Title: Prevalence and Regression for Pool-Tested (Group-Tested) Data
Description: An easy-to-use tool for working with presence/absence tests on 'pooled'
or 'grouped' samples. The primary application is for estimating prevalence of
a marker in a population based on the results of tests on pooled specimens.
This sampling method is often employed in surveillance of rare conditions in
humans or animals (e.g. molecular xenomonitoring). The package was initially
conceived as an R-based alternative to the molecular xenomonitoring software,
'PoolScreen' <https://sites.uab.edu/statgenetics/software/>. However, it goes
further, allowing for estimates of prevalence to be adjusted for hierarchical
sampling frames, and perform flexible mixed-effect regression analyses
(McLure et al. Environmental Modelling and Software.
<DOI:10.1016/j.envsoft.2021.105158>). The package is currently in early stages,
however more features are planned or in the works: e.g. adjustments for
imperfect test specificity/sensitivity, functions for helping with optimal
experimental design, and functions for spatial modelling.
Author: Angus McLure [aut, cre] (<https://orcid.org/0000-0003-2551-3059>)
Maintainer: Angus McLure <angus.mclure@anu.edu.au>
Diff between PoolTestR versions 0.1.1 dated 2021-02-15 and 0.1.2 dated 2022-01-18
PoolTestR-0.1.1/PoolTestR/inst/stan/BayesianPoolScreenJeffreys.stan |only PoolTestR-0.1.1/PoolTestR/src/stanExports_BayesianPoolScreenJeffreys.cc |only PoolTestR-0.1.1/PoolTestR/src/stanExports_BayesianPoolScreenJeffreys.h |only PoolTestR-0.1.2/PoolTestR/DESCRIPTION | 17 PoolTestR-0.1.2/PoolTestR/MD5 | 60 - PoolTestR-0.1.2/PoolTestR/NEWS.md | 15 PoolTestR-0.1.2/PoolTestR/R/ExampleData.R | 4 PoolTestR-0.1.2/PoolTestR/R/HierPoolPrev.R | 63 + PoolTestR-0.1.2/PoolTestR/R/PoolPrev.R | 95 +- PoolTestR-0.1.2/PoolTestR/R/PoolReg.R | 6 PoolTestR-0.1.2/PoolTestR/R/PoolRegBayes.R | 345 +++++++++- PoolTestR-0.1.2/PoolTestR/R/PoolTestR-package.R | 4 PoolTestR-0.1.2/PoolTestR/R/SimpleExampleData.R | 2 PoolTestR-0.1.2/PoolTestR/R/TruePrev.R | 16 PoolTestR-0.1.2/PoolTestR/R/getPrevalence.R | 79 +- PoolTestR-0.1.2/PoolTestR/R/stanmodels.R | 3 PoolTestR-0.1.2/PoolTestR/README.md | 6 PoolTestR-0.1.2/PoolTestR/configure.win | 3 PoolTestR-0.1.2/PoolTestR/inst/CITATION |only PoolTestR-0.1.2/PoolTestR/inst/stan/BayesianPoolScreen.stan | 18 PoolTestR-0.1.2/PoolTestR/inst/stan/HierBayesianPoolScreen.stan | 17 PoolTestR-0.1.2/PoolTestR/man/ExampleData.Rd | 4 PoolTestR-0.1.2/PoolTestR/man/HierPoolPrev.Rd | 46 + PoolTestR-0.1.2/PoolTestR/man/PoolPrev.Rd | 38 - PoolTestR-0.1.2/PoolTestR/man/PoolReg.Rd | 9 PoolTestR-0.1.2/PoolTestR/man/PoolRegBayes.Rd | 28 PoolTestR-0.1.2/PoolTestR/man/PoolTestR-package.Rd | 4 PoolTestR-0.1.2/PoolTestR/man/SimpleExampleData.Rd | 2 PoolTestR-0.1.2/PoolTestR/man/TruePrev.Rd | 16 PoolTestR-0.1.2/PoolTestR/man/getPrevalence.Rd | 40 - PoolTestR-0.1.2/PoolTestR/src/RcppExports.cpp | 7 PoolTestR-0.1.2/PoolTestR/src/stanExports_BayesianPoolScreen.h | 117 ++- PoolTestR-0.1.2/PoolTestR/src/stanExports_HierBayesianPoolScreen.h | 87 +- 33 files changed, 862 insertions(+), 289 deletions(-)
Title: Padé Approximant Coefficients
Description: Given a vector of Taylor series coefficients of sufficient length
as input, the function returns the numerator and denominator coefficients
for the Padé approximant of appropriate order (Baker, 1975)
<ISBN:9780120748556>.
Author: Avraham Adler [aut, cph, cre] (<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Pade versions 1.0.3 dated 2020-11-10 and 1.0.4 dated 2022-01-18
Pade-1.0.3/Pade/tests/testthat |only Pade-1.0.3/Pade/tests/testthat.R |only Pade-1.0.4/Pade/DESCRIPTION | 11 +++++------ Pade-1.0.4/Pade/MD5 | 14 +++++++------- Pade-1.0.4/Pade/README.md | 20 +++++++++++++------- Pade-1.0.4/Pade/build/partial.rdb |binary Pade-1.0.4/Pade/inst/CITATION | 8 +++++--- Pade-1.0.4/Pade/inst/NEWS.Rd | 9 +++++++++ Pade-1.0.4/Pade/inst/tinytest |only Pade-1.0.4/Pade/tests/tinytest.R |only 10 files changed, 39 insertions(+), 23 deletions(-)
Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function
(Corless et al, 1996) <doi:10.1007/BF02124750> without the need for
installing the entire GSL.
Author: Avraham Adler [aut, cph, cre] (<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between lamW versions 2.1.0 dated 2021-05-21 and 2.1.1 dated 2022-01-18
lamW-2.1.0/lamW/inst/News.Rd |only lamW-2.1.0/lamW/tests/testthat |only lamW-2.1.0/lamW/tests/testthat.R |only lamW-2.1.1/lamW/DESCRIPTION | 11 +++++------ lamW-2.1.1/lamW/MD5 | 17 ++++++++--------- lamW-2.1.1/lamW/README.md | 14 +++++++------- lamW-2.1.1/lamW/build/partial.rdb |binary lamW-2.1.1/lamW/inst/CITATION | 8 +++++--- lamW-2.1.1/lamW/inst/NEWS.Rd |only lamW-2.1.1/lamW/inst/tinytest |only lamW-2.1.1/lamW/src/RcppExports.cpp | 5 +++++ lamW-2.1.1/lamW/tests/tinytest.R |only 12 files changed, 30 insertions(+), 25 deletions(-)
Title: Tools for Exploring Multiple Response Data
Description: Interaction and analysis of multiple response data,
along with other tools for analysing these types of data including
missing value analysis and calculation of standard errors for
a range of covariance matrix results (proportions, multinomial,
independent samples, and multiple response).
Author: Tom Elliott [aut, cre] (<https://orcid.org/0000-0002-7815-6318>),
Junjie Zeng [aut] (Original author),
Simon Potter [aut]
Maintainer: Tom Elliott <tom.elliott@auckland.ac.nz>
Diff between iNZightMR versions 2.2.5 dated 2020-05-05 and 2.2.6 dated 2022-01-18
DESCRIPTION | 9 ++++----- MD5 | 6 +++--- R/vmro.R | 14 +++++++++----- tests/testthat/test_vmro.R | 4 ++++ 4 files changed, 20 insertions(+), 13 deletions(-)
Title: Tools for 'iNZight'
Description: Provides a collection of wrapper functions for common variable and dataset manipulation workflows primarily used by 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions. Additionally, many of the functions return the 'tidyverse' code used to obtain the result in an effort to bridge the gap between GUI and coding.
Author: Tom Elliott [aut, cre] (<https://orcid.org/0000-0002-7815-6318>),
Daniel Barnett [aut],
Owen Jin [aut],
Yiwen He [aut],
Christoph Knopf [ctb],
Akshay Gupta [ctb],
Lushi Cai [ctb]
Maintainer: Tom Elliott <tom.elliott@auckland.ac.nz>
Diff between iNZightTools versions 1.12.1 dated 2021-11-04 and 1.12.2 dated 2022-01-18
iNZightTools-1.12.1/iNZightTools/man/iNZightTools.Rd |only iNZightTools-1.12.1/iNZightTools/man/url_to_temp.Rd |only iNZightTools-1.12.2/iNZightTools/DESCRIPTION | 24 ++-- iNZightTools-1.12.2/iNZightTools/MD5 | 24 ++-- iNZightTools-1.12.2/iNZightTools/NAMESPACE | 1 iNZightTools-1.12.2/iNZightTools/R/code_writing.R | 22 ++++ iNZightTools-1.12.2/iNZightTools/R/combine_cat_var.R | 1 iNZightTools-1.12.2/iNZightTools/R/iNZightTools.R | 16 -- iNZightTools-1.12.2/iNZightTools/R/import_data.R | 55 ++++++---- iNZightTools-1.12.2/iNZightTools/inst/pkgdown |only iNZightTools-1.12.2/iNZightTools/man/aggregateData.Rd | 2 iNZightTools-1.12.2/iNZightTools/man/print_code.Rd |only iNZightTools-1.12.2/iNZightTools/man/sheets.Rd | 14 +- iNZightTools-1.12.2/iNZightTools/man/smart_read.Rd | 32 +++-- iNZightTools-1.12.2/iNZightTools/tests/testthat/test_tidy_code.R | 14 ++ 15 files changed, 127 insertions(+), 78 deletions(-)
Title: Shiny/R Wrapper for 'clipboard.js'
Description: Leverages the functionality of 'clipboard.js', a JavaScript library
for HMTL5-based copy to clipboard from web pages (see <https://clipboardjs.com>
for more information), and provides a reactive copy-to-clipboard UI button
component, called 'rclipButton', and a a reactive copy-to-clipboard UI link
component, called 'rclipLink', for 'shiny' R applications.
Author: Sebastien Bihorel
Maintainer: Sebastien Bihorel <sb.pmlab@gmail.com>
Diff between rclipboard versions 0.1.3 dated 2021-01-13 and 0.1.4 dated 2022-01-18
DESCRIPTION | 10 +++++----- MD5 | 13 +++++++------ NAMESPACE | 4 ++-- NEWS |only R/rclipButton.R | 46 ++++++++++++++++++++++++++-------------------- README.md | 11 +++++++++-- inst/lib/clipboard.min.js | 8 ++++---- man/rclipButton.Rd | 13 +++++++------ 8 files changed, 60 insertions(+), 45 deletions(-)
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided. Furthermore, methods for the simulation of extreme value random fields are provided. Main geostatistical parts are based among others on the books by Christian Lantuejoul <doi:10.1007/978-3-662-04808-5>.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Paulo Ribeiro [ctb], Brian D. Ripley [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.3.13 dated 2021-11-02 and 3.3.14 dated 2022-01-18
DESCRIPTION | 10 +++---- MD5 | 55 ++++++++++++++++++++--------------------- inst/LICENCE.for.sse2neon.h |only man/Bayesian.Rd | 2 - man/RMmodelsTrend.Rd | 3 +- src/Coordinate_systems.cc | 4 +- src/Gneiting.cc | 16 +++++------ src/Huetchen.cc | 10 +++---- src/InternalCov.noncritical.cc | 2 - src/KeyInfo.cc | 4 +- src/MLE.cc | 12 ++++---- src/Machine.h | 2 - src/RMS.cc | 14 +++++----- src/extremes.cc | 12 ++++---- src/families.cc | 38 ++++++++++++++-------------- src/gausslikeli.cc | 20 +++++++------- src/getNset.cc | 10 +++---- src/hyperplan.cc | 10 +++---- src/nugget.cc | 4 +- src/operator.cc | 20 +++++++------- src/plusmal.cc | 10 +++---- src/primitive.cov.cc | 8 ++--- src/primitive.gauss.mix.cc | 4 +- src/primitive.others.cc | 6 ++-- src/rf_interfaces.cc | 6 ++-- src/shape.cc | 4 +- src/startGetNset.cc | 18 ++++++------- src/userinterfaces.cc | 20 +++++++------- src/variogramAndCo.cc | 10 +++---- 29 files changed, 168 insertions(+), 166 deletions(-)
Title: Estimate Gaussian and Student's t Mixture Vector Autoregressive
Models
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive, Student's t mixture vector autoregressive, and Gaussian and Student's t
mixture vector autoregressive models, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function and generalized
forecast error variance decomposition.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (2021) <arXiv:2007.04713>,
Savi Virolainen (2021) <arXiv:2109.13648>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 2.0.1 dated 2021-12-14 and 2.0.2 dated 2022-01-18
DESCRIPTION | 10 MD5 | 51 ++- NAMESPACE | 1 NEWS.md | 8 R/MAINest.R | 2 R/WaldAndLR.R | 82 ++--- R/argumentChecks.R | 6 R/generateParams.R | 2 R/geneticAlgorithm.R | 6 R/gmvarkit.R | 3 R/printMethods.R | 20 + build/vignette.rds |binary inst/doc/gmvarkit-vignette.R | 109 ------- inst/doc/gmvarkit-vignette.Rnw | 482 +++++++++++++++++++++++++++-------- inst/doc/gmvarkit-vignette.pdf |binary man/LR_test.Rd | 14 - man/Wald_test.Rd | 12 man/fitGSMVAR.Rd | 2 man/gmvarkit.Rd | 3 man/print.hypotest.Rd |only man/warn_eigens.Rd | 11 tests/testthat/test_argumentChecks.R | 10 tests/testthat/test_waldAndLR.R | 12 vignettes/figures |only vignettes/gmvarkit-vignette.Rnw | 482 +++++++++++++++++++++++++++-------- vignettes/refs.bib | 16 - 26 files changed, 911 insertions(+), 433 deletions(-)
Title: Estimate Univariate Gaussian and Student's t Mixture
Autoregressive Models
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR),
Student's t Mixture Autoregressive (StMAR), and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models,
quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>,
Mika Meitz, Daniel Preve, Pentti Saikkonen (2021) <doi:10.1080/03610926.2021.1916531>,
Savi Virolainen (2021) <doi:10.1515/snde-2020-0060>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between uGMAR versions 3.4.0 dated 2021-09-02 and 3.4.1 dated 2022-01-18
DESCRIPTION | 13 - MD5 | 36 ++--- NEWS.md | 4 R/MAINest.R | 2 R/parameterReforms.R | 140 ++++--------------- R/pickAndChangeParams.R | 2 build/vignette.rds |binary inst/doc/uGMARpaper.Rnw | 235 +++++++++++++++++---------------- inst/doc/uGMARpaper.pdf |binary man/fitGSMAR.Rd | 2 man/pick_pars.Rd | 2 vignettes/figures/diagplotfit42gsr.png |binary vignettes/figures/figsimuexp.png |binary vignettes/figures/pacfplot.png |binary vignettes/figures/plotfit42gs.png |binary vignettes/figures/predictfit42gs.png |binary vignettes/figures/proflogfit42gs.png |binary vignettes/refs.bib | 88 +++++++----- vignettes/uGMARpaper.Rnw | 235 +++++++++++++++++---------------- 19 files changed, 361 insertions(+), 398 deletions(-)
Title: Covariate Balancing Propensity Score
Description: Implements the covariate balancing propensity score (CBPS) proposed
by Imai and Ratkovic (2014) <DOI:10.1111/rssb.12027>. The propensity score is
estimated such that it maximizes the resulting covariate balance as well as the
prediction of treatment assignment. The method, therefore, avoids an iteration
between model fitting and balance checking. The package also implements optimal
CBPS from Fan et al. (in-press) <DOI:10.1080/07350015.2021.2002159>,
several extensions of the CBPS beyond the cross-sectional, binary treatment setting.
They include the CBPS for longitudinal settings so that it can be used in
conjunction with marginal structural models from Imai and Ratkovic (2015)
<DOI:10.1080/01621459.2014.956872>, treatments with three- and four-valued treatment
variables, continuous-valued treatments from Fong, Hazlett, and Imai (2018)
<DOI:10.1214/17-AOAS1101>, propensity score estimation with a large number of
covariates from Ning, Peng, and Imai (2020) <DOI:10.1093/biomet/asaa020>, and the situation
with multiple distinct binary treatments administered simultaneously. In the future
it will be extended to other settings including the generalization of experimental
and instrumental variable estimates.
Author: Christian Fong [aut, cre],
Marc Ratkovic [aut],
Kosuke Imai [aut],
Chad Hazlett [ctb],
Xiaolin Yang [ctb],
Sida Peng [ctb],
Inbeom Lee [ctb]
Maintainer: Christian Fong <cjfong@umich.edu>
Diff between CBPS versions 0.22 dated 2021-03-29 and 0.23 dated 2022-01-18
CBPS-0.22/CBPS/data/Blackwell.tab |only CBPS-0.22/CBPS/data/LaLonde.tab |only CBPS-0.23/CBPS/ChangeLog | 5 +-- CBPS-0.23/CBPS/DESCRIPTION | 30 +++++++++--------- CBPS-0.23/CBPS/MD5 | 36 +++++++++++----------- CBPS-0.23/CBPS/NAMESPACE | 2 + CBPS-0.23/CBPS/R/AsyVar.R |only CBPS-0.23/CBPS/data/Blackwell.tab.gz |only CBPS-0.23/CBPS/data/LaLonde.tab.gz |only CBPS-0.23/CBPS/man/AsyVar.Rd |only CBPS-0.23/CBPS/man/Blackwell.Rd | 6 ++- CBPS-0.23/CBPS/man/CBIV.Rd | 12 ++++++- CBPS-0.23/CBPS/man/CBMSM.Rd | 21 +++++++++--- CBPS-0.23/CBPS/man/CBMSM.fit.Rd | 14 +++++++- CBPS-0.23/CBPS/man/CBPS.Rd | 18 ++++++++--- CBPS-0.23/CBPS/man/CBPS.fit.Rd | 15 +++++++-- CBPS-0.23/CBPS/man/LaLonde.Rd | 6 ++- CBPS-0.23/CBPS/man/hdCBPS.Rd | 11 +++++- CBPS-0.23/CBPS/man/plot.CBMSM.Rd | 3 - CBPS-0.23/CBPS/man/plot.CBPS.Rd | 3 - CBPS-0.23/CBPS/man/plot.CBPSContinuous.Rd | 3 - CBPS-0.23/CBPS/man/vcov_outcome.CBPSContinuous.Rd | 3 - 22 files changed, 126 insertions(+), 62 deletions(-)
Title: Multiple Imputation of Covariates by Substantive Model
Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by
Substantive Model Compatible Fully Conditional Specification.
This is a modification of the popular FCS/chained equations
multiple imputation approach, and allows imputation of missing
covariate values from models which are compatible with the user
specified substantive model.
Author: Jonathan Bartlett [aut, cre],
Ruth Keogh [aut],
Edouard F. Bonneville [aut],
Claus Thorn Ekstrøm [ctb]
Maintainer: Jonathan Bartlett <j.w.bartlett@bath.ac.uk>
Diff between smcfcs versions 1.6.0 dated 2021-06-17 and 1.6.1 dated 2022-01-18
DESCRIPTION | 8 MD5 | 80 - NAMESPACE | 22 R/data.r | 286 ++-- R/plot_convergence.R | 426 +++--- R/smcfcs.r | 2333 ++++++++++++++++----------------- R/smcfcs_parallel.r | 342 ++-- README.md | 22 build/partial.rdb |binary build/vignette.rds |binary inst/doc/smcfcs-vignette.R | 96 - inst/doc/smcfcs-vignette.Rmd | 278 +-- inst/doc/smcfcs-vignette.html | 734 +++++----- inst/doc/smcfcs_coverror-vignette.R | 168 +- inst/doc/smcfcs_coverror-vignette.Rmd | 262 +-- inst/doc/smcfcs_coverror-vignette.html | 682 ++++----- man/ex_cc.Rd | 50 man/ex_compet.Rd | 48 man/ex_coxquad.Rd | 50 man/ex_dtsam.Rd | 44 man/ex_lininter.Rd | 44 man/ex_linquad.Rd | 48 man/ex_logisticquad.Rd | 48 man/ex_ncc.Rd | 52 man/ex_poisson.Rd | 46 man/plot.smcfcs.Rd | 118 - man/smcfcs.Rd | 442 +++--- man/smcfcs.casecohort.Rd | 202 +- man/smcfcs.dtsam.Rd | 230 +-- man/smcfcs.nestedcc.Rd | 216 +-- man/smcfcs.parallel.Rd | 164 +- tests/testthat/test_casecohort.r | 166 +- tests/testthat/test_coxph.r | 96 - tests/testthat/test_dtsam.r | 878 ++++++------ tests/testthat/test_errorchecks.R | 452 +++--- tests/testthat/test_measerror.r | 172 +- tests/testthat/test_nestedcc.R | 272 +-- tests/testthat/test_parallel.r | 418 ++--- tests/testthat/test_weibull.r | 126 - vignettes/smcfcs-vignette.Rmd | 278 +-- vignettes/smcfcs_coverror-vignette.Rmd | 262 +-- 41 files changed, 5341 insertions(+), 5320 deletions(-)
Title: Univariate GARCH Models
Description: ARFIMA, in-mean, external regressors and various GARCH flavors, with methods for fit, forecast, simulation, inference and plotting.
Author: Alexios Galanos [aut, cre],
Tobias Kley [ctb]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between rugarch versions 1.4-4 dated 2020-07-16 and 1.4-6 dated 2022-01-18
ChangeLog | 95 +++++++------- DESCRIPTION | 18 +- MD5 | 118 ++++++++--------- NAMESPACE | 1 R/arfima-classes.R | 2 R/arfima-main.R | 2 R/arfima-methods.R | 2 R/arfima-multi.R | 2 R/rugarch-aparch.R | 2 R/rugarch-armafor.R | 2 R/rugarch-benchmarks.R | 2 R/rugarch-bootstrap.R | 2 R/rugarch-classes.R | 2 R/rugarch-csgarch.R | 2 R/rugarch-cv.R | 2 R/rugarch-cwrappers.R | 2 R/rugarch-distributions.R | 16 +- R/rugarch-egarch.R | 2 R/rugarch-fgarch.R | 2 R/rugarch-figarch.R | 2 R/rugarch-gjrgarch.R | 2 R/rugarch-graphs.R | 2 R/rugarch-helperfn.R | 2 R/rugarch-igarch.R | 2 R/rugarch-imports.R | 2 R/rugarch-kappa.R | 14 +- R/rugarch-lossfn.R | 2 R/rugarch-mcsgarch.R | 2 R/rugarch-methods.R | 2 R/rugarch-multi.R | 2 R/rugarch-numderiv.R | 2 R/rugarch-plots.R | 2 R/rugarch-realgarch.R | 2 R/rugarch-rolling.R | 2 R/rugarch-series.R | 2 R/rugarch-sgarch.R | 2 R/rugarch-solvers.R | 152 +++++++++++------------ R/rugarch-startpars.R | 2 R/rugarch-tests.R | 2 R/rugarch-uncertainty.R | 2 R/zzz.R | 2 README.md | 4 build/vignette.rds |binary inst/doc/Introduction_to_the_rugarch_package.pdf |binary inst/rugarch.tests/rugarch.test1.R | 4 inst/rugarch.tests/rugarch.test10.R | 4 inst/rugarch.tests/rugarch.test11.R | 2 inst/rugarch.tests/rugarch.test12.R | 4 inst/rugarch.tests/rugarch.test13.R | 4 inst/rugarch.tests/rugarch.test14.R | 2 inst/rugarch.tests/rugarch.test2.R | 4 inst/rugarch.tests/rugarch.test3.R | 4 inst/rugarch.tests/rugarch.test4.R | 4 inst/rugarch.tests/rugarch.test5.R | 4 inst/rugarch.tests/rugarch.test6.R | 4 inst/rugarch.tests/rugarch.test7.R | 4 inst/rugarch.tests/rugarch.test8.R | 4 inst/rugarch.tests/rugarch.test9.R | 2 inst/rugarch.tests/runtests.R | 4 src/distributions.c | 16 ++ 60 files changed, 291 insertions(+), 265 deletions(-)
Title: Tools for Designing and Weighting Survey Samples
Description: Functions and datasets to support Valliant, Dever, and Kreuter, Practical Tools for Designing and Weighting Survey Samples (2nd edition, 2018). Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example data sets are included.
Author: Richard Valliant, Jill A. Dever, Frauke Kreuter
Maintainer: Richard Valliant <valliant@umich.edu>
Diff between PracTools versions 1.2.4 dated 2021-12-20 and 1.2.5 dated 2022-01-18
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 4 ++-- R/deffCR.R | 4 ++-- inst/doc/Singlestage-samsize.pdf |binary inst/doc/Varcomps-multistage.pdf |binary man/deffCR.Rd | 4 ++-- vignettes/Singlestage-samsize.html | 4 ++-- vignettes/Varcomps-multistage.html | 4 ++-- 9 files changed, 23 insertions(+), 23 deletions(-)
Title: Multi-Calibration Boosting
Description: Implements 'Multi-Calibration Boosting' (2018) <https://proceedings.mlr.press/v80/hebert-johnson18a.html> and
'Multi-Accuracy Boosting' (2019) <arXiv:1805.12317> for the multi-calibration of a machine learning model's prediction.
'MCBoost' updates predictions for sub-groups in an iterative fashion in order to mitigate biases like poor calibration or large accuracy differences across subgroups.
Multi-Calibration works best in scenarios where the underlying data & labels are unbiased, but resulting models are.
This is often the case, e.g. when an algorithm fits a majority population while ignoring or under-fitting minority populations.
Author: Florian Pfisterer [cre, aut] (<https://orcid.org/0000-0001-8867-762X>),
Susanne Dandl [ctb] (<https://orcid.org/0000-0003-4324-4163>),
Christoph Kern [ctb] (<https://orcid.org/0000-0001-7363-4299>),
Carolin Becker [ctb],
Bernd Bischl [ctb] (<https://orcid.org/0000-0001-6002-6980>)
Maintainer: Florian Pfisterer <pfistererf@googlemail.com>
Diff between mcboost versions 0.3.3.0 dated 2021-08-03 and 0.4.0 dated 2022-01-18
DESCRIPTION | 24 +- MD5 | 74 ++++--- NAMESPACE | 8 NEWS.md | 6 R/AuditorFitters.R | 46 ++-- R/MCBoost.R | 315 +++++++++++++++++------------- R/MCBoostSurv.R |only R/PipeOpLearnerPred.R |only R/PipeOpMCBoost.R | 46 ---- R/PipeOpMCBoostSurv.R |only R/PipelineMCBoost.R |only R/Predictor.R | 22 +- R/ProbRange.R | 3 R/ProbRange2D.R |only R/helpers.R | 68 +++++- R/zzz.R | 13 - README.md | 20 + build/partial.rdb |only build/vignette.rds |binary inst/CITATION |only inst/doc/mcboost_basics_extensions.Rmd | 2 inst/doc/mcboost_basics_extensions.html | 2 inst/doc/mcboost_example.Rmd | 7 inst/doc/mcboost_example.html | 292 ++++++++++++++------------- inst/doc/mcboostsurv_basics.R |only inst/doc/mcboostsurv_basics.Rmd |only inst/doc/mcboostsurv_basics.html |only man/MCBoost.Rd | 38 ++- man/MCBoostSurv.Rd |only man/make_survival_curve.Rd |only man/mcboost-package.Rd | 11 - man/mlr_pipeops_mcboost.Rd | 153 +++++++++++++- man/mlr_pipeops_mcboostsurv.Rd |only man/ppl_mcboost.Rd | 7 man/ppl_mcboostsurv.Rd |only tests/testthat.R | 4 tests/testthat/setup.R |only tests/testthat/teardown.R |only tests/testthat/test_auditor_fitters.R | 1 tests/testthat/test_mcboost.R | 52 ++-- tests/testthat/test_mcboostsurv.R |only tests/testthat/test_pipeop_learner_pred.R |only tests/testthat/test_pipeop_mcboost.R | 17 + tests/testthat/test_pipeop_mcboostsurv.R |only tests/testthat/test_probrange2d.R |only tests/testthat/test_sonar_usecase.R |only vignettes/mcboost_basics_extensions.Rmd | 2 vignettes/mcboost_example.Rmd | 7 vignettes/mcboostsurv_basics.Rmd |only 49 files changed, 791 insertions(+), 449 deletions(-)
Title: Causal Inference for a Binary Treatment and Continuous Outcome
using Bayesian Causal Forests
Description: Causal inference for a binary treatment and continuous outcome using Bayesian Causal Forests. See Hahn, Murray and Carvalho (2017) <arXiv:1706.09523> for additional information. This implementation relies on code originally accompanying Pratola et. al. (2013) <arXiv:1309.1906>.
Author: P. Richard Hahn, Jared S. Murray, and Carlos Carvalho
Maintainer: Jared S. Murray <jared.murray@mccombs.utexas.edu>
Diff between bcf versions 1.3 dated 2019-08-28 and 1.3.1 dated 2022-01-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- src/Makevars | 2 +- src/Makevars.win | 2 +- src/RcppExports.cpp | 5 +++++ src/funs.cpp | 2 +- 6 files changed, 17 insertions(+), 12 deletions(-)
Title: Generate Tidy Charts Inspired by 'IBCS'
Description: There is a wide range of R packages created for data visualization, but still, there was no simple and easily accessible way to create clean and transparent charts - up to now. The 'tidycharts' package enables the user to generate charts compliant with International Business Communication Standards ('IBCS').
It means unified bar widths, colors, chart sizes, etc. Creating homogeneous reports has never been that easy! Additionally, users can apply semantic notation to indicate different data scenarios (plan, budget, forecast). What's more, it is possible to customize the charts by creating a personal color pallet with the possibility of switching to default options after the experiments.
We wanted the package to be helpful in writing reports, so we also made joining charts in a one, clear image possible.
All charts are generated in SVG format and can be shown in the 'RStudio' viewer pane or exported to HTML output of 'knitr'/'markdown'.
Author: Przemysław Biecek [aut] (<https://orcid.org/0000-0001-8423-1823>),
Piotr Piątyszek [aut],
Kinga Ułasik [aut],
Bartosz Sawicki [aut, cre]
Maintainer: Bartosz Sawicki <sawicki.bartosz@interia.pl>
Diff between tidycharts versions 0.1.2 dated 2021-08-23 and 0.1.3 dated 2022-01-18
tidycharts-0.1.2/tidycharts/man/get_gray_color_stacked.Rd |only tidycharts-0.1.3/tidycharts/DESCRIPTION | 16 tidycharts-0.1.3/tidycharts/MD5 | 153 ++-- tidycharts-0.1.3/tidycharts/NAMESPACE | 7 tidycharts-0.1.3/tidycharts/R/bar_chart.R | 101 +- tidycharts-0.1.3/tidycharts/R/bar_chart_grouped.R | 27 tidycharts-0.1.3/tidycharts/R/bar_chart_waterfall.R | 10 tidycharts-0.1.3/tidycharts/R/chart_utils.R | 48 + tidycharts-0.1.3/tidycharts/R/column_chart_functions.R | 160 ++-- tidycharts-0.1.3/tidycharts/R/drawing_utils.R | 8 tidycharts-0.1.3/tidycharts/R/drawing_utils_K.R | 24 tidycharts-0.1.3/tidycharts/R/env_functions.R | 84 ++ tidycharts-0.1.3/tidycharts/R/join_charts.R | 17 tidycharts-0.1.3/tidycharts/R/line_chart.R | 45 - tidycharts-0.1.3/tidycharts/R/line_chart_dense.R | 49 - tidycharts-0.1.3/tidycharts/R/line_chart_markers.R | 61 - tidycharts-0.1.3/tidycharts/R/line_chart_normalized.R | 54 - tidycharts-0.1.3/tidycharts/R/line_chart_stacked.R | 57 - tidycharts-0.1.3/tidycharts/R/parse_time_series.R | 2 tidycharts-0.1.3/tidycharts/R/scatter_and_bubble_plot.R | 125 ++- tidycharts-0.1.3/tidycharts/R/tidychart.R |only tidycharts-0.1.3/tidycharts/README.md | 28 tidycharts-0.1.3/tidycharts/inst/doc/EDA-for-palmer-penguins-data-set.R | 74 -- tidycharts-0.1.3/tidycharts/inst/doc/EDA-for-palmer-penguins-data-set.Rmd | 79 -- tidycharts-0.1.3/tidycharts/inst/doc/EDA-for-palmer-penguins-data-set.html | 218 +----- tidycharts-0.1.3/tidycharts/inst/doc/Getting_Started.R | 130 ++- tidycharts-0.1.3/tidycharts/inst/doc/Getting_Started.Rmd | 156 ++-- tidycharts-0.1.3/tidycharts/inst/doc/Getting_Started.html | 355 +++++----- tidycharts-0.1.3/tidycharts/inst/doc/customize-package.R | 8 tidycharts-0.1.3/tidycharts/inst/doc/customize-package.Rmd | 11 tidycharts-0.1.3/tidycharts/inst/doc/customize-package.html | 138 +-- tidycharts-0.1.3/tidycharts/inst/doc/join_charts.R | 7 tidycharts-0.1.3/tidycharts/inst/doc/join_charts.Rmd | 7 tidycharts-0.1.3/tidycharts/inst/doc/join_charts.html | 128 +-- tidycharts-0.1.3/tidycharts/man/SVGsave.Rd | 4 tidycharts-0.1.3/tidycharts/man/add_title.Rd | 11 tidycharts-0.1.3/tidycharts/man/add_waterfall_bars.Rd | 6 tidycharts-0.1.3/tidycharts/man/bar_chart.Rd | 4 tidycharts-0.1.3/tidycharts/man/bar_chart_absolute_variance.Rd | 17 tidycharts-0.1.3/tidycharts/man/bar_chart_grouped.Rd | 6 tidycharts-0.1.3/tidycharts/man/bar_chart_normalized.Rd | 6 tidycharts-0.1.3/tidycharts/man/bar_chart_reference.Rd | 5 tidycharts-0.1.3/tidycharts/man/bar_chart_relative_variance.Rd | 17 tidycharts-0.1.3/tidycharts/man/bar_chart_waterfall.Rd | 8 tidycharts-0.1.3/tidycharts/man/column_chart.Rd | 8 tidycharts-0.1.3/tidycharts/man/column_chart_absolute_variance.Rd | 13 tidycharts-0.1.3/tidycharts/man/column_chart_grouped.Rd | 8 tidycharts-0.1.3/tidycharts/man/column_chart_normalized.Rd | 10 tidycharts-0.1.3/tidycharts/man/column_chart_reference.Rd | 12 tidycharts-0.1.3/tidycharts/man/column_chart_relative_variance.Rd | 13 tidycharts-0.1.3/tidycharts/man/column_chart_waterfall.Rd | 4 tidycharts-0.1.3/tidycharts/man/column_chart_waterfall_variance.Rd | 11 tidycharts-0.1.3/tidycharts/man/draw_triangle.Rd | 4 tidycharts-0.1.3/tidycharts/man/facet_chart.Rd | 8 tidycharts-0.1.3/tidycharts/man/get_color_stacked.Rd |only tidycharts-0.1.3/tidycharts/man/join_charts.Rd | 10 tidycharts-0.1.3/tidycharts/man/knit_print.tidychart.Rd |only tidycharts-0.1.3/tidycharts/man/line_chart.Rd | 10 tidycharts-0.1.3/tidycharts/man/line_chart_dense.Rd | 5 tidycharts-0.1.3/tidycharts/man/line_chart_dense_custom.Rd | 4 tidycharts-0.1.3/tidycharts/man/line_chart_markers.Rd | 7 tidycharts-0.1.3/tidycharts/man/line_chart_markers_reference.Rd | 4 tidycharts-0.1.3/tidycharts/man/line_chart_normalized.Rd | 8 tidycharts-0.1.3/tidycharts/man/line_chart_stacked.Rd | 9 tidycharts-0.1.3/tidycharts/man/parse_time_series.Rd | 2 tidycharts-0.1.3/tidycharts/man/print.tidychart.Rd |only tidycharts-0.1.3/tidycharts/man/reset_margins.Rd |only tidycharts-0.1.3/tidycharts/man/restore_defaults.Rd | 6 tidycharts-0.1.3/tidycharts/man/scatter_plot.Rd | 14 tidycharts-0.1.3/tidycharts/man/set_colors.Rd | 4 tidycharts-0.1.3/tidycharts/man/set_margins.Rd |only tidycharts-0.1.3/tidycharts/man/set_scatter_colors.Rd |only tidycharts-0.1.3/tidycharts/man/set_styles.Rd | 6 tidycharts-0.1.3/tidycharts/man/show.Rd |only tidycharts-0.1.3/tidycharts/man/str_width.Rd | 4 tidycharts-0.1.3/tidycharts/tests/testthat/Rplots.pdf |binary tidycharts-0.1.3/tidycharts/tests/testthat/test-utils.R | 14 tidycharts-0.1.3/tidycharts/tests/testthat/test_scatterplots.R | 8 tidycharts-0.1.3/tidycharts/vignettes/EDA-for-palmer-penguins-data-set.Rmd | 79 -- tidycharts-0.1.3/tidycharts/vignettes/Getting_Started.Rmd | 156 ++-- tidycharts-0.1.3/tidycharts/vignettes/customize-package.Rmd | 11 tidycharts-0.1.3/tidycharts/vignettes/join_charts.Rmd | 7 82 files changed, 1461 insertions(+), 1469 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] (<https://orcid.org/0000-0001-5231-5184>)
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 4.5.0 dated 2022-01-06 and 4.5.1 dated 2022-01-18
DESCRIPTION | 8 +++--- MD5 | 30 +++++++++++------------ NEWS | 11 ++++++++ R/fastsecrloglik.R | 14 +++++++---- R/generalsecrloglik.R | 20 ++++++++++----- R/preparedata.R | 4 ++- R/utility.R | 53 ++++++++++++++++++++++-------------------- inst/doc/secr-datainput.pdf |binary inst/doc/secr-overview.pdf |binary man/secr-package.Rd | 4 +-- src/autils.cpp | 9 +++++-- src/polygonN.cpp | 2 - src/secr.h | 2 - src/simsecr.cpp | 3 -- src/trapping.cpp | 11 +++----- tests/testthat/test-initial.R | 19 +++++++++++++++ 16 files changed, 120 insertions(+), 70 deletions(-)
Title: Utilities for the Simulation and Analysis of Random Fields and
Genetic Data
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used.
Author: Martin Schlather [aut, cre], Alexander FreudenBerg [aut], Reinhard Furrer [ctb], Martin Kroll [ctb], Brian D. Ripley [ctb], John W. Ratcliff et al. (cph)
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFieldsUtils versions 1.0.11 dated 2021-11-20 and 1.1.0 dated 2022-01-18
RandomFieldsUtils-1.0.11/RandomFieldsUtils/inst/include/immintrin.h |only RandomFieldsUtils-1.0.11/RandomFieldsUtils/inst/include/intrinsics_specific.h |only RandomFieldsUtils-1.0.11/RandomFieldsUtils/src/avx.cc |only RandomFieldsUtils-1.0.11/RandomFieldsUtils/src/avx2.cc |only RandomFieldsUtils-1.0.11/RandomFieldsUtils/src/immintrin.h |only RandomFieldsUtils-1.0.11/RandomFieldsUtils/src/intrinsics_specific.h |only RandomFieldsUtils-1.0.11/RandomFieldsUtils/src/solve_gpu.cu |only RandomFieldsUtils-1.1.0/RandomFieldsUtils/DESCRIPTION | 13 RandomFieldsUtils-1.1.0/RandomFieldsUtils/MD5 | 138 +- RandomFieldsUtils-1.1.0/RandomFieldsUtils/NAMESPACE | 9 RandomFieldsUtils-1.1.0/RandomFieldsUtils/R/RFoptions.R | 119 +- RandomFieldsUtils-1.1.0/RandomFieldsUtils/R/aaa_auto.R | 53 RandomFieldsUtils-1.1.0/RandomFieldsUtils/R/gpu.R |only RandomFieldsUtils-1.1.0/RandomFieldsUtils/R/internal_use.R | 16 RandomFieldsUtils-1.1.0/RandomFieldsUtils/R/utils.R | 31 RandomFieldsUtils-1.1.0/RandomFieldsUtils/R/zzz.R | 7 RandomFieldsUtils-1.1.0/RandomFieldsUtils/configure | 215 ++- RandomFieldsUtils-1.1.0/RandomFieldsUtils/configure.ac | 188 ++- RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/CITATION | 5 RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/AutoRandomFieldsUtils.h | 1 RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/AutoRandomFieldsUtilsLocal.h | 7 RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/Basic_utils.h | 161 +- RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/Basic_utils_local.h | 2 RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/RandomFieldsUtils.h | 10 RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/def.h | 2 RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/errors_messages.h | 53 RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/extern.h | 7 RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/intrinsics.h | 578 ++++++++-- RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/kleinkram.h | 39 RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/options.h | 99 + RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/parallel_base.h | 112 + RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/parallel_simd.h | 4 RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/solve_gpu.h | 5 RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/sse2neon.H |only RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/win_linux_aux.h | 2 RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/xport_import.h | 1 RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/zzz_RandomFieldsUtils.h | 357 +----- RandomFieldsUtils-1.1.0/RandomFieldsUtils/inst/include/zzz_calls.h | 380 +++--- RandomFieldsUtils-1.1.0/RandomFieldsUtils/man/RFoptions.Rd | 367 +++--- RandomFieldsUtils-1.1.0/RandomFieldsUtils/man/uses.instruction.set.Rd |only RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/AutoRandomFieldsUtils.cc | 22 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/AutoRandomFieldsUtils.h | 1 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/AutoRandomFieldsUtilsLocal.h | 7 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/Basic_utils.h | 161 +- RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/Basic_utils_local.h | 2 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/Makevars.in | 41 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/RFoptions.cc | 507 ++++++-- RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/RandomFieldsUtils.h | 10 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/avx2_fctns.cc |only RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/avx_fctns.cc |only RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/beskf.cc | 2 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/def.h | 2 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/errors_messages.h | 53 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/extern.h | 7 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/gpu_info.cc |only RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/gpu_info_61.cu |only RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/intrinsics.h | 578 ++++++++-- RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/kleinkram.cc | 164 +- RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/kleinkram.h | 39 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/maths.cc | 22 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/obsolete.cc | 52 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/options.cc | 328 +++-- RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/options.h | 99 + RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/parallel_base.h | 112 + RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/parallel_simd.h | 4 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/solve.cc | 392 +++--- RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/solve_61.cu |only RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/solve_gpu.h | 5 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/sort.cc | 14 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/sse2neon.H |only RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/utils.cc | 139 -- RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/win_linux_aux.cc | 33 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/win_linux_aux.h | 2 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/xport_import.cc | 41 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/xport_import.h | 1 RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/zzz.c | 69 - RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/zzz_RandomFieldsUtils.h | 357 +----- RandomFieldsUtils-1.1.0/RandomFieldsUtils/src/zzz_calls.h | 380 +++--- 78 files changed, 4139 insertions(+), 2488 deletions(-)
More information about RandomFieldsUtils at CRAN
Permanent link
Title: Fast and Scalable Approximate k-Nearest Neighbor Search Methods
using 'N2' Library
Description: Implements methods to perform fast approximate K-nearest neighbor search on input matrix. Algorithm based on the 'N2' implementation of an approximate nearest neighbor search using hierarchical Navigable Small World (NSW) graphs. The original algorithm is described in "Efficient and Robust Approximate Nearest Neighbor Search Using Hierarchical Navigable Small World Graphs", Y. Malkov and D. Yashunin, <doi:10.1109/TPAMI.2018.2889473>, <arXiv:1603.09320>.
Author: Peter Kharchenko [aut],
Viktor Petukhov [aut],
Dirk Eddelbuettel [ctb],
Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between N2R versions 1.0.0 dated 2021-11-19 and 1.0.1 dated 2022-01-18
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ README.md | 4 ++-- src/Makevars | 2 +- src/n2/distance.cc | 3 ++- src/n2/heuristic.cc | 3 +-- src/n2/hnsw.cc | 3 ++- src/n2/include/n2/simd.h |only 8 files changed, 19 insertions(+), 17 deletions(-)
Title: Resampling-Based Analysis of Multivariate Data and Repeated
Measures Designs
Description: Implemented are various tests for semi-parametric repeated measures
and general MANOVA designs that do neither assume multivariate normality nor
covariance homogeneity, i.e., the procedures are applicable for a wide range
of general multivariate factorial designs. In addition to asymptotic inference
methods, novel bootstrap and permutation approaches are implemented as well. These provide more
accurate results in case of small to moderate sample sizes. Furthermore, post-hoc
comparisons are provided for the multivariate analyses.
Friedrich, S., Konietschke, F. and Pauly, M. (2019) <doi:10.32614/RJ-2019-051>.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly
Maintainer: Sarah Friedrich <sarah.friedrich@math.uni-augsburg.de>
Diff between MANOVA.RM versions 0.5.2 dated 2021-09-17 and 0.5.3 dated 2022-01-18
MANOVA.RM-0.5.2/MANOVA.RM/R/plot_function.R |only MANOVA.RM-0.5.2/MANOVA.RM/R/plot_helper_fct.R |only MANOVA.RM-0.5.2/MANOVA.RM/R/plot_new.R |only MANOVA.RM-0.5.3/MANOVA.RM/DESCRIPTION | 10 MANOVA.RM-0.5.3/MANOVA.RM/MD5 | 42 - MANOVA.RM-0.5.3/MANOVA.RM/R/GUI.R | 257 ++----- MANOVA.RM-0.5.3/MANOVA.RM/R/RM-function.R | 12 MANOVA.RM-0.5.3/MANOVA.RM/R/plot_RM.R |only MANOVA.RM-0.5.3/MANOVA.RM/R/prepdata.R | 4 MANOVA.RM-0.5.3/MANOVA.RM/R/utility_functions.R | 79 -- MANOVA.RM-0.5.3/MANOVA.RM/inst/doc/Introduction_to_MANOVA.RM.R | 15 MANOVA.RM-0.5.3/MANOVA.RM/inst/doc/Introduction_to_MANOVA.RM.Rmd | 31 MANOVA.RM-0.5.3/MANOVA.RM/inst/doc/Introduction_to_MANOVA.RM.html | 329 +++++++--- MANOVA.RM-0.5.3/MANOVA.RM/man/EEG.Rd | 6 MANOVA.RM-0.5.3/MANOVA.RM/man/EEGwide.Rd | 6 MANOVA.RM-0.5.3/MANOVA.RM/man/MANOVA.Rd | 16 MANOVA.RM-0.5.3/MANOVA.RM/man/MANOVA.wide.Rd | 18 MANOVA.RM-0.5.3/MANOVA.RM/man/MANOVARM.Rd | 1 MANOVA.RM-0.5.3/MANOVA.RM/man/RM.Rd | 18 MANOVA.RM-0.5.3/MANOVA.RM/man/multRM.Rd | 15 MANOVA.RM-0.5.3/MANOVA.RM/man/o2cons.Rd | 6 MANOVA.RM-0.5.3/MANOVA.RM/man/plot.RM.Rd | 13 MANOVA.RM-0.5.3/MANOVA.RM/man/simCI.Rd | 13 MANOVA.RM-0.5.3/MANOVA.RM/vignettes/Introduction_to_MANOVA.RM.Rmd | 31 24 files changed, 530 insertions(+), 392 deletions(-)
Title: Firth's Bias-Reduced Logistic Regression
Description: Fit a logistic regression model using Firth's bias reduction method, equivalent to penalization of the log-likelihood by the Jeffreys
prior. Confidence intervals for regression coefficients can be computed by penalized profile likelihood. Firth's method was proposed as ideal
solution to the problem of separation in logistic regression, see Heinze and Schemper (2002) <doi:10.1002/sim.1047>. If needed, the bias reduction can be turned off such that ordinary
maximum likelihood logistic regression is obtained. Two new modifications of Firth's method, FLIC and FLAC, lead to unbiased predictions and are now available
in the package as well, see Puhr et al (2017) <doi:10.1002/sim.7273>.
Author: Georg Heinze [aut, cre],
Meinhard Ploner [aut],
Daniela Dunkler [ctb],
Harry Southworth [ctb],
Lena Jiricka [aut]
Maintainer: Georg Heinze <georg.heinze@meduniwien.ac.at>
Diff between logistf versions 1.24 dated 2020-09-16 and 1.24.1 dated 2022-01-18
logistf-1.24.1/logistf/DESCRIPTION | 12 logistf-1.24.1/logistf/MD5 | 116 - logistf-1.24.1/logistf/NAMESPACE | 211 +-- logistf-1.24.1/logistf/NEWS.md |only logistf-1.24.1/logistf/R/CLIP.confint.r | 15 logistf-1.24.1/logistf/R/CLIP.profile.r | 4 logistf-1.24.1/logistf/R/PVR.confint.r | 2 logistf-1.24.1/logistf/R/add1.R | 30 logistf-1.24.1/logistf/R/anova.logistf.r | 194 --- logistf-1.24.1/logistf/R/backward.r | 166 -- logistf-1.24.1/logistf/R/data.R | 4 logistf-1.24.1/logistf/R/extractAIC.R | 11 logistf-1.24.1/logistf/R/flac.R | 167 +- logistf-1.24.1/logistf/R/flic.R | 115 + logistf-1.24.1/logistf/R/logistf-package.R | 66 - logistf-1.24.1/logistf/R/logistf.R | 146 +- logistf-1.24.1/logistf/R/logistf.control.R | 18 logistf-1.24.1/logistf/R/logistf.fit.R | 71 - logistf-1.24.1/logistf/R/logistf.mod.control.R |only logistf-1.24.1/logistf/R/logistf.pdf.R | 20 logistf-1.24.1/logistf/R/logistftest.R | 69 - logistf-1.24.1/logistf/R/logistpl.R | 27 logistf-1.24.1/logistf/R/logistpl.control.r | 6 logistf-1.24.1/logistf/R/plot.logistf.profile.r | 2 logistf-1.24.1/logistf/R/predict.flac.R | 9 logistf-1.24.1/logistf/R/predict.flic.R | 9 logistf-1.24.1/logistf/R/predict.logistf.R | 146 +- logistf-1.24.1/logistf/R/print.flac.R | 2 logistf-1.24.1/logistf/R/print.flic.R | 2 logistf-1.24.1/logistf/R/print.logistf.R | 2 logistf-1.24.1/logistf/R/print.logistftest.R | 4 logistf-1.24.1/logistf/R/profile.logistf.r | 217 +-- logistf-1.24.1/logistf/R/summary.flac.R | 68 - logistf-1.24.1/logistf/R/summary.flic.R | 69 - logistf-1.24.1/logistf/R/summary.logistf.R | 31 logistf-1.24.1/logistf/R/terms.logistf.R |only logistf-1.24.1/logistf/README.md | 16 logistf-1.24.1/logistf/man/CLIP.confint.Rd | 57 logistf-1.24.1/logistf/man/CLIP.profile.Rd | 34 logistf-1.24.1/logistf/man/PVR.confint.Rd | 28 logistf-1.24.1/logistf/man/add1.Rd | 10 logistf-1.24.1/logistf/man/anova.Rd | 54 logistf-1.24.1/logistf/man/backward.Rd | 23 logistf-1.24.1/logistf/man/flac.Rd | 102 + logistf-1.24.1/logistf/man/flic.Rd | 95 - logistf-1.24.1/logistf/man/logistf-package.Rd |only logistf-1.24.1/logistf/man/logistf.Rd | 133 +- logistf-1.24.1/logistf/man/logistf.control.Rd | 38 logistf-1.24.1/logistf/man/logistf.mod.control.Rd |only logistf-1.24.1/logistf/man/logistftest.Rd | 58 logistf-1.24.1/logistf/man/logistpl.control.Rd | 28 logistf-1.24.1/logistf/man/plot.logistf.profile.Rd | 12 logistf-1.24.1/logistf/man/predict.flac.Rd | 14 logistf-1.24.1/logistf/man/predict.flic.Rd | 14 logistf-1.24.1/logistf/man/predict.logistf.Rd | 24 logistf-1.24.1/logistf/man/profile.logistf.Rd | 31 logistf-1.24.1/logistf/man/sex2.Rd | 12 logistf-1.24.1/logistf/man/sexagg.Rd | 18 logistf-1.24.1/logistf/src/init.c | 18 logistf-1.24.1/logistf/src/logistf.c | 1265 +++++++++++++-------- logistf-1.24.1/logistf/src/veclib.h | 14 logistf-1.24/logistf/R/helpfunc.R |only 62 files changed, 2214 insertions(+), 1915 deletions(-)
Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
Corrections
Description: Provides several cluster-robust variance estimators (i.e.,
sandwich estimators) for ordinary and weighted least squares linear regression
models, including the bias-reduced linearization estimator introduced by Bell
and McCaffrey (2002)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2002002/article/9058-eng.pdf> and
developed further by Pustejovsky and Tipton (2017)
<DOI:10.1080/07350015.2016.1247004>. The package includes functions for estimating
the variance- covariance matrix and for testing single- and multiple-
contrast hypotheses based on Wald test statistics. Tests of single regression
coefficients use Satterthwaite or saddle-point corrections. Tests of multiple-
contrast hypotheses use an approximation to Hotelling's T-squared distribution.
Methods are provided for a variety of fitted models, including lm() and mlm
objects, glm(), ivreg() (from package 'AER'), plm() (from package 'plm'), gls()
and lme() (from 'nlme'), lmer() (from `lme4`), robu() (from 'robumeta'), and
rma.uni() and rma.mv() (from 'metafor').
Author: James Pustejovsky [aut, cre] (<https://orcid.org/0000-0003-0591-9465>)
Maintainer: James Pustejovsky <jepusto@gmail.com>
Diff between clubSandwich versions 0.5.4 dated 2022-01-08 and 0.5.5 dated 2022-01-18
DESCRIPTION | 6 - MD5 | 28 ++--- NAMESPACE | 1 NEWS | 7 + R/conf_int.R | 173 +++++++++++++++++++++++++++++++ build/partial.rdb |binary inst/doc/Wald-tests-in-clubSandwich.html | 4 inst/doc/meta-analysis-with-CRVE.html | 8 - inst/doc/panel-data-CRVE.html | 4 man/linear_contrast.Rd |only tests/testthat/test_coef.R | 16 +- tests/testthat/test_conf_int.R | 4 tests/testthat/test_linear_contrast.R |only tests/testthat/test_rma-mv.R | 16 +- tests/testthat/test_rma-uni.R | 47 +++++--- tests/testthat/test_robu.R | 2 16 files changed, 253 insertions(+), 63 deletions(-)
Title: Statistics Tutorials for Biologists
Description: Tutorials for statistics, aimed at biological scientists.
Subjects range from basic descriptive statistics
through to complex linear modelling. The tutorials
include text, videos, interactive coding exercises
and multiple choice quizzes. The package also
includes 19 datasets which are used in the
tutorials.
Author: Rob Knell
Maintainer: Rob Knell <r.knell@qmul.ac.uk>
Diff between Biostatistics versions 1.0.3 dated 2021-09-02 and 1.0.4 dated 2022-01-18
DESCRIPTION | 6 +- MD5 | 14 +++--- NEWS.md | 2 inst/tutorials/13_Single_factor_ANOVA/Linear_models_1_single_factor_ANOVA.Rmd | 3 - inst/tutorials/15_Model_assumptions/Linear_models_3_Assumptions_and_diagnostics.Rmd | 2 inst/tutorials/17_Multiple_regression/Linear_models_5_multiple_regression.Rmd | 21 ++++++---- inst/tutorials/18_Factors_and_continuous_variables/Linear_models_6.Rmd | 11 +++-- inst/tutorials/19_Model_selection/Linear_models_7_Model_selection.Rmd | 14 +++--- 8 files changed, 44 insertions(+), 29 deletions(-)
Title: Log-Concave Density Estimation in Arbitrary Dimensions
Description: Software for computing a log-concave (maximum likelihood) estimator for i.i.d. data in any number of dimensions. For a detailed description of the method see Cule, Samworth and Stewart (2010, Journal of Royal Statistical Society Series B, <doi:10.1111/j.1467-9868.2010.00753.x>).
Author: Madeleine Cule, Robert Gramacy, Richard Samworth, Yining Chen
Maintainer: Yining Chen <Y.Chen101@lse.ac.uk>
Diff between LogConcDEAD versions 1.6-4 dated 2020-12-02 and 1.6-5 dated 2022-01-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 2 +- build/vignette.rds |binary configure.ac | 4 ++-- inst/doc/LogConcDEAD.pdf |binary 6 files changed, 12 insertions(+), 12 deletions(-)
Title: Simulation Tools for Planning Vitamin D Studies
Description: Simulation tools for planning Vitamin D studies. Individual vitamin D status
profiles are simulated, modelling population heterogeneity in trial arms.
Exposures to infectious agents are generated, with infection depending on vitamin D status.
Author: Rebecca Mangan [aut],
Jason Wyse [aut, cre],
Lina Zgaga [aut]
Maintainer: Jason Wyse <wyseja@tcd.ie>
Diff between SimVitD versions 1.0 dated 2021-01-05 and 1.0.1 dated 2022-01-18
DESCRIPTION | 7 +++---- MD5 | 26 ++++++++++++++------------ NEWS.md | 11 ++++++++++- R/exposure.levels.R | 8 ++++---- R/plot.vitd.curve.R | 4 ++-- R/power.calc.0.R | 4 ++-- R/rr.curve.plot.R | 2 +- R/vitd.curve.2.function.R |only R/vitd.curve.R | 1 + README.md |only build/vignette.rds |binary inst/doc/SimVitD.pdf |binary man/exposure.levels.Rd | 3 ++- man/plot.vitd.curve.Rd | 2 +- man/rr.curve.plot.Rd | 2 +- 15 files changed, 41 insertions(+), 29 deletions(-)
Title: Population Down-Scaling
Description: Areal interpolation of population data obtained
by census surveys. Given a set of source zone polygons such as
census tracts or city blocks alongside with population counts and a
target zone of incogruent yet superimposed polygon features (such as
individual buildings) populR transforms population counts from the
former to the latter using Areal Weighted and Volume Weighted
Interpolation methods.
Author: Marios Batsaris
Maintainer: Marios Batsaris <m.batsaris@aegean.gr>
Diff between populR versions 0.1.3 dated 2021-12-19 and 0.1.4 dated 2022-01-18
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/pp_round.R | 4 +++- R/utils.R | 20 ++++++++------------ man/pp_round.Rd | 4 +++- 5 files changed, 21 insertions(+), 21 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] (<https://orcid.org/0000-0003-2672-7841>)
Maintainer: David M. Phillippo <david.phillippo@bristol.ac.uk>
Diff between multinma versions 0.3.0 dated 2021-03-18 and 0.4.0 dated 2022-01-18
multinma-0.3.0/multinma/vignettes/example_plaque_psoriasis_files |only multinma-0.4.0/multinma/DESCRIPTION | 12 multinma-0.4.0/multinma/MD5 | 150 multinma-0.4.0/multinma/NAMESPACE | 17 multinma-0.4.0/multinma/NEWS.md | 35 multinma-0.4.0/multinma/R/data.R | 4 multinma-0.4.0/multinma/R/doc-examples.R | 22 multinma-0.4.0/multinma/R/integration.R | 236 multinma-0.4.0/multinma/R/multinma-package.R | 4 multinma-0.4.0/multinma/R/nma.R | 251 - multinma-0.4.0/multinma/R/nma_data-class.R | 213 multinma-0.4.0/multinma/R/nma_data.R | 152 multinma-0.4.0/multinma/R/nma_nodesplit-class.R |only multinma-0.4.0/multinma/R/nodesplit_summary-class.R |only multinma-0.4.0/multinma/R/predict.R | 51 multinma-0.4.0/multinma/R/ranks.R | 36 multinma-0.4.0/multinma/R/relative_effects.R | 97 multinma-0.4.0/multinma/R/stan_nma-class.R | 17 multinma-0.4.0/multinma/R/stanmodels.R | 3 multinma-0.4.0/multinma/README.md | 24 multinma-0.4.0/multinma/build/partial.rdb |binary multinma-0.4.0/multinma/build/vignette.rds |binary multinma-0.4.0/multinma/data/plaque_psoriasis_ipd.rda |binary multinma-0.4.0/multinma/inst/REFERENCES.bib | 51 multinma-0.4.0/multinma/inst/REFERENCES.bib.sav.tmp |only multinma-0.4.0/multinma/inst/doc/example_atrial_fibrillation.html | 2403 ++++------ multinma-0.4.0/multinma/inst/doc/example_bcg_vaccine.html | 861 +-- multinma-0.4.0/multinma/inst/doc/example_blocker.html | 348 - multinma-0.4.0/multinma/inst/doc/example_diabetes.html | 1224 ++--- multinma-0.4.0/multinma/inst/doc/example_dietary_fat.html | 710 +- multinma-0.4.0/multinma/inst/doc/example_hta_psoriasis.html | 710 +- multinma-0.4.0/multinma/inst/doc/example_parkinsons.html | 1664 +++--- multinma-0.4.0/multinma/inst/doc/example_plaque_psoriasis.html | 418 - multinma-0.4.0/multinma/inst/doc/example_smoking.html | 797 +-- multinma-0.4.0/multinma/inst/doc/example_statins.html | 639 -- multinma-0.4.0/multinma/inst/doc/example_thrombolytics.html | 1056 ++-- multinma-0.4.0/multinma/inst/doc/example_transfusion.html | 533 -- multinma-0.4.0/multinma/inst/doc/vignette_overview.Rmd | 7 multinma-0.4.0/multinma/inst/doc/vignette_overview.html | 8 multinma-0.4.0/multinma/inst/stan/include/data_common.stan | 3 multinma-0.4.0/multinma/inst/stan/include/model_common.stan | 3 multinma-0.4.0/multinma/inst/stan/include/transformed_parameters_common.stan | 10 multinma-0.4.0/multinma/inst/stan/predict_delta_new.stan |only multinma-0.4.0/multinma/man/aa_example_smk_nodesplit.Rd |only multinma-0.4.0/multinma/man/add_integration.Rd | 61 multinma-0.4.0/multinma/man/get_nodesplits.Rd |only multinma-0.4.0/multinma/man/hta_psoriasis.Rd | 2 multinma-0.4.0/multinma/man/nma.Rd | 32 multinma-0.4.0/multinma/man/nma_nodesplit-class.Rd |only multinma-0.4.0/multinma/man/nodesplit_summary-class.Rd |only multinma-0.4.0/multinma/man/nodesplit_summary-methods.Rd |only multinma-0.4.0/multinma/man/plot.nodesplit_summary.Rd |only multinma-0.4.0/multinma/man/posterior_ranks.Rd | 7 multinma-0.4.0/multinma/man/predict.stan_nma.Rd | 15 multinma-0.4.0/multinma/man/print.nma_nodesplit_df.Rd |only multinma-0.4.0/multinma/man/relative_effects.Rd | 5 multinma-0.4.0/multinma/man/summary.nma_nodesplit_df.Rd |only multinma-0.4.0/multinma/man/thrombolytics.Rd | 2 multinma-0.4.0/multinma/src/RcppExports.cpp | 7 multinma-0.4.0/multinma/src/stanExports_binomial_1par.h | 796 +-- multinma-0.4.0/multinma/src/stanExports_binomial_2par.h | 864 +-- multinma-0.4.0/multinma/src/stanExports_normal.h | 764 +-- multinma-0.4.0/multinma/src/stanExports_ordered_multinomial.h | 1002 ++-- multinma-0.4.0/multinma/src/stanExports_poisson.h | 736 +-- multinma-0.4.0/multinma/src/stanExports_predict_delta_new.cc |only multinma-0.4.0/multinma/src/stanExports_predict_delta_new.h |only multinma-0.4.0/multinma/tests/testthat/test-add_integration.R | 435 + multinma-0.4.0/multinma/tests/testthat/test-data_combine.R | 121 multinma-0.4.0/multinma/tests/testthat/test-data_set.R | 274 + multinma-0.4.0/multinma/tests/testthat/test-example_atrial_fibrillation.R | 130 multinma-0.4.0/multinma/tests/testthat/test-example_bcg_vaccine.R | 53 multinma-0.4.0/multinma/tests/testthat/test-example_blocker.R | 46 multinma-0.4.0/multinma/tests/testthat/test-example_diabetes.R | 60 multinma-0.4.0/multinma/tests/testthat/test-example_parkinsons.R | 231 multinma-0.4.0/multinma/tests/testthat/test-example_plaque_psoriasis.R | 22 multinma-0.4.0/multinma/tests/testthat/test-example_smoking.R | 108 multinma-0.4.0/multinma/tests/testthat/test-example_statins.R | 67 multinma-0.4.0/multinma/tests/testthat/test-example_thrombolytics.R | 156 multinma-0.4.0/multinma/tests/testthat/test-nodesplit.R |only multinma-0.4.0/multinma/tests/testthat/test-posterior_ranks.R | 18 multinma-0.4.0/multinma/vignettes/vignette_overview.Rmd | 7 81 files changed, 10065 insertions(+), 8725 deletions(-)
Title: Animal Movement Tools
Description: Manage and analyze animal movement data. The functionality of 'amt' includes methods to calculate home ranges, track statistics (e.g. step lengths, speed, or turning angles), prepare data for fitting habitat selection analyses, and simulation of space-use from fitted step-selection functions.
Author: Johannes Signer [aut, cre],
Brian Smith [ctb],
Bjoern Reineking [ctb],
Ulrike Schlaegel [ctb],
John Fieberg [ctb],
Josh O'Brien [ctb],
Bernardo Niebuhr [ctb],
Scott LaPoint [dtc]
Maintainer: Johannes Signer <jsigner@gwdg.de>
Diff between amt versions 0.1.5 dated 2021-12-03 and 0.1.6 dated 2022-01-18
DESCRIPTION | 6 MD5 | 53 ++++---- NAMESPACE | 5 NEWS.md | 10 + R/bbox.R | 3 R/coercion.R | 38 ++---- R/extract_covariates.R | 32 ++--- R/hr_area.R | 5 R/hr_isopleths.R | 34 +++-- R/hr_kde.R | 9 + R/hr_locoh.R | 1 R/hr_od.R | 2 R/nsd.R | 26 +++- R/steps.R | 2 build/partial.rdb |binary inst/doc/p1_getting_started.html | 171 ++++++++++++++------------- inst/doc/p2_hr.html | 113 +++++++++--------- inst/doc/p3_rsf.html | 121 ++++++++++--------- inst/doc/p4_SSF.html | 233 +++++++++++++++++++------------------- inst/doc/p5_other_packages.html | 109 +++++++++-------- inst/tinytest/test_hr.R | 60 +++++++++ inst/tinytest/test_nsd.R |only inst/tinytest/test_random_steps.R | 9 - man/as_sf_points.Rd | 5 man/bbox.Rd | 3 man/hr_isopleths.Rd | 12 + man/nsd.Rd | 16 ++ src/track_methods.cpp | 2 28 files changed, 614 insertions(+), 466 deletions(-)
Title: Variance Components Testing for Linear and Nonlinear Mixed
Effects Models
Description: An implementation of the Likelihood ratio Test (LRT) for testing that,
in a (non)linear mixed effects model, the variances of a subset of the random
effects are equal to zero. There is no restriction on the subset of variances
that can be tested: for example, it is possible to test that all the variances
are equal to zero. Note that the implemented test is asymptotic.
This package should be used on model fits from packages 'nlme', 'lmer', and 'saemix'.
Charlotte Baey, Paul-Henry Cournède and Estelle Kuhn (2019) <doi:10.1016/j.csda.2019.01.014>.
Author: Charlotte Baey [aut, cre] (<https://orcid.org/0000-0002-1413-1058>),
Estelle Kuhn [aut]
Maintainer: Charlotte Baey <charlotte.baey@univ-lille.fr>
Diff between varTestnlme versions 1.2.0 dated 2021-12-07 and 1.3.0 dated 2022-01-18
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 7 +++++-- R/generics.R | 15 ++++----------- R/varCompTest.lme.R | 10 +++++----- R/varCompTest.merMod.R | 11 +++++------ R/varCompTest.saemixObject.R | 8 ++++---- man/varCompTest.Rd | 14 ++++++++++---- 8 files changed, 43 insertions(+), 42 deletions(-)
Title: Bayesian Hierarchical Models for Basket Trials
Description: Provides functions for the evaluation of basket
trial designs with binary endpoints. Operating characteristics of a
basket trial design are assessed by simulating trial data according to
scenarios, analyzing the data with Bayesian hierarchical models (BHMs), and
assessing decision probabilities on stratum and trial-level based on Go / No-go decision making.
The package is build for high flexibility regarding decision rules,
number of interim analyses, number of strata, and recruitment.
The BHMs proposed by
Berry et al. (2013) <doi:10.1177/1740774513497539>
and Neuenschwander et al. (2016) <doi:10.1002/pst.1730>,
as well as a model that combines both approaches are implemented.
Functions are provided to implement Bayesian decision rules as for example
proposed by Fisch et al. (2015) <doi:10.1177/2168479014533970>.
In addition, posterior point estimates (mean/median) and credible intervals
for response rates and some model parameters can be calculated.
For simulated trial data, bias and mean squared errors of posterior
point estimates for response rates can be provided.
Author: Stephan Wojciekowski [aut, cre]
Maintainer: Stephan Wojciekowski <stephan.wojciekowski@boehringer-ingelheim.com>
Diff between bhmbasket versions 0.9.3 dated 2021-10-11 and 0.9.4 dated 2022-01-18
bhmbasket-0.9.3/bhmbasket/R/BUGSModels.R |only bhmbasket-0.9.3/bhmbasket/R/GraveyardOfOldFunctions.R |only bhmbasket-0.9.4/bhmbasket/DESCRIPTION | 10 bhmbasket-0.9.4/bhmbasket/MD5 | 44 bhmbasket-0.9.4/bhmbasket/NEWS.md | 32 bhmbasket-0.9.4/bhmbasket/R/AnalysisFunctions.R | 421 ++++----- bhmbasket-0.9.4/bhmbasket/R/DataFunctions.R | 107 -- bhmbasket-0.9.4/bhmbasket/R/Misc.R | 43 bhmbasket-0.9.4/bhmbasket/R/OCFunctions.R | 81 - bhmbasket-0.9.4/bhmbasket/build/vignette.rds |binary bhmbasket-0.9.4/bhmbasket/inst/CITATION | 5 bhmbasket-0.9.4/bhmbasket/inst/doc/Running_bhmbasket_on_HPC.R |only bhmbasket-0.9.4/bhmbasket/inst/doc/Running_bhmbasket_on_HPC.Rmd |only bhmbasket-0.9.4/bhmbasket/inst/doc/Running_bhmbasket_on_HPC.html |only bhmbasket-0.9.4/bhmbasket/inst/doc/reproduceExNex.Rmd | 2 bhmbasket-0.9.4/bhmbasket/inst/doc/reproduceExNex.html | 446 +++++----- bhmbasket-0.9.4/bhmbasket/inst/jags_models |only bhmbasket-0.9.4/bhmbasket/man/continueRecruitment.Rd | 3 bhmbasket-0.9.4/bhmbasket/man/getEstimates.Rd | 6 bhmbasket-0.9.4/bhmbasket/man/getGoDecisions.Rd | 3 bhmbasket-0.9.4/bhmbasket/man/getGoProbabilities.Rd | 3 bhmbasket-0.9.4/bhmbasket/man/negateGoDecisions.Rd | 3 bhmbasket-0.9.4/bhmbasket/man/scaleRoundList.Rd | 3 bhmbasket-0.9.4/bhmbasket/vignettes/Running_bhmbasket_on_HPC.Rmd |only bhmbasket-0.9.4/bhmbasket/vignettes/bhmbasket_on_HPC.R |only bhmbasket-0.9.4/bhmbasket/vignettes/reproduceExNex.Rmd | 2 26 files changed, 602 insertions(+), 612 deletions(-)
Title: Assessment Models for Agriculture Soil Conditions and Crop
Suitability
Description: Soil assessment builds information for improved decision in soil management. It analyzes soil conditions with regard to agriculture
crop suitability requirements [such as those given by FAO <https://www.fao.org/land-water/databases-and-software/crop-information/en/>] soil fertility classes,
soil erosion models and soil salinity classification. Suitability requirements are for crops grouped into cereal crops, nuts, legumes, fruits, vegetables,
industrial crops, and root crops.
Author: Christian Thine Omuto
Maintainer: Christian Thine Omuto <thineomuto@yahoo.com>
Diff between soilassessment versions 0.2.1 dated 2020-08-30 and 0.2.2 dated 2022-01-18
DESCRIPTION | 13 +++---- MD5 | 84 +++++++++++++++++++++++++--------------------- NAMESPACE | 1 R/CECSuit.R | 14 +++++++ R/ECSuit.R | 13 +++++++ R/ECconversion2.R | 22 ++++++++++-- R/ESPSuit.R | 14 +++++++ R/LGPSuit.R | 12 ++++++ R/ME_ECharm.R |only R/ME_PHharm.R |only R/PHConversion.R |only R/PHSuit.R | 12 ++++++ R/SOCSuit.R | 12 ++++++ R/carbonateSuit.R | 13 +++++++ R/classCode.R | 6 +-- R/depthSuit.R | 13 ++++++- R/drainageSuit.R | 14 +++++++ R/fertilitySuit.R | 14 +++++++ R/imageIndices.R | 7 ++- R/rainSuit.R | 12 ++++++ R/saltSeverity.R | 2 - R/slopeSuit.R | 14 +++++++ R/stoneSuit.R | 12 ++++++ R/tempSuit.R | 12 ++++++ R/textureSuit.R | 28 ++++++++++----- data/ME_ECharmserve.RData |only data/ME_PHharmserve.RData |only man/CECSuit.Rd | 4 +- man/ECSuit.Rd | 4 +- man/ECconversion1.Rd | 4 +- man/ECconversion2.Rd | 5 ++ man/ESPSuit.Rd | 4 +- man/LGPSuit.Rd | 4 +- man/ME_ECharm.Rd |only man/ME_ECharmserve.Rd |only man/ME_PHharm.Rd |only man/ME_PHharmserve.Rd |only man/PHConversion.Rd |only man/PHSuit.Rd | 4 +- man/SOCSuit.Rd | 4 +- man/carbonateSuit.Rd | 4 +- man/depthSuit.Rd | 4 +- man/drainageSuit.Rd | 4 +- man/rainSuit.Rd | 4 +- man/slopeSuit.Rd | 4 +- man/stoneSuit.Rd | 4 +- man/tempSuit.Rd | 4 +- man/textureSuit.Rd | 4 +- 48 files changed, 313 insertions(+), 96 deletions(-)
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Title: Broadly Useful Convenient and Efficient R Functions
Description: Broadly useful convenient and efficient R functions
that bring users concise and elegant R data analyses.
This package includes easy-to-use functions for
(1) basic R programming
(e.g., set working directory to the path of currently opened file,
import/export data from/to files with any format,
print strings with rich formats and colors);
(2) multivariate computation
(e.g., compute scale sums/means/... with reverse scoring);
(3) reliability analyses and factor analyses;
(4) descriptive statistics and correlation analyses;
(5) t-test, multi-factor analysis of variance (ANOVA),
simple-effect analysis, and post-hoc multiple comparison;
(6) tidy report of statistical models
(to R Console and Microsoft Word);
(7) mediation and moderation analyses (PROCESS);
and (8) additional toolbox for statistics and graphics.
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between bruceR versions 0.8.2 dated 2021-12-12 and 0.8.3 dated 2022-01-18
DESCRIPTION | 8 +++--- MD5 | 20 ++++++++-------- NEWS.md | 12 +++++++++ R/bruceR.R | 53 +++++++++++++++++++++++--------------------- R/bruceR_basic.R | 24 +++++++++---------- R/bruceR_stats_01_basic.R | 4 +-- R/bruceR_stats_04_regress.R | 2 - R/bruceR_stats_05_advance.R | 5 ++-- README.md | 6 +++- build/partial.rdb |binary inst/CITATION | 4 +-- 11 files changed, 78 insertions(+), 60 deletions(-)
Title: Access Forest Ecology Layers for British Columbia in 2001-2018
Description: R-based access to a large set of data variables relevant to forest ecology in British Columbia (BC), Canada. Layers
are in raster format at 100m resolution in the BC Albers projection, hosted at the Federated Research Data Repository (FRDR)
with <doi:10.20383/101.0283>. The collection includes: elevation; biogeoclimatic zone; wildfire; cutblocks; forest attributes from
Hansen et al. (2013) <doi:10.1139/cjfr-2013-0401> and Beaudoin et al. (2017) <doi:10.1139/cjfr-2017-0184>; and rasterized
Forest Insect and Disease Survey (FIDS) maps for a number of insect pest species, all covering the period 2001-2018.
Users supply a polygon or point location in the province of BC, and 'rasterbc' will download the overlapping raster tiles
hosted at FRDR, merging them as needed and returning the result in R as a 'SpatRaster' object. Metadata associated with these
layers, and code for downloading them from their original sources can be found in the 'github' repository
<https://github.com/deankoch/rasterbc_src>.
Author: Dean Koch [aut, cre] (<https://orcid.org/0000-0002-8849-859X>)
Maintainer: Dean Koch <dkoch@ualberta.ca>
Diff between rasterbc versions 1.0.0 dated 2021-12-16 and 1.0.1 dated 2022-01-18
rasterbc-1.0.0/rasterbc/vignettes/man |only rasterbc-1.0.1/rasterbc/DESCRIPTION | 6 rasterbc-1.0.1/rasterbc/MD5 | 29 - rasterbc-1.0.1/rasterbc/NEWS.md | 8 rasterbc-1.0.1/rasterbc/README.md | 27 + rasterbc-1.0.1/rasterbc/build/partial.rdb |binary rasterbc-1.0.1/rasterbc/inst/doc/vignette_intro.R | 67 ++- rasterbc-1.0.1/rasterbc/inst/doc/vignette_intro.Rmd | 186 +++++++--- rasterbc-1.0.1/rasterbc/inst/doc/vignette_intro.html | 65 +-- rasterbc-1.0.1/rasterbc/vignettes/vignette_intro.Rmd | 186 +++++++--- rasterbc-1.0.1/rasterbc/vignettes/vignette_intro.Rmd.orig |only rasterbc-1.0.1/rasterbc/vignettes/vignette_intro.md |only rasterbc-1.0.1/rasterbc/vignettes/vignette_intro_okanagan_bgcz-1.png |only rasterbc-1.0.1/rasterbc/vignettes/vignette_intro_okanagan_elevation-1.png |only rasterbc-1.0.1/rasterbc/vignettes/vignette_intro_okanagan_elevation_clipped-1.png |only rasterbc-1.0.1/rasterbc/vignettes/vignette_intro_okanagan_elevation_tiles-1.png |only rasterbc-1.0.1/rasterbc/vignettes/vignette_intro_okanagan_location-1.png |only rasterbc-1.0.1/rasterbc/vignettes/vignette_pinebeetle_DEVELOPMENT.R |only 18 files changed, 396 insertions(+), 178 deletions(-)
Title: Psychometric Meta-Analysis Toolkit
Description: Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more. Bugs can be reported to <https://github.com/psychmeta/psychmeta/issues> or <issues@psychmeta.com>.
Author: Jeffrey A. Dahlke [aut, cre],
Brenton M. Wiernik [aut],
Wesley Gardiner [ctb] (Unit tests),
Michael T. Brannick [ctb] (Testing),
Jack Kostal [ctb] (Code for reshape_mat2dat function),
Sean Potter [ctb] (Testing; Code for cumulative and leave1out plots),
John Sakaluk [ctb] (Code for funnel and forest plots),
Yuejia (Mandy) Teng [ctb] (Testing)
Maintainer: Jeffrey A. Dahlke <jdahlke@humrro.org>
Diff between psychmeta versions 2.6.1 dated 2022-01-03 and 2.6.2 dated 2022-01-18
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++++ build/partial.rdb |binary build/psychmeta.pdf |binary inst/doc/ma_r.html | 4 ++-- inst/doc/overview.Rmd | 2 +- vignettes/overview.Rmd | 2 +- 8 files changed, 20 insertions(+), 15 deletions(-)
Title: Marginal Effects, Marginal Means, Predictions, and Contrasts
Description: Compute, summarize, and plot marginal effects, adjusted predictions, contrasts, and marginal means for a wide variety of models.
Author: Vincent Arel-Bundock [aut, cre, cph]
(<https://orcid.org/0000-0003-2042-7063>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between marginaleffects versions 0.3.1 dated 2022-01-09 and 0.3.2 dated 2022-01-18
marginaleffects-0.3.1/marginaleffects/inst/doc/lme4.R |only marginaleffects-0.3.1/marginaleffects/inst/doc/lme4.Rmd |only marginaleffects-0.3.1/marginaleffects/inst/doc/lme4.html |only marginaleffects-0.3.1/marginaleffects/man/get_marginalmeans.Rd |only marginaleffects-0.3.1/marginaleffects/man/sanity_type.Rd |only marginaleffects-0.3.1/marginaleffects/man/type_dictionary.Rd |only marginaleffects-0.3.1/marginaleffects/vignettes/lme4.Rmd |only marginaleffects-0.3.2/marginaleffects/DESCRIPTION | 32 - marginaleffects-0.3.2/marginaleffects/MD5 | 106 ++--- marginaleffects-0.3.2/marginaleffects/NAMESPACE | 6 marginaleffects-0.3.2/marginaleffects/NEWS.md | 17 marginaleffects-0.3.2/marginaleffects/R/datagrid.R | 2 marginaleffects-0.3.2/marginaleffects/R/get_dydx.R | 4 marginaleffects-0.3.2/marginaleffects/R/get_gradient.R |only marginaleffects-0.3.2/marginaleffects/R/get_jacobian.R |only marginaleffects-0.3.2/marginaleffects/R/marginaleffects.R | 31 + marginaleffects-0.3.2/marginaleffects/R/marginalmeans.R | 1 marginaleffects-0.3.2/marginaleffects/R/methods_brglm2.R | 13 marginaleffects-0.3.2/marginaleffects/R/methods_mclogit.R |only marginaleffects-0.3.2/marginaleffects/R/methods_scam.R |only marginaleffects-0.3.2/marginaleffects/R/predictions.R | 34 + marginaleffects-0.3.2/marginaleffects/R/sanity_model.R | 6 marginaleffects-0.3.2/marginaleffects/R/sanity_type.R | 1 marginaleffects-0.3.2/marginaleffects/R/standard_errors_delta.R | 5 marginaleffects-0.3.2/marginaleffects/R/summary.R | 4 marginaleffects-0.3.2/marginaleffects/R/type_dictionary.R | 4 marginaleffects-0.3.2/marginaleffects/README.md | 4 marginaleffects-0.3.2/marginaleffects/build/vignette.rds |binary marginaleffects-0.3.2/marginaleffects/inst/doc/case_studies.R |only marginaleffects-0.3.2/marginaleffects/inst/doc/case_studies.Rmd |only marginaleffects-0.3.2/marginaleffects/inst/doc/case_studies.html |only marginaleffects-0.3.2/marginaleffects/inst/doc/mfx.R | 3 marginaleffects-0.3.2/marginaleffects/inst/doc/mfx.Rmd | 18 marginaleffects-0.3.2/marginaleffects/inst/doc/mfx.html | 201 +++++----- marginaleffects-0.3.2/marginaleffects/inst/doc/predictions.R | 12 marginaleffects-0.3.2/marginaleffects/inst/doc/predictions.Rmd | 30 + marginaleffects-0.3.2/marginaleffects/inst/doc/predictions.html | 101 +++-- marginaleffects-0.3.2/marginaleffects/inst/doc/supported_models.html | 95 ++++ marginaleffects-0.3.2/marginaleffects/man/datagrid.Rd | 2 marginaleffects-0.3.2/marginaleffects/man/get_coef.Rd | 9 marginaleffects-0.3.2/marginaleffects/man/get_group_names.Rd | 9 marginaleffects-0.3.2/marginaleffects/man/get_vcov.Rd | 5 marginaleffects-0.3.2/marginaleffects/man/marginaleffects.Rd | 31 + marginaleffects-0.3.2/marginaleffects/man/meffects.Rd | 31 + marginaleffects-0.3.2/marginaleffects/man/predictions.Rd | 34 + marginaleffects-0.3.2/marginaleffects/man/set_coef.Rd | 5 marginaleffects-0.3.2/marginaleffects/tests/testthat/_snaps/summary.md | 13 marginaleffects-0.3.2/marginaleffects/tests/testthat/test-numDeriv.R |only marginaleffects-0.3.2/marginaleffects/tests/testthat/test-pkg-MASS.R | 1 marginaleffects-0.3.2/marginaleffects/tests/testthat/test-pkg-brglm2.R | 10 marginaleffects-0.3.2/marginaleffects/tests/testthat/test-pkg-brms.R | 1 marginaleffects-0.3.2/marginaleffects/tests/testthat/test-pkg-estimatr.R | 5 marginaleffects-0.3.2/marginaleffects/tests/testthat/test-pkg-lmerTest.R |only marginaleffects-0.3.2/marginaleffects/tests/testthat/test-pkg-mclogit.R |only marginaleffects-0.3.2/marginaleffects/tests/testthat/test-pkg-scam.R |only marginaleffects-0.3.2/marginaleffects/tests/testthat/test-pkg-speedglm.R | 1 marginaleffects-0.3.2/marginaleffects/tests/testthat/test-pkg-survey.R | 5 marginaleffects-0.3.2/marginaleffects/tests/testthat/test-pkg-truncreg.R | 1 marginaleffects-0.3.2/marginaleffects/tests/testthat/test-summary.R | 11 marginaleffects-0.3.2/marginaleffects/tests/testthat/test-tidy.R | 2 marginaleffects-0.3.2/marginaleffects/vignettes/case_studies.Rmd |only marginaleffects-0.3.2/marginaleffects/vignettes/lme4.html |only marginaleffects-0.3.2/marginaleffects/vignettes/mfx.Rmd | 18 marginaleffects-0.3.2/marginaleffects/vignettes/predictions.Rmd | 30 + 64 files changed, 694 insertions(+), 260 deletions(-)
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Title: Train and Apply a Gaussian Stochastic Process Model
Description: Train a Gaussian stochastic process model of an unknown function, possibly observed with error, via maximum likelihood or MAP estimation, run model diagnostics, and make predictions, following Sacks, J., Welch, W.J., Mitchell, T.J., and Wynn, H.P. (1989) "Design and Analysis of Computer Experiments", Statistical Science, <doi:10.1214/ss/1177012413>. Perform sensitivity analysis and visualize low-order effects, following Schonlau, M. and Welch, W.J. (2006), "Screening the Input Variables to a Computer Model Via Analysis of Variance and Visualization", <doi:10.1007/0-387-28014-6_14>.
Author: William J. Welch [aut, cre, cph]
(<https://orcid.org/0000-0002-4575-3124>),
Yilin Yang [aut] (<https://orcid.org/0000-0003-0885-6017>)
Maintainer: William J. Welch <will@stat.ubc.ca>
Diff between GaSP versions 1.0.0 dated 2021-06-07 and 1.0.1 dated 2022-01-18
DESCRIPTION | 11 ++++----- MD5 | 41 +++++++++++++++++++--------------- R/Check.R | 3 -- R/Fit.R | 18 ++++++++------ R/PlotEffects.R | 12 +++------ R/RegMod.R | 3 -- README.md | 11 +++++++-- build |only inst |only man/Fit.Rd | 18 ++++++++------ src/RCconvert.h | 2 + src/RtoC.c | 65 +++++++++++++++++++++++++++++------------------------- src/gaspcv.c | 16 ++++++------- src/gaspfit.c | 33 ++++++++++++++++----------- src/gasppredict.c | 16 ++++++------- src/gaspvis.c | 18 +++++++------- src/lib.h | 4 ++- src/libout.c | 7 ++--- src/libreg.c | 32 ++++++++++++++++---------- src/matutil.c | 9 +++---- vignettes |only 21 files changed, 178 insertions(+), 141 deletions(-)
Title: Prioritizing Cancer Driver Genes Using Genomics Data
Description: Cancer genomes contain large numbers of somatic alterations but few
genes drive tumor development. Identifying cancer driver genes is critical
for precision oncology. Most of current approaches either identify driver
genes based on mutational recurrence or using estimated scores predicting
the functional consequences of mutations. 'driveR' is a tool for
personalized or batch analysis of genomic data for driver gene prioritization
by combining genomic information and prior biological knowledge. As features,
'driveR' uses coding impact metaprediction scores, non-coding impact scores,
somatic copy number alteration scores, hotspot gene/double-hit gene
condition, 'phenolyzer' gene scores and memberships to cancer-related KEGG
pathways. It uses these features to estimate cancer-type-specific
probability for each gene of being a cancer driver using the related task of
a multi-task learning classification model. The method is described in detail
in Ulgen E, Sezerman OU. 2021. driveR: driveR: a novel method for
prioritizing cancer driver genes using somatic genomics data. BMC
Bioinformatics <doi:10.1186/s12859-021-04203-7>.
Author: Ege Ulgen [aut, cre, cph] (<https://orcid.org/0000-0003-2090-3621>)
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between driveR versions 0.2.1 dated 2020-11-25 and 0.3.0 dated 2022-01-18
DESCRIPTION | 14 - MD5 | 18 - NEWS.md | 10 README.md | 17 - build/vignette.rds |binary data/specific_thresholds.rda |binary inst/CITATION | 10 inst/doc/how_to_use.Rmd | 2 inst/doc/how_to_use.html | 458 ++++++++++--------------------------------- vignettes/how_to_use.Rmd | 2 10 files changed, 157 insertions(+), 374 deletions(-)