat/test-req-perform-stream.R | 4 tests/testthat/test-req-perform.R | 90 ++++++++++ tests/testthat/test-req-retries.R | 10 + tests/testthat/test-req-throttle.R | 19 +- tests/testthat/test-resp-body.R | 12 + tests/testthat/test-resp-stream.R |only tests/testthat/test-resp.R | 3 tests/testthat/test-utils.R | 28 ++- vignettes/httr2.Rmd | 3 107 files changed, 837 insertions(+), 385 deletions(-)
Title: Experimental Design and Analysis for Tree Improvement
Description: Provides data sets and R Codes for E.R. Williams, C.E. Harwood and A.C. Matheson (2023). Experimental Design and Analysis for Tree Improvement, CSIRO Publishing.
Author: Muhammad Yaseen [aut, cre, cph]
,
Sami Ullah [aut, ctb],
Kent Eskridge [aut, ctb],
Emlyn Williams [aut, ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between eda4treeR versions 0.6.0 dated 2023-05-01 and 1.1.0 dated 2024-09-13
DESCRIPTION | 19 ++-- MD5 | 116 ++++++++++++++--------------- NEWS.md | 56 +++++++------- R/DataExam2.1.R | 2 R/DataExam2.2.R | 2 R/DataExam3.1.1.R | 9 +- R/DataExam3.1.R | 8 +- R/DataExam4.3.R | 16 ++-- R/DataExam4.4.R | 10 +- R/DataExam5.1.R | 8 +- R/DataExam5.2.R | 8 +- R/DataExam8.2.R | 24 +++--- R/Exam2.1.R | 9 -- R/Exam2.2.R | 13 +-- R/Exam3.1.1.R | 12 +-- R/Exam3.1.R | 76 ++++++++++++++----- R/Exam4.3.1.R | 14 +-- R/Exam4.3.R | 36 +++++---- R/Exam4.4.R | 12 +-- R/Exam5.1.R | 124 ++++++++++++++++++------------- R/Exam5.2.R | 95 +++++++++++++++--------- R/Exam6.2.R | 57 +++++++------- R/Exam8.1.1.R | 154 ++++++++++++++++++++------------------ R/Exam8.1.2.R | 33 +++++--- R/Exam8.1.R | 27 ++++-- R/Exam8.2.R | 126 +++++++++++++++---------------- README.md | 186 +++++++++++++++++++++++------------------------ data/DataExam2.1.RData |binary data/DataExam2.2.RData |binary data/DataExam3.1.1.RData |binary data/DataExam3.1.RData |binary data/DataExam4.3.RData |binary data/DataExam4.4.RData |binary data/DataExam5.1.RData |binary data/DataExam5.2.RData |binary data/DataExam8.2.RData |binary man/DataExam2.1.Rd | 2 man/DataExam2.2.Rd | 2 man/DataExam3.1.1.Rd | 9 +- man/DataExam3.1.Rd | 8 +- man/DataExam4.3.Rd | 16 ++-- man/DataExam4.4.Rd | 10 +- man/DataExam5.1.Rd | 8 +- man/DataExam5.2.Rd | 8 +- man/DataExam8.2.Rd | 24 +++--- man/Exam2.1.Rd | 8 -- man/Exam2.2.Rd | 12 +-- man/Exam3.1.1.Rd | 11 +- man/Exam3.1.Rd | 76 ++++++++++++++----- man/Exam4.3.1.Rd | 13 +-- man/Exam4.3.Rd | 35 +++++--- man/Exam4.4.Rd | 11 +- man/Exam5.1.Rd | 123 ++++++++++++++++++------------- man/Exam5.2.Rd | 92 +++++++++++++++-------- man/Exam6.2.Rd | 56 +++++++------- man/Exam8.1.1.Rd | 33 +++++--- man/Exam8.1.2.Rd | 32 +++++--- man/Exam8.1.Rd | 26 ++++-- man/Exam8.2.Rd | 17 ++-- 59 files changed, 1081 insertions(+), 803 deletions(-)
Title: Diallel Analysis with R
Description: Performs Diallel Analysis with R using Griffing's and Hayman's approaches. Four different Methods (1: Method-I (Parents + F1's + reciprocals); 2: Method-II (Parents and one set of F1's); 3: Method-III (One set of F1's and reciprocals); 4: Method-IV (One set of F1's only)) and two Models (1: Fixed Effects Model; 2: Random Effects Model) can be applied using Griffing's approach.
Author: Muhammad Yaseen [aut, cre, cph]
,
Kent Eskridge [ctb, aut],
Pedro Barbosa [ctb, aut],
Yuhang Guo [ctb, aut]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between DiallelAnalysisR versions 0.5.0 dated 2023-03-31 and 0.6.0 dated 2024-09-13
DESCRIPTION | 23 +++---- MD5 | 6 - NEWS.md | 56 +++++++++-------- README.md | 197 +++++++++++++++++++++++++++++------------------------------- 4 files changed, 142 insertions(+), 140 deletions(-)
More information about DiallelAnalysisR at CRAN
Permanent link
Title: 'Java' Environments for R Projects
Description: Quickly install 'Java Development Kit (JDK)' without
administrative privileges and set environment variables in current R
session or project to solve common issues with 'Java' environment
management in 'R'. Recommended to users of 'Java'/'rJava'-dependent
'R' packages such as 'r5r', 'opentripplanner', 'xlsx', 'openNLP',
'rWeka', 'RJDBC', 'tabulapdf', and many more. 'rJavaEnv' prevents
common problems like 'Java' not found, 'Java' version conflicts,
missing 'Java' installations, and the inability to install 'Java' due
to lack of administrative privileges. 'rJavaEnv' automates the
download, installation, and setup of the 'Java' on a per-project basis
by setting the relevant 'JAVA_HOME' in the current 'R' session or the
current working directory (via '.Rprofile', with the user's consent).
Similar to what 'renv' does for 'R' packages, 'rJavaEnv' allows
different 'Java' versions to be used across different projects, but
can also be configured to allow multiple versions within the same
proj [...truncated...]
Author: Egor Kotov [aut, cre, cph] ,
Mauricio Vargas [ctb] ,
Hadley Wickham [ctb]
Maintainer: Egor Kotov <kotov.egor@gmail.com>
Diff between rJavaEnv versions 0.2.1 dated 2024-09-03 and 0.2.2 dated 2024-09-13
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 6 ++++++ R/java_env.R | 8 +++++--- README.md | 2 +- inst/schemaorg.json | 2 +- 7 files changed, 23 insertions(+), 14 deletions(-)
Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, stats, geoms and scales for plotting
"light" spectra with 'ggplot2', together with specializations of ggplot()
and autoplot() methods for spectral data and waveband definitions
stored in objects of classes defined in package 'photobiology'. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggspectra versions 0.3.12 dated 2023-10-21 and 0.3.13 dated 2024-09-13
ggspectra-0.3.12/ggspectra/inst/doc/userguide3-data-manip.R |only ggspectra-0.3.12/ggspectra/inst/doc/userguide3-data-manip.Rmd |only ggspectra-0.3.12/ggspectra/inst/doc/userguide3-data-manip.html |only ggspectra-0.3.12/ggspectra/vignettes/userguide3-data-manip.Rmd |only ggspectra-0.3.13/ggspectra/DESCRIPTION | 14 ggspectra-0.3.13/ggspectra/MD5 | 158 - ggspectra-0.3.13/ggspectra/NEWS.md | 31 ggspectra-0.3.13/ggspectra/R/autoplot-calibration-spct.R | 116 ggspectra-0.3.13/ggspectra/R/autoplot-cps-spct.r | 152 - ggspectra-0.3.13/ggspectra/R/autoplot-filter-spct.r | 425 +-- ggspectra-0.3.13/ggspectra/R/autoplot-generic-spct.R | 87 ggspectra-0.3.13/ggspectra/R/autoplot-raw-spct.r | 113 ggspectra-0.3.13/ggspectra/R/autoplot-response-spct.r | 128 ggspectra-0.3.13/ggspectra/R/autoplot-source-spct.r | 181 - ggspectra-0.3.13/ggspectra/R/autotitle.R | 211 + ggspectra-0.3.13/ggspectra/R/axis-labels-texts.R | 159 - ggspectra-0.3.13/ggspectra/R/axis-utils-calibration-spct.R | 41 ggspectra-0.3.13/ggspectra/R/axis-utils-cps-spct.R | 41 ggspectra-0.3.13/ggspectra/R/axis-utils-filter-spct.R | 283 +- ggspectra-0.3.13/ggspectra/R/axis-utils-raw-spct.R | 45 ggspectra-0.3.13/ggspectra/R/axis-utils-response-spct.R | 148 - ggspectra-0.3.13/ggspectra/R/axis-utils-source-spct.R | 99 ggspectra-0.3.13/ggspectra/R/axis-utils-wlength.R | 180 + ggspectra-0.3.13/ggspectra/R/ggplot-methods.R | 27 ggspectra-0.3.13/ggspectra/README.md | 18 ggspectra-0.3.13/ggspectra/build/partial.rdb |binary ggspectra-0.3.13/ggspectra/build/vignette.rds |binary ggspectra-0.3.13/ggspectra/inst/doc/userguide-0-r4p-introduction.html | 4 ggspectra-0.3.13/ggspectra/inst/doc/userguide1-grammar.R | 8 ggspectra-0.3.13/ggspectra/inst/doc/userguide1-grammar.Rmd | 16 ggspectra-0.3.13/ggspectra/inst/doc/userguide1-grammar.html | 1296 +++++----- ggspectra-0.3.13/ggspectra/inst/doc/userguide2-autoplot-methods.R | 47 ggspectra-0.3.13/ggspectra/inst/doc/userguide2-autoplot-methods.Rmd | 99 ggspectra-0.3.13/ggspectra/inst/doc/userguide2-autoplot-methods.html | 472 ++- ggspectra-0.3.13/ggspectra/man/A_label.Rd | 13 ggspectra-0.3.13/ggspectra/man/Afr_label.Rd | 22 ggspectra-0.3.13/ggspectra/man/O_plot.Rd | 5 ggspectra-0.3.13/ggspectra/man/Rfr_label.Rd | 17 ggspectra-0.3.13/ggspectra/man/Tfr_label.Rd | 19 ggspectra-0.3.13/ggspectra/man/autoplot.calibration_spct.Rd | 90 ggspectra-0.3.13/ggspectra/man/autoplot.cps_spct.Rd | 89 ggspectra-0.3.13/ggspectra/man/autoplot.filter_spct.Rd | 124 ggspectra-0.3.13/ggspectra/man/autoplot.generic_spct.Rd | 76 ggspectra-0.3.13/ggspectra/man/autoplot.object_spct.Rd | 111 ggspectra-0.3.13/ggspectra/man/autoplot.raw_spct.Rd | 88 ggspectra-0.3.13/ggspectra/man/autoplot.reflector_spct.Rd | 96 ggspectra-0.3.13/ggspectra/man/autoplot.response_spct.Rd | 96 ggspectra-0.3.13/ggspectra/man/autoplot.source_spct.Rd | 110 ggspectra-0.3.13/ggspectra/man/autotitle.Rd | 30 ggspectra-0.3.13/ggspectra/man/axis_labels.Rd | 27 ggspectra-0.3.13/ggspectra/man/counts_label.Rd | 6 ggspectra-0.3.13/ggspectra/man/cps_label.Rd | 6 ggspectra-0.3.13/ggspectra/man/cps_plot.Rd | 5 ggspectra-0.3.13/ggspectra/man/e_plot.Rd | 13 ggspectra-0.3.13/ggspectra/man/e_rsp_plot.Rd | 5 ggspectra-0.3.13/ggspectra/man/figures/README-example0-1.png |binary ggspectra-0.3.13/ggspectra/man/figures/README-example1-1.png |binary ggspectra-0.3.13/ggspectra/man/figures/README-example2-1.png |binary ggspectra-0.3.13/ggspectra/man/generic_plot.Rd | 9 ggspectra-0.3.13/ggspectra/man/multipliers_label.Rd | 8 ggspectra-0.3.13/ggspectra/man/q_plot.Rd | 5 ggspectra-0.3.13/ggspectra/man/q_rsp_plot.Rd | 5 ggspectra-0.3.13/ggspectra/man/raw_plot.Rd | 5 ggspectra-0.3.13/ggspectra/man/s.e.irrad_label.Rd | 28 ggspectra-0.3.13/ggspectra/man/s.e.response_label.Rd | 15 ggspectra-0.3.13/ggspectra/man/scale_x_energy_eV_continuous.Rd | 11 ggspectra-0.3.13/ggspectra/man/scale_x_frequency_continuous.Rd | 7 ggspectra-0.3.13/ggspectra/man/scale_x_wavenumber_continuous.Rd | 7 ggspectra-0.3.13/ggspectra/man/scale_x_wl_continuous.Rd | 7 ggspectra-0.3.13/ggspectra/man/scale_y_A_continuous.Rd | 20 ggspectra-0.3.13/ggspectra/man/scale_y_Afr_continuous.Rd | 20 ggspectra-0.3.13/ggspectra/man/scale_y_Rfr_continuous.Rd | 33 ggspectra-0.3.13/ggspectra/man/scale_y_Tfr_continuous.Rd | 33 ggspectra-0.3.13/ggspectra/man/scale_y_counts_continuous.Rd | 10 ggspectra-0.3.13/ggspectra/man/scale_y_cps_continuous.Rd | 7 ggspectra-0.3.13/ggspectra/man/scale_y_multipliers_continuous.Rd | 7 ggspectra-0.3.13/ggspectra/man/scale_y_s.e.irrad_continuous.Rd | 19 ggspectra-0.3.13/ggspectra/man/scale_y_s.e.response_continuous.Rd | 19 ggspectra-0.3.13/ggspectra/man/sec_axis_w_number.Rd | 33 ggspectra-0.3.13/ggspectra/man/w_length_label.Rd | 27 ggspectra-0.3.13/ggspectra/vignettes/userguide1-grammar.Rmd | 16 ggspectra-0.3.13/ggspectra/vignettes/userguide2-autoplot-methods.Rmd | 99 82 files changed, 3651 insertions(+), 2446 deletions(-)
Title: Boldness-Recalibration of Binary Events
Description: Boldness-recalibration maximally spreads out probability predictions while maintaining a user specified level of calibration, facilitated the brcal() function. Supporting functions to assess calibration via Bayesian and Frequentist approaches, Maximum Likelihood Estimator (MLE) recalibration, Linear in Log Odds (LLO)-adjust via any specified parameters, and visualize results are also provided. Methodological details can be found in Guthrie & Franck (2024) <doi:10.1080/00031305.2024.2339266>.
Author: Adeline P. Guthrie [aut, cre] ,
Christopher T. Franck [aut]
Maintainer: Adeline P. Guthrie <apguthrie47@gmail.com>
Diff between BRcal versions 0.0.4 dated 2024-06-25 and 1.0.0 dated 2024-09-13
BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br90_ac47b5dd88ca2583e3d44e9682cbe57f.RData |only BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br90_ac47b5dd88ca2583e3d44e9682cbe57f.rdb |only BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br90_ac47b5dd88ca2583e3d44e9682cbe57f.rdx |only BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br90_tau_0145ca272a70355028da45bd15f5589a.RData |only BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br90_tau_0145ca272a70355028da45bd15f5589a.rdb |only BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br90_tau_0145ca272a70355028da45bd15f5589a.rdx |only BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br95_09588f0c17d7957638d385fbffa61064.RData |only BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br95_09588f0c17d7957638d385fbffa61064.rdb |only BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br95_09588f0c17d7957638d385fbffa61064.rdx |only BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br95_2_4eb1a9e9235c9c6ed392a27e3d820a98.RData |only BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br95_2_4eb1a9e9235c9c6ed392a27e3d820a98.rdb |only BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br95_2_4eb1a9e9235c9c6ed392a27e3d820a98.rdx |only BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br95_3_4701cfca89cc7ddfb92daf695ef21c15.RData |only BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br95_3_4701cfca89cc7ddfb92daf695ef21c15.rdb |only BRcal-0.0.4/BRcal/vignettes/hockey_vignette_cache/html/br95_3_4701cfca89cc7ddfb92daf695ef21c15.rdx |only BRcal-1.0.0/BRcal/DESCRIPTION | 12 BRcal-1.0.0/BRcal/MD5 | 57 +-- BRcal-1.0.0/BRcal/NAMESPACE | 2 BRcal-1.0.0/BRcal/R/boldness_recalib.R | 42 -- BRcal-1.0.0/BRcal/R/data.R | 57 ++- BRcal-1.0.0/BRcal/R/plotting_functions.R | 161 ++++++---- BRcal-1.0.0/BRcal/README.md | 2 BRcal-1.0.0/BRcal/build/partial.rdb |only BRcal-1.0.0/BRcal/data/foreclosure.rda |only BRcal-1.0.0/BRcal/inst/doc/hockey_vignette.R | 27 + BRcal-1.0.0/BRcal/inst/doc/hockey_vignette.Rmd | 44 +- BRcal-1.0.0/BRcal/inst/doc/hockey_vignette.html | 145 +++++---- BRcal-1.0.0/BRcal/man/foreclosure.Rd |only BRcal-1.0.0/BRcal/man/lineplot.Rd | 27 + BRcal-1.0.0/BRcal/man/plot_params.Rd | 17 - BRcal-1.0.0/BRcal/vignettes/hockey_vignette.Rmd | 44 +- BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br90_833624141bc7c2f984bd2a2aa5589f83.RData |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br90_833624141bc7c2f984bd2a2aa5589f83.rdb |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br90_833624141bc7c2f984bd2a2aa5589f83.rdx |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br90_tau_5cbcbb517f5ea9a6a92958ce86c80468.RData |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br90_tau_5cbcbb517f5ea9a6a92958ce86c80468.rdb |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br90_tau_5cbcbb517f5ea9a6a92958ce86c80468.rdx |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_2_bc84195f5545bbeeb9459ba87cee4579.RData |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_2_bc84195f5545bbeeb9459ba87cee4579.rdb |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_2_bc84195f5545bbeeb9459ba87cee4579.rdx |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_3_a15138f2ae67678b519d05efb23146d1.RData |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_3_a15138f2ae67678b519d05efb23146d1.rdb |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_3_a15138f2ae67678b519d05efb23146d1.rdx |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_49c34b170b17be939d8b4874d4c661aa.RData |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_49c34b170b17be939d8b4874d4c661aa.rdb |only BRcal-1.0.0/BRcal/vignettes/hockey_vignette_cache/html/br95_49c34b170b17be939d8b4874d4c661aa.rdx |only 46 files changed, 387 insertions(+), 250 deletions(-)
More information about timeSeriesDataSets at CRAN
Permanent link
More information about power.transform at CRAN
Permanent link
Title: Manipulate Date, POSIXct and hms Vectors
Description: Manipulates date ('Date'), date time ('POSIXct') and time
('hms') vectors. Date/times are considered discrete and are floored
whenever encountered. Times are wrapped and time zones are maintained
unless explicitly altered by the user.
Author: Joe Thorley [aut] ,
Ayla Pearson [aut, cre] ,
Poisson Consulting [cph, fnd]
Maintainer: Ayla Pearson <ayla@poissonconsulting.ca>
Diff between dttr2 versions 0.5.0 dated 2023-11-14 and 0.5.1 dated 2024-09-13
dttr2-0.5.0/dttr2/R/namespace.R |only dttr2-0.5.1/dttr2/DESCRIPTION | 13 +++---- dttr2-0.5.1/dttr2/LICENSE | 4 +- dttr2-0.5.1/dttr2/MD5 | 51 ++++++++++++++--------------- dttr2-0.5.1/dttr2/NAMESPACE | 5 ++ dttr2-0.5.1/dttr2/NEWS.md | 7 +++ dttr2-0.5.1/dttr2/R/complete.R | 6 +-- dttr2-0.5.1/dttr2/R/dttr2-package.R | 3 - dttr2-0.5.1/dttr2/R/excel_to_date_time.R | 2 - dttr2-0.5.1/dttr2/R/internal.R | 3 + dttr2-0.5.1/dttr2/R/utils.R | 2 + dttr2-0.5.1/dttr2/README.md | 9 ++--- dttr2-0.5.1/dttr2/man/dtt_adjust_units.Rd | 4 +- dttr2-0.5.1/dttr2/man/dtt_date.Rd | 2 - dttr2-0.5.1/dttr2/man/dtt_date_time.Rd | 2 - dttr2-0.5.1/dttr2/man/dtt_days_in_month.Rd | 4 +- dttr2-0.5.1/dttr2/man/dtt_days_in_year.Rd | 4 +- dttr2-0.5.1/dttr2/man/dtt_daytt.Rd | 4 +- dttr2-0.5.1/dttr2/man/dtt_excel_to_date.Rd | 4 +- dttr2-0.5.1/dttr2/man/dtt_floor.Rd | 2 - dttr2-0.5.1/dttr2/man/dtt_floored.Rd | 2 - dttr2-0.5.1/dttr2/man/dtt_sys_time.Rd | 4 +- dttr2-0.5.1/dttr2/man/dtt_time.Rd | 6 +-- dttr2-0.5.1/dttr2/man/dttr2-package.Rd | 3 + dttr2-0.5.1/dttr2/man/is_date_time.Rd | 4 +- dttr2-0.5.1/dttr2/tests/spelling.R | 9 +++-- dttr2-0.5.1/dttr2/tests/testthat.R | 8 ++++ 27 files changed, 98 insertions(+), 69 deletions(-)
Title: EcoPhyloMapper
Description: Facilitates the aggregation of species' geographic ranges from vector or raster spatial data, and that enables the calculation of various morphological and phylogenetic community metrics across geography. Citation: Title, PO, DL Swiderski and ML Zelditch (2022) <doi:10.1111/2041-210X.13914>.
Author: Pascal Title [aut, cre] ,
Donald Swiderski [aut],
Miriam Zelditch [aut]
Maintainer: Pascal Title <pascal.title@stonybrook.edu>
Diff between epm versions 1.1.2 dated 2023-12-19 and 1.1.3 dated 2024-09-13
DESCRIPTION | 8 +-- MD5 | 24 +++++------ R/addTraits.R | 4 + R/createEPMgrid.R | 3 + R/customBetaDiv.R | 2 R/epm-package.R | 3 - R/gridMetrics.R | 111 +++++++++++++++++++++++++++++++++++++++++++-------- R/tableFromEpmGrid.R | 29 +++++++++++++ build/partial.rdb |binary man/createEPMgrid.Rd | 2 man/customBetaDiv.Rd | 2 man/epm.Rd | 9 ++++ man/gridMetrics.Rd | 15 +++++- 13 files changed, 173 insertions(+), 39 deletions(-)
Title: Nonparametric Bootstrap Test with Pooled Resampling
Description: Addressing crucial research questions often necessitates a small
sample size due to factors such as distinctive target populations, rarity
of the event under study, time and cost constraints, ethical concerns, or
group-level unit of analysis. Many readily available analytic methods,
however, do not accommodate small sample sizes, and the choice of the best
method can be unclear. The 'npboottprm' package enables the execution of
nonparametric bootstrap tests with pooled resampling to help fill this gap.
Grounded in the statistical methods for small sample size studies detailed
in Dwivedi, Mallawaarachchi, and Alvarado (2017) <doi:10.1002/sim.7263>, the
package facilitates a range of statistical tests, encompassing independent
t-tests, paired t-tests, and one-way Analysis of Variance (ANOVA) F-tests.
The nonparboot() function undertakes essential computations, yielding
detailed outputs which include test statistics, effect sizes, confidence
intervals, and bootstrap distributions. F [...truncated...]
Author: Mackson Ncube [aut, cre],
mightymetrika, LLC [cph, fnd]
Maintainer: Mackson Ncube <macksonncube.stats@gmail.com>
Diff between npboottprm versions 0.3.1 dated 2024-07-16 and 0.3.2 dated 2024-09-13
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Title: Deconvolution of Bulk RNA-Seq Data Based on Deep Learning
Description: Deconvolution of bulk RNA-Seq data using context-specific deconvolution models based on Deep Neural Networks using scRNA-Seq data as input. These models are able to make accurate estimates of the cell composition of bulk RNA-Seq samples from the same context using the advances provided by Deep Learning and the meaningful information provided by scRNA-Seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> for more details.
Author: Diego Mananes [aut, cre] ,
Carlos Torroja [aut] ,
Fatima Sanchez-Cabo [aut]
Maintainer: Diego Mananes <dmananesc@cnic.es>
Diff between digitalDLSorteR versions 1.0.1 dated 2024-02-07 and 1.1.0 dated 2024-09-13
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More information about digitalDLSorteR at CRAN
Permanent link
Title: Tools for Handling Indices and Proportions in Small Area
Estimation
Description: It allows for mapping proportions and indicators defined on the unit interval. It implements Beta-based small area methods comprising the classical Beta regression models, the Flexible Beta model and Zero and/or One Inflated extensions (Janicki 2020 <doi:10.1080/03610926.2019.1570266>). Such methods, developed within a Bayesian framework through Stan <https://mc-stan.org/>, come equipped with a set of diagnostics and complementary tools, visualizing and exporting functions. A Shiny application with a user-friendly interface can be launched to further simplify the process. For further details, refer to De Nicolò and Gardini (2024 <doi:10.18637/jss.v108.i01>).
Author: Silvia De Nicolo [aut, cre] ,
Aldo Gardini [aut]
Maintainer: Silvia De Nicolo <silvia.denicolo@unibo.it>
Diff between tipsae versions 1.0.2 dated 2024-07-30 and 1.0.3 dated 2024-09-13
DESCRIPTION | 10 - MD5 | 35 ++-- R/fit_sae.R | 2 build/partial.rdb |binary inst/doc/tipsae_vignette.pdf |binary inst/shiny_tipsae/server_files/data_load_server.R | 4 inst/shiny_tipsae/server_files/plots/data_summary_plot_map.R | 7 inst/shiny_tipsae/server_files/plots/results_estimates_map.R | 5 inst/shiny_tipsae/server_files/plots/results_raneff_map_spat.R | 5 inst/shiny_tipsae/server_files/plots/results_raneff_map_temp.R | 5 inst/shiny_tipsae/server_files/plots/results_raneff_map_unstr.R | 5 inst/shiny_tipsae/server_files/plots/results_summary_map_resid.R | 5 inst/shiny_tipsae/server_files/results_estimates_server.R | 4 inst/shiny_tipsae/ui_files/results_estimates.R | 4 inst/shiny_tipsae/www/complement_theme.css | 1 inst/stan/include/transf_par_ZIBalt.stan | 4 man/fit_sae.Rd | 2 src/stanExports_global.h | 80 +++++----- vignettes/tipsae_vignette_output.pdf |only 19 files changed, 91 insertions(+), 87 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics
Description: A collection of functions to create spatial weights matrix
objects from polygon 'contiguities', from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial 'autocorrelation',
including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord'
(1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel'
general cross product statistic, Empirical Bayes estimates and
'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992)
<doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured
join count statistics, 'APLE' ('Li 'et al.' )
<doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I', 'Gearys C'
('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and
'Getis/Ord' G ('Ord' and 'Getis' 1995)
< [...truncated...]
Author: Roger Bivand [cre, aut] ,
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assuncao [ctb],
Anil Bera [ctb],
Olaf Berke [ctb],
F. Guillaume Blanchet [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Steph [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 1.3-5 dated 2024-06-10 and 1.3-6 dated 2024-09-13
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Title: Interpolation From C
Description: Simple interpolation methods designed to be used from C
code. Supports constant, linear and spline interpolation. An R
wrapper is included but this package is primarily designed to be
used from C code using 'LinkingTo'. The spline calculations are
classical cubic interpolation, e.g., Forsythe, Malcolm and Moler
(1977) <ISBN: 9780131653320>.
Author: Rich FitzJohn [aut, cre],
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between cinterpolate versions 1.0.1 dated 2023-11-29 and 1.0.2 dated 2024-09-13
DESCRIPTION | 6 +++--- LICENSE | 2 +- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/cinterpolate.html | 4 ++-- src/interpolate.c | 16 ++++++++-------- 6 files changed, 19 insertions(+), 19 deletions(-)
Title: Linear Predictive Models Based on the LIBLINEAR C/C++ Library
Description: A wrapper around the LIBLINEAR C/C++ library for machine
learning (available at
<https://www.csie.ntu.edu.tw/~cjlin/liblinear/>). LIBLINEAR is
a simple library for solving large-scale regularized linear
classification and regression. It currently supports
L2-regularized classification (such as logistic regression,
L2-loss linear SVM and L1-loss linear SVM) as well as
L1-regularized classification (such as L2-loss linear SVM and
logistic regression) and L2-regularized support vector
regression (with L1- or L2-loss). The main features of
LiblineaR include multi-class classification (one-vs-the rest,
and Crammer & Singer method), cross validation for model
selection, probability estimates (logistic regression only) or
weights for unbalanced data. The estimation of the models is
particularly fast as compared to other libraries.
Author: Thibault Helleputte [cre, aut, cph],
Jerome Paul [aut],
Pierre Gramme [aut]
Maintainer: Thibault Helleputte <thibault.helleputte@dnalytics.com>
Diff between LiblineaR versions 2.10-23 dated 2023-12-11 and 2.10-24 dated 2024-09-13
DESCRIPTION | 9 +++--- MD5 | 12 ++++----- NAMESPACE | 2 - NEWS | 3 ++ src/linear.cpp | 68 ++++++++++++++++++++++++++-------------------------- src/predictLinear.c | 10 +++---- src/trainLinear.c | 10 +++---- 7 files changed, 57 insertions(+), 57 deletions(-)
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana [aut, cre] ,
Joan Salvador [ctb]
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 4.8.0 dated 2024-01-29 and 4.9.0 dated 2024-09-13
compareGroups-4.8.0/compareGroups/inst/app/rsconnect |only compareGroups-4.8.0/compareGroups/vignettes/file20385ed07b92.html |only compareGroups-4.8.0/compareGroups/vignettes/file4b40486364bd.html |only compareGroups-4.9.0/compareGroups/DESCRIPTION | 12 compareGroups-4.9.0/compareGroups/MD5 | 94 - compareGroups-4.9.0/compareGroups/NAMESPACE | 1 compareGroups-4.9.0/compareGroups/NEWS.md | 8 compareGroups-4.9.0/compareGroups/R/chisq.test2.R | 7 compareGroups-4.9.0/compareGroups/R/compare.i.R | 6 compareGroups-4.9.0/compareGroups/R/compareGroups.R | 12 compareGroups-4.9.0/compareGroups/R/compareGroups.fit.R | 4 compareGroups-4.9.0/compareGroups/R/createTable.R | 5 compareGroups-4.9.0/compareGroups/R/descrTable.R | 4 compareGroups-4.9.0/compareGroups/R/export2csv.R | 8 compareGroups-4.9.0/compareGroups/R/export2html.R | 8 compareGroups-4.9.0/compareGroups/R/export2latex.cbind.createTable.R | 8 compareGroups-4.9.0/compareGroups/R/export2latex.createTable.R | 8 compareGroups-4.9.0/compareGroups/R/export2md.R | 30 compareGroups-4.9.0/compareGroups/R/export2mdcbind.R | 19 compareGroups-4.9.0/compareGroups/R/export2mdword.R | 6 compareGroups-4.9.0/compareGroups/R/export2mdwordcbind.R | 17 compareGroups-4.9.0/compareGroups/R/export2xls.R | 8 compareGroups-4.9.0/compareGroups/R/format2.R | 12 compareGroups-4.9.0/compareGroups/R/prepare.r | 10 compareGroups-4.9.0/compareGroups/R/print.cbind.createTable.R | 10 compareGroups-4.9.0/compareGroups/R/print.createTable.R | 8 compareGroups-4.9.0/compareGroups/R/table.i.R | 6 compareGroups-4.9.0/compareGroups/build/vignette.rds |binary compareGroups-4.9.0/compareGroups/inst/app/global.R | 8 compareGroups-4.9.0/compareGroups/inst/app/server.R | 20 compareGroups-4.9.0/compareGroups/inst/app/ui.R | 34 compareGroups-4.9.0/compareGroups/inst/app/www/ReGiCor.jpg |only compareGroups-4.9.0/compareGroups/inst/app/www/ciberCV.png |only compareGroups-4.9.0/compareGroups/inst/app/www/datarus.jpg |only compareGroups-4.9.0/compareGroups/inst/app/www/imim.png |only compareGroups-4.9.0/compareGroups/inst/doc/compareGroups_vignette.R | 92 - compareGroups-4.9.0/compareGroups/inst/doc/compareGroups_vignette.Rmd | 30 compareGroups-4.9.0/compareGroups/inst/doc/compareGroups_vignette.html | 726 +++++----- compareGroups-4.9.0/compareGroups/man/compareGroups-internal.Rd | 22 compareGroups-4.9.0/compareGroups/man/compareGroups-package.Rd | 4 compareGroups-4.9.0/compareGroups/man/compareGroups.Rd | 7 compareGroups-4.9.0/compareGroups/man/createTable.Rd | 11 compareGroups-4.9.0/compareGroups/man/descrTable.Rd | 8 compareGroups-4.9.0/compareGroups/man/export2csv.Rd | 7 compareGroups-4.9.0/compareGroups/man/export2html.Rd | 7 compareGroups-4.9.0/compareGroups/man/export2latex.Rd | 10 compareGroups-4.9.0/compareGroups/man/export2md.Rd | 10 compareGroups-4.9.0/compareGroups/man/export2xls.Rd | 4 compareGroups-4.9.0/compareGroups/man/figures/var1age.pdf |binary compareGroups-4.9.0/compareGroups/man/figures/var1sex.pdf |binary compareGroups-4.9.0/compareGroups/vignettes/compareGroups_vignette.Rmd | 30 51 files changed, 705 insertions(+), 636 deletions(-)
Title: Spatial Dependence for Simple Features
Description: An interface to 'spdep' to integrate with 'sf' objects and the 'tidyverse'.
Author: Josiah Parry [aut] ,
Dexter Locke [aut, cre]
Maintainer: Dexter Locke <dexter.locke@gmail.com>
Diff between sfdep versions 0.2.4 dated 2024-02-20 and 0.2.5 dated 2024-09-13
DESCRIPTION | 12 +++++----- MD5 | 13 +++++------ R/spacetime-constructor.R | 4 +-- R/spacetime-methods.R | 2 - R/utils-set-operations.R | 3 ++ build/partial.rdb |binary man/as_spacetime.Rd | 2 - tests/testthat/test-spacetime-constructor_cli_update_patch.R |only 8 files changed, 20 insertions(+), 16 deletions(-)
Title: 'La Societe Nouvelle' API Access
Description: Tools facilitating access to the 'macro_data' service of the
'La Societe Nouvelle' API. It ensures an easy and fully-disclosed
access to all macro-level data used in the 'La Societe Nouvelle'
systems and the related metadata. Related API can be accessed from
<https://api.lasocietenouvelle.org/>.
Author: Joris Blain [aut, cre]
Maintainer: Joris Blain <joris.blain@lasocietenouvelle.org>
Diff between lsnstat versions 1.0.0 dated 2023-04-22 and 1.0.1 dated 2024-09-13
DESCRIPTION | 13 +++--- MD5 | 21 ++++++--- NAMESPACE | 6 ++ NEWS.md |only R/lsnstat-package.R | 18 ++++---- R/lsnstat_macrodata.R | 70 ++++++++++++++++++-------------- R/lsnstat_metadata.R | 46 +++++++++++---------- R/utils.R |only README.md | 4 - man/from_filter_list_to_sql.Rd |only man/get_endpoint.Rd |only man/get_lsn_dataset_list.Rd |only man/lsnstat_macrodata.Rd | 87 ++++++++++++++++++++++------------------- man/lsnstat_metadata.Rd | 70 +++++++++++++++----------------- 14 files changed, 181 insertions(+), 154 deletions(-)
Title: Equating of Multiple Forms
Description: Equating of multiple forms using Item Response Theory (IRT) methods (Battauz M. (2017) <doi:10.1007/s11336-016-9517-x>, Battauz and 'Leoncio' (2023) <doi:10.1177/01466216231151702>, Haberman S. J. (2009) <doi:10.1002/j.2333-8504.2009.tb02197.x>).
Author: Michela Battauz [aut, cre],
Waldir Leoncio [ctb]
Maintainer: Michela Battauz <michela.battauz@uniud.it>
Diff between equateMultiple versions 0.1.2 dated 2024-02-13 and 1.0.0 dated 2024-09-13
DESCRIPTION | 23 MD5 | 32 - NAMESPACE | 8 R/EqMult.r | 911 ++++++++++++++++++---------------- R/RcppExports.R | 8 build/vignette.rds |binary data |only inst/doc/equateMultiple_tutorial.R | 53 - inst/doc/equateMultiple_tutorial.Rmd | 74 +- inst/doc/equateMultiple_tutorial.html | 356 ++++++------- man/equateMultiple-package.Rd | 18 man/itm.Rd | 2 man/mathTest.Rd |only man/multiec.Rd | 41 + src/EqMult.cpp | 164 ++++++ src/Makevars |only src/Makevars.win |only src/RcppExports.cpp | 40 + vignettes/equateMultiple_tutorial.Rmd | 74 +- 19 files changed, 1078 insertions(+), 726 deletions(-)
More information about equateMultiple at CRAN
Permanent link
Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre] ,
Andreas Rappold [ctb]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between Deriv versions 4.1.3 dated 2021-02-24 and 4.1.6 dated 2024-09-13
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NEWS | 21 ++++++++++++++++++++- R/Deriv.R | 20 +++++++++++++------- R/Simplify.R | 32 +++++++++++++++++++++++++++----- inst/CITATION | 2 +- man/Deriv-package.Rd | 4 ++-- man/Deriv.Rd | 17 +++++++++++++---- tests/testthat/test_Deriv.R | 7 +++++-- 9 files changed, 95 insertions(+), 36 deletions(-)
Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers
that disseminate data by means of SDMX web services.
SDMX (Statistical Data and Metadata eXchange) is a standard that
has been developed with the aim of simplifying the exchange of
statistical information.
More about the SDMX standard and the SDMX Web Services
can be found at: <https://sdmx.org>.
Author: Attilio Mattiocco [aut, cre]
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>
Diff between RJSDMX versions 3.3-0 dated 2024-06-04 and 3.4-0 dated 2024-09-13
DESCRIPTION | 10 ++++++---- MD5 | 6 +++--- inst/java/SDMX.jar |binary man/RJSDMX-package.Rd | 2 +- 4 files changed, 10 insertions(+), 8 deletions(-)
Title: Quality Control for Label-Free Proteomics Expression Data
Description: Label-free bottom-up proteomics expression data is often affected by data heterogeneity and missing values. Normalization and missing value imputation are commonly used techniques to address these issues and make the dataset suitable for further downstream analysis. This package provides an optimal combination of normalization and imputation methods for the dataset. The package utilizes three normalization methods and three imputation methods.The statistical evaluation measures named pooled co-efficient of variance, pooled estimate of variance and pooled median absolute deviation are used for selecting the best combination of normalization and imputation method for the given dataset. The user can also visualize the results by using various plots available in this package. The user can also perform the differential expression analysis between two sample groups with the function included in this package. The chosen three normalization methods, three imputation methods and three evaluati [...truncated...]
Author: Kabilan S [aut, cre],
Dr Shashi Bhushan Lal [aut, ths],
Dr Sudhir Srivastava [aut, ths],
Dr Krishna Kumar Chaturvedi [ths],
Dr Yasin Jeshima K [ths],
Dr Ramasubramanian V [ths],
Dr Girish Kumar Jha [ctb]
Maintainer: Kabilan S <kabilan151414@gmail.com>
Diff between lfproQC versions 0.2.0 dated 2024-09-06 and 0.3.0 dated 2024-09-13
lfproQC-0.2.0/lfproQC/R/knn_rlr_yeast_data.R |only lfproQC-0.2.0/lfproQC/data/knn_rlr_yeast_data.rda |only lfproQC-0.2.0/lfproQC/man/knn_rlr_yeast_data.Rd |only lfproQC-0.3.0/lfproQC/DESCRIPTION | 8 lfproQC-0.3.0/lfproQC/MD5 | 49 - lfproQC-0.3.0/lfproQC/NEWS | 7 lfproQC-0.3.0/lfproQC/R/Boxplot_data.R | 2 lfproQC-0.3.0/lfproQC/R/Corrplot_data.R | 2 lfproQC-0.3.0/lfproQC/R/Densityplot_data.R | 2 lfproQC-0.3.0/lfproQC/R/MDSplot_data.R | 2 lfproQC-0.3.0/lfproQC/R/QQplot_data.R | 2 lfproQC-0.3.0/lfproQC/R/best_combination.R | 747 ++++++++++------------ lfproQC-0.3.0/lfproQC/R/rlr_knn_yeast_data.R |only lfproQC-0.3.0/lfproQC/R/top_table_fn.R | 2 lfproQC-0.3.0/lfproQC/README.md |only lfproQC-0.3.0/lfproQC/data/rlr_knn_yeast_data.rda |only lfproQC-0.3.0/lfproQC/inst/doc/user_guide.R | 14 lfproQC-0.3.0/lfproQC/inst/doc/user_guide.Rmd | 14 lfproQC-0.3.0/lfproQC/inst/doc/user_guide.html | 170 ++--- lfproQC-0.3.0/lfproQC/man/Boxplot_data.Rd | 2 lfproQC-0.3.0/lfproQC/man/Corrplot_data.Rd | 2 lfproQC-0.3.0/lfproQC/man/Densityplot_data.Rd | 2 lfproQC-0.3.0/lfproQC/man/MDSplot_data.Rd | 2 lfproQC-0.3.0/lfproQC/man/QQplot_data.Rd | 2 lfproQC-0.3.0/lfproQC/man/best_combination.Rd | 36 - lfproQC-0.3.0/lfproQC/man/lfproQC-package.Rd | 8 lfproQC-0.3.0/lfproQC/man/rlr_knn_yeast_data.Rd |only lfproQC-0.3.0/lfproQC/man/top_table_fn.Rd | 2 lfproQC-0.3.0/lfproQC/vignettes/user_guide.Rmd | 14 29 files changed, 556 insertions(+), 535 deletions(-)
Title: Lightening One-Code Resolving Microbial Ecology Solution
Description: Provides a robust collection of functions tailored for microbial ecology analysis, encompassing both data analysis and visualization. It introduces an encapsulation feature that streamlines the process into a summary object. With the initial configuration of this summary object, users can execute a wide range of analyses with a single line of code, requiring only two essential parameters for setup. The package delivers comprehensive outputs including analysis objects, statistical outcomes, and visualization-ready data, enhancing the efficiency of research workflows. Designed with user-friendliness in mind, it caters to both novices and seasoned researchers, offering an intuitive interface coupled with adaptable customization options to meet diverse analytical needs.
Author: Ningqi Wang [aut, cre, cph],
Yaozhong Zhang [aut],
Gaofei Jiang [aut]
Maintainer: Ningqi Wang <2434066068@qq.com>
Diff between LorMe versions 1.0.0 dated 2024-08-29 and 1.1.0 dated 2024-09-13
LorMe-1.0.0/LorMe/README.md |only LorMe-1.1.0/LorMe/DESCRIPTION | 10 +-- LorMe-1.1.0/LorMe/MD5 | 53 +++++++++----------- LorMe-1.1.0/LorMe/R/Alpha_diversity_calculator.R | 6 +- LorMe-1.1.0/LorMe/R/Deseq_analysis.R | 4 - LorMe-1.1.0/LorMe/R/Filter_function.R | 15 +---- LorMe-1.1.0/LorMe/R/Module_abundance.R | 7 ++ LorMe-1.1.0/LorMe/R/Module_composition.R | 4 - LorMe-1.1.0/LorMe/R/Pre_assumption.R | 4 - LorMe-1.1.0/LorMe/R/community_plot.R | 4 - LorMe-1.1.0/LorMe/R/differential_bar.R | 8 +-- LorMe-1.1.0/LorMe/R/indicator_analysis.R | 4 - LorMe-1.1.0/LorMe/R/network_analysis.R | 46 ++++++++++------- LorMe-1.1.0/LorMe/R/object_config.R | 11 ++++ LorMe-1.1.0/LorMe/R/structure_plot.R | 6 +- LorMe-1.1.0/LorMe/R/tax_summary.R | 3 + LorMe-1.1.0/LorMe/R/tbRDA_analysis.R | 2 LorMe-1.1.0/LorMe/man/Alpha_diversity_calculator.Rd | 4 - LorMe-1.1.0/LorMe/man/Deseq_analysis.Rd | 4 - LorMe-1.1.0/LorMe/man/Filter_function.Rd | 15 +---- LorMe-1.1.0/LorMe/man/Module_composition.Rd | 4 - LorMe-1.1.0/LorMe/man/auto_signif_test.Rd | 4 - LorMe-1.1.0/LorMe/man/community_plot.Rd | 2 LorMe-1.1.0/LorMe/man/differential_bar.Rd | 6 +- LorMe-1.1.0/LorMe/man/indicator_analysis.Rd | 4 - LorMe-1.1.0/LorMe/man/network_analysis.Rd | 3 + LorMe-1.1.0/LorMe/man/structure_plot.Rd | 2 LorMe-1.1.0/LorMe/man/tbRDA_analysis.Rd | 2 28 files changed, 128 insertions(+), 109 deletions(-)
Title: Handle Strings as Vectors of Characters
Description: Creates a new chars class which looks like a string but is actually
a vector of individual characters, making 'strings' iterable. This class
enables vector operations on 'strings' such as reverse, sort, head, and set
operations.
Author: Jonathan Carroll [aut, cre]
Maintainer: Jonathan Carroll <rpkg@jcarroll.com.au>
Diff between charcuterie versions 0.0.3 dated 2024-09-10 and 0.0.4 dated 2024-09-13
DESCRIPTION | 6 +++--- MD5 | 21 ++++++++++++++------- NAMESPACE | 4 ++++ NEWS.md | 5 +++++ R/classes.R |only README.md | 13 ++++++++++++- inst/doc/use_cases.R | 2 +- inst/doc/use_cases.Rmd | 2 +- man/is_alnum.Rd |only man/is_letter.Rd |only man/is_number.Rd |only man/is_punct.Rd |only tests/testthat/test-classes.R |only vignettes/spongebob.jpg |only vignettes/use_cases.Rmd | 2 +- 15 files changed, 41 insertions(+), 14 deletions(-)
Title: Individual Dose Optimization using Population Pharmacokinetics
Description: Optimize drug regimens through model-informed precision dosing,
using individual pharmacokinetic (PK) and pharmacokinetic-pharmacodynamic
(PK-PD) profiles. By integrating therapeutic drug monitoring (TDM) data with
population models, 'posologyr' provides accurate posterior estimates and
enables the calculation of personalized dosing regimens. The empirical Bayes
estimates are computed following the method described by Kang et al. (2012)
<doi:10.4196/kjpp.2012.16.2.97>.
Author: Cyril Leven [aut, cre, cph] ,
Matthew Fidler [ctb] ,
Emmanuelle Comets [ctb],
Audrey Lavenu [ctb],
Marc Lavielle [ctb]
Maintainer: Cyril Leven <cyril.leven@chu-brest.fr>
Diff between posologyr versions 1.2.6 dated 2024-08-27 and 1.2.7 dated 2024-09-13
posologyr-1.2.6/posologyr/build |only posologyr-1.2.6/posologyr/inst/doc |only posologyr-1.2.6/posologyr/tests/testthat/test_issue_53.R |only posologyr-1.2.6/posologyr/vignettes |only posologyr-1.2.7/posologyr/DESCRIPTION | 24 +++---- posologyr-1.2.7/posologyr/MD5 | 48 ++------------- posologyr-1.2.7/posologyr/NAMESPACE | 1 posologyr-1.2.7/posologyr/NEWS.md | 6 + posologyr-1.2.7/posologyr/R/et.R |only posologyr-1.2.7/posologyr/R/param_estim.R | 35 +++------- posologyr-1.2.7/posologyr/R/utils.R | 12 +-- posologyr-1.2.7/posologyr/man/poso_replace_et.Rd |only posologyr-1.2.7/posologyr/man/poso_simu_pop.Rd | 3 13 files changed, 46 insertions(+), 83 deletions(-)
Title: Compute Scagnostics on Pairs of Numeric Variables in a Data Set
Description: Computes a range of scatterplot diagnostics (scagnostics) on pairs
of numerical variables in a data set. A range of scagnostics, including graph
and association-based scagnostics described by Leland Wilkinson and Graham
Wills (2008) <doi:10.1198/106186008X320465> and association-based
scagnostics described by Katrin Grimm (2016,ISBN:978-3-8439-3092-5) can be
computed. Summary and plotting functions are provided.
Author: Harriet Mason [aut, cre] ,
Stuart Lee [aut] ,
Ursula Laa [aut] ,
Dianne Cook [aut]
Maintainer: Harriet Mason <harriet.m.mason@gmail.com>
Diff between cassowaryr versions 2.0.0 dated 2022-08-09 and 2.0.2 dated 2024-09-13
DESCRIPTION | 22 ++-- MD5 | 15 +-- NEWS.md | 10 +- R/scree.R | 5 - build/vignette.rds |binary inst/CITATION | 24 +++- inst/doc/cassowaryr.R | 4 inst/doc/cassowaryr.html | 232 ++++++++++++++++++++++++----------------------- man/figures |only 9 files changed, 172 insertions(+), 140 deletions(-)
Title: Fitting and Forecasting Gegenbauer ARMA Time Series Models
Description: Methods for estimating univariate long memory-seasonal/cyclical
Gegenbauer time series processes. See for example (2022) <doi:10.1007/s00362-022-01290-3>.
Refer to the vignette for details of fitting these processes.
Author: Richard Hunt [aut, cre]
Maintainer: Richard Hunt <maint@huntemail.id.au>
Diff between garma versions 0.9.22 dated 2024-09-05 and 0.9.23 dated 2024-09-12
DESCRIPTION | 8 MD5 | 13 - R/garma_main.R | 3 inst/doc/introduction.html | 4 tests/testthat/_snaps |only tests/testthat/test-garma.R |only tests/testthat/test-garma2.R |only tests/testthat/test-predict.R |only tests/testthat/test_garma.R | 492 +++++++++++++++++++++--------------------- 9 files changed, 263 insertions(+), 257 deletions(-)
Title: Visualization of Viral Protein Sequence Diversity Dynamics
Description: To ease the visualization of outputs from Diversity Motif Analyser ('DiMA';
<https://github.com/BVU-BILSAB/DiMA>). 'vDiveR' allows visualization of the diversity
motifs (index and its variants – major, minor and unique) for elucidation of
the underlying inherent dynamics. Please refer <https://vdiver-manual.readthedocs.io/en/latest/>
for more information.
Author: Pendy Tok [aut, cre],
Li Chuin Chong [aut],
Evgenia Chikina [aut],
Yin Cheng Chen [aut],
Mohammad Asif Khan [aut]
Maintainer: Pendy Tok <pendytok0518@gmail.com>
Diff between vDiveR versions 1.2.1 dated 2024-01-09 and 2.0.0 dated 2024-09-12
DESCRIPTION | 12 +- MD5 | 35 ++++---- NAMESPACE | 3 NEWS.md | 4 R/json2csv.R | 2 R/metadata_extraction.R | 182 ++++++++++++++++++++++++++++--------------- R/plot_time.R | 36 ++++---- R/plot_worldmap.R | 63 +++++++++----- R/sample_data.R | 8 - data/metadata.rda |binary inst/extdata/city_mapper.csv |only man/JSON_sample.Rd | 2 man/json2csv.Rd | 2 man/metadata.Rd | 2 man/metadata_extraction.Rd | 9 +- man/plot_time.Rd | 11 -- man/plot_worldmap.Rd | 4 man/protein_2hosts.Rd | 2 man/proteins_1host.Rd | 2 19 files changed, 226 insertions(+), 153 deletions(-)
Title: Seismic Time Series Analysis Tools
Description: Multiple interactive codes to view and analyze seismic data, via spectrum analysis, wavelet transforms, particle motion, hodograms. Includes general time-series tools, plotting, filtering, interactive display.
Author: Jonathan M. Lees [aut, cre],
Jake Anderson [ctb],
Leonard Lisapaly [ctb],
Dave Harris [aut, cph]
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between RSEIS versions 4.2-0 dated 2024-02-25 and 4.2-4 dated 2024-09-12
DESCRIPTION | 12 +- MD5 | 194 ++++++++++++++++++------------------ NAMESPACE | 2 R/ASCII.SEISN.R | 5 R/DECIMATE.SEISN.R | 22 +++- R/FAKEDATA.R |only R/JSAC.seis.R | 222 ++++++++--------------------------------- R/ReadSet.Instr.R | 36 ++++-- R/X2RSEIS.R | 5 R/Zdate.R | 2 R/butfilt.R | 15 ++ R/dateStamp.R | 2 R/downsample.R |only R/filedatetime.R | 2 R/getANSS.R | 4 R/getIRIS.R | 2 R/getPDEcsv.R | 2 R/getPDEscreen.R | 2 R/getseis24.R | 269 +++++++++++++++++--------------------------------- R/infoDB.R | 30 ++--- R/markseis24.R | 8 + R/pickseis24.R | 38 ++----- R/plotseis24.R | 31 ++++- R/read1segy.R | 6 - R/rseis2sac.R | 36 +----- R/rseis2segy.R | 38 ++++--- R/saveWPX.R | 4 R/view.seis.R | 19 ++- R/winseis24.R | 10 + R/wlet.do.R | 2 R/write1segy.R | 17 ++- man/ASCII.SEISN.Rd | 9 + man/AUGMENTbutfilt.Rd | 6 - man/DECIMATE.SEISN.Rd | 50 ++++++++- man/DISPLACE.SEISN.Rd | 23 ---- man/DISTxsec.Rd | 7 - man/DO.PMOT.ARR.Rd | 20 +++ man/FAKEDATA.Rd |only man/GET.seis.Rd | 87 ++++++++-------- man/Get1Dvel.Rd | 4 man/JSAC.seis.Rd | 49 ++------- man/MTMgabor.Rd | 6 - man/Mine.seis.Rd | 44 +++++--- man/P2GH.Rd | 7 - man/PLOT.ALLPX.Rd | 15 ++ man/PMOT.drive.Rd | 2 man/ReadInstr.Rd | 30 ++--- man/ReadSet.Instr.Rd | 11 -- man/SEARCHPIX.Rd | 7 + man/SEIS2list.Rd | 10 - man/SELBUT.Rd | 2 man/SPECT.drive.Rd | 31 ----- man/VELOCITY.SEISN.Rd | 20 --- man/WINGH.Rd | 2 man/X2RSEIS.Rd | 3 man/X2SAC.Rd | 6 - man/XTR.Rd | 2 man/YPIX.Rd | 2 man/ZOOM.SEISN.Rd | 4 man/Zdate.Rd | 6 - man/butfilt.Rd | 5 man/combineSEIS.Rd | 16 +- man/convert2Rseis.Rd | 62 ++--------- man/downsample.Rd |only man/editDB.Rd | 61 +++++++---- man/filedatetime.Rd | 2 man/getIRIS.Rd | 19 ++- man/getPDEcsv.Rd | 40 +++---- man/getseis24.Rd | 46 +++++++- man/grotseis.Rd | 17 ++- man/infoDB.Rd | 40 +++++-- man/lagplot.Rd | 11 -- man/longfft.Rd | 64 ++++++----- man/makeDB.Rd | 78 +++++--------- man/markseis24.Rd | 62 ++++++++--- man/parse.pde.Rd | 13 ++ man/pickseis24.Rd | 73 ++++++++++--- man/plotDB.Rd | 37 +++++- man/plotGH.Rd | 22 ++-- man/plotJGET.Rd | 19 ++- man/plotseis24.Rd | 43 ++++++- man/prepSEIS.Rd | 67 ------------ man/rdistaz.Rd | 25 ++++ man/read1segy.Rd | 21 +-- man/rseis2segy.Rd | 19 ++- man/ruler.Rd | 4 man/saveWPX.Rd | 4 man/segy2rseis.Rd | 23 ++-- man/seisorder.Rd | 2 man/setstas.Rd | 12 +- man/setupDB.Rd | 44 +++++--- man/swig.ALLPX.Rd | 13 +- man/tung.pulse.Rd | 11 +- man/view.seis.Rd | 112 +++++++++----------- man/winseis24.Rd | 49 +++++++-- man/wlet.do.Rd | 21 --- man/write1segy.Rd | 23 +++- src/ARAIC.c | 4 src/GetCornerFreq.c | 2 src/TTray.c | 48 ++++---- 100 files changed, 1410 insertions(+), 1326 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. [...truncated...]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 5.10 dated 2024-07-01 and 5.11 dated 2024-09-12
DESCRIPTION | 8 +- MD5 | 134 +++++++++++++++++++++++----------------------- R/abc.R | 4 - R/accumulators.R | 2 R/basic_components.R | 2 R/basic_probes.R | 36 ++++++------ R/betabinom.R | 2 R/bsflu.R | 6 +- R/bsmc2.R | 2 R/bsplines.R | 4 - R/childhood.R | 2 R/conc.R | 2 R/concat.R | 4 - R/covariate_table.R | 2 R/csnippet.R | 2 R/dacca.R | 22 +++---- R/design.R | 4 - R/ebola.R | 6 +- R/eff_sample_size.R | 6 +- R/elementary_algorithms.R | 4 - R/estimation_algorithms.R | 2 R/filter_traj.R | 2 R/flow.R | 2 R/kalman.R | 9 +-- R/kf.R | 2 R/logmeanexp.R | 2 R/mcap.R | 16 ++--- R/mif2.R | 8 +- R/nlf.R | 40 ++++++------- R/objfun.R | 2 R/package.R | 4 - R/parameter_trans.R | 2 R/parmat.R | 2 R/parus.R | 3 - R/pfilter.R | 6 +- R/pmcmc.R | 8 +- R/pomp_examp.R | 6 +- R/probe.R | 2 R/probe_match.R | 12 ++-- R/profile_design.R | 6 +- R/proposals.R | 6 +- R/saved_states.R | 4 - R/sir.R | 42 +++++++------- R/skeleton_spec.R | 8 +- R/slice_design.R | 2 R/sobol_design.R | 4 - R/spect.R | 28 ++++----- R/spect_match.R | 4 - R/spy.R | 1 R/templates.R | 2 R/traj_match.R | 4 - R/trajectory.R | 4 - R/window.R | 2 R/workhorses.R | 2 R/wpfilter.R | 8 +- README.md | 2 inst/NEWS | 6 ++ inst/NEWS.Rd | 5 + man/bsplines.Rd | 2 man/macros/citations.Rd | 74 ++++++++++++------------- man/mcap.Rd | 2 man/probe_match.Rd | 5 + man/spy.Rd | 7 ++ src/distributions.c | 6 +- src/logmeanexp.c | 2 src/probe_marginal.c | 30 +++++----- src/synth_lik.c | 6 +- src/trajectory.c | 34 +++++------ 68 files changed, 359 insertions(+), 333 deletions(-)
Title: Many Ways to Make, Modify, Map, Mark, and Measure Myriad
Networks
Description: Many tools for making, modifying, mapping, marking, measuring,
and motifs and memberships of many different types of networks.
All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
and on one-mode, two-mode (bipartite), and sometimes three-mode networks.
The package includes functions for importing and exporting, creating and generating networks,
modifying networks and node and tie attributes,
and describing and visualizing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Christian Steglich [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manynet versions 1.0.5 dated 2024-08-30 and 1.1.0 dated 2024-09-12
manynet-1.0.5/manynet/R/map_layout_configurations.R |only manynet-1.0.5/manynet/R/map_layout_partition.R |only manynet-1.0.5/manynet/R/mark_is.R |only manynet-1.0.5/manynet/R/print_classes.R |only manynet-1.0.5/manynet/data/ison_monastery_esteem.rda |only manynet-1.0.5/manynet/data/ison_monastery_influence.rda |only manynet-1.0.5/manynet/data/ison_monastery_like.rda |only manynet-1.0.5/manynet/data/ison_monastery_praise.rda |only manynet-1.0.5/manynet/man/add_nodes.Rd |only manynet-1.0.5/manynet/man/add_ties.Rd |only manynet-1.0.5/manynet/man/as.Rd |only manynet-1.0.5/manynet/man/between_centrality.Rd |only manynet-1.0.5/manynet/man/close_centrality.Rd |only manynet-1.0.5/manynet/man/cluster.Rd |only manynet-1.0.5/manynet/man/configuration_layouts.Rd |only manynet-1.0.5/manynet/man/degree_centrality.Rd |only manynet-1.0.5/manynet/man/eigenv_centrality.Rd |only manynet-1.0.5/manynet/man/features.Rd |only manynet-1.0.5/manynet/man/from.Rd |only manynet-1.0.5/manynet/man/graphr.Rd |only manynet-1.0.5/manynet/man/graphs.Rd |only manynet-1.0.5/manynet/man/grapht.Rd |only manynet-1.0.5/manynet/man/is.Rd |only manynet-1.0.5/manynet/man/is_format.Rd |only manynet-1.0.5/manynet/man/ison_monastery.Rd |only manynet-1.0.5/manynet/man/kselect.Rd |only manynet-1.0.5/manynet/man/learning.Rd |only manynet-1.0.5/manynet/man/make_generate.Rd |only manynet-1.0.5/manynet/man/many_palettes.Rd |only manynet-1.0.5/manynet/man/measure_infection.Rd |only manynet-1.0.5/manynet/man/measure_net_diffusion.Rd |only manynet-1.0.5/manynet/man/measure_node_diffusion.Rd |only manynet-1.0.5/manynet/man/miss.Rd |only manynet-1.0.5/manynet/man/over.Rd |only manynet-1.0.5/manynet/man/partition_layouts.Rd |only manynet-1.0.5/manynet/man/play.Rd |only manynet-1.0.5/manynet/man/read.Rd |only manynet-1.0.5/manynet/man/reformat.Rd |only manynet-1.0.5/manynet/man/scales.Rd |only manynet-1.0.5/manynet/man/themes.Rd |only manynet-1.0.5/manynet/man/to_levels.Rd |only manynet-1.0.5/manynet/man/to_paths.Rd |only manynet-1.0.5/manynet/man/to_project.Rd |only manynet-1.0.5/manynet/man/to_scope.Rd |only manynet-1.0.5/manynet/man/write.Rd |only manynet-1.1.0/manynet/DESCRIPTION | 30 manynet-1.1.0/manynet/MD5 | 318 +++++----- manynet-1.1.0/manynet/NAMESPACE | 24 manynet-1.1.0/manynet/NEWS.md | 68 ++ manynet-1.1.0/manynet/R/class_marks.R | 13 manynet-1.1.0/manynet/R/class_measures.R | 11 manynet-1.1.0/manynet/R/class_networks.R |only manynet-1.1.0/manynet/R/data_ison.R | 472 +++++++-------- manynet-1.1.0/manynet/R/make_create.R | 8 manynet-1.1.0/manynet/R/make_generate.R | 179 +++-- manynet-1.1.0/manynet/R/make_play.R | 18 manynet-1.1.0/manynet/R/make_read.R | 127 +++- manynet-1.1.0/manynet/R/manip_as.R | 71 +- manynet-1.1.0/manynet/R/manip_correlation.R | 6 manynet-1.1.0/manynet/R/manip_from.R | 20 manynet-1.1.0/manynet/R/manip_miss.R | 8 manynet-1.1.0/manynet/R/manip_nodes.R | 36 - manynet-1.1.0/manynet/R/manip_reformat.R | 49 - manynet-1.1.0/manynet/R/manip_reformed.R | 69 +- manynet-1.1.0/manynet/R/manip_split.R | 10 manynet-1.1.0/manynet/R/manip_ties.R | 43 - manynet-1.1.0/manynet/R/manynet-tutorials.R | 49 - manynet-1.1.0/manynet/R/manynet-utils.R | 5 manynet-1.1.0/manynet/R/map_autograph.R | 14 manynet-1.1.0/manynet/R/map_layouts.R |only manynet-1.1.0/manynet/R/map_palettes.R | 5 manynet-1.1.0/manynet/R/map_plot.R | 6 manynet-1.1.0/manynet/R/map_theme.R | 72 +- manynet-1.1.0/manynet/R/mark_net.R |only manynet-1.1.0/manynet/R/mark_nodes.R | 10 manynet-1.1.0/manynet/R/mark_ties.R | 86 ++ manynet-1.1.0/manynet/R/measure_attributes.R | 2 manynet-1.1.0/manynet/R/measure_centrality.R | 90 +- manynet-1.1.0/manynet/R/measure_closure.R | 10 manynet-1.1.0/manynet/R/measure_cohesion.R | 2 manynet-1.1.0/manynet/R/measure_diffusion.R | 42 - manynet-1.1.0/manynet/R/measure_features.R | 20 manynet-1.1.0/manynet/R/measure_heterogeneity.R | 4 manynet-1.1.0/manynet/R/measure_hierarchy.R | 2 manynet-1.1.0/manynet/R/measure_holes.R | 2 manynet-1.1.0/manynet/R/measure_over.R | 17 manynet-1.1.0/manynet/R/measure_properties.R | 2 manynet-1.1.0/manynet/R/member_cliques.R | 4 manynet-1.1.0/manynet/R/member_community.R | 2 manynet-1.1.0/manynet/R/member_components.R | 6 manynet-1.1.0/manynet/R/member_core.R | 4 manynet-1.1.0/manynet/R/member_equivalence.R | 2 manynet-1.1.0/manynet/R/model_cluster.R | 6 manynet-1.1.0/manynet/R/model_k.R | 10 manynet-1.1.0/manynet/R/motif_census.R | 30 manynet-1.1.0/manynet/R/reexports_classes.R | 24 manynet-1.1.0/manynet/R/zzz.R |only manynet-1.1.0/manynet/README.md | 59 - manynet-1.1.0/manynet/data/ison_adolescents.rda |binary manynet-1.1.0/manynet/data/ison_algebra.rda |binary manynet-1.1.0/manynet/data/ison_brandes.rda |binary manynet-1.1.0/manynet/data/ison_friends.rda |binary manynet-1.1.0/manynet/data/ison_greys.rda |binary manynet-1.1.0/manynet/data/ison_hightech.rda |binary manynet-1.1.0/manynet/data/ison_karateka.rda |binary manynet-1.1.0/manynet/data/ison_koenigsberg.rda |binary 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manynet-1.1.0/manynet/man/ison_friends.Rd | 2 manynet-1.1.0/manynet/man/ison_greys.Rd | 2 manynet-1.1.0/manynet/man/ison_hightech.Rd | 2 manynet-1.1.0/manynet/man/ison_karateka.Rd | 2 manynet-1.1.0/manynet/man/ison_koenigsberg.Rd | 2 manynet-1.1.0/manynet/man/ison_laterals.Rd | 8 manynet-1.1.0/manynet/man/ison_lawfirm.Rd | 2 manynet-1.1.0/manynet/man/ison_lotr.Rd | 2 manynet-1.1.0/manynet/man/ison_marvel.Rd | 4 manynet-1.1.0/manynet/man/ison_monks.Rd |only manynet-1.1.0/manynet/man/ison_networkers.Rd | 2 manynet-1.1.0/manynet/man/ison_physicians.Rd | 8 manynet-1.1.0/manynet/man/ison_potter.Rd | 12 manynet-1.1.0/manynet/man/ison_southern_women.Rd | 2 manynet-1.1.0/manynet/man/ison_starwars.Rd | 14 manynet-1.1.0/manynet/man/ison_thrones.Rd |only manynet-1.1.0/manynet/man/ison_usstates.Rd | 2 manynet-1.1.0/manynet/man/make_cran.Rd |only manynet-1.1.0/manynet/man/make_create.Rd | 12 manynet-1.1.0/manynet/man/make_explicit.Rd | 12 manynet-1.1.0/manynet/man/make_learning.Rd |only manynet-1.1.0/manynet/man/make_play.Rd |only manynet-1.1.0/manynet/man/make_random.Rd |only manynet-1.1.0/manynet/man/make_read.Rd |only manynet-1.1.0/manynet/man/make_stochastic.Rd |only manynet-1.1.0/manynet/man/make_write.Rd |only manynet-1.1.0/manynet/man/manip_as.Rd |only manynet-1.1.0/manynet/man/manip_correlation.Rd | 20 manynet-1.1.0/manynet/man/manip_from.Rd |only manynet-1.1.0/manynet/man/manip_levels.Rd |only manynet-1.1.0/manynet/man/manip_miss.Rd |only manynet-1.1.0/manynet/man/manip_nodes.Rd |only manynet-1.1.0/manynet/man/manip_paths.Rd |only manynet-1.1.0/manynet/man/manip_permutation.Rd | 20 manynet-1.1.0/manynet/man/manip_project.Rd |only manynet-1.1.0/manynet/man/manip_reformat.Rd |only manynet-1.1.0/manynet/man/manip_scope.Rd |only manynet-1.1.0/manynet/man/manip_split.Rd | 20 manynet-1.1.0/manynet/man/manip_ties.Rd |only manynet-1.1.0/manynet/man/map_graphr.Rd |only manynet-1.1.0/manynet/man/map_graphs.Rd |only manynet-1.1.0/manynet/man/map_grapht.Rd |only 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manynet-1.1.0/manynet/man/reexports.Rd | 4 manynet-1.1.0/manynet/tests/testthat/test-manip_grab.R | 2 206 files changed, 1563 insertions(+), 1088 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc]
,
Christoph Burow [aut, trl, dtc]
,
Michael Dietze [aut] ,
Margret C. Fuchs [aut] ,
Christoph Schmidt [aut] ,
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] ,
Norbert Mercier [aut] ,
Rachel K. Smedley [ct [...truncated...]
Maintainer: Sebastian Kreutzer <maintainer_luminescence@r-luminescence.org>
Diff between Luminescence versions 0.9.24 dated 2024-06-07 and 0.9.25 dated 2024-09-12
Luminescence-0.9.24/Luminescence/tests/testthat/test_RLum.R |only Luminescence-0.9.24/Luminescence/tests/testthat/test_analyse_IRSARRF.R |only Luminescence-0.9.24/Luminescence/tests/testthat/test_analyse_SARCWOSL.R |only Luminescence-0.9.24/Luminescence/tests/testthat/test_analyse_SARTL.R |only Luminescence-0.9.24/Luminescence/tests/testthat/test_calc_CobbeDoseRate.R |only Luminescence-0.9.24/Luminescence/tests/testthat/test_convert_XYSG2CSV.R |only Luminescence-0.9.24/Luminescence/tests/testthat/test_merge_RLumDataCurve.R |only Luminescence-0.9.24/Luminescence/tests/testthat/test_merge_RLumResults.R |only Luminescence-0.9.24/Luminescence/tests/testthat/test_merge_RisoeBINfileData.R |only Luminescence-0.9.25/Luminescence/DESCRIPTION | 79 - Luminescence-0.9.25/Luminescence/MD5 | 716 +++++----- Luminescence-0.9.25/Luminescence/NAMESPACE | 6 Luminescence-0.9.25/Luminescence/NEWS.md | 312 ++-- Luminescence-0.9.25/Luminescence/R/Analyse_SAR.OSLdata.R | 2 Luminescence-0.9.25/Luminescence/R/CW2pHMi.R | 7 Luminescence-0.9.25/Luminescence/R/PSL2Risoe.BINfileData.R | 17 Luminescence-0.9.25/Luminescence/R/RLum.Analysis-class.R | 89 - Luminescence-0.9.25/Luminescence/R/RLum.Data.Curve-class.R | 6 Luminescence-0.9.25/Luminescence/R/RLum.Data.Image-class.R | 8 Luminescence-0.9.25/Luminescence/R/RLum.Results-class.R | 37 Luminescence-0.9.25/Luminescence/R/Risoe.BINfileData-class.R | 2 Luminescence-0.9.25/Luminescence/R/Risoe.BINfileData2RLum.Analysis.R | 128 - Luminescence-0.9.25/Luminescence/R/Risoe.BINfileData2RLum.Data.Curve.R | 8 Luminescence-0.9.25/Luminescence/R/Second2Gray.R | 2 Luminescence-0.9.25/Luminescence/R/addins_RLum.R | 17 Luminescence-0.9.25/Luminescence/R/analyse_Al2O3C_CrossTalk.R | 18 Luminescence-0.9.25/Luminescence/R/analyse_Al2O3C_ITC.R | 28 Luminescence-0.9.25/Luminescence/R/analyse_Al2O3C_Measurement.R | 90 - Luminescence-0.9.25/Luminescence/R/analyse_FadingMeasurement.R | 121 - Luminescence-0.9.25/Luminescence/R/analyse_IRSAR.RF.R | 217 +-- Luminescence-0.9.25/Luminescence/R/analyse_SAR.CWOSL.R | 173 -- Luminescence-0.9.25/Luminescence/R/analyse_SAR.TL.R | 63 Luminescence-0.9.25/Luminescence/R/analyse_baSAR.R | 423 ++--- Luminescence-0.9.25/Luminescence/R/analyse_pIRIRSequence.R | 38 Luminescence-0.9.25/Luminescence/R/analyse_portableOSL.R | 52 Luminescence-0.9.25/Luminescence/R/apply_CosmicRayRemoval.R | 11 Luminescence-0.9.25/Luminescence/R/calc_AliquotSize.R | 26 Luminescence-0.9.25/Luminescence/R/calc_AverageDose.R | 28 Luminescence-0.9.25/Luminescence/R/calc_CommonDose.R | 38 Luminescence-0.9.25/Luminescence/R/calc_CosmicDoseRate.R | 13 Luminescence-0.9.25/Luminescence/R/calc_FadingCorr.R | 15 Luminescence-0.9.25/Luminescence/R/calc_FastRatio.R | 72 - Luminescence-0.9.25/Luminescence/R/calc_FiniteMixture.R | 62 Luminescence-0.9.25/Luminescence/R/calc_FuchsLang2001.R | 2 Luminescence-0.9.25/Luminescence/R/calc_Huntley2006.R | 67 Luminescence-0.9.25/Luminescence/R/calc_Lamothe2003.R | 13 Luminescence-0.9.25/Luminescence/R/calc_MinDose.R | 96 - Luminescence-0.9.25/Luminescence/R/calc_OSLLxTxDecomposed.R | 30 Luminescence-0.9.25/Luminescence/R/calc_Statistics.R | 5 Luminescence-0.9.25/Luminescence/R/calc_TLLxTxRatio.R | 1 Luminescence-0.9.25/Luminescence/R/calc_ThermalLifetime.R | 27 Luminescence-0.9.25/Luminescence/R/calc_WodaFuchs2008.R | 72 - Luminescence-0.9.25/Luminescence/R/calc_gSGC.R | 44 Luminescence-0.9.25/Luminescence/R/calc_gSGC_feldspar.R | 4 Luminescence-0.9.25/Luminescence/R/combine_De_Dr.R | 6 Luminescence-0.9.25/Luminescence/R/convert_Daybreak2CSV.R | 10 Luminescence-0.9.25/Luminescence/R/convert_Wavelength2Energy.R | 3 Luminescence-0.9.25/Luminescence/R/convert_XSYG2CSV.R | 2 Luminescence-0.9.25/Luminescence/R/extract_IrradiationTimes.R | 109 - Luminescence-0.9.25/Luminescence/R/fit_CWCurve.R | 53 Luminescence-0.9.25/Luminescence/R/fit_EmissionSpectra.R | 49 Luminescence-0.9.25/Luminescence/R/fit_LMCurve.R | 70 Luminescence-0.9.25/Luminescence/R/fit_OSLLifeTimes.R | 113 - Luminescence-0.9.25/Luminescence/R/fit_SurfaceExposure.R | 27 Luminescence-0.9.25/Luminescence/R/fit_ThermalQuenching.R | 8 Luminescence-0.9.25/Luminescence/R/get_Layout.R | 5 Luminescence-0.9.25/Luminescence/R/import_Data.R | 5 Luminescence-0.9.25/Luminescence/R/install_DevelopmentVersion.R | 7 Luminescence-0.9.25/Luminescence/R/internal_as.latex.table.R | 26 Luminescence-0.9.25/Luminescence/R/internals_RLum.R | 142 + Luminescence-0.9.25/Luminescence/R/internals_Thermochronometry.R | 149 ++ Luminescence-0.9.25/Luminescence/R/merge_RLum.Analysis.R | 21 Luminescence-0.9.25/Luminescence/R/merge_RLum.Data.Curve.R | 32 Luminescence-0.9.25/Luminescence/R/merge_RLum.R | 10 Luminescence-0.9.25/Luminescence/R/merge_RLum.Results.R | 15 Luminescence-0.9.25/Luminescence/R/merge_Risoe.BINfileData.R | 13 Luminescence-0.9.25/Luminescence/R/methods_RLum.R | 13 Luminescence-0.9.25/Luminescence/R/plot_AbanicoPlot.R | 131 - Luminescence-0.9.25/Luminescence/R/plot_DRCSummary.R | 25 Luminescence-0.9.25/Luminescence/R/plot_DRTResults.R | 23 Luminescence-0.9.25/Luminescence/R/plot_DetPlot.R | 59 Luminescence-0.9.25/Luminescence/R/plot_FilterCombinations.R | 50 Luminescence-0.9.25/Luminescence/R/plot_GrowthCurve.R | 152 -- Luminescence-0.9.25/Luminescence/R/plot_Histogram.R | 53 Luminescence-0.9.25/Luminescence/R/plot_KDE.R | 114 - Luminescence-0.9.25/Luminescence/R/plot_NRt.R | 25 Luminescence-0.9.25/Luminescence/R/plot_RLum.Analysis.R | 106 - Luminescence-0.9.25/Luminescence/R/plot_RLum.Data.Curve.R | 7 Luminescence-0.9.25/Luminescence/R/plot_RLum.Data.Spectrum.R | 89 - Luminescence-0.9.25/Luminescence/R/plot_RLum.R | 2 Luminescence-0.9.25/Luminescence/R/plot_RLum.Results.R | 23 Luminescence-0.9.25/Luminescence/R/plot_RadialPlot.R | 71 Luminescence-0.9.25/Luminescence/R/plot_Risoe.BINfileData.R | 13 Luminescence-0.9.25/Luminescence/R/plot_ViolinPlot.R | 37 Luminescence-0.9.25/Luminescence/R/read_BIN2R.R | 713 ++++----- Luminescence-0.9.25/Luminescence/R/read_Daybreak2R.R | 9 Luminescence-0.9.25/Luminescence/R/read_HeliosOSL2R.R |only Luminescence-0.9.25/Luminescence/R/read_PSL2R.R | 80 - Luminescence-0.9.25/Luminescence/R/read_RF2R.R | 7 Luminescence-0.9.25/Luminescence/R/read_SPE2R.R | 70 Luminescence-0.9.25/Luminescence/R/read_TIFF2R.R | 3 Luminescence-0.9.25/Luminescence/R/read_XSYG2R.R | 123 - Luminescence-0.9.25/Luminescence/R/report_RLum.R | 29 Luminescence-0.9.25/Luminescence/R/scale_GammaDose.R | 4 Luminescence-0.9.25/Luminescence/R/template_DRAC.R | 3 Luminescence-0.9.25/Luminescence/R/use_DRAC.R | 18 Luminescence-0.9.25/Luminescence/R/verify_SingleGrainData.R | 18 Luminescence-0.9.25/Luminescence/R/write_R2BIN.R | 38 Luminescence-0.9.25/Luminescence/R/write_R2TIFF.R | 3 Luminescence-0.9.25/Luminescence/R/write_RLum2CSV.R | 9 Luminescence-0.9.25/Luminescence/R/zzz.R | 2 Luminescence-0.9.25/Luminescence/README.md | 21 Luminescence-0.9.25/Luminescence/build/partial.rdb |binary Luminescence-0.9.25/Luminescence/build/vignette.rds |binary Luminescence-0.9.25/Luminescence/inst/CITATION | 2 Luminescence-0.9.25/Luminescence/inst/extdata/HeliosOSL_Example.osl |only Luminescence-0.9.25/Luminescence/man/Analyse_SAR.OSLdata.Rd | 4 Luminescence-0.9.25/Luminescence/man/CW2pHMi.Rd | 2 Luminescence-0.9.25/Luminescence/man/CW2pLM.Rd | 2 Luminescence-0.9.25/Luminescence/man/CW2pLMi.Rd | 2 Luminescence-0.9.25/Luminescence/man/CW2pPMi.Rd | 2 Luminescence-0.9.25/Luminescence/man/GitHub-API.Rd | 2 Luminescence-0.9.25/Luminescence/man/Luminescence-package.Rd | 5 Luminescence-0.9.25/Luminescence/man/PSL2Risoe.BINfileData.Rd | 8 Luminescence-0.9.25/Luminescence/man/RLum-class.Rd | 2 Luminescence-0.9.25/Luminescence/man/RLum.Analysis-class.Rd | 2 Luminescence-0.9.25/Luminescence/man/RLum.Data.Curve-class.Rd | 2 Luminescence-0.9.25/Luminescence/man/RLum.Data.Image-class.Rd | 2 Luminescence-0.9.25/Luminescence/man/RLum.Data.Spectrum-class.Rd | 2 Luminescence-0.9.25/Luminescence/man/RLum.Results-class.Rd | 2 Luminescence-0.9.25/Luminescence/man/Risoe.BINfileData-class.Rd | 2 Luminescence-0.9.25/Luminescence/man/Risoe.BINfileData2RLum.Analysis.Rd | 4 Luminescence-0.9.25/Luminescence/man/Second2Gray.Rd | 2 Luminescence-0.9.25/Luminescence/man/analyse_Al2O3C_CrossTalk.Rd | 2 Luminescence-0.9.25/Luminescence/man/analyse_Al2O3C_ITC.Rd | 2 Luminescence-0.9.25/Luminescence/man/analyse_Al2O3C_Measurement.Rd | 6 Luminescence-0.9.25/Luminescence/man/analyse_FadingMeasurement.Rd | 7 Luminescence-0.9.25/Luminescence/man/analyse_IRSAR.RF.Rd | 6 Luminescence-0.9.25/Luminescence/man/analyse_SAR.CWOSL.Rd | 2 Luminescence-0.9.25/Luminescence/man/analyse_SAR.TL.Rd | 2 Luminescence-0.9.25/Luminescence/man/analyse_baSAR.Rd | 6 Luminescence-0.9.25/Luminescence/man/analyse_pIRIRSequence.Rd | 2 Luminescence-0.9.25/Luminescence/man/analyse_portableOSL.Rd | 4 Luminescence-0.9.25/Luminescence/man/apply_CosmicRayRemoval.Rd | 4 Luminescence-0.9.25/Luminescence/man/apply_EfficiencyCorrection.Rd | 2 Luminescence-0.9.25/Luminescence/man/bin_RLum.Data.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_AliquotSize.Rd | 4 Luminescence-0.9.25/Luminescence/man/calc_AverageDose.Rd | 4 Luminescence-0.9.25/Luminescence/man/calc_CentralDose.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_CobbleDoseRate.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_CommonDose.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_CosmicDoseRate.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_FadingCorr.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_FastRatio.Rd | 10 Luminescence-0.9.25/Luminescence/man/calc_FiniteMixture.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_FuchsLang2001.Rd | 4 Luminescence-0.9.25/Luminescence/man/calc_HomogeneityTest.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_Huntley2006.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_IEU.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_Kars2008.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_Lamothe2003.Rd | 4 Luminescence-0.9.25/Luminescence/man/calc_MaxDose.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_MinDose.Rd | 13 Luminescence-0.9.25/Luminescence/man/calc_OSLLxTxDecomposed.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_OSLLxTxRatio.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_SourceDoseRate.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_Statistics.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_TLLxTxRatio.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_ThermalLifetime.Rd | 2 Luminescence-0.9.25/Luminescence/man/calc_WodaFuchs2008.Rd | 8 Luminescence-0.9.25/Luminescence/man/calc_gSGC.Rd | 4 Luminescence-0.9.25/Luminescence/man/calc_gSGC_feldspar.Rd | 2 Luminescence-0.9.25/Luminescence/man/combine_De_Dr.Rd | 4 Luminescence-0.9.25/Luminescence/man/convert_Activity2Concentration.Rd | 2 Luminescence-0.9.25/Luminescence/man/convert_BIN2CSV.Rd | 2 Luminescence-0.9.25/Luminescence/man/convert_Concentration2DoseRate.Rd | 2 Luminescence-0.9.25/Luminescence/man/convert_Daybreak2CSV.Rd | 4 Luminescence-0.9.25/Luminescence/man/convert_PSL2CSV.Rd | 2 Luminescence-0.9.25/Luminescence/man/convert_RLum2Risoe.BINfileData.Rd | 2 Luminescence-0.9.25/Luminescence/man/convert_SG2MG.Rd | 2 Luminescence-0.9.25/Luminescence/man/convert_Wavelength2Energy.Rd | 2 Luminescence-0.9.25/Luminescence/man/convert_XSYG2CSV.Rd | 2 Luminescence-0.9.25/Luminescence/man/extract_IrradiationTimes.Rd | 12 Luminescence-0.9.25/Luminescence/man/extract_ROI.Rd | 2 Luminescence-0.9.25/Luminescence/man/fit_CWCurve.Rd | 15 Luminescence-0.9.25/Luminescence/man/fit_EmissionSpectra.Rd | 2 Luminescence-0.9.25/Luminescence/man/fit_LMCurve.Rd | 2 Luminescence-0.9.25/Luminescence/man/fit_OSLLifeTimes.Rd | 5 Luminescence-0.9.25/Luminescence/man/fit_SurfaceExposure.Rd | 2 Luminescence-0.9.25/Luminescence/man/fit_ThermalQuenching.Rd | 2 Luminescence-0.9.25/Luminescence/man/get_Layout.Rd | 2 Luminescence-0.9.25/Luminescence/man/get_Quote.Rd | 2 Luminescence-0.9.25/Luminescence/man/get_RLum.Rd | 2 Luminescence-0.9.25/Luminescence/man/get_Risoe.BINfileData.Rd | 2 Luminescence-0.9.25/Luminescence/man/get_rightAnswer.Rd | 2 Luminescence-0.9.25/Luminescence/man/import_Data.Rd | 4 Luminescence-0.9.25/Luminescence/man/length_RLum.Rd | 2 Luminescence-0.9.25/Luminescence/man/merge_RLum.Analysis.Rd | 6 Luminescence-0.9.25/Luminescence/man/merge_RLum.Data.Curve.Rd | 2 Luminescence-0.9.25/Luminescence/man/merge_RLum.Rd | 6 Luminescence-0.9.25/Luminescence/man/merge_RLum.Results.Rd | 2 Luminescence-0.9.25/Luminescence/man/merge_Risoe.BINfileData.Rd | 2 Luminescence-0.9.25/Luminescence/man/methods_RLum.Rd | 7 Luminescence-0.9.25/Luminescence/man/names_RLum.Rd | 2 Luminescence-0.9.25/Luminescence/man/plot_AbanicoPlot.Rd | 13 Luminescence-0.9.25/Luminescence/man/plot_DRCSummary.Rd | 4 Luminescence-0.9.25/Luminescence/man/plot_DRTResults.Rd | 2 Luminescence-0.9.25/Luminescence/man/plot_DetPlot.Rd | 5 Luminescence-0.9.25/Luminescence/man/plot_FilterCombinations.Rd | 2 Luminescence-0.9.25/Luminescence/man/plot_GrowthCurve.Rd | 9 Luminescence-0.9.25/Luminescence/man/plot_Histogram.Rd | 2 Luminescence-0.9.25/Luminescence/man/plot_KDE.Rd | 9 Luminescence-0.9.25/Luminescence/man/plot_NRt.Rd | 6 Luminescence-0.9.25/Luminescence/man/plot_OSLAgeSummary.Rd | 2 Luminescence-0.9.25/Luminescence/man/plot_RLum.Analysis.Rd | 9 Luminescence-0.9.25/Luminescence/man/plot_RLum.Data.Curve.Rd | 8 Luminescence-0.9.25/Luminescence/man/plot_RLum.Data.Image.Rd | 2 Luminescence-0.9.25/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 2 Luminescence-0.9.25/Luminescence/man/plot_RLum.Rd | 2 Luminescence-0.9.25/Luminescence/man/plot_RLum.Results.Rd | 2 Luminescence-0.9.25/Luminescence/man/plot_ROI.Rd | 2 Luminescence-0.9.25/Luminescence/man/plot_RadialPlot.Rd | 7 Luminescence-0.9.25/Luminescence/man/plot_Risoe.BINfileData.Rd | 2 Luminescence-0.9.25/Luminescence/man/plot_ViolinPlot.Rd | 9 Luminescence-0.9.25/Luminescence/man/read_BIN2R.Rd | 10 Luminescence-0.9.25/Luminescence/man/read_Daybreak2R.Rd | 2 Luminescence-0.9.25/Luminescence/man/read_HeliosOSL2R.Rd |only Luminescence-0.9.25/Luminescence/man/read_PSL2R.Rd | 15 Luminescence-0.9.25/Luminescence/man/read_RF2R.Rd | 2 Luminescence-0.9.25/Luminescence/man/read_SPE2R.Rd | 8 Luminescence-0.9.25/Luminescence/man/read_TIFF2R.Rd | 2 Luminescence-0.9.25/Luminescence/man/read_XSYG2R.Rd | 12 Luminescence-0.9.25/Luminescence/man/replicate_RLum.Rd | 2 Luminescence-0.9.25/Luminescence/man/report_RLum.Rd | 2 Luminescence-0.9.25/Luminescence/man/sTeve.Rd | 2 Luminescence-0.9.25/Luminescence/man/scale_GammaDose.Rd | 6 Luminescence-0.9.25/Luminescence/man/set_RLum.Rd | 2 Luminescence-0.9.25/Luminescence/man/set_Risoe.BINfileData.Rd | 2 Luminescence-0.9.25/Luminescence/man/smooth_RLum.Rd | 2 Luminescence-0.9.25/Luminescence/man/structure_RLum.Rd | 2 Luminescence-0.9.25/Luminescence/man/subset_SingleGrainData.Rd | 2 Luminescence-0.9.25/Luminescence/man/template_DRAC.Rd | 2 Luminescence-0.9.25/Luminescence/man/trim_RLum.Data.Rd | 2 Luminescence-0.9.25/Luminescence/man/tune_Data.Rd | 2 Luminescence-0.9.25/Luminescence/man/use_DRAC.Rd | 2 Luminescence-0.9.25/Luminescence/man/verify_SingleGrainData.Rd | 14 Luminescence-0.9.25/Luminescence/man/write_R2BIN.Rd | 12 Luminescence-0.9.25/Luminescence/man/write_R2TIFF.Rd | 2 Luminescence-0.9.25/Luminescence/man/write_RLum2CSV.Rd | 2 Luminescence-0.9.25/Luminescence/tests/testthat/_data |only Luminescence-0.9.25/Luminescence/tests/testthat/test_Analyse_SAROSLdata.R | 5 Luminescence-0.9.25/Luminescence/tests/testthat/test_CW2pX.R | 2 Luminescence-0.9.25/Luminescence/tests/testthat/test_PSL2RisoeBINfiledata.R | 17 Luminescence-0.9.25/Luminescence/tests/testthat/test_RLum.Analysis-class.R | 174 ++ Luminescence-0.9.25/Luminescence/tests/testthat/test_RLum.Data.Curve.R | 1 Luminescence-0.9.25/Luminescence/tests/testthat/test_RLum.Data.Image.R | 1 Luminescence-0.9.25/Luminescence/tests/testthat/test_RLum.Data.Spectrum.R | 1 Luminescence-0.9.25/Luminescence/tests/testthat/test_RLum.Results-class.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_Risoe.BINfileData2RLum.Analysis.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_Risoe.BINfileData2RLum.Data.Curve.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_RisoeBINfileData-class.R | 20 Luminescence-0.9.25/Luminescence/tests/testthat/test_Second2Gray.R | 24 Luminescence-0.9.25/Luminescence/tests/testthat/test_analyse_Al2O3C_CrossTalk.R | 40 Luminescence-0.9.25/Luminescence/tests/testthat/test_analyse_Al2O3C_ITC.R | 54 Luminescence-0.9.25/Luminescence/tests/testthat/test_analyse_Al2O3C_Measurement.R | 84 - Luminescence-0.9.25/Luminescence/tests/testthat/test_analyse_FadingMeasurement.R | 57 Luminescence-0.9.25/Luminescence/tests/testthat/test_analyse_IRSAR.RF.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_analyse_SAR.CWOSL.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_analyse_SAR.TL.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_analyse_baSAR.R | 220 ++- Luminescence-0.9.25/Luminescence/tests/testthat/test_analyse_pIRIRSequence.R | 59 Luminescence-0.9.25/Luminescence/tests/testthat/test_analyse_portableOSL.R | 72 - Luminescence-0.9.25/Luminescence/tests/testthat/test_apply_CosmicRayRemoval.R | 8 Luminescence-0.9.25/Luminescence/tests/testthat/test_apply_EfficiencyCorrection.R | 7 Luminescence-0.9.25/Luminescence/tests/testthat/test_as_latex_table.R | 37 Luminescence-0.9.25/Luminescence/tests/testthat/test_bin_RLumData.R | 2 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_AliquotSize.R | 34 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_AverageDose.R | 32 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_CentralDose.R | 14 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_CobbleDoseRate.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_CommonDose.R | 31 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_CosmicDoseRate.R | 52 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_FadingCorr.R | 27 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_FastRatio.R | 67 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_FiniteMixture.R | 30 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_FuchsLang2001.R | 12 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_HomogeneityTest.R | 14 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_Huntley2006.R | 78 - Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_IEU.R | 12 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_Lamothe2003.R | 59 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_MaxDose.R | 4 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_MinDose.R | 55 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_OSLLxTxDecomposed.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_OSLLxTxRatio.R | 8 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_SourceDoseRate.R | 3 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_Statistics.R | 19 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_TLLxTxRatio.R | 8 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_ThermalLifetime.R | 26 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_WodaFuchs2008.R | 50 Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_gSGC.R | 85 - Luminescence-0.9.25/Luminescence/tests/testthat/test_calc_gSGC_feldspar.R | 21 Luminescence-0.9.25/Luminescence/tests/testthat/test_combine_De_Dr.R | 34 Luminescence-0.9.25/Luminescence/tests/testthat/test_convert_Activity2Concentration.R | 15 Luminescence-0.9.25/Luminescence/tests/testthat/test_convert_Concentration2DoseRate.R | 3 Luminescence-0.9.25/Luminescence/tests/testthat/test_convert_Daybreak2CSV.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_convert_PSL2CSV.R | 3 Luminescence-0.9.25/Luminescence/tests/testthat/test_convert_RLum2Risoe.BINfileData.R | 14 Luminescence-0.9.25/Luminescence/tests/testthat/test_convert_SG2MG.R | 12 Luminescence-0.9.25/Luminescence/tests/testthat/test_convert_Wavelength2Energy.R | 8 Luminescence-0.9.25/Luminescence/tests/testthat/test_convert_XSYG2CSV.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_extract_IrradiationTimes.R | 50 Luminescence-0.9.25/Luminescence/tests/testthat/test_extract_ROI.R | 2 Luminescence-0.9.25/Luminescence/tests/testthat/test_fit_CWCurve.R | 67 Luminescence-0.9.25/Luminescence/tests/testthat/test_fit_EmissionSpectra.R | 42 Luminescence-0.9.25/Luminescence/tests/testthat/test_fit_LMCurve.R | 83 - Luminescence-0.9.25/Luminescence/tests/testthat/test_fit_OSLLifeTimes.R | 102 + Luminescence-0.9.25/Luminescence/tests/testthat/test_fit_SurfaceExposure.R | 74 - Luminescence-0.9.25/Luminescence/tests/testthat/test_fit_ThermalQuenching.R | 13 Luminescence-0.9.25/Luminescence/tests/testthat/test_get_Layout.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_get_RLum.R | 14 Luminescence-0.9.25/Luminescence/tests/testthat/test_github.R | 5 Luminescence-0.9.25/Luminescence/tests/testthat/test_import_Data.R | 8 Luminescence-0.9.25/Luminescence/tests/testthat/test_internals.R | 121 + Luminescence-0.9.25/Luminescence/tests/testthat/test_merge_RLum.Analysis.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_merge_RLum.Data.Curve.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_merge_RLum.R | 18 Luminescence-0.9.25/Luminescence/tests/testthat/test_merge_RLum.Results.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_merge_Risoe.BINfileData.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_methods_DRAC.R | 13 Luminescence-0.9.25/Luminescence/tests/testthat/test_methods_S3.R | 158 +- Luminescence-0.9.25/Luminescence/tests/testthat/test_names_RLum.R | 1 Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_AbanicoPlot.R | 89 + Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_DRCSummary.R | 57 Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_DRTResults.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_DetPlot.R | 89 + Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_FilterCombinations.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_Functions.R | 45 Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_GrowthCurve.R | 147 +- Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_Histogram.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_KDE.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_NRt.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_OSLAgeSummary.R | 5 Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_RLum.Analysis.R | 95 - Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_RLum.Data.Curve.R | 11 Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_RLum.Data.Image.R | 7 Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_RLum.Data.Spectrum.R | 52 Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_RLum.R | 1 Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_RLum.Results.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_ROI.R | 1 Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_RadialPlot.R | 95 + Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_Risoe.BINfileData.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_plot_ViolinPlot.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_read_BIN2R.R | 211 +- Luminescence-0.9.25/Luminescence/tests/testthat/test_read_Daybreak2R.R | 75 - Luminescence-0.9.25/Luminescence/tests/testthat/test_read_HeliosOSL2R.R |only Luminescence-0.9.25/Luminescence/tests/testthat/test_read_PSL2R.R | 31 Luminescence-0.9.25/Luminescence/tests/testthat/test_read_RF2R.R | 20 Luminescence-0.9.25/Luminescence/tests/testthat/test_read_SPE2R.R | 69 Luminescence-0.9.25/Luminescence/tests/testthat/test_read_TIFF2R.R | 1 Luminescence-0.9.25/Luminescence/tests/testthat/test_read_XSYG2R.R | 76 - Luminescence-0.9.25/Luminescence/tests/testthat/test_replicate_RLum.R | 1 Luminescence-0.9.25/Luminescence/tests/testthat/test_report_RLum.R | 17 Luminescence-0.9.25/Luminescence/tests/testthat/test_scale_GammaDose.R | 12 Luminescence-0.9.25/Luminescence/tests/testthat/test_smooth_RLum.R | 2 Luminescence-0.9.25/Luminescence/tests/testthat/test_structure_RLum.R | 1 Luminescence-0.9.25/Luminescence/tests/testthat/test_subset_RLum.R | 12 Luminescence-0.9.25/Luminescence/tests/testthat/test_subset_SingleGrainData.R | 1 Luminescence-0.9.25/Luminescence/tests/testthat/test_template_DRAC.R | 20 Luminescence-0.9.25/Luminescence/tests/testthat/test_trim_RLum.Data.R | 10 Luminescence-0.9.25/Luminescence/tests/testthat/test_use_DRAC.R | 31 Luminescence-0.9.25/Luminescence/tests/testthat/test_verify_SingleGrainData.R | 49 Luminescence-0.9.25/Luminescence/tests/testthat/test_write_R2BIN.R | 72 - Luminescence-0.9.25/Luminescence/tests/testthat/test_write_R2TIFF.R | 1 Luminescence-0.9.25/Luminescence/tests/testthat/test_write_RLum2CSV.R | 27 Luminescence-0.9.25/Luminescence/tests/testthat/test_zzz.R | 7 375 files changed, 6085 insertions(+), 4646 deletions(-)
Title: Analytics & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
MMM, Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and
robust results, without the need of repetitive coding or advanced R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.2.8 dated 2024-06-11 and 5.2.9 dated 2024-09-12
DESCRIPTION | 16 MD5 | 514 +++---- NAMESPACE | 1077 ++++++++-------- R/apis.R | 68 - R/audio.R | 359 ++--- R/cache.R | 326 ++-- R/chatgpt.R | 938 ++++++------- R/checks.R | 304 ++-- R/clusters.R | 694 +++++----- R/colour_palettes.R | 394 ++--- R/confidence.R | 172 +- R/correlations.R | 1116 ++++++++-------- R/cran.R | 176 +- R/credentials.R | 196 +- R/crosstab.R | 202 +-- R/currency.R | 146 +- R/dalex_explainers.R | 441 +++--- R/dataframe_str.R | 462 +++--- R/datasets.R | 160 +- R/dim_reduction.R | 336 ++--- R/distribution.R | 950 +++++++------- R/dropbox.R | 246 +-- R/encoding.R | 44 R/facebook.R | 1528 +++++++++++----------- R/forecasting.R | 710 +++++----- R/frequencies.R | 1724 ++++++++++++------------- R/gemini.R | 166 +- R/geodata.R | 524 +++---- R/google_analytics.R | 130 - R/google_sheets.R | 258 +-- R/google_trends.R | 380 ++--- R/hubspot.R | 398 ++--- R/hubspot_f1.R | 502 +++---- R/lares.R | 300 ++-- R/lasso.R | 262 +-- R/linkedin.R | 114 - R/logo.R | 98 - R/mails.R | 190 +- R/maze.R | 669 ++++----- R/missings.R | 260 +-- R/model_functions.R | 1954 ++++++++++++++--------------- R/model_metrics.R | 1232 +++++++++--------- R/model_plots.R | 2928 +++++++++++++++++++++---------------------- R/model_predict.R | 326 ++-- R/model_preprocessing.R | 490 +++---- R/numble.R | 54 R/object_detection.R | 120 - R/onehotencoding.R | 1050 +++++++-------- R/other_functions.R | 2264 ++++++++++++++++----------------- R/other_plots.R | 548 ++++---- R/outliers.R | 358 ++--- R/plot_scales.R | 224 +-- R/querieSQL.R | 64 R/robyn.R | 1169 +++++++++-------- R/rtistry.R | 96 - R/scrabble.R | 959 +++++++------- R/shapley.R | 538 ++++---- R/shiny.R | 2 R/slack.R | 92 - R/statusbar.R | 158 +- R/stocks.R | 3016 ++++++++++++++++++++++----------------------- R/sudoku.R | 178 +- R/surveys.R | 84 - R/text_mining.R | 1124 ++++++++-------- R/theme_lares.R | 818 ++++++------ R/tictoc.R | 188 +- R/trees.R | 297 ++-- R/twitter.R | 56 R/typeform.R | 98 - R/update.R | 74 - R/wordle.R | 596 ++++---- R/wrangling.R | 1722 ++++++++++++------------- R/x2y.R | 736 +++++----- R/zzz.R | 198 +- README.md | 146 +- inst/_pkgdown.yml | 20 inst/docs/config.yml | 28 inst/docs/stocksReport.Rmd | 160 +- man/ROC.Rd | 132 - man/autoline.Rd | 154 +- man/balance_data.Rd | 126 - man/bind_files.Rd | 114 - man/bring_api.Rd | 154 +- man/cache_write.Rd | 160 +- man/categ_reducer.Rd | 172 +- man/checks.Rd | 144 +- man/chr2num.Rd | 142 +- man/ci_lower.Rd | 74 - man/ci_var.Rd | 72 - man/clean_text.Rd | 214 +-- man/clusterKmeans.Rd | 236 +-- man/clusterOptimalK.Rd | 116 - man/clusterVisualK.Rd | 86 - man/conf_mat.Rd | 144 +- man/corr.Rd | 208 +-- man/corr_cross.Rd | 218 +-- man/corr_var.Rd | 230 +-- man/cran_logs.Rd | 74 - man/crosstab.Rd | 146 +- man/dalex_local.Rd | 64 man/dalex_residuals.Rd | 48 man/dalex_variable.Rd | 88 - man/date_cuts.Rd | 102 - man/date_feats.Rd | 206 +-- man/db_download.Rd | 212 +-- man/db_upload.Rd | 174 +- man/df_str.Rd | 122 - man/dfr.Rd | 70 - man/dft.Rd | 98 - man/dist2d.Rd | 70 - man/distr.Rd | 268 +-- man/errors.Rd | 132 - man/etf_sector.Rd | 68 - man/export_plot.Rd | 180 +- man/export_results.Rd | 196 +- man/fb_accounts.Rd | 144 +- man/fb_ads.Rd | 174 +- man/fb_creatives.Rd | 134 - man/fb_insights.Rd | 294 ++-- man/fb_process.Rd | 114 - man/fb_report_check.Rd | 150 +- man/fb_rf.Rd | 306 ++-- man/fb_token.Rd | 116 - man/file_name.Rd | 156 +- man/filesGD.Rd | 86 - man/files_functions.Rd | 148 +- man/filterdata.Rd | 246 +-- man/font_exists.Rd | 138 +- man/forecast_arima.Rd | 162 +- man/formatColoured.Rd | 144 +- man/format_string.Rd | 322 ++-- man/freqs.Rd | 272 ++-- man/freqs_df.Rd | 178 +- man/freqs_list.Rd | 258 +-- man/freqs_plot.Rd | 180 +- man/gain_lift.Rd | 142 +- man/gemini_ask.Rd | 200 +- man/get_credentials.Rd | 268 +-- man/get_currency.Rd | 88 - man/get_mp3.Rd | 174 +- man/get_tweets.Rd | 68 - man/gg_fill_customs.Rd | 162 +- man/glued.Rd | 192 +- man/google_sheets.Rd | 174 +- man/google_trends.Rd | 106 - man/gpt_ask.Rd | 354 ++--- man/gpt_prompter.Rd | 276 ++-- man/grepl_letters.Rd | 68 - man/grepm.Rd | 158 +- man/h2o_automl.Rd | 426 +++--- man/h2o_explainer.Rd | 140 +- man/h2o_results.Rd | 142 +- man/h2o_selectmodel.Rd | 154 +- man/h2o_shap.Rd | 154 +- man/haveInternet.Rd | 118 - man/holidays.Rd | 174 +- man/image_metadata.Rd | 112 - man/importxlsx.Rd | 114 - man/impute.Rd | 140 +- man/install_recommended.Rd | 38 man/ip_data.Rd | 156 +- man/is_url.Rd | 110 - man/iter_seeds.Rd | 84 - man/json2vector.Rd | 122 - man/lares-exports.Rd | 18 man/lares.Rd | 44 man/lares_logo.Rd | 36 man/lares_pal.Rd | 114 - man/lasso_vars.Rd | 188 +- man/left_right.Rd | 106 - man/li_auth.Rd | 88 - man/li_profile.Rd | 78 - man/list_cats.Rd | 134 - man/listfiles.Rd | 152 +- man/loglossBinary.Rd | 58 man/mail_send.Rd | 218 +-- man/markdown2df.Rd | 120 - man/maze_solve.Rd | 182 +- man/missingness.Rd | 140 +- man/model_metrics.Rd | 248 +-- man/model_preprocess.Rd | 230 +-- man/move_files.Rd | 120 - man/mplot_conf.Rd | 180 +- man/mplot_cuts.Rd | 134 - man/mplot_cuts_error.Rd | 128 - man/mplot_density.Rd | 138 +- man/mplot_full.Rd | 188 +- man/mplot_gain.Rd | 192 +- man/mplot_importance.Rd | 164 +- man/mplot_lineal.Rd | 118 - man/mplot_metrics.Rd | 104 - man/mplot_response.Rd | 186 +- man/mplot_roc.Rd | 174 +- man/mplot_splits.Rd | 158 +- man/mplot_topcats.Rd | 98 - man/msplit.Rd | 172 +- man/myip.Rd | 116 - man/ngrams.Rd | 98 - man/noPlot.Rd | 82 - man/normalize.Rd | 102 - man/num_abbr.Rd | 114 - man/ohe_commas.Rd | 140 +- man/ohse.Rd | 248 +-- man/outlier_turkey.Rd | 60 man/outlier_zscore.Rd | 68 - man/outlier_zscore_plot.Rd | 86 - man/plot_cats.Rd | 72 - man/plot_chord.Rd | 110 - man/plot_df.Rd | 72 - man/plot_nums.Rd | 80 - man/plot_palette.Rd | 82 - man/plot_survey.Rd | 74 - man/plot_timeline.Rd | 182 +- man/prophesize.Rd | 104 - man/quants.Rd | 132 - man/queryDB.Rd | 72 - man/queryGA.Rd | 160 +- man/quiet.Rd | 118 - man/read.file.Rd | 128 - man/reduce_pca.Rd | 128 - man/reduce_tsne.Rd | 102 - man/remove_stopwords.Rd | 82 - man/replaceall.Rd | 182 +- man/replacefactor.Rd | 114 - man/robyn_hypsbuilder.Rd | 124 - man/robyn_modelselector.Rd | 164 +- man/robyn_performance.Rd | 119 - man/rtistry_sphere.Rd | 36 man/scale_x_comma.Rd | 208 +-- man/scrabble.Rd | 310 ++-- man/sentimentBreakdown.Rd | 110 - man/shap_var.Rd | 118 - man/slackSend.Rd | 124 - man/spread_list.Rd | 82 - man/statusbar.Rd | 182 +- man/stocks_hist.Rd | 170 +- man/stocks_report.Rd | 334 ++-- man/sudoku_solver.Rd | 96 - man/target_set.Rd | 56 man/textCloud.Rd | 112 - man/textFeats.Rd | 134 - man/textTokenizer.Rd | 204 +-- man/theme_lares.Rd | 206 +-- man/tic.Rd | 200 +- man/topics_rake.Rd | 72 - man/tree_var.Rd | 270 +--- man/trim_mp3.Rd | 72 - man/try_require.Rd | 148 +- man/updateLares.Rd | 130 - man/vector2text.Rd | 132 - man/warnifnot.Rd | 118 - man/weighted_value.Rd | 102 - man/what_size.Rd | 146 +- man/winsorize.Rd | 64 man/wordle.Rd | 156 +- man/x2y.Rd | 256 +-- man/year_month.Rd | 110 - man/zerovar.Rd | 98 - 258 files changed, 33920 insertions(+), 33824 deletions(-)
Title: Generalized Additive Models
Description: Functions for fitting and working with generalized additive models, as described in chapter 7 of "Statistical Models in S" (Chambers and Hastie (eds), 1991), and "Generalized Additive Models" (Hastie and Tibshirani, 1990).
Author: Trevor Hastie [aut, cre],
Balasubramanian Narasimhan [ctb]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between gam versions 1.22-4 dated 2024-07-18 and 1.22-5 dated 2024-09-12
ChangeLog | 14 +++++++++++--- DESCRIPTION | 21 +++++++++++++-------- MD5 | 6 +++--- src/loessc.c | 12 ++++++------ 4 files changed, 33 insertions(+), 20 deletions(-)
Title: Dynamic Web-Based Analytics for the Energy Industry
Description: A 'Shiny' web application for energy industry analytics.
Take an overview of the industry, measure Key Performance Indicators,
identify changes in the industry over time, and discover new relationships in the data.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
Diff between eAnalytics versions 0.3 dated 2023-06-26 and 0.3.1 dated 2024-09-12
DESCRIPTION | 16 ++++++++-------- MD5 | 7 ++++--- NEWS.md | 2 -- README.md | 14 ++++++++++---- inst/CITATION |only 5 files changed, 22 insertions(+), 17 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex
macroevolutionary dynamics on phylogenetic trees. It is a companion
package to the command line program BAMM (Bayesian Analysis of
Macroevolutionary Mixtures) and is entirely oriented towards the analysis,
interpretation, and visualization of evolutionary rates. Functionality
includes visualization of rate shifts on phylogenies, estimating
evolutionary rates through time, comparing posterior distributions of
evolutionary rates across clades, comparing diversification models using
Bayes factors, and more.
Author: Dan Rabosky [aut],
Michael Grundler [aut],
Pascal Title [aut, cre] ,
Carlos Anderson [aut],
Jeff Shi [aut],
Joseph Brown [aut],
Huateng Huang [aut],
Jon Mitchell [aut]
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between BAMMtools versions 2.1.11 dated 2023-12-19 and 2.1.12 dated 2024-09-12
DESCRIPTION | 29 ++++++++++++++++++++++------- MD5 | 14 +++++++------- R/BAMMtools-package.R | 3 +-- R/cohorts.R | 2 +- man/BAMMtools.Rd | 8 ++++++++ man/cohorts.Rd | 2 +- src/jenksBrks.c | 17 +++++++++-------- src/treetraverse.c | 40 ++++++++++++++++++++-------------------- 8 files changed, 69 insertions(+), 46 deletions(-)
Title: Conducts Analyses Informing Ecosystem Restoration Decisions
Description: Three sets of data and functions for informing ecosystem restoration
decisions, particularly in the context of the U.S. Army Corps of Engineers.
First, model parameters are compiled as a data set and associated metadata
for over 300 habitat suitability models developed by the U.S. Fish and
Wildlife Service (USFWS 1980, <https://www.fws.gov/policy-library/870fw1>).
Second, functions for conducting habitat suitability analyses both for the
models described above as well as generic user-specified model parameterizations.
Third, a suite of decision support tools for conducting cost-effectiveness and
incremental cost analyses (Robinson et al. 1995, IWR Report 95-R-1, U.S.
Army Corps of Engineers).
Author: S. Kyle McKay [aut, cre] ,
Darixa D. Hernandez-Abrams [aut],
Kiara C. Cushway [aut]
Maintainer: S. Kyle McKay <kyle.mckay@usace.army.mil>
Diff between ecorest versions 1.0.0 dated 2020-06-26 and 2.0.0 dated 2024-09-12
DESCRIPTION | 30 ++++---- MD5 | 24 +++--- NAMESPACE | 2 R/HSIeqtn.R | 135 +++++++++++++++++++++++++++--------- R/HSImetadata.R | 38 +++++++++- R/HSImodels.R | 11 +- R/SIcalc.R | 3 data/HSImetadata.RData |binary data/HSImodels.RData |binary man/HSIeqtn.Rd | 24 +++++- man/HSImetadata.Rd | 182 ++++++++++++++++++++++++++++--------------------- man/HSImodels.Rd | 65 +++++++++-------- man/SIcalc.Rd | 3 13 files changed, 341 insertions(+), 176 deletions(-)
Title: Statistical Tools for Ranks
Description: Account for uncertainty when working with ranks.
Estimate standard errors consistently in linear regression with ranked variables.
Construct confidence sets of various kinds for positions of populations in a ranking
based on values of a certain feature and their estimation errors.
Theory based on Mogstad, Romano, Shaikh, and Wilhelm (2023)<doi:10.1093/restud/rdad006> and
Chetverikov and Wilhelm (2023) <doi:10.48550/arXiv.2310.15512>.
Author: Daniel Wilhelm [aut, cre],
Pawel Morgen [aut]
Maintainer: Daniel Wilhelm <d.wilhelm@lmu.de>
Diff between csranks versions 1.2.2 dated 2024-01-24 and 1.2.3 dated 2024-09-12
csranks-1.2.2/csranks/tests/spelling.Rout.save |only csranks-1.2.3/csranks/DESCRIPTION | 10 csranks-1.2.3/csranks/MD5 | 57 +-- csranks-1.2.3/csranks/NAMESPACE | 3 csranks-1.2.3/csranks/NEWS.md | 12 csranks-1.2.3/csranks/R/data.R | 4 csranks-1.2.3/csranks/R/lmranks.R | 2 csranks-1.2.3/csranks/R/lmranks_model_selection.R | 15 csranks-1.2.3/csranks/R/lmranks_model_usage.R | 2 csranks-1.2.3/csranks/R/lmranks_summary.R | 21 - csranks-1.2.3/csranks/R/plotranking.R | 3 csranks-1.2.3/csranks/R/rank_utils.R | 40 +- csranks-1.2.3/csranks/R/ranks.R | 6 csranks-1.2.3/csranks/build/partial.rdb |binary csranks-1.2.3/csranks/build/vignette.rds |binary csranks-1.2.3/csranks/inst/doc/Inference-for-Ranks.html | 17 csranks-1.2.3/csranks/inst/doc/Inference-for-Ranks.rmd | 2 csranks-1.2.3/csranks/inst/doc/Rank-Rank-Reg.html | 188 ++++------ csranks-1.2.3/csranks/inst/doc/Rank-Rank-Reg.rmd | 2 csranks-1.2.3/csranks/man/csranks.Rd | 6 csranks-1.2.3/csranks/man/cstaubest.Rd | 2 csranks-1.2.3/csranks/man/irank.Rd | 15 csranks-1.2.3/csranks/man/irank_against.Rd | 36 + csranks-1.2.3/csranks/man/lmranks.Rd | 16 csranks-1.2.3/csranks/man/pisa.Rd | 2 csranks-1.2.3/csranks/man/pisa2018.Rd | 2 csranks-1.2.3/csranks/tests/testthat/test_grouped_lmranks_vcov.R | 8 csranks-1.2.3/csranks/tests/testthat/test_lmranks_vcov.R | 8 csranks-1.2.3/csranks/vignettes/Inference-for-Ranks.rmd | 2 csranks-1.2.3/csranks/vignettes/Rank-Rank-Reg.rmd | 2 30 files changed, 272 insertions(+), 211 deletions(-)
Title: "Risk Model Regression and Analysis with Complex Non-Linear
Models"
Description: Performs survival analysis using general non-linear models. Risk models can be the sum or product of terms. Each term is the product of exponential/linear functions of covariates. Additionally sub-terms can be defined as a sum of exponential, linear threshold, and step functions. Cox Proportional hazards <https://en.wikipedia.org/wiki/Proportional_hazards_model>, Poisson <https://en.wikipedia.org/wiki/Poisson_regression>, and Fine-Grey competing risks <https://www.publichealth.columbia.edu/research/population-health-methods/competing-risk-analysis> regression are supported. This work was sponsored by NASA Grant 80NSSC19M0161 through a subcontract from the National Council on Radiation Protection and Measurements (NCRP). The computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CNS-1006860, EPS-1006860, EPS-0919443, ACI-1440548, CHE-1726332, and NIH P20GM113109.
Author: Eric Giunta [aut, cre] ,
Amir Bahadori [ctb] ,
Dan Andresen [ctb],
Linda Walsh [ctb] ,
Benjamin French [ctb] ,
Lawrence Dauer [ctb],
John Boice Jr [ctb] ,
Kansas State University [cph],
NASA [fnd],
NCRP [fnd],
NRC [fnd]
Maintainer: Eric Giunta <egiunta@ksu.edu>
Diff between Colossus versions 1.1.3 dated 2024-09-06 and 1.1.3.1 dated 2024-09-12
DESCRIPTION | 6 - MD5 | 48 ++++---- NEWS.md | 4 README.md | 2 inst/doc/Alt_Distrib_Starts.Rmd | 8 - inst/doc/Alt_Distrib_Starts.html | 8 - inst/doc/Alt_Run_Opt.R | 12 ++ inst/doc/Alt_Run_Opt.Rmd | 28 +++- inst/doc/Alt_Run_Opt.html | 36 ++++-- inst/doc/Control_Options.Rmd | 7 + inst/doc/Control_Options.html | 214 ++++++++++++++++++++++++++++++------ inst/doc/Plotting_And_Analysis.Rmd | 2 inst/doc/Plotting_And_Analysis.html | 2 inst/doc/Starting-Description.R | 2 inst/doc/Starting-Description.Rmd | 20 +-- inst/doc/Starting-Description.html | 20 +-- src/R_Interface.cpp | 1 tests/testthat/test-multidose.R | 14 +- tests/testthat/test-omnibus.R | 8 + tools/config/configure.R | 4 vignettes/Alt_Distrib_Starts.Rmd | 8 - vignettes/Alt_Run_Opt.Rmd | 28 +++- vignettes/Control_Options.Rmd | 7 + vignettes/Plotting_And_Analysis.Rmd | 2 vignettes/Starting-Description.Rmd | 20 +-- 25 files changed, 376 insertions(+), 135 deletions(-)
Title: Ensembles of Caret Models
Description: Functions for creating ensembles of caret models: caretList()
and caretStack(). caretList() is a convenience function for fitting multiple
caret::train() models to the same dataset. caretStack() will make linear or
non-linear combinations of these models, using a caret::train() model as a
meta-model.
Author: Zachary A. Deane-Mayer [aut, cre, cph],
Jared E. Knowles [ctb],
Anton Lopez [ctb]
Maintainer: Zachary A. Deane-Mayer <zach.mayer@gmail.com>
Diff between caretEnsemble versions 4.0.0 dated 2024-08-17 and 4.0.1 dated 2024-09-12
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NEWS.md | 3 +++ R/caretStack.R | 2 +- inst/doc/Version-4.0-New-Features.html | 18 +++++++++--------- inst/doc/caretEnsemble-intro.html | 32 ++++++++++++++++---------------- man/autoplot.caretStack.Rd | 2 +- 7 files changed, 42 insertions(+), 39 deletions(-)
Title: Dereplicate and Cherry-Pick Mass Spectrometry Spectra
Description: Convenient wrapper functions for the analysis of
matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF)
spectra data in order to select only representative spectra (also
called cherry-pick). The package covers the preprocessing and
dereplication steps (based on Strejcek, Smrhova, Junkova and Uhlik
(2018) <doi:10.3389/fmicb.2018.01294>) needed to cluster MALDI-TOF
spectra before the final cherry-picking step. It enables the easy
exclusion of spectra and/or clusters to accommodate complex
cherry-picking strategies. Alternatively, cherry-picking using
taxonomic identification MALDI-TOF data is made easy with functions to
import inconsistently formatted reports.
Author: Charlie Pauvert [aut, cre, cph]
,
David Wylensek [ctb] ,
Selina Nuechtern [ctb],
Thomas Clavel [ctb, fnd, cph]
Maintainer: Charlie Pauvert <cpauvert@ukaachen.de>
Diff between maldipickr versions 1.3.0 dated 2023-12-14 and 1.3.1 dated 2024-09-12
maldipickr-1.3.0/maldipickr/man/figures/logo.png |only maldipickr-1.3.1/maldipickr/DESCRIPTION | 13 maldipickr-1.3.1/maldipickr/MD5 | 44 +- maldipickr-1.3.1/maldipickr/NAMESPACE | 1 maldipickr-1.3.1/maldipickr/NEWS.md | 28 + maldipickr-1.3.1/maldipickr/R/gather_spectra_stats.R |only maldipickr-1.3.1/maldipickr/R/import_biotyper_spectra.R | 4 maldipickr-1.3.1/maldipickr/R/merge_processed_spectra.R | 21 + maldipickr-1.3.1/maldipickr/README.md | 163 +++------- maldipickr-1.3.1/maldipickr/build/vignette.rds |binary maldipickr-1.3.1/maldipickr/inst/WORDLIST | 17 - maldipickr-1.3.1/maldipickr/inst/doc/dereplicate-bruker-maldi-biotyper-spectra.R | 8 maldipickr-1.3.1/maldipickr/inst/doc/dereplicate-bruker-maldi-biotyper-spectra.Rmd | 8 maldipickr-1.3.1/maldipickr/inst/doc/dereplicate-bruker-maldi-biotyper-spectra.html | 12 maldipickr-1.3.1/maldipickr/inst/doc/import-data-from-bruker-maldi-biotyper.html | 14 maldipickr-1.3.1/maldipickr/inst/doc/maldipickr.R |only maldipickr-1.3.1/maldipickr/inst/doc/maldipickr.Rmd |only maldipickr-1.3.1/maldipickr/inst/doc/maldipickr.html |only maldipickr-1.3.1/maldipickr/man/figures/logo.svg |only maldipickr-1.3.1/maldipickr/man/figures/maldipickr-data-flow-portrait-thumb.png |only maldipickr-1.3.1/maldipickr/man/figures/maldipickr-data-flow-portrait.png |only maldipickr-1.3.1/maldipickr/man/figures/maldipickr-data-flow-portrait.svg |only maldipickr-1.3.1/maldipickr/man/gather_spectra_stats.Rd |only maldipickr-1.3.1/maldipickr/man/maldipickr-package.Rd | 3 maldipickr-1.3.1/maldipickr/man/merge_processed_spectra.Rd | 16 maldipickr-1.3.1/maldipickr/tests/testthat/test-gather_spectra_stats.R |only maldipickr-1.3.1/maldipickr/tests/testthat/test-merge_processed_spectra.R | 8 maldipickr-1.3.1/maldipickr/vignettes/dereplicate-bruker-maldi-biotyper-spectra.Rmd | 8 maldipickr-1.3.1/maldipickr/vignettes/maldipickr.Rmd |only 29 files changed, 218 insertions(+), 150 deletions(-)
Title: Variational Inference for Hierarchical Generalized Linear Models
Description: Estimates hierarchical models using mean-field variational Bayes.
At present, it can estimate logistic, linear, and negative binomial models.
It can accommodate models with an arbitrary number of random effects and
requires no integration to estimate. It also provides the ability to improve
the quality of the approximation using marginal augmentation.
Goplerud (2022) <doi:10.1214/21-BA1266> and Goplerud (2024) <doi:10.1017/S0003055423000035>
provide details on the variational algorithms.
Author: Max Goplerud [aut, cre]
Maintainer: Max Goplerud <mgoplerud@austin.utexas.edu>
Diff between vglmer versions 1.0.3 dated 2022-10-27 and 1.0.5 dated 2024-09-12
vglmer-1.0.3/vglmer/.Rinstignore |only vglmer-1.0.5/vglmer/DESCRIPTION | 18 vglmer-1.0.5/vglmer/MD5 | 37 vglmer-1.0.5/vglmer/NAMESPACE | 8 vglmer-1.0.5/vglmer/NEWS.md | 12 vglmer-1.0.5/vglmer/R/RcppExports.R | 4 vglmer-1.0.5/vglmer/R/mgcv_functions.R |only vglmer-1.0.5/vglmer/R/predict_functions.R | 105 ++ vglmer-1.0.5/vglmer/R/print_functions.R | 2 vglmer-1.0.5/vglmer/R/spline_functions.R | 385 +++++++--- vglmer-1.0.5/vglmer/R/vglmer_regression.R | 92 +- vglmer-1.0.5/vglmer/README.md | 8 vglmer-1.0.5/vglmer/man/LinRegChol.Rd | 4 vglmer-1.0.5/vglmer/man/Predict.matrix.randwalk.smooth.Rd |only vglmer-1.0.5/vglmer/man/fallback_subbars.Rd |only vglmer-1.0.5/vglmer/man/smooth.construct.randwalk.smooth.spec.Rd |only vglmer-1.0.5/vglmer/man/v_s.Rd | 23 vglmer-1.0.5/vglmer/man/vglmer_predict.Rd | 6 vglmer-1.0.5/vglmer/src/eigen_alpha.cpp | 4 vglmer-1.0.5/vglmer/tests/testthat/test-errors.R | 56 + vglmer-1.0.5/vglmer/tests/testthat/test-gKRLS.R |only vglmer-1.0.5/vglmer/tests/testthat/test-predict.R | 25 vglmer-1.0.5/vglmer/tests/testthat/test-splines.R | 85 +- 23 files changed, 654 insertions(+), 220 deletions(-)
Title: Star Trek Color Palettes
Description: Provides a dataset of predefined color palettes based on the Star Trek science fiction series, associated color palette functions,
and additional functions for generating customized palettes that are on theme. The package also offers functions for applying
the palettes to plots made using the 'ggplot2' package.
Author: Matthew Leonawicz [aut, cre]
Maintainer: Matthew Leonawicz <rpkgs@pm.me>
Diff between trekcolors versions 0.1.3 dated 2021-06-01 and 0.2.0 dated 2024-09-12
DESCRIPTION | 16 ++-- MD5 | 51 ++++++------- NEWS.md | 4 + R/lcars.R | 59 ++++++++------- R/trekcolors.R | 30 +++++-- README.md | 97 +++++++++++++----------- inst/WORDLIST | 8 -- man/figures/README-ex2-1.png |binary man/figures/README-ex3-1.png |binary man/figures/README-ex3-2.png |binary man/figures/README-ex3-3.png |binary man/figures/README-ex3-4.png |binary man/figures/README-ex3-5.png |binary man/figures/README-ex3-6.png |binary man/figures/README-ex3-7.png |binary man/figures/README-ex3-8.png |binary man/figures/README-ex3-9.png |binary man/figures/README-ex5-1.png |binary man/figures/README-ex5-2.png |binary man/figures/README-ex5-3.png |binary man/figures/README-ex6-1.png |binary man/lcars_colors.Rd | 81 ++++++++++---------- man/lcars_pals.Rd | 112 +++++++++++++++------------- man/scale_lcars.Rd | 168 ++++++++++++++++++++++--------------------- man/scale_trek.Rd | 74 +++++++++--------- man/trek_pal.Rd | 81 ++++++++++---------- man/trekcolors.Rd |only 27 files changed, 413 insertions(+), 368 deletions(-)
Title: Read Cancer Records in the NAACCR Format
Description: Functions for reading cancer record files which follow a format
defined by the North American Association of Central Cancer Registries
(NAACCR).
Author: Nathan Werth [aut, cre],
Pennsylvania Department of Health [cph],
North American Association of Cancer Registries [cph],
World Health Organization [cph],
United States Centers for Disease Control and Prevention [cph],
United States Bureau of the Cens [...truncated...]
Maintainer: Nathan Werth <nwerth@pa.gov>
Diff between naaccr versions 2.0.2 dated 2022-11-23 and 3.0.1 dated 2024-09-12
DESCRIPTION | 52 ++++++-- MD5 | 43 +++--- NAMESPACE | 12 + NEWS | 21 +++ R/data-item-interpreting.R | 37 ++++- R/gis.R |only R/onLoad.R | 5 R/read_naaccr.R | 2 R/record_format.R | 8 + R/sysdata.rda |binary R/write_naaccr.R | 207 +++++++++++++++++++------------- README.md | 3 data/field_levels.RData |binary man/field_levels.Rd | 2 man/naaccr_datetime.Rd | 15 +- man/naaccr_formats.Rd | 12 + man/parse_geocoding_quality_codes.Rd |only man/read_naaccr.Rd | 2 man/write_naaccr_xml.Rd | 5 tests/testthat/test-gis.R |only tests/testthat/test-item-interpreting.R | 67 ++++++++-- tests/testthat/test-naaccr_record.R | 30 ++++ tests/testthat/test-utilities.R | 17 +- tests/testthat/test-write_naaccr.R | 2 24 files changed, 382 insertions(+), 160 deletions(-)
Title: Practical Functions for Biostatistics Beginners
Description: A set of user-friendly functions designed to fill gaps in existing introductory biostatistics R tools, making it easier for newcomers to perform basic biostatistical analyses without needing advanced programming skills.
The methods implemented in this package are based on the works:
Connor (1987) <doi:10.2307/2531961>
Fleiss, Levin, & Paik (2013, ISBN:978-1-118-62561-3)
Levin & Chen (1999) <doi:10.1080/00031305.1999.10474431>
McNemar (1947) <doi:10.1007/BF02295996>.
Author: Marina Mautner Wizentier [aut, cre]
,
Melody S. Goodman [aut] ,
Jemar R. Bather [aut]
Maintainer: Marina Mautner Wizentier <mm12025@nyu.edu>
Diff between biostats101 versions 0.1.0 dated 2024-09-04 and 0.1.1 dated 2024-09-12
DESCRIPTION | 6 - MD5 | 12 +-- R/power.2p.2n.R | 6 + R/power.paired.prop.R | 156 +++++++++++++++++++++++++++++++++-------------- README.md | 2 inst/CITATION | 2 man/power.paired.prop.Rd | 13 +-- 7 files changed, 135 insertions(+), 62 deletions(-)
Title: Stock Status Plots (SSPs)
Description: Pauly et al. (2008) <http://legacy.seaaroundus.s3.amazonaws.com/doc/Researcher+Publications/dpauly/PDF/2008/Books%26Chapters/FisheriesInLargeMarineEcosystems.pdf> created (and coined the name) 'Stock Status Plots' for a UNEP compendium on Large Marine Ecosystems(LMEs, Sherman and Hempel (2009)<https://marineinfo.org/imis?module=ref&refid=142061&printversion=1&dropIMIStitle=1>). Stock status plots are bivariate graphs summarizing the status (e.g., developing, fully exploited, overexploited, etc.), through time, of the multispecies fisheries of a fished area or ecosystem. This package contains three functions to generate stock status plots viz., SSplots_pauly() (as per the criteria proposed by Pauly et al.,2008), SSplots_kleisner() (as per the criteria proposed by Kleisner and Pauly (2011) <http://www.ecomarres.com/downloads/regional.pdf> and Kleisner et al. (2013) <doi:10.1111/j.1467-2979.2012.00469.x>)and SSplots_EPI() (as per the criteria proposed b [...truncated...]
Author: Eldho Varghese [aut, cre],
J Jayasankar [aut],
Sreepriya V [aut],
Reshma Gills [ctb],
Ashutosh Dalal [ctb]
Maintainer: Eldho Varghese <eldhoiasri@gmail.com>
Diff between SSplots versions 0.1.1 dated 2023-05-08 and 0.1.2 dated 2024-09-12
DESCRIPTION | 10 +++++----- MD5 | 12 +++++++----- NAMESPACE | 1 + R/SSplots_EPI.R |only R/SSplots_kleisner.R | 43 ++++++++++++++++++------------------------- R/SSplots_pauly.R | 41 ++++++++++++++++++----------------------- man/SSplots_EPI.Rd |only man/SSplots_pauly.Rd | 5 +++-- 8 files changed, 52 insertions(+), 60 deletions(-)
Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on
'Windows', 'Linux' and 'macOS'.
Author: Jay Loden [aut],
Dave Daeschler [aut],
Giampaolo Rodola' [aut],
Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between ps versions 1.7.7 dated 2024-07-02 and 1.8.0 dated 2024-09-12
DESCRIPTION | 10 MD5 | 112 +++--- NAMESPACE | 6 NEWS.md | 31 + R/cleancall.R |only R/disk.R | 302 ++++++++++++++++ R/iso-date.R |only R/kill-tree.R | 39 +- R/linux.R | 107 +++++ R/low-level.R | 260 ++++++++++++-- R/macos.R |only R/ps.R | 10 R/rematch2.R |only R/testthat-reporter.R | 59 ++- R/utils.R | 42 ++ README.md | 449 ++++++++---------------- configure | 9 man/CleanupReporter.Rd | 5 man/ps-package.Rd | 1 man/ps_apps.Rd |only man/ps_disk_io_counters.Rd |only man/ps_disk_partitions.Rd | 1 man/ps_disk_usage.Rd | 1 man/ps_environ.Rd | 25 + man/ps_fs_info.Rd |only man/ps_fs_mount_point.Rd |only man/ps_fs_stat.Rd |only man/ps_interrupt.Rd | 2 man/ps_kill.Rd | 26 + man/ps_kill_tree.Rd | 8 man/ps_memory_info.Rd | 2 man/ps_resume.Rd | 2 man/ps_send_signal.Rd | 2 man/ps_status.Rd | 28 + man/ps_suspend.Rd | 2 man/ps_terminate.Rd | 2 man/ps_wait.Rd |only src/api-linux.c | 582 +++++++++++++++++++++++++++++-- src/api-macos.c | 446 +++++++++++++++++++++--- src/api-posix.c | 301 ++++++++++++++++ src/api-windows.c | 603 +++++++++++++++++++++++++++++---- src/arch/macos/apps.m |only src/arch/macos/disk.c |only src/cleancall.c |only src/cleancall.h |only src/dummy.c | 16 src/extra.c | 24 - src/init.c | 17 src/ps-internal.h | 9 src/ps.h | 9 src/px.c | 57 +++ tests/testthat.R | 4 tests/testthat/_snaps |only tests/testthat/fixtures |only tests/testthat/helpers.R | 1 tests/testthat/test-cleanup-reporter.R | 14 tests/testthat/test-common.R | 83 ++++ tests/testthat/test-connections.R | 2 tests/testthat/test-disk.R |only tests/testthat/test-finished.R | 4 tests/testthat/test-kill-tree.R | 1 tests/testthat/test-macos.R | 8 tests/testthat/test-pid-reuse.R | 4 tests/testthat/test-posix.R | 49 ++ tests/testthat/test-wait-inotify.R |only tests/testthat/test-wait.R |only tools |only 67 files changed, 3168 insertions(+), 609 deletions(-)
Title: Package Dependency Resolution and Downloads
Description: Find recursive dependencies of 'R' packages from various
sources. Solve the dependencies to obtain a consistent set of packages
to install. Download packages, and install them. It supports packages
on 'CRAN', 'Bioconductor' and other 'CRAN-like' repositories,
'GitHub', package 'URLs', and local package trees and files. It caches
metadata and package files via the 'pkgcache' package, and performs
all 'HTTP' requests, downloads, builds and installations in parallel.
'pkgdepends' is the workhorse of the 'pak' package.
Author: Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pkgdepends versions 0.7.2 dated 2024-03-17 and 0.8.0 dated 2024-09-12
DESCRIPTION | 15 MD5 | 289 ++++++------ NAMESPACE | 4 R/builder.R |only R/gh-mirror.R |only R/gh-releases.R |only R/gh-repo.R |only R/ghcr.R |only R/git-app.R | 7 R/git-auth.R | 21 R/git-protocol.R | 79 ++- R/git-submodules.R |only R/install-plan.R | 58 +- R/iso-date.R |only R/parse-remotes.R | 13 R/repo.R |only R/resolution-df.R | 14 R/resolution.R | 2 R/solve.R | 34 + R/sysreqs2.R | 12 R/system-packages.R | 42 + R/time.R | 2 R/type-cran.R | 4 R/type-git.R | 43 - R/type-gitlab.R | 34 + R/utils.R | 14 R/zzz-pkgdepends-config.R | 12 inst/WORDLIST | 3 inst/docs/pak-config-docs.rds |binary inst/docs/pkg-refs.rds |binary inst/sysreqs/HEAD | 2 inst/sysreqs/rules/apparmor.json | 11 inst/sysreqs/rules/atk.json | 41 + inst/sysreqs/rules/automake.json | 9 inst/sysreqs/rules/berkeleydb.json | 9 inst/sysreqs/rules/blender.json | 10 inst/sysreqs/rules/boost.json |only inst/sysreqs/rules/cairo.json | 9 inst/sysreqs/rules/chrome.json | 38 + inst/sysreqs/rules/cmake.json | 9 inst/sysreqs/rules/eigen.json |only inst/sysreqs/rules/exiftool.json | 9 inst/sysreqs/rules/fftw3.json | 9 inst/sysreqs/rules/flint.json |only inst/sysreqs/rules/fluidsynth.json |only inst/sysreqs/rules/fontconfig.json | 9 inst/sysreqs/rules/freetype.json | 9 inst/sysreqs/rules/fribidi.json | 9 inst/sysreqs/rules/gdal.json | 14 inst/sysreqs/rules/geos.json | 9 inst/sysreqs/rules/git.json | 11 inst/sysreqs/rules/glib.json | 9 inst/sysreqs/rules/glpk.json | 14 inst/sysreqs/rules/glu.json | 9 inst/sysreqs/rules/gmp.json | 9 inst/sysreqs/rules/gnumake.json | 9 inst/sysreqs/rules/gpgme.json | 9 inst/sysreqs/rules/grpcpp.json |only inst/sysreqs/rules/gsl.json | 9 inst/sysreqs/rules/gtk.json | 9 inst/sysreqs/rules/harfbuzz.json | 9 inst/sysreqs/rules/haveged.json | 9 inst/sysreqs/rules/hdf5.json | 9 inst/sysreqs/rules/hiredis.json | 9 inst/sysreqs/rules/imagemagick.json | 9 inst/sysreqs/rules/java.json | 13 inst/sysreqs/rules/latex.json | 9 inst/sysreqs/rules/leptonica.json | 9 inst/sysreqs/rules/libarchive.json | 9 inst/sysreqs/rules/libavfilter.json | 11 inst/sysreqs/rules/libbsd.json | 9 inst/sysreqs/rules/libcurl.json | 10 inst/sysreqs/rules/libgit2.json | 15 inst/sysreqs/rules/libicu.json | 28 + inst/sysreqs/rules/libjpeg.json | 9 inst/sysreqs/rules/libjq.json | 9 inst/sysreqs/rules/libmagic.json | 9 inst/sysreqs/rules/libmysqlclient.json | 13 inst/sysreqs/rules/libpng.json | 9 inst/sysreqs/rules/libprotobuf.json | 9 inst/sysreqs/rules/librsvg2.json | 9 inst/sysreqs/rules/libsecret.json | 9 inst/sysreqs/rules/libsndfile.json | 9 inst/sysreqs/rules/libsodium.json | 9 inst/sysreqs/rules/libssh.json |only inst/sysreqs/rules/libssh2.json | 9 inst/sysreqs/rules/libtiff.json | 9 inst/sysreqs/rules/libtool.json |only inst/sysreqs/rules/libwebp.json | 9 inst/sysreqs/rules/libxml2.json | 9 inst/sysreqs/rules/libxslt.json | 9 inst/sysreqs/rules/libzstd.json |only inst/sysreqs/rules/mongodb.json | 9 inst/sysreqs/rules/mpfr.json | 9 inst/sysreqs/rules/mysql.json | 9 inst/sysreqs/rules/netcdf4.json | 9 inst/sysreqs/rules/odbc.json | 9 inst/sysreqs/rules/openbabel.json |only inst/sysreqs/rules/opencl.json | 10 inst/sysreqs/rules/opencv.json | 11 inst/sysreqs/rules/opengl.json | 9 inst/sysreqs/rules/openmpi.json | 9 inst/sysreqs/rules/openssl.json | 9 inst/sysreqs/rules/pandoc-citeproc.json | 3 inst/sysreqs/rules/pandoc.json | 20 inst/sysreqs/rules/pango.json | 9 inst/sysreqs/rules/perl.json | 9 inst/sysreqs/rules/pkg-config.json | 9 inst/sysreqs/rules/poppler.json | 11 inst/sysreqs/rules/postgresql.json | 35 - inst/sysreqs/rules/proj.json | 11 inst/sysreqs/rules/protobuf-compiler.json | 11 inst/sysreqs/rules/protobuf-grpc.json |only inst/sysreqs/rules/python.json | 9 inst/sysreqs/rules/python3.json | 9 inst/sysreqs/rules/redland.json | 9 inst/sysreqs/rules/rust.json | 9 inst/sysreqs/rules/sasl.json | 9 inst/sysreqs/rules/sdl2.json |only inst/sysreqs/rules/sqlite3.json | 9 inst/sysreqs/rules/suitesparse.json | 9 inst/sysreqs/rules/tcltk.json | 9 inst/sysreqs/rules/tesseract.json | 9 inst/sysreqs/rules/tk.json | 11 inst/sysreqs/rules/udunits2.json | 14 inst/sysreqs/rules/v8.json | 2 inst/sysreqs/rules/wget.json | 9 inst/sysreqs/rules/xft.json | 9 inst/sysreqs/rules/xz.json |only inst/sysreqs/rules/zeromq.json | 9 inst/sysreqs/rules/zlib.json | 9 man/ghr.Rd |only man/ghrepo.Rd |only man/pkg_build.Rd |only man/pkg_config.Rd | 5 man/pkg_refs.Rd | 22 man/repo.Rd |only tests/testthat/_snaps/assertions.md | 6 tests/testthat/_snaps/git-protocol.md | 49 +- tests/testthat/_snaps/git-submodules.md |only tests/testthat/_snaps/parse-remotes.md | 561 +++++++++++++++++++++--- tests/testthat/_snaps/pillar-1.9.0/type-bioc.md | 3 tests/testthat/_snaps/pillar-1.9.0/type-git.md | 5 tests/testthat/_snaps/pkg-dependencies.md | 22 tests/testthat/_snaps/pkg-downloads.md | 22 tests/testthat/_snaps/pkg-installation.md | 22 tests/testthat/_snaps/pkgdepends-config.md | 22 tests/testthat/_snaps/sysreqs.md | 22 tests/testthat/_snaps/type-cran.md | 84 +-- tests/testthat/_snaps/type-gitlab.md | 2 tests/testthat/fixtures/git-repo.tar.gz |binary tests/testthat/fixtures/submodules.ini |only tests/testthat/fixtures/submodules2.ini |only tests/testthat/fixtures/submodules3.ini |only tests/testthat/helper-install.R | 2 tests/testthat/test-git-submodules.R |only tests/testthat/test-parse-remotes.R | 27 - tests/testthat/test-sysreqs.R | 2 tests/testthat/test-type-git.R | 21 tests/testthat/test-type-gitlab.R | 4 160 files changed, 2054 insertions(+), 497 deletions(-)
Title: Cache 'CRAN'-Like Metadata and R Packages
Description: Metadata and package cache for CRAN-like repositories. This
is a utility package to be used by package management tools that want
to take advantage of caching.
Author: Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pkgcache versions 2.2.2 dated 2024-04-04 and 2.2.3 dated 2024-09-12
DESCRIPTION | 8 MD5 | 46 +-- NAMESPACE | 1 NEWS.md | 15 + R/aaa-async.R | 1 R/archive.R | 2 R/bioc.R | 1 R/installed.R | 2 R/metadata-cache.R | 3 R/onload.R | 438 ------------------------------------- R/packages-gz.R | 15 - R/ppm.R | 39 --- R/repo-set.R | 16 - man/pkgcache-package.Rd | 83 +++---- man/repo_get.Rd | 2 src/lib.c | 4 tests/async/test-call-function.R | 1 tests/testthat/_snaps/installed.md | 7 tests/testthat/_snaps/platform.md | 11 tests/testthat/_snaps/ppm.md | 39 +-- tests/testthat/test-installed.R | 9 tests/testthat/test-platform.R | 7 tests/testthat/test-ppm.R | 35 -- tests/testthat/test-repo-set.R | 25 -- 24 files changed, 169 insertions(+), 641 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm, the Generalized
Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC)
and some related functions are implemented. Functions for incorporating
background knowledge are provided.
Author: Markus Kalisch [aut, cre],
Alain Hauser [aut],
Martin Maechler [aut],
Diego Colombo [ctb],
Doris Entner [ctb],
Patrik Hoyer [ctb],
Antti Hyttinen [ctb],
Jonas Peters [ctb],
Nicoletta Andri [ctb],
Emilija Perkovic [ctb],
Preetam Nandy [ctb],
Philipp R [...truncated...]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.7-11 dated 2024-02-12 and 2.7-12 dated 2024-09-12
pcalg-2.7-11/pcalg/tests/test_randDAG.Rout.save |only pcalg-2.7-12/pcalg/DESCRIPTION | 8 +-- pcalg-2.7-12/pcalg/MD5 | 56 ++++++++++++------------ pcalg-2.7-12/pcalg/build/partial.rdb |binary pcalg-2.7-12/pcalg/build/vignette.rds |binary pcalg-2.7-12/pcalg/inst/doc/vignette2018.pdf |binary pcalg-2.7-12/pcalg/man/LINGAM.Rd | 2 pcalg-2.7-12/pcalg/man/ages.Rd | 8 ++- pcalg-2.7-12/pcalg/man/amatType.Rd | 2 pcalg-2.7-12/pcalg/man/corGraph.Rd | 2 pcalg-2.7-12/pcalg/man/dag2essgraph.Rd | 4 - pcalg-2.7-12/pcalg/man/fciPlus.Rd | 5 +- pcalg-2.7-12/pcalg/man/ges.Rd | 4 + pcalg-2.7-12/pcalg/man/getGraph.Rd | 8 +-- pcalg-2.7-12/pcalg/man/gmG.Rd | 2 pcalg-2.7-12/pcalg/man/gmI.Rd | 2 pcalg-2.7-12/pcalg/man/opt.target.Rd | 2 pcalg-2.7-12/pcalg/man/optAdjSet.Rd | 2 pcalg-2.7-12/pcalg/man/pcAlgo-class.Rd | 2 pcalg-2.7-12/pcalg/man/pdag2allDags.Rd | 2 pcalg-2.7-12/pcalg/man/possAn.Rd | 2 pcalg-2.7-12/pcalg/man/possDe.Rd | 2 pcalg-2.7-12/pcalg/man/randDAG.Rd | 33 +++++++------- pcalg-2.7-12/pcalg/man/randomDAG.Rd | 3 - pcalg-2.7-12/pcalg/tests/Rplots.pdf |binary pcalg-2.7-12/pcalg/tests/filesToFix_Tests.txt |only pcalg-2.7-12/pcalg/tests/test_addBgKnowledge.R | 2 pcalg-2.7-12/pcalg/tests/test_possDeAn.R | 2 pcalg-2.7-12/pcalg/tests/test_randDAG.R | 18 ++++--- pcalg-2.7-12/pcalg/tests/test_rfci.R | 7 +-- 30 files changed, 97 insertions(+), 83 deletions(-)
Title: Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
Description: Lp_solve is freely available (under LGPL 2) software for
solving linear, integer and mixed integer programs. In this
implementation we supply a "wrapper" function in C and some R
functions that solve general linear/integer problems,
assignment problems, and transportation problems. This version
calls lp_solve version 5.5.
Author: Gabor Csardi [cre],
Michel Berkelaar [aut]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between lpSolve versions 5.6.20 dated 2023-12-10 and 5.6.21 dated 2024-09-12
DESCRIPTION | 15 ++++++++++----- MD5 | 7 ++++--- NEWS.md |only src/commonlib.c | 6 +----- src/lp_utils.c | 1 - 5 files changed, 15 insertions(+), 14 deletions(-)
Title: Local Likelihood Inference for Conditional Copula Models
Description: Implements a local likelihood estimator for the dependence parameter in bivariate conditional copula models. Copula family and local likelihood bandwidth parameters are selected by leave-one-out cross-validation. The models are implemented in 'TMB', meaning that the local score function is efficiently calculated via automated differentiation (AD), such that quasi-Newton algorithms may be used for parameter estimation.
Author: Elif Fidan Acar [aut],
Martin Lysy [aut, cre],
Alan Kuchinsky [ctb]
Maintainer: Martin Lysy <mlysy@uwaterloo.ca>
Diff between LocalCop versions 0.0.1 dated 2024-03-21 and 0.0.2 dated 2024-09-12
LocalCop-0.0.1/LocalCop/inst/doc/LocalCop-vignette.R |only LocalCop-0.0.1/LocalCop/inst/doc/LocalCop-vignette.Rmd |only LocalCop-0.0.1/LocalCop/inst/doc/LocalCop-vignette.html |only LocalCop-0.0.1/LocalCop/vignettes/LocalCop-vignette.Rmd |only LocalCop-0.0.2/LocalCop/DESCRIPTION | 17 ++-- LocalCop-0.0.2/LocalCop/MD5 | 58 ++++++++-------- LocalCop-0.0.2/LocalCop/NEWS.md | 14 +++ LocalCop-0.0.2/LocalCop/R/CondiCopLikCV.R | 4 - LocalCop-0.0.2/LocalCop/R/CondiCopLocFit.R | 4 - LocalCop-0.0.2/LocalCop/R/CondiCopLocFun.R | 7 - LocalCop-0.0.2/LocalCop/R/CondiCopSelect.R | 26 ++++--- LocalCop-0.0.2/LocalCop/R/ConvertPar.R | 16 +++- LocalCop-0.0.2/LocalCop/R/utils.R | 26 ++++++- LocalCop-0.0.2/LocalCop/build/vignette.rds |binary LocalCop-0.0.2/LocalCop/inst/doc/LocalCop.R |only LocalCop-0.0.2/LocalCop/inst/doc/LocalCop.Rmd |only LocalCop-0.0.2/LocalCop/inst/doc/LocalCop.html |only LocalCop-0.0.2/LocalCop/man/ConvertPar.Rd | 6 + LocalCop-0.0.2/LocalCop/src/TMB/LocalLikelihood.hpp | 40 ++++++++--- LocalCop-0.0.2/LocalCop/src/TMB/dclayton.hpp | 2 LocalCop-0.0.2/LocalCop/src/TMB/dfrank.hpp | 2 LocalCop-0.0.2/LocalCop/src/TMB/dgumbel.hpp | 2 LocalCop-0.0.2/LocalCop/src/TMB/hclayton.hpp | 22 +++--- LocalCop-0.0.2/LocalCop/src/TMB/hfrank.hpp | 2 LocalCop-0.0.2/LocalCop/src/TMB/hgaussian.hpp | 2 LocalCop-0.0.2/LocalCop/src/TMB/hgumbel.hpp | 2 LocalCop-0.0.2/LocalCop/src/TMB/pclayton.hpp | 22 +++--- LocalCop-0.0.2/LocalCop/src/TMB/pfrank.hpp | 2 LocalCop-0.0.2/LocalCop/src/TMB/pgumbel.hpp | 22 +++--- LocalCop-0.0.2/LocalCop/src/TMB/pt.hpp | 18 ++-- LocalCop-0.0.2/LocalCop/src/TMB/qt.hpp | 18 ++-- LocalCop-0.0.2/LocalCop/tests/testthat/helper.R | 16 +++- LocalCop-0.0.2/LocalCop/tests/testthat/test-LocLikFun.R | 29 +++++--- LocalCop-0.0.2/LocalCop/vignettes/LocalCop.Rmd |only 34 files changed, 236 insertions(+), 143 deletions(-)