Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor Analysis (Parafac) model-1 fit to a three-way or four-way data tensor/array. See Harshman (1994) <doi:10.1016/0167-9473(94)90132-5>. Uses Parafac factor weights from one mode of this model as predictors to tune parameters for one or more classification methods via a k-fold cross-validation procedure. Supports penalized logistic regression, support vector machine, random forest, and feed-forward neural network. Supports binary and multiclass classification. Predicts class labels or class probabilities and calculates multiple classification performance measures. Parallel computing is implemented via the 'parallel' and 'doParallel' packages.
Author: Matthew A. Snodgress <snodg031@umn.edu>
Maintainer: Matthew A. Snodgress <snodg031@umn.edu>
Diff between cpfa versions 1.0-2 dated 2022-05-16 and 1.0-3 dated 2022-06-15
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- inst/doc/cpfa.R | 4 ++-- inst/doc/cpfa.Rmd | 11 +++++------ inst/doc/cpfa.pdf |binary vignettes/cpfa.Rmd | 11 +++++------ 6 files changed, 23 insertions(+), 25 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] ,
RStudio, PBC [cph],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.39 dated 2022-05-16 and 0.40 dated 2022-06-15
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/install.R | 27 +++++++++++++++++++++------ man/install_tinytex.Rd | 12 +++++++++--- man/tinytex-package.Rd | 2 +- 5 files changed, 39 insertions(+), 18 deletions(-)
Title: Tools for Bayesian Analyses
Description: Provides tools for conducting Bayesian analyses. The package contains
functions for creating a wide range of prior distribution objects, mixing posterior
samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc...
The tools for working with prior distribution span from visualization, generating 'JAGS'
and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.
Author: Frantisek Bartos [aut, cre]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between BayesTools versions 0.2.10 dated 2022-05-10 and 0.2.11 dated 2022-06-15
DESCRIPTION | 6 MD5 | 112 +- NAMESPACE | 8 NEWS.md | 12 R/JAGS-diagnostics.R | 22 R/JAGS-fit.R | 148 ++- R/JAGS-formula.R | 102 +- R/JAGS-marglik.R | 104 +- R/priors-density.R | 42 R/priors-plot.R | 184 ++++ R/priors-print.R | 18 R/priors-tools.R | 20 R/priors.R | 142 +++ R/summary-tables.R | 218 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 99 +- inst/doc/ComparisonR.R | 4 inst/doc/ComparisonR.Rmd | 9 inst/doc/ComparisonR.html | 366 +++++++- inst/doc/SpikeAndSlab.R |only inst/doc/SpikeAndSlab.Rmd |only inst/doc/SpikeAndSlab.html |only man/BayesTools_model_tables.Rd | 55 + man/is.prior.Rd | 6 man/prior_spike_and_slab.Rd |only tests/testthat/_snaps/JAGS-diagnostics/diagnostics-plot-spike-and-slab-1.svg |only tests/testthat/_snaps/JAGS-diagnostics/diagnostics-plot-spike-and-slab-2.svg |only tests/testthat/_snaps/JAGS-diagnostics/diagnostics-plot-spike-and-slab-3.svg |only tests/testthat/_snaps/JAGS-fit/jags-fit-formula-spike-and-slab-1.svg |only tests/testthat/_snaps/JAGS-fit/jags-fit-formula-spike-and-slab-2.svg |only tests/testthat/_snaps/JAGS-fit/jags-model-prior-1.svg | 198 ++-- tests/testthat/_snaps/JAGS-fit/jags-model-prior-10.svg | 196 ++-- tests/testthat/_snaps/JAGS-fit/jags-model-prior-12.svg | 202 ++-- tests/testthat/_snaps/JAGS-fit/jags-model-prior-13.svg | 202 ++-- tests/testthat/_snaps/JAGS-fit/jags-model-prior-14.svg |only tests/testthat/_snaps/JAGS-fit/jags-model-prior-2.svg | 236 ++--- tests/testthat/_snaps/JAGS-fit/jags-model-prior-3.svg | 211 ++-- tests/testthat/_snaps/JAGS-fit/jags-model-prior-4.svg | 218 +--- tests/testthat/_snaps/JAGS-fit/jags-model-prior-5.svg | 218 ++-- tests/testthat/_snaps/JAGS-fit/jags-model-prior-6.svg | 243 ++--- tests/testthat/_snaps/JAGS-fit/jags-model-prior-7.svg | 190 ++-- tests/testthat/_snaps/JAGS-fit/jags-model-prior-8.svg | 231 ++--- tests/testthat/_snaps/JAGS-fit/jags-model-prior-9.svg | 210 ++-- tests/testthat/_snaps/JAGS-fit/jags-model-prior-spike-and-slab-1.svg |only tests/testthat/_snaps/JAGS-fit/jags-model-prior-spike-and-slab-2.svg |only tests/testthat/_snaps/priors-plot/priors-plot-15-1.svg |only tests/testthat/_snaps/priors-plot/priors-plot-15-10.svg |only tests/testthat/_snaps/priors-plot/priors-plot-15-11.svg |only tests/testthat/_snaps/priors-plot/priors-plot-15-2.svg |only tests/testthat/_snaps/priors-plot/priors-plot-15-3.svg |only tests/testthat/_snaps/priors-plot/priors-plot-15-4.svg |only tests/testthat/_snaps/priors-plot/priors-plot-15-5.svg |only tests/testthat/_snaps/priors-plot/priors-plot-15-6.svg |only tests/testthat/_snaps/priors-plot/priors-plot-15-7.svg |only tests/testthat/_snaps/priors-plot/priors-plot-15-8.svg |only tests/testthat/_snaps/priors-plot/priors-plot-15-9.svg |only tests/testthat/_snaps/priors-print/priors-print-4.svg |only tests/testthat/_snaps/priors/prior-bernoulli-1.svg |only tests/testthat/_snaps/priors/prior-bernoulli-2.svg |only tests/testthat/_snaps/priors/prior-spike-and-slab-1.svg |only tests/testthat/test-JAGS-diagnostics.R | 52 + tests/testthat/test-JAGS-fit.R | 152 +++ tests/testthat/test-JAGS-marglik.R | 30 tests/testthat/test-priors-plot.R | 286 +++--- tests/testthat/test-priors-print.R | 233 ++--- tests/testthat/test-priors-tools.R | 86 - tests/testthat/test-priors.R | 457 +++++----- tests/testthat/test-summary-tables.R | 100 ++ vignettes/ComparisonR.Rmd | 9 vignettes/SpikeAndSlab.Rmd |only 71 files changed, 3660 insertions(+), 1977 deletions(-)
Title: User-Friendly Tables with Color Helpers for Data Exploration
Description: Make it easy to deal with multiple cross-tables in data
exploration, by creating them, manipulating them, and adding color
helpers to highlight important informations (differences from totals,
comparisons between lines or columns, contributions to variance, margins
of error, etc.). All functions are pipe-friendly and render data frames
which can be easily manipulated. In the same time, time-taking operations
are done with `data.table` to go faster with big dataframes. Tables can
be exported to Excel and in html with formats and colors.
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@gmail.com>
Diff between tabxplor versions 1.0.3 dated 2022-04-09 and 1.1.0 dated 2022-06-15
tabxplor-1.0.3/tabxplor/man/get_ci_type.Rd |only tabxplor-1.0.3/tabxplor/man/get_col_var.Rd |only tabxplor-1.0.3/tabxplor/man/get_color.Rd |only tabxplor-1.0.3/tabxplor/man/get_comp_all.Rd |only tabxplor-1.0.3/tabxplor/man/get_diff_type.Rd |only tabxplor-1.0.3/tabxplor/man/is_refcol.Rd |only tabxplor-1.0.3/tabxplor/man/is_refrow.Rd |only tabxplor-1.1.0/tabxplor/DESCRIPTION | 17 tabxplor-1.1.0/tabxplor/MD5 | 83 tabxplor-1.1.0/tabxplor/NAMESPACE | 340 - tabxplor-1.1.0/tabxplor/NEWS.md | 8 tabxplor-1.1.0/tabxplor/R/fmt_class.R | 818 +- tabxplor-1.1.0/tabxplor/R/tab.R | 3353 +++++++++-- tabxplor-1.1.0/tabxplor/R/tab_classes.R | 3926 +++++++------- tabxplor-1.1.0/tabxplor/R/tab_xl.R | 469 + tabxplor-1.1.0/tabxplor/R/utils.R | 1 tabxplor-1.1.0/tabxplor/README.md | 265 tabxplor-1.1.0/tabxplor/inst/doc/tabxplor.R | 38 tabxplor-1.1.0/tabxplor/inst/doc/tabxplor.Rmd | 152 tabxplor-1.1.0/tabxplor/inst/doc/tabxplor.html | 1136 +++- tabxplor-1.1.0/tabxplor/man/cash-.tabxplor_fmt.Rd |only tabxplor-1.1.0/tabxplor/man/fmt.Rd | 140 tabxplor-1.1.0/tabxplor/man/fmt_get_color_code.Rd | 19 tabxplor-1.1.0/tabxplor/man/get_ci_type.data.frame.Rd |only tabxplor-1.1.0/tabxplor/man/get_ci_type.default.Rd |only tabxplor-1.1.0/tabxplor/man/get_ci_type.tabxplor_fmt.Rd |only tabxplor-1.1.0/tabxplor/man/get_col_var.data.frame.Rd |only tabxplor-1.1.0/tabxplor/man/get_col_var.default.Rd |only tabxplor-1.1.0/tabxplor/man/get_col_var.tabxplor_fmt.Rd |only tabxplor-1.1.0/tabxplor/man/get_color.data.frame.Rd |only tabxplor-1.1.0/tabxplor/man/get_color.default.Rd |only tabxplor-1.1.0/tabxplor/man/get_color.tabxplor_fmt.Rd |only tabxplor-1.1.0/tabxplor/man/get_diff_type.data.frame.Rd |only tabxplor-1.1.0/tabxplor/man/get_diff_type.default.Rd |only tabxplor-1.1.0/tabxplor/man/get_diff_type.tabxplor_fmt.Rd |only tabxplor-1.1.0/tabxplor/man/get_display.Rd | 4 tabxplor-1.1.0/tabxplor/man/is_refcol.data.frame.Rd |only tabxplor-1.1.0/tabxplor/man/is_refcol.default.Rd |only tabxplor-1.1.0/tabxplor/man/is_refcol.tabxplor_fmt.Rd |only tabxplor-1.1.0/tabxplor/man/is_refrow.data.frame.Rd |only tabxplor-1.1.0/tabxplor/man/is_refrow.default.Rd |only tabxplor-1.1.0/tabxplor/man/is_refrow.tabxplor_fmt.Rd |only tabxplor-1.1.0/tabxplor/man/mutate.tabxplor_fmt.Rd |only tabxplor-1.1.0/tabxplor/man/tab.Rd | 33 tabxplor-1.1.0/tabxplor/man/tab_chi2.Rd | 10 tabxplor-1.1.0/tabxplor/man/tab_ci.Rd | 65 tabxplor-1.1.0/tabxplor/man/tab_many.Rd | 89 tabxplor-1.1.0/tabxplor/man/tab_num.Rd |only tabxplor-1.1.0/tabxplor/man/tab_pct.Rd | 14 tabxplor-1.1.0/tabxplor/man/tab_plain.Rd | 107 tabxplor-1.1.0/tabxplor/man/tab_prepare.Rd | 19 tabxplor-1.1.0/tabxplor/man/tab_spread.Rd | 12 tabxplor-1.1.0/tabxplor/man/tab_totaltab.Rd | 2 tabxplor-1.1.0/tabxplor/man/tabxplor-data.table.Rd |only tabxplor-1.1.0/tabxplor/tests/testthat/test-fmt_class.R | 261 tabxplor-1.1.0/tabxplor/tests/testthat/test-tab.R | 497 + tabxplor-1.1.0/tabxplor/vignettes/tabxplor.Rmd | 152 57 files changed, 7909 insertions(+), 4121 deletions(-)
Title: Multiple-Scaled Clustering
Description: Model based clustering using
the multivariate multiple Scaled t (MST) and multivariate multiple
scaled contaminated normal (MSCN) distributions. The MST is an
extension of the multivariate Student-t distribution to include
flexible tail behaviors, Forbes, F. & Wraith, D. (2014) <doi:10.1007/s11222-013-9414-4>. The MSCN represents a heavy-tailed
generalization of the multivariate normal (MN) distribution to
model elliptical contoured scatters in the presence of mild outliers
(also referred to as "bad" points) and automatically detect bad points, Punzo, A. & Tortora, C. (2021) <doi:10.1177/1471082X19890935>.
Author: Cristina Tortora [aut, cre, cph]
,
Antonio Punzo [aut] ,
Louis Tran [aut]
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between MSclust versions 1.0 dated 2022-04-08 and 1.0.1 dated 2022-06-15
DESCRIPTION | 8 +- MD5 | 12 ++-- R/MSmixt.R | 4 - R/extra.R | 150 +++++++++++++++++++++++++++------------------------- man/mscn.Rd | 2 man/mst.Rd | 4 - man/plot.MSclust.Rd | 2 7 files changed, 94 insertions(+), 88 deletions(-)
Title: Information Matrices for 'lmeStruct' and 'glsStruct' Objects
Description: Provides analytic derivatives and information matrices for
fitted linear mixed effects (lme) models and generalized least squares (gls) models
estimated using lme() (from package 'nlme') and gls() (from package 'nlme'), respectively.
The package includes functions for estimating the sampling variance-covariance of variance
component parameters using the inverse Fisher information. The variance components include
the parameters of the random effects structure (for lme models), the variance structure,
and the correlation structure. The expected and average forms of the Fisher information matrix
are used in the calculations, and models estimated by full maximum likelihood or
restricted maximum likelihood are supported. The package also includes a function for estimating
standardized mean difference effect sizes (Pustejovsky, Hedges, and Shadish (2014) <DOI:10.3102/1076998614547577>)
based on fitted lme or gls models.
Author: James Pustejovsky [aut] ,
Man Chen [aut, cre]
Maintainer: Man Chen <manchen9005@gmail.com>
Diff between lmeInfo versions 0.1.3 dated 2021-02-02 and 0.2.0 dated 2022-06-15
DESCRIPTION | 14 MD5 | 61 - NAMESPACE | 3 NEWS.md | 8 R/build-variance-matrices.R | 31 R/confidence-interval-functions.R | 2 R/derivatives.R | 37 R/function-checking.R | 40 - R/g_mlm.R | 117 +- R/information-matrices.R | 172 +++- R/matrix-functions.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Information-matrices-for-fitted-LME-models.html | 600 ++++++++++++--- man/CI_g.Rd | 2 man/Fisher_info.Rd | 32 man/extract_varcomp.Rd | 37 man/g_mlm.Rd | 69 + man/varcomp_vcov.Rd | 18 tests/testthat.R | 8 tests/testthat/test-against-merDeriv.R | 4 tests/testthat/test-equivalent-models.R | 2 tests/testthat/test-fixed-sigma-models.R | 2 tests/testthat/test-gls-models.R | 6 tests/testthat/test-meta-analysis-model.R |only tests/testthat/test-multi-model-g_mlm.R |only tests/testthat/test-multivariate-models.R | 186 +++- tests/testthat/test-scdhlm-examples.R | 7 tests/testthat/test-separate-random-effects.R | 11 tests/testthat/test-seperate-variances.R |only tests/testthat/test-three-level-models.R | 2 tests/testthat/test-two-level-models.R | 3 vignettes/references.bib | 4 33 files changed, 1152 insertions(+), 328 deletions(-)
Title: Data Sets for Econometrics
Description: Data sets for econometrics, including political science.
Author: Yves Croissant <yves.croissant@let.ish-lyon.cnrs.fr> and Spencer Graves
Maintainer: Spencer Graves <spencer.graves@effectivedefense.org>
Diff between Ecdat versions 0.3-9 dated 2020-11-03 and 0.4-0 dated 2022-06-15
DESCRIPTION | 10 - MD5 | 334 +++++++++++++++++++------------------- NEWS | 3 README | 2 README.md |only build |only data/Accident.rda |binary data/AccountantsAuditorsPct.rda |binary data/Airline.rda |binary data/Airq.rda |binary data/Benefits.rda |binary data/Bids.rda |binary data/BudgetFood.rda |binary data/BudgetItaly.rda |binary data/BudgetUK.rda |binary data/Bwages.rda |binary data/CPSch3.rda |binary data/CRANpackages.rda |binary data/CRSPday.rda |binary data/Capm.rda |binary data/Car.rda |binary data/Caschool.rda |binary data/Catsup.rda |binary data/Cigar.rda |binary data/Cigarette.rda |binary data/Clothing.rda |binary data/Computers.rda |binary data/Consumption.rda |binary data/Cracker.rda |binary data/Crime.rda |binary data/DM.rda |binary data/Doctor.rda |binary data/DoctorAUS.rda |binary data/DoctorContacts.rda |binary data/Earnings.rda |binary data/Fair.rda |binary data/FinancialCrisisFiles.rda |binary data/Fishing.rda |binary data/Forward.rda |binary data/Garch.rda |binary data/Gasoline.rda |binary data/Griliches.rda |binary data/HC.rda |binary data/HHSCyberSecurityBreaches.rda |binary data/HI.rda |binary data/Hdma.rda |binary data/Heating.rda |binary data/Hedonic.rda |binary data/Hmda.rda |binary data/Housing.rda |binary data/Hstarts.rda |binary data/Icecream.rda |binary data/IncomeUK.rda |binary data/Irates.rda |binary data/Journals.rda |binary data/Ketchup.rda |binary data/Klein.rda |binary data/LT.rda |binary data/LaborSupply.rda |binary data/Labour.rda |binary data/Longley.rda |binary data/MCAS.rda |binary data/MW.rda |binary data/Macrodat.rda |binary data/Males.rda |binary data/ManufCost.rda |binary data/MedExp.rda |binary data/Metal.rda |binary data/Mishkin.rda |binary data/ModeChoice.rda |binary data/Mofa.rda |binary data/Money.rda |binary data/MoneyUS.rda |binary data/Mpyr.rda |binary data/Mroz.rda |binary data/MunExp.rda |binary data/NaturalPark.rda |binary data/OCC1950.rda |binary data/OFP.rda |binary data/Oil.rda |binary data/PE.rda |binary data/PPP.rda |binary data/PSID.rda |binary data/Participation.rda |binary data/PatentsHGH.rda |binary data/PatentsRD.rda |binary data/Pound.rda |binary data/Produc.rda |binary data/RetSchool.rda |binary data/SP500.rda |binary data/Schooling.rda |binary data/Solow.rda |binary data/Somerville.rda |binary data/Star.rda |binary data/Strike.rda |binary data/StrikeNb.rda |binary data/SumHes.rda |binary data/Tbrate.rda |binary data/Tobacco.rda |binary data/Train.rda |binary data/TranspEq.rda |binary data/Treatment.rda |binary data/Tuna.rda |binary data/USFinanceIndustry.rda |binary data/USGDPpresidents.rda |binary data/USPS.rda |only data/USclassifiedDocuments.rda |binary data/USincarcerations.rda |only data/USnewspapers.rda |only data/UStaxWords.rda |binary data/UnempDur.rda |binary data/Unemployment.rda |binary data/VietNamH.rda |binary data/VietNamI.rda |binary data/Wages.rda |binary data/Wages1.rda |binary data/Workinghours.rda |binary data/Yogurt.rda |binary data/bankingCrises.rda |binary data/breaches.rda |binary data/coolingFromNuclearWar.rda |binary data/incomeInequality.rda |binary data/nkill.byCountryYr.rda |binary data/nonEnglishNames.rda |binary data/nuclearWeaponStates.rda |binary data/terrorism.rda |binary inst/WORDLIST | 3 man/Accident.Rd | 2 man/AccountantsAuditorsPct.Rd | 7 man/Airline.Rd | 4 man/Benefits.Rd | 2 man/CRSPday.Rd | 4 man/CRSPmon.Rd | 4 man/Diamond.Rd | 2 man/DoctorContacts.Rd | 2 man/Electricity.Rd | 4 man/Fair.Rd | 4 man/Grunfeld.Rd | 2 man/HC.Rd | 2 man/Hedonic.Rd | 2 man/Index.Econometrics.Rd | 4 man/Index.Economics.Rd | 4 man/Index.Observations.Rd | 4 man/Index.Source.Rd | 10 - man/Index.Time.Series.Rd | 2 man/Klein.Rd | 2 man/Longley.Rd | 2 man/ManufCost.Rd | 2 man/MedExp.Rd | 2 man/Metal.Rd | 2 man/Mode.Rd | 2 man/ModeChoice.Rd | 2 man/Mroz.Rd | 2 man/MunExp.Rd | 2 man/Nerlove.Rd | 4 man/OCC1950.Rd | 4 man/OFP.Rd | 2 man/PE.Rd | 4 man/PatentsHGH.Rd | 2 man/PatentsRD.Rd | 6 man/SP500.Rd | 4 man/Solow.Rd | 2 man/Strike.Rd | 2 man/TranspEq.Rd | 2 man/USGDPpresidents.Rd | 177 ++++++++++++++++---- man/USPS.Rd |only man/USincarcerations.Rd |only man/USnewspapers.Rd |only man/UnempDur.Rd | 2 man/Wages1.Rd | 2 man/breaches.Rd | 2 man/nuclearWeaponStates.Rd | 16 - 172 files changed, 397 insertions(+), 269 deletions(-)
Title: moDel Agnostic Language for Exploration and eXplanation
Description: Any unverified black box model is the path to failure. Opaqueness leads to distrust.
Distrust leads to ignoration. Ignoration leads to rejection.
DALEX package xrays any model and helps to explore and explain its behaviour.
Machine Learning (ML) models are widely used and have various applications in classification
or regression. Models created with boosting, bagging, stacking or similar techniques are often
used due to their high performance. But such black-box models usually lack direct interpretability.
DALEX package contains various methods that help to understand the link between input variables
and model output. Implemented methods help to explore the model on the level of a single instance
as well as a level of the whole dataset.
All model explainers are model agnostic and can be compared across different models.
DALEX package is the cornerstone for 'DrWhy.AI' universe of packages for visual model exploration.
Find more details in (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] ,
Szymon Maksymiuk [aut] ,
Hubert Baniecki [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between DALEX versions 2.4.1 dated 2022-05-21 and 2.4.2 dated 2022-06-15
DESCRIPTION | 8 +++--- MD5 | 14 ++++++++-- R/data_covid.R |only R/data_happiness.R |only R/misc_loss_functions.R | 61 +++++++++++++++-------------------------------- data/covid_spring.rda |only data/covid_summer.rda |only data/happiness_test.rda |only data/happiness_train.rda |only man/covid.Rd |only man/happiness.Rd |only man/loss_yardstick.Rd | 45 ++++++---------------------------- 12 files changed, 43 insertions(+), 85 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] ,
Gregor Gorjanc [ctb] ,
John Hickey [ctb] ,
Daniel Money [ctb] ,
David Wilson [ctb],
Thiago Oliveira [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 1.1.2 dated 2022-02-17 and 1.2 dated 2022-06-15
AlphaSimR-1.1.2/AlphaSimR/R/OCS.R |only AlphaSimR-1.1.2/AlphaSimR/cleanup |only AlphaSimR-1.1.2/AlphaSimR/configure |only AlphaSimR-1.1.2/AlphaSimR/configure.ac |only AlphaSimR-1.1.2/AlphaSimR/src/Makevars.in |only AlphaSimR-1.1.2/AlphaSimR/src/OCS.cpp |only AlphaSimR-1.2/AlphaSimR/DESCRIPTION | 19 AlphaSimR-1.2/AlphaSimR/MD5 | 302 - AlphaSimR-1.2/AlphaSimR/NAMESPACE | 13 AlphaSimR-1.2/AlphaSimR/NEWS | 14 AlphaSimR-1.2/AlphaSimR/R/AlphaSimR.R | 8 AlphaSimR-1.2/AlphaSimR/R/Class-HybridPop.R | 3 AlphaSimR-1.2/AlphaSimR/R/Class-LociMap.R | 16 AlphaSimR-1.2/AlphaSimR/R/Class-Pop.R | 133 AlphaSimR-1.2/AlphaSimR/R/Class-RRsol.R | 1 AlphaSimR-1.2/AlphaSimR/R/Class-SimParam.R | 301 + AlphaSimR-1.2/AlphaSimR/R/GS.R | 236 + AlphaSimR-1.2/AlphaSimR/R/crossing.R | 153 AlphaSimR-1.2/AlphaSimR/R/founderPop.R | 9 AlphaSimR-1.2/AlphaSimR/R/hybrids.R | 4 AlphaSimR-1.2/AlphaSimR/R/importData.R |only AlphaSimR-1.2/AlphaSimR/R/mergePops.R | 4 AlphaSimR-1.2/AlphaSimR/R/misc.R | 258 + AlphaSimR-1.2/AlphaSimR/R/phenotypes.R | 5 AlphaSimR-1.2/AlphaSimR/R/polyploids.R | 157 AlphaSimR-1.2/AlphaSimR/R/popSummary.R | 117 AlphaSimR-1.2/AlphaSimR/R/pullGeno.R | 396 +- AlphaSimR-1.2/AlphaSimR/R/selection.R | 22 AlphaSimR-1.2/AlphaSimR/build/vignette.rds |binary AlphaSimR-1.2/AlphaSimR/inst/doc/intro.html | 374 + AlphaSimR-1.2/AlphaSimR/inst/doc/traits.pdf |binary AlphaSimR-1.2/AlphaSimR/man/AlphaSimR-package.Rd | 91 AlphaSimR-1.2/AlphaSimR/man/HybridPop-class.Rd | 106 AlphaSimR-1.2/AlphaSimR/man/LociMap-class.Rd | 40 AlphaSimR-1.2/AlphaSimR/man/MapPop-class.Rd | 86 AlphaSimR-1.2/AlphaSimR/man/MegaPop-class.Rd | 86 AlphaSimR-1.2/AlphaSimR/man/NamedMapPop-class.Rd | 80 AlphaSimR-1.2/AlphaSimR/man/Pop-class.Rd | 154 AlphaSimR-1.2/AlphaSimR/man/RRBLUP.Rd | 138 AlphaSimR-1.2/AlphaSimR/man/RRBLUP2.Rd | 230 - AlphaSimR-1.2/AlphaSimR/man/RRBLUPMemUse.Rd | 56 AlphaSimR-1.2/AlphaSimR/man/RRBLUP_D.Rd | 140 AlphaSimR-1.2/AlphaSimR/man/RRBLUP_D2.Rd | 184 AlphaSimR-1.2/AlphaSimR/man/RRBLUP_GCA.Rd | 142 AlphaSimR-1.2/AlphaSimR/man/RRBLUP_GCA2.Rd | 182 AlphaSimR-1.2/AlphaSimR/man/RRBLUP_SCA.Rd | 140 AlphaSimR-1.2/AlphaSimR/man/RRBLUP_SCA2.Rd | 190 AlphaSimR-1.2/AlphaSimR/man/RRsol-class.Rd | 52 AlphaSimR-1.2/AlphaSimR/man/RawPop-class.Rd | 106 AlphaSimR-1.2/AlphaSimR/man/SimParam.Rd | 3312 ++++++++--------- AlphaSimR-1.2/AlphaSimR/man/TraitA-class.Rd | 36 AlphaSimR-1.2/AlphaSimR/man/TraitA2-class.Rd | 34 AlphaSimR-1.2/AlphaSimR/man/TraitA2D-class.Rd | 32 AlphaSimR-1.2/AlphaSimR/man/TraitAD-class.Rd | 32 AlphaSimR-1.2/AlphaSimR/man/TraitADE-class.Rd | 32 AlphaSimR-1.2/AlphaSimR/man/TraitADEG-class.Rd | 40 AlphaSimR-1.2/AlphaSimR/man/TraitADG-class.Rd | 40 AlphaSimR-1.2/AlphaSimR/man/TraitAE-class.Rd | 32 AlphaSimR-1.2/AlphaSimR/man/TraitAEG-class.Rd | 40 AlphaSimR-1.2/AlphaSimR/man/TraitAG-class.Rd | 40 AlphaSimR-1.2/AlphaSimR/man/aa.Rd | 62 AlphaSimR-1.2/AlphaSimR/man/attrition.Rd | 72 AlphaSimR-1.2/AlphaSimR/man/bv.Rd | 60 AlphaSimR-1.2/AlphaSimR/man/cChr.Rd | 54 AlphaSimR-1.2/AlphaSimR/man/calcGCA.Rd | 72 AlphaSimR-1.2/AlphaSimR/man/dd.Rd | 60 AlphaSimR-1.2/AlphaSimR/man/dot-newPop.Rd |only AlphaSimR-1.2/AlphaSimR/man/doubleGenome.Rd | 78 AlphaSimR-1.2/AlphaSimR/man/ebv.Rd | 58 AlphaSimR-1.2/AlphaSimR/man/editGenome.Rd | 96 AlphaSimR-1.2/AlphaSimR/man/editGenomeTopQtl.Rd | 88 AlphaSimR-1.2/AlphaSimR/man/fastRRBLUP.Rd | 154 AlphaSimR-1.2/AlphaSimR/man/genParam.Rd | 128 AlphaSimR-1.2/AlphaSimR/man/genicVarA.Rd | 60 AlphaSimR-1.2/AlphaSimR/man/genicVarAA.Rd | 62 AlphaSimR-1.2/AlphaSimR/man/genicVarD.Rd | 60 AlphaSimR-1.2/AlphaSimR/man/genicVarG.Rd | 60 AlphaSimR-1.2/AlphaSimR/man/getMisc.Rd |only AlphaSimR-1.2/AlphaSimR/man/getNumThreads.Rd | 38 AlphaSimR-1.2/AlphaSimR/man/getQtlMap.Rd | 86 AlphaSimR-1.2/AlphaSimR/man/getSnpMap.Rd | 88 AlphaSimR-1.2/AlphaSimR/man/gv.Rd | 56 AlphaSimR-1.2/AlphaSimR/man/hybridCross.Rd | 100 AlphaSimR-1.2/AlphaSimR/man/importGenMap.Rd |only AlphaSimR-1.2/AlphaSimR/man/importHaplo.Rd |only AlphaSimR-1.2/AlphaSimR/man/importInbredGeno.Rd |only AlphaSimR-1.2/AlphaSimR/man/isFemale.Rd |only AlphaSimR-1.2/AlphaSimR/man/makeCross.Rd | 82 AlphaSimR-1.2/AlphaSimR/man/makeCross2.Rd | 86 AlphaSimR-1.2/AlphaSimR/man/makeDH.Rd | 84 AlphaSimR-1.2/AlphaSimR/man/meanG.Rd | 56 AlphaSimR-1.2/AlphaSimR/man/meanP.Rd | 56 AlphaSimR-1.2/AlphaSimR/man/mergeGenome.Rd | 84 AlphaSimR-1.2/AlphaSimR/man/mergePops.Rd | 64 AlphaSimR-1.2/AlphaSimR/man/mutate.Rd | 92 AlphaSimR-1.2/AlphaSimR/man/nInd.Rd | 56 AlphaSimR-1.2/AlphaSimR/man/newMapPop.Rd | 103 AlphaSimR-1.2/AlphaSimR/man/newMegaPop.Rd | 66 AlphaSimR-1.2/AlphaSimR/man/newPop.Rd | 81 AlphaSimR-1.2/AlphaSimR/man/pedigreeCross.Rd | 154 AlphaSimR-1.2/AlphaSimR/man/pheno.Rd | 56 AlphaSimR-1.2/AlphaSimR/man/popVar.Rd | 40 AlphaSimR-1.2/AlphaSimR/man/pullIbdHaplo.Rd | 80 AlphaSimR-1.2/AlphaSimR/man/pullMarkerGeno.Rd |only AlphaSimR-1.2/AlphaSimR/man/pullMarkerHaplo.Rd |only AlphaSimR-1.2/AlphaSimR/man/pullQtlGeno.Rd | 80 AlphaSimR-1.2/AlphaSimR/man/pullQtlHaplo.Rd | 95 AlphaSimR-1.2/AlphaSimR/man/pullSegSiteGeno.Rd | 76 AlphaSimR-1.2/AlphaSimR/man/pullSegSiteHaplo.Rd | 90 AlphaSimR-1.2/AlphaSimR/man/pullSnpGeno.Rd | 80 AlphaSimR-1.2/AlphaSimR/man/pullSnpHaplo.Rd | 95 AlphaSimR-1.2/AlphaSimR/man/quickHaplo.Rd | 70 AlphaSimR-1.2/AlphaSimR/man/randCross.Rd | 106 AlphaSimR-1.2/AlphaSimR/man/randCross2.Rd | 124 AlphaSimR-1.2/AlphaSimR/man/reduceGenome.Rd | 108 AlphaSimR-1.2/AlphaSimR/man/resetPop.Rd | 72 AlphaSimR-1.2/AlphaSimR/man/runMacs.Rd | 124 AlphaSimR-1.2/AlphaSimR/man/runMacs2.Rd | 154 AlphaSimR-1.2/AlphaSimR/man/sampleHaplo.Rd | 66 AlphaSimR-1.2/AlphaSimR/man/selIndex.Rd | 90 AlphaSimR-1.2/AlphaSimR/man/selInt.Rd | 36 AlphaSimR-1.2/AlphaSimR/man/selectCross.Rd | 174 AlphaSimR-1.2/AlphaSimR/man/selectFam.Rd | 164 AlphaSimR-1.2/AlphaSimR/man/selectInd.Rd | 148 AlphaSimR-1.2/AlphaSimR/man/selectOP.Rd | 154 AlphaSimR-1.2/AlphaSimR/man/selectWithinFam.Rd | 166 AlphaSimR-1.2/AlphaSimR/man/self.Rd | 82 AlphaSimR-1.2/AlphaSimR/man/setEBV.Rd | 132 AlphaSimR-1.2/AlphaSimR/man/setMisc.Rd |only AlphaSimR-1.2/AlphaSimR/man/setPheno.Rd | 190 AlphaSimR-1.2/AlphaSimR/man/setPhenoGCA.Rd | 208 - AlphaSimR-1.2/AlphaSimR/man/setPhenoProgTest.Rd | 158 AlphaSimR-1.2/AlphaSimR/man/smithHazel.Rd | 60 AlphaSimR-1.2/AlphaSimR/man/solveMKM.Rd | 48 AlphaSimR-1.2/AlphaSimR/man/solveMVM.Rd | 48 AlphaSimR-1.2/AlphaSimR/man/solveRRBLUP.Rd | 36 AlphaSimR-1.2/AlphaSimR/man/solveRRBLUPMK.Rd | 40 AlphaSimR-1.2/AlphaSimR/man/solveRRBLUPMV.Rd | 44 AlphaSimR-1.2/AlphaSimR/man/solveRRBLUP_EM.Rd | 60 AlphaSimR-1.2/AlphaSimR/man/solveRRBLUP_EM2.Rd | 68 AlphaSimR-1.2/AlphaSimR/man/solveRRBLUP_EM3.Rd | 76 AlphaSimR-1.2/AlphaSimR/man/solveUVM.Rd | 40 AlphaSimR-1.2/AlphaSimR/man/transMat.Rd |only AlphaSimR-1.2/AlphaSimR/man/usefulness.Rd | 122 AlphaSimR-1.2/AlphaSimR/man/varA.Rd | 60 AlphaSimR-1.2/AlphaSimR/man/varAA.Rd | 62 AlphaSimR-1.2/AlphaSimR/man/varD.Rd | 60 AlphaSimR-1.2/AlphaSimR/man/varG.Rd | 56 AlphaSimR-1.2/AlphaSimR/man/varP.Rd | 56 AlphaSimR-1.2/AlphaSimR/man/writePlink.Rd | 130 AlphaSimR-1.2/AlphaSimR/man/writeRecords.Rd | 80 AlphaSimR-1.2/AlphaSimR/src/Makevars |only AlphaSimR-1.2/AlphaSimR/src/Makevars.win | 3 AlphaSimR-1.2/AlphaSimR/src/algorithm.cpp | 2 AlphaSimR-1.2/AlphaSimR/src/datastructures.cpp | 6 AlphaSimR-1.2/AlphaSimR/src/getGeno.cpp | 60 AlphaSimR-1.2/AlphaSimR/src/getHybridGv.cpp | 4 AlphaSimR-1.2/AlphaSimR/src/ibd.cpp | 18 AlphaSimR-1.2/AlphaSimR/src/meiosis.cpp | 16 AlphaSimR-1.2/AlphaSimR/tests/testthat/test-addTrait.R | 66 AlphaSimR-1.2/AlphaSimR/tests/testthat/test-crossing.R | 20 161 files changed, 8637 insertions(+), 6996 deletions(-)
Title: Eigenvectors from Eigenvalues Sparse Principal Component
Analysis (EESPCA)
Description: Contains logic for computing sparse principal components via the EESPCA method,
which is based on an approximation of the eigenvector/eigenvalue identity.
Includes logic to support execution of the TPower and rifle sparse PCA methods,
as well as logic to estimate the sparsity parameters used by EESPCA, TPower and rifle
via cross-validation to minimize the out-of-sample reconstruction error.
H. Robert Frost (2021) <doi:10.1080/10618600.2021.1987254>.
Author: H. Robert Frost
Maintainer: H. Robert Frost <rob.frost@dartmouth.edu>
Diff between EESPCA versions 0.6.0 dated 2022-05-16 and 0.7.0 dated 2022-06-15
DESCRIPTION | 6 ++--- MD5 | 10 ++++---- R/EESPCA.R | 50 +++++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/EESPCA_Example.pdf |binary man/EESPCA-package.Rd | 4 +-- 6 files changed, 37 insertions(+), 33 deletions(-)
Title: R Speaks 'Monolix'
Description: Provides methods for model building and model evaluation of mixed effects models using
'Monolix' <https://monolix.lixoft.com>. 'Monolix' is a software tool for nonlinear mixed effects
modeling that must have been installed in order to use 'Rsmlx'.
Among other tasks, 'Rsmlx' provides a powerful tool for automatic PK model building, performs
statistical tests for model assessment, bootstrap simulation and likelihood profiling for
computing confidence intervals. 'Rsmlx' also proposes several automatic covariate search methods for
mixed effects models.
Author: Marc Lavielle [aut, cre],
Jonathan Chauvin [ctb],
Clemence Pinaud [ctb]
Maintainer: Marc Lavielle <Marc.Lavielle@inria.fr>
Diff between Rsmlx versions 4.0.2 dated 2022-03-04 and 5.0.1 dated 2022-06-15
DESCRIPTION | 10 MD5 | 44 - NAMESPACE | 14 R/RsmlxTools.R | 112 ++ R/bootstrap.R | 1462 ++++++++++++++++++------------------ R/buildAll.R | 172 +++- R/buildVar.R | 376 ++++++--- R/buildmlx.R | 696 +++++++++++------ R/confintmlx.R | 4 R/correlationModelSelection.R | 107 +- R/covariateModelSelection.R | 322 +++++++ R/errorModelSelection.R | 34 R/newConnectors.R | 44 - R/pkbuild.R | 183 +++- R/pkpopini.R | 547 ------------- R/readDatamlx.R |only R/testmlx.R | 117 ++ R/writeDataSmlx.R | 634 +++++++-------- man/buildAll.Rd | 275 +++--- man/buildVar.Rd | 169 ++-- man/buildmlx.Rd | 19 man/getEstimatedCovarianceMatrix.Rd | 46 - man/pkbuild.Rd | 6 man/readDatamlx.Rd |only 24 files changed, 2968 insertions(+), 2425 deletions(-)
Title: A Toolbox for Conditional Inference Trees and Random Forests
Description: Additions to 'party' and 'partykit' packages : tools for the interpretation of forests (surrogate trees, prototypes, etc.), feature selection (see Gregorutti et al (2017) <arXiv:1310.5726>, Hapfelmeier and Ulm (2013) <doi:10.1016/j.csda.2012.09.020>, Altmann et al (2010) <doi:10.1093/bioinformatics/btq134>) and parallelized versions of conditional forest and variable importance functions. Also modules and a shiny app for conditional inference trees.
Author: Nicolas Robette
Maintainer: Nicolas Robette <nicolas.robette@uvsq.fr>
Diff between moreparty versions 0.2.1 dated 2021-07-14 and 0.3 dated 2022-06-15
DESCRIPTION | 13 MD5 | 40 - NAMESPACE | 55 ++ NEWS.md | 25 - R/ALT.R | 8 R/BivariateAssoc.R | 15 R/EasyTreeVarImp.R |only R/GetSplitStats.R | 12 R/HAPF.R | 8 R/NRFE.R | 12 R/NiceTreePlot.R |only R/RFE.R | 12 R/ctree-module.R |only R/ictree.R |only README.md | 7 build/vignette.rds |binary inst/doc/Titanic_example.R | 3 inst/doc/Titanic_example.Rmd | 3 inst/doc/Titanic_example.html | 1049 +++++++++++++++++++++++++++++++++++++----- man/EasyTreeVarImp.Rd |only man/GetSplitStats.Rd | 2 man/NiceTreePlot.Rd |only man/ctree-module.Rd |only man/ictree.Rd |only vignettes/Titanic_example.Rmd | 3 25 files changed, 1098 insertions(+), 169 deletions(-)
Title: Recurrent Event Regression
Description: A comprehensive collection of practical and easy-to-use tools for regression analysis of recurrent events, with or without the presence of a (possibly) informative terminal event. The modeling framework is based on a joint frailty scale-change model, that includes models described in Wang et al. (2001) <doi:10.1198/016214501753209031>, Huang and Wang (2004) <doi:10.1198/016214504000001033>, Xu et al. (2017) <doi:10.1080/01621459.2016.1173557>, and Xu et al. (2019) <doi:10.5705/SS.202018.0224> as special cases. The implemented estimating procedure does not require any parametric assumption on the frailty distribution. The package also allows the users to specify different model forms for both the recurrent event process and the terminal event.
Author: Sy Han Chiou [aut, cre],
Chiung-Yu Huang [aut]
Maintainer: Sy Han (Steven) Chiou <schiou@utdallas.edu>
Diff between reReg versions 1.4.3 dated 2022-04-19 and 1.4.4 dated 2022-06-15
DESCRIPTION | 6 MD5 | 22 - NEWS.md | 5 R/plot.R | 371 +++++++++++++--------- R/reReg.R | 22 - R/regGeneral.R | 759 +++++++++++++++++++++++----------------------- R/summary.R | 394 ++++++++++++----------- man/plotEvents.Rd | 2 man/plotEvents.control.Rd | 42 ++ man/reReg.Rd | 2 src/RcppExports.cpp | 15 src/regRec.cpp | 358 +++++++++++++++------ 12 files changed, 1134 insertions(+), 864 deletions(-)
More information about germinationmetrics at CRAN
Permanent link
Title: Functions for Wayne W. Daniel's Biostatistics, Tenth Edition
Description: Functions to accompany Wayne W. Daniel's Biostatistics: A Foundation for Analysis in the Health Sciences, Tenth Edition.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DanielBiostatistics10th versions 0.1.5 dated 2022-06-07 and 0.1.6 dated 2022-06-15
DESCRIPTION | 11 MD5 | 98 + NAMESPACE | 15 NEWS.md | 3 R/0S4_Boolean.R |only R/0S4_freqs.R |only R/DanielBiostatistics10th.R | 16 R/chp09.R |only R/chp11.R |only R/chp12.R | 18 R/chp2.R | 45 R/chp3.R | 25 R/chp4.R | 21 R/chp5.6.7.R | 2 R/chp7.power.R | 49 inst/example/Chapter1.R | 28 inst/example/Chapter10.R | 32 inst/example/Chapter11.R | 162 -- inst/example/Chapter12.R | 24 inst/example/Chapter13.R | 17 inst/example/Chapter14.R | 8 inst/example/Chapter2.R | 8 inst/example/Chapter3.R | 12 inst/example/Chapter4.R | 8 inst/example/Chapter5.6.7.R | 11 inst/example/Chapter7.power.R | 22 inst/example/Chapter8.R | 49 inst/example/Chapter9.R | 70 - inst/example/LDS_C10.R | 2 inst/example/LDS_C12.R | 15 inst/extdata/EXA_C07_S07_01.csv |only inst/extdata/EXA_C08_S02_01.csv | 199 ++- inst/extdata/EXA_C09_S03_01_corrected.csv |only inst/extdata/EXA_C11_S01_01.csv |only inst/extdata/EXA_C11_S01_02.csv |only inst/extdata/EXA_C11_S05_01.csv |only inst/extdata/EXR_C08_S04_03.csv | 98 - inst/extdata/EXR_C11_S05_01.csv |only inst/extdata/EXR_C11_S05_02.csv |only inst/extdata/EXR_C13_S05_01.csv |only inst/extdata/EXR_C13_S05_02.csv |only inst/extdata/LDS_C12_SMOKING.csv | 1702 +++++++++++++++++++++--------- inst/extdata/REV_C02_16.csv | 108 - inst/extdata/REV_C07_18.csv |only man/BooleanRisk-class.Rd |only man/BooleanTest-class.Rd |only man/Chapter01.Rd | 28 man/Chapter02.Rd | 12 man/Chapter03.Rd | 14 man/Chapter04.Rd | 10 man/Chapter05to07.Rd | 11 man/Chapter07_power.Rd | 24 man/Chapter09.Rd |only man/Chapter11.Rd |only man/Chapter12.Rd | 26 man/DanielBiostatistics10th-package.Rd | 9 man/binom2pois.Rd | 2 man/freqs-class.Rd |only man/show-BooleanRisk-method.Rd |only man/show-BooleanTest-method.Rd |only man/show-freqs-method.Rd |only 61 files changed, 1757 insertions(+), 1257 deletions(-)
More information about DanielBiostatistics10th at CRAN
Permanent link
Title: Data from Access to Information Law
Description: Downloads the public data available from the Brazilian Access to Information Law and and performs a search on information requests and appeals made since 2015.
Author: Igor Laltuf [aut, cre]
Maintainer: Igor Laltuf <igorlaltuf@gmail.com>
Diff between dail versions 1.3 dated 2022-04-01 and 1.3.1 dated 2022-06-15
DESCRIPTION | 8 ++--- MD5 | 6 ++-- R/appeals.R | 16 ++++------ R/requests.R | 86 ++++++++++++++++++++++++++--------------------------------- 4 files changed, 53 insertions(+), 63 deletions(-)
Title: Time Series and Econometric Modeling
Description: Time series analysis, (dis)aggregation and manipulation, e.g. time series extension, merge, projection, lag, lead, delta, moving and cumulative average and product, selection by index, date and year-period, conversion to daily, monthly, quarterly, (semi)annually. Simultaneous equation models definition, estimation, simulation and forecasting with coefficient restrictions, error autocorrelation, exogenization, add-factors, impact and interim multipliers analysis, conditional equation evaluation, endogenous targeting and model renormalization, structural stability, stochastic simulation and forecast, optimal control.
Author: Andrea Luciani [aut, cre] ,
Roberto Stok [aut],
Bank of Italy [cph]
Maintainer: Andrea Luciani <andrea.luciani@bancaditalia.it>
Diff between bimets versions 2.1.0 dated 2022-04-02 and 2.1.1 dated 2022-06-15
DESCRIPTION | 8 +- MD5 | 80 ++++++++++++++--------------- NEWS.md | 6 ++ R/bimets_model_functions.R | 14 +++-- R/bimets_ts_functions.R | 2 build/vignette.rds |binary data/bimets_12F_YP2D__.RData |binary data/bimets_12L_YP2D__.RData |binary data/bimets_12_D2YP__.RData |binary data/bimets_1F_YP2D__.RData |binary data/bimets_1L_YP2D__.RData |binary data/bimets_1_D2YP__.RData |binary data/bimets_24F_YP2D__.RData |binary data/bimets_24L_YP2D__.RData |binary data/bimets_24_D2YP__.RData |binary data/bimets_2F_YP2D__.RData |binary data/bimets_2L_YP2D__.RData |binary data/bimets_2_D2YP__.RData |binary data/bimets_366_D2YP__.RData |binary data/bimets_366_YP2D__.RData |binary data/bimets_36F_YP2D__.RData |binary data/bimets_36L_YP2D__.RData |binary data/bimets_36_D2YP__.RData |binary data/bimets_3F_YP2D__.RData |binary data/bimets_3L_YP2D__.RData |binary data/bimets_3_D2YP__.RData |binary data/bimets_4F_YP2D__.RData |binary data/bimets_4L_YP2D__.RData |binary data/bimets_4_D2YP__.RData |binary data/bimets_53F_YP2D__.RData |binary data/bimets_53L_YP2D__.RData |binary data/bimets_53_D2YP__.RData |binary data/bimets_static_G90__.RData |binary data/bimets_static_TD90__.RData |binary data/bimets_static_startYear___.RData |binary data/bimets_static_totalLength___.RData |binary inst/doc/bimets.R | 88 ++++++++++++++++---------------- inst/doc/bimets.Rnw | 7 ++ inst/doc/bimets.pdf |binary man/RENORM.Rd | 2 vignettes/bimets.Rnw | 7 ++ 41 files changed, 117 insertions(+), 97 deletions(-)
Title: Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It provides various routines for importing bibliographic data from 'SCOPUS',
'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions'
(<https://www.dimensions.ai/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>),
and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut],
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 3.2.1 dated 2022-02-21 and 4.0.0 dated 2022-06-15
DESCRIPTION | 12 MD5 | 86 NAMESPACE | 8 NEWS | 11 R/authorProdOverTime.R | 64 R/biblioAnalysis.R | 9 R/biblioshiny.R | 6 R/bibtag.R | 29 R/bradford.R | 12 R/cocMatrix.R | 41 R/conceptualStructure.R | 52 R/couplingMap.R | 9 R/csvLens2df.R | 1 R/dimensions2df.R | 50 R/dominance.R | 2 R/fieldByYear.R | 13 R/keywordGrowth.R | 2 R/lotka.R | 6 R/networkPlot.R | 33 R/networkStat.R | 2 R/plot.bibliometrix.R | 125 R/retrievalByAuthorID.R | 370 +- R/rpys.R | 16 R/summary.bibliometrix.R | 28 R/summary.bibliometrix_netstat.R | 2 R/tableTag.R | 10 R/termExtraction.R | 78 R/thematicEvolution.R | 5 R/thematicMap.R | 236 + R/zzz.R | 9 build/partial.rdb |binary data/bibtag.rda |binary data/countries.rda |binary data/logo.rda |binary data/stopwords.rda |binary inst/biblioshiny/server.R | 5213 +++++++++++++++++++++++++++------------ inst/biblioshiny/ui.R | 4892 +++++++++--------------------------- inst/biblioshiny/utils.R |only inst/biblioshiny/www/logo.jpg |binary inst/biblioshiny/www/logo2.jpg |only man/biblioAnalysis.Rd | 2 man/bibtag.Rd | 3 man/networkPlot.Rd | 4 man/thematicEvolution.Rd | 5 man/thematicMap.Rd | 5 45 files changed, 5829 insertions(+), 5622 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: Jose Pinheiro [aut] ,
Douglas Bates [aut] ,
Saikat DebRoy [ctb] ,
Deepayan Sarkar [ctb] ,
EISPACK authors [ctb] ,
Siem Heisterkamp [ctb] ,
Bert Van Willigen [ctb] ,
Johannes Ranke [ctb] ),
R Core Team [aut, cre]
Maintainer: R Core Team <R-core@R-project.org>
Diff between nlme versions 3.1-157 dated 2022-03-25 and 3.1-158 dated 2022-06-15
ChangeLog | 9 ++++++++- DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/lme.R | 3 +-- R/nlsList.R | 2 +- man/Soybean.Rd | 4 ++-- man/anova.gls.Rd | 12 ++++++------ tests/scoping.R | 5 ++--- 8 files changed, 31 insertions(+), 26 deletions(-)
Title: A Fast and Light Package to Compute Polygenic Risk Scores
Description: Quickly computes polygenic scores from GWAS summary statistics of either case-control or quantitative traits, without LD matrix computation or parameter tuning. Reales,G., Vigorito, E., Kelemen,M., Wallace,C. (2021) <doi:10.1101/2020.07.24.220392> "RápidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset".
Author: Guillermo Reales [aut, cre] ,
Chris Wallace [aut] ,
Olly Burren [ctb]
Maintainer: Guillermo Reales <gr440@cam.ac.uk>
Diff between RapidoPGS versions 2.1.0 dated 2021-06-17 and 2.2.0 dated 2022-06-15
DESCRIPTION | 8 MD5 | 33 +- NEWS.md | 31 ++ R/data.R | 8 R/rapfunc.R | 25 - README.md | 35 -- build/vignette.rds |binary data/EUR_ld.blocks38.RData |binary inst/CITATION |only inst/doc/Computing_RapidoPGSmulti.R | 3 inst/doc/Computing_RapidoPGSmulti.Rmd | 15 - inst/doc/Computing_RapidoPGSmulti.html | 382 ++++++++++++++++++++++--- inst/doc/Computing_RapidoPGSsingle.R | 3 inst/doc/Computing_RapidoPGSsingle.Rmd | 12 inst/doc/Computing_RapidoPGSsingle.html | 472 +++++++++++++++++++++++++------- man/EUR_ld.blocks38.Rd | 8 vignettes/Computing_RapidoPGSmulti.Rmd | 15 - vignettes/Computing_RapidoPGSsingle.Rmd | 12 18 files changed, 832 insertions(+), 230 deletions(-)
Title: Finds the Inflection Point of a Curve
Description: Implementation of methods Extremum Surface Estimator (ESE) and
Extremum Distance Estimator (EDE) to identify the inflection point of a curve .
Christopoulos, DT (2014) <doi:10.48550/arXiv.1206.5478> .
Christopoulos, DT (2016) <https://veltech.edu.in/wp-content/uploads/2016/04/Paper-04-2016.pdf> .
Christopoulos, DT (2016) <doi:10.2139/ssrn.3043076> .
Author: Demetris T. Christopoulos
Maintainer: Demetris T. Christopoulos <dchristop@econ.uoa.gr>
Diff between inflection versions 1.3.5 dated 2019-06-28 and 1.3.6 dated 2022-06-15
DESCRIPTION | 10 MD5 | 40 +- NEWS.md | 6 build/vignette.rds |binary inst/doc/inflection.R | 2 inst/doc/inflection.Rmd | 2 inst/doc/inflection.html | 243 +++++++++------ inst/doc/inflectionDevelopingMethods.R | 8 inst/doc/inflectionDevelopingMethods.Rmd | 2 inst/doc/inflectionDevelopingMethods.html | 407 ++++++++++++++----------- inst/doc/inflectionMissionImpossible.R | 24 - inst/doc/inflectionMissionImpossible.Rmd | 2 inst/doc/inflectionMissionImpossible.html | 473 ++++++++++++++++-------------- man/ede.Rd | 6 man/ese.Rd | 6 man/findipl.Rd | 2 man/findiplist.Rd | 12 man/inflection-package.Rd | 2 vignettes/inflection.Rmd | 2 vignettes/inflectionDevelopingMethods.Rmd | 2 vignettes/inflectionMissionImpossible.Rmd | 2 21 files changed, 715 insertions(+), 538 deletions(-)
Title: Hierarchical and Geographically Weighted Regression
Description: This model divides coefficients into three types,
i.e., local fixed effects, global fixed effects, and random effects (Hu et al., 2022)<doi:10.1177/23998083211063885>.
If data have spatial hierarchical structures (especially are overlapping on some locations),
it is worth trying this model to reach better fitness.
Author: Yigong Hu, Richard Harris, Richard Timmerman
Maintainer: Yigong Hu <yigong.hu@bristol.ac.uk>
Diff between hgwrr versions 0.2-2 dated 2022-05-20 and 0.2-3 dated 2022-06-15
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++++----------- R/hgwr.R | 13 +++++++------ build/partial.rdb |binary configure | 18 +++++++++--------- configure.ac | 2 +- data/datalist | 4 +++- data/multisampling.large.rda |only data/multisampling.rda |binary data/wuhan.hp.rda |only man/hgwr.Rd | 2 +- man/multisampling.Rd | 5 ++--- man/multisampling.large.Rd |only man/print.hgwrm.Rd | 2 +- man/print.summary.hgwrm.Rd | 2 +- man/wuhan.hp.Rd |only 16 files changed, 45 insertions(+), 39 deletions(-)
Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut],
Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>
Diff between rpact versions 3.2.3 dated 2022-03-02 and 3.3.0 dated 2022-06-15
DESCRIPTION | 10 MD5 | 235 NAMESPACE | 2 NEWS.md | 172 R/RcppExports.R | 8 R/class_analysis_dataset.R | 5 R/class_core_parameter_set.R | 21 R/class_core_plot_settings.R | 1330 +-- R/class_design.R | 1708 ++-- R/class_design_plan.R | 3775 +++++----- R/class_design_power_and_asn.R | 519 - R/class_design_set.R | 1537 ++-- R/class_simulation_results.R | 25 R/class_summary.R | 186 R/class_time.R | 20 R/f_analysis_base.R | 44 R/f_analysis_base_means.R | 26 R/f_analysis_base_rates.R | 25 R/f_analysis_base_survival.R | 27 R/f_analysis_enrichment_means.R | 6 R/f_analysis_enrichment_rates.R | 6 R/f_analysis_enrichment_survival.R | 6 R/f_analysis_multiarm_means.R | 6 R/f_analysis_multiarm_rates.R | 6 R/f_analysis_multiarm_survival.R | 6 R/f_analysis_utilities.R | 5 R/f_core_assertions.R | 41 R/f_core_constants.R | 222 R/f_core_output_formats.R | 17 R/f_core_plot.R | 23 R/f_core_utilities.R | 32 R/f_design_fisher_combination_test.R | 18 R/f_design_group_sequential.R | 820 +- R/f_design_sample_size_calculator.R | 28 R/f_design_utilities.R | 34 R/f_parameter_set_utilities.R | 4 R/f_simulation_base_survival.R | 16 R/f_simulation_enrichment.R | 35 R/f_simulation_enrichment_survival.R | 8 R/f_simulation_multiarm_rates.R | 8 R/f_simulation_multiarm_survival.R | 46 R/f_simulation_utilities.R | 14 R/pkgname.R | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/rpact_getting_started.html | 5 man/PowerAndAverageSampleNumberResult.Rd | 2 man/TrialDesign.Rd | 6 man/TrialDesignCharacteristics.Rd | 2 man/TrialDesignFisher.Rd | 2 man/TrialDesignGroupSequential.Rd | 2 man/TrialDesignInverseNormal.Rd | 2 man/TrialDesignPlan.Rd | 6 man/TrialDesignPlanMeans.Rd | 2 man/TrialDesignPlanRates.Rd | 2 man/TrialDesignPlanSurvival.Rd | 2 man/TrialDesignSet.Rd | 2 man/TrialDesignSet_as.data.frame.Rd | 2 man/TrialDesignSet_length.Rd | 2 man/getAnalysisResults.Rd | 75 man/getAvailablePlotTypes.Rd | 1 man/getClosedCombinationTestResults.Rd | 6 man/getDesignCharacteristics.Rd | 1 man/getDesignConditionalDunnett.Rd | 11 man/getDesignFisher.Rd | 1 man/getDesignGroupSequential.Rd | 20 man/getDesignInverseNormal.Rd | 7 man/getDesignSet.Rd | 38 man/getGroupSequentialProbabilities.Rd |only man/getLogLevel.Rd | 1 man/getObjectRCode.Rd | 5 man/getObservedInformationRates.Rd | 1 man/getOutputFormat.Rd | 25 man/getParameterCaption.Rd | 1 man/getParameterName.Rd | 1 man/getPowerAndAverageSampleNumber.Rd | 3 man/getSimulatedRejectionsDelayedResponse.Rd |only man/getSimulationEnrichmentMeans.Rd | 70 man/getSimulationEnrichmentRates.Rd | 27 man/getSimulationEnrichmentSurvival.Rd | 22 man/getSimulationMultiArmMeans.Rd | 4 man/plot.TrialDesign.Rd | 18 man/plot.TrialDesignSet.Rd | 14 man/printCitation.Rd | 1 man/readDataset.Rd | 1 man/rpact.Rd | 2 man/setOutputFormat.Rd | 25 man/sub-TrialDesignSet-method.Rd | 2 man/utilitiesForPiecewiseExponentialDistribution.Rd | 1 src/RcppExports.cpp | 22 src/f_design_fisher_combination_test.cpp | 6 src/f_design_group_sequential.cpp | 500 + src/f_simulation_base_survival.cpp | 5 src/f_utilities.cpp | 22 src/f_utilities.h | 5 tests/testthat/helper-class_analysis_dataset.R | 53 tests/testthat/helper-f_analysis_base_means.R | 74 tests/testthat/helper-f_analysis_base_rates.R | 78 tests/testthat/helper-f_analysis_base_survival.R | 78 tests/testthat/helper-f_core_assertions.R | 80 tests/testthat/helper-f_core_utilities.R | 165 tests/testthat/test-class_analysis_dataset.R | 39 tests/testthat/test-f_analysis_base_rates.R | 11 tests/testthat/test-f_analysis_enrichment_means.R | 20 tests/testthat/test-f_analysis_enrichment_rates.R | 10 tests/testthat/test-f_analysis_enrichment_survival.R | 8 tests/testthat/test-f_analysis_multiarm_means.R | 913 +- tests/testthat/test-f_analysis_multiarm_rates.R | 1284 +-- tests/testthat/test-f_analysis_multiarm_survival.R | 2164 ++--- tests/testthat/test-f_analysis_utilities.R | 18 tests/testthat/test-f_core_utilities.R | 95 tests/testthat/test-f_design_group_sequential.R | 5 tests/testthat/test-f_design_group_sequential_beta_spending.R |only tests/testthat/test-f_design_sample_size_calculator.R | 331 tests/testthat/test-f_parameter_set_utilities.R | 10 tests/testthat/test-f_simulation_base_survival.R | 229 tests/testthat/test-f_simulation_enrichment_means.R | 22 tests/testthat/test-f_simulation_enrichment_rates.R | 35 tests/testthat/test-f_simulation_enrichment_survival.R | 24 tests/testthat/test-f_simulation_multiarm_survival.R | 142 120 files changed, 9858 insertions(+), 8101 deletions(-)
Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Creates styled tables for data presentation. Export to HTML, LaTeX,
RTF, 'Word', 'Excel', and 'PowerPoint'. Simple, modern interface to manipulate
borders, size, position, captions, colours, text styles and number formatting.
Table cells can span multiple rows and/or columns.
Includes a 'huxreg' function for creation of regression tables, and 'quick_*'
one-liners to print data to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 5.4.0 dated 2021-05-14 and 5.5.0 dated 2022-06-15
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huxtable-5.5.0/huxtable/DESCRIPTION | 19 huxtable-5.5.0/huxtable/MD5 | 147 -- huxtable-5.5.0/huxtable/NAMESPACE | 4 huxtable-5.5.0/huxtable/NEWS.md | 19 huxtable-5.5.0/huxtable/R/aaa-utils.R | 12 huxtable-5.5.0/huxtable/R/bookdown.R | 7 huxtable-5.5.0/huxtable/R/clean-contents.R | 14 huxtable-5.5.0/huxtable/R/column-to-header.R |only huxtable-5.5.0/huxtable/R/creation.R | 29 huxtable-5.5.0/huxtable/R/flextable.R | 7 huxtable-5.5.0/huxtable/R/huxreg.R | 9 huxtable-5.5.0/huxtable/R/knitr.R | 13 huxtable-5.5.0/huxtable/R/markdown.R | 3 huxtable-5.5.0/huxtable/R/merge.R | 22 huxtable-5.5.0/huxtable/R/misc.R | 4 huxtable-5.5.0/huxtable/R/number-format-functions.R | 9 huxtable-5.5.0/huxtable/R/package-docs.R | 9 huxtable-5.5.0/huxtable/R/properties-cell.R | 10 huxtable-5.5.0/huxtable/R/screen.R | 29 huxtable-5.5.0/huxtable/R/stripes.R |only huxtable-5.5.0/huxtable/build/vignette.rds |binary huxtable-5.5.0/huxtable/data/jams.rda |binary huxtable-5.5.0/huxtable/inst/doc/design-principles.html | 298 ++++ huxtable-5.5.0/huxtable/inst/doc/huxreg.html | 640 ++++++---- huxtable-5.5.0/huxtable/inst/doc/huxtable.R | 10 huxtable-5.5.0/huxtable/inst/doc/huxtable.Rmd | 24 huxtable-5.5.0/huxtable/inst/doc/huxtable.pdf |only huxtable-5.5.0/huxtable/inst/doc/themes.html | 4 huxtable-5.5.0/huxtable/man/add_footnote.Rd | 4 huxtable-5.5.0/huxtable/man/as_huxtable.Rd | 13 huxtable-5.5.0/huxtable/man/column_to_header.Rd |only huxtable-5.5.0/huxtable/man/fmt_percent.Rd | 4 huxtable-5.5.0/huxtable/man/huxtable-FAQ.Rd | 50 huxtable-5.5.0/huxtable/man/huxtable-news.Rd | 86 + huxtable-5.5.0/huxtable/man/huxtable-package.Rd | 18 huxtable-5.5.0/huxtable/man/mapping-functions.Rd | 24 huxtable-5.5.0/huxtable/man/merge_across.Rd | 9 huxtable-5.5.0/huxtable/man/merge_cells.Rd | 13 huxtable-5.5.0/huxtable/man/merge_repeated_rows.Rd | 9 huxtable-5.5.0/huxtable/man/number_format.Rd | 4 huxtable-5.5.0/huxtable/man/spans.Rd | 9 huxtable-5.5.0/huxtable/man/stripes.Rd |only huxtable-5.5.0/huxtable/man/subset-.brdr.Rd | 4 huxtable-5.5.0/huxtable/man/tidy_override.Rd | 3 huxtable-5.5.0/huxtable/man/wrap.Rd | 4 huxtable-5.5.0/huxtable/tests/testthat/404.html |only huxtable-5.5.0/huxtable/tests/testthat/bookdown-test.Rmd | 4 huxtable-5.5.0/huxtable/tests/testthat/quarto-test.qmd |only huxtable-5.5.0/huxtable/tests/testthat/siunitx-test.Rmd |only huxtable-5.5.0/huxtable/tests/testthat/test-column-to-header.R |only huxtable-5.5.0/huxtable/tests/testthat/test-dplyr.R | 3 huxtable-5.5.0/huxtable/tests/testthat/test-huxreg.R | 1 huxtable-5.5.0/huxtable/tests/testthat/test-huxtable-creation.R | 11 huxtable-5.5.0/huxtable/tests/testthat/test-manipulation-helpers.R | 9 huxtable-5.5.0/huxtable/tests/testthat/test-number-format-functions.R | 2 huxtable-5.5.0/huxtable/tests/testthat/test-number-formatting.R | 16 huxtable-5.5.0/huxtable/tests/testthat/test-print.R | 16 huxtable-5.5.0/huxtable/tests/testthat/test-stripes.R |only huxtable-5.5.0/huxtable/tests/testthat/test-yy-end-to-end.R | 37 huxtable-5.5.0/huxtable/vignettes/huxtable.Rmd | 24 90 files changed, 1261 insertions(+), 458 deletions(-)
Title: Estimating the Number of Factors in EFA with Out-of-Sample
Prediction Errors
Description: Estimating the number of factors in Exploratory Factor Analysis (EFA) with out-of-sample prediction errors using a cross-validation scheme. Haslbeck & van Bork (Preprint) <https://psyarxiv.com/qktsd>.
Author: Jonas Haslbeck [aut, cre],
Riet van Bork [ctb]
Maintainer: Jonas Haslbeck <jonashaslbeck@gmail.com>
Diff between fspe versions 0.1.0 dated 2021-02-24 and 0.1.1 dated 2022-06-15
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/fspe.R | 9 +++++++-- R/helpers.R | 5 ++++- README.md | 5 +++++ 5 files changed, 23 insertions(+), 10 deletions(-)
Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Statistics: locate and tag peaks and valleys; label plot with the
equation of a fitted polynomial or other types of models; labels
with P-value, R^2 or adjusted R^2 or information criteria for fitted models;
label with ANOVA table for fitted models; label with summary for fitted
models. Model fit classes for which suitable methods are provided by package
'broom' and 'broom.mixed' are supported. Scales and stats to build volcano
and quadrant plots based on outcomes, fold changes, p-values and false
discovery rates.
Author: Pedro J. Aphalo [aut, cre] ,
Kamil Slowikowski [ctb] ,
Samer Mouksassi [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpmisc versions 0.4.6 dated 2022-04-10 and 0.4.7 dated 2022-06-15
ggpmisc-0.4.6/ggpmisc/R/stat-quant-line.R |only ggpmisc-0.4.7/ggpmisc/DESCRIPTION | 22 ggpmisc-0.4.7/ggpmisc/MD5 | 54 ggpmisc-0.4.7/ggpmisc/NEWS.md | 19 ggpmisc-0.4.7/ggpmisc/R/stat-fit-deviations.R | 92 - ggpmisc-0.4.7/ggpmisc/R/stat-fit-residuals.R | 78 ggpmisc-0.4.7/ggpmisc/R/stat-ma-eq.R | 123 + ggpmisc-0.4.7/ggpmisc/R/stat-ma-line.R | 114 + ggpmisc-0.4.7/ggpmisc/R/stat-poly-eq.R | 91 - ggpmisc-0.4.7/ggpmisc/R/stat-poly-line.R | 87 - ggpmisc-0.4.7/ggpmisc/R/stat-quant-band.R | 66 ggpmisc-0.4.7/ggpmisc/R/stat-quant-eq.R | 162 + ggpmisc-0.4.7/ggpmisc/R/stat-quant-line.r |only ggpmisc-0.4.7/ggpmisc/README.md | 125 - ggpmisc-0.4.7/ggpmisc/build/vignette.rds |binary ggpmisc-0.4.7/ggpmisc/inst/doc/model-based-annotations.Rmd | 31 ggpmisc-0.4.7/ggpmisc/inst/doc/model-based-annotations.html | 869 +++++----- ggpmisc-0.4.7/ggpmisc/man/figures/README-unnamed-chunk-1-1.png |binary ggpmisc-0.4.7/ggpmisc/man/ggpmisc-ggproto.Rd | 2 ggpmisc-0.4.7/ggpmisc/man/stat_fit_deviations.Rd | 19 ggpmisc-0.4.7/ggpmisc/man/stat_fit_residuals.Rd | 10 ggpmisc-0.4.7/ggpmisc/man/stat_ma_eq.Rd | 651 +++---- ggpmisc-0.4.7/ggpmisc/man/stat_ma_line.Rd | 13 ggpmisc-0.4.7/ggpmisc/man/stat_poly_eq.Rd | 12 ggpmisc-0.4.7/ggpmisc/man/stat_poly_line.Rd | 23 ggpmisc-0.4.7/ggpmisc/man/stat_quant_band.Rd | 11 ggpmisc-0.4.7/ggpmisc/man/stat_quant_eq.Rd | 831 ++++----- ggpmisc-0.4.7/ggpmisc/man/stat_quant_line.Rd | 516 ++--- ggpmisc-0.4.7/ggpmisc/vignettes/model-based-annotations.Rmd | 31 29 files changed, 2255 insertions(+), 1797 deletions(-)
Title: Companion to Applied Regression
Description: Functions to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Third Edition, Sage, 2019.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Brad Price [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Ben Bolker [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [c [...truncated...]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between car versions 3.0-13 dated 2022-05-02 and 3.1-0 dated 2022-06-15
DESCRIPTION | 12 +-- MD5 | 32 ++++---- NAMESPACE | 7 + NEWS | 10 ++ R/Anova.R | 11 ++ R/avPlot3d.R |only R/crPlot3d.R |only R/recode.R | 135 ++++++++++++++++++----------------- R/scatter3d.R | 11 +- R/vif.R | 114 ++++++++++------------------- build/vignette.rds |binary inst/doc/embedding.pdf |binary man/Anova.Rd | 9 +- man/avPlots.Rd | 30 ++++++- man/crPlots.Rd | 63 ++++++++++++++-- man/recode.Rd | 189 ++++++++++++++++++++++++++----------------------- man/scatter3d.Rd | 4 - man/vif.Rd | 14 +-- 18 files changed, 365 insertions(+), 276 deletions(-)
More information about worldfootballR at CRAN
Permanent link
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts
with a suite of web services for chemical information. Sources include: Alan
Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver,
ChEBI, Chemical Translation Service, ChemIDplus, ChemSpider, ETOX,
Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem,
SRS, Wikidata.
Author: Eduard Szoecs [aut],
Robert Allaway [ctb],
Daniel Muench [ctb],
Johannes Ranke [ctb],
Andreas Scharmueller [ctb],
Eric R Scott [ctb],
Jan Stanstrup [ctb],
Joao Vitor F Cavalcante [ctb],
Gordon Getzinger [ctb],
Tamas Stirling [ctb, cre]
Maintainer: Tamas Stirling <stirling.tamas@gmail.com>
Diff between webchem versions 1.1.2 dated 2021-12-06 and 1.1.3 dated 2022-06-15
DESCRIPTION | 10 - MD5 | 80 ++++++------ NAMESPACE | 1 NEWS.md | 14 ++ R/bcpc.R | 14 +- R/chebi.R | 4 R/chemid.R | 6 R/cir.R | 42 ++++-- R/cts.R | 12 - R/etox.R | 9 - R/opsin.R | 2 R/pubchem.R | 34 +++-- R/srs.R | 2 R/utils.R | 8 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/webchem.html | 242 +++++++++++++++++++++++++++++++++++++-- man/chebi_comp_entity.Rd | 2 man/ci_query.Rd | 2 man/cir_img.Rd | 2 man/cir_query.Rd | 4 man/cts_compinfo.Rd | 2 man/cts_convert.Rd | 6 man/cts_from.Rd | 2 man/cts_to.Rd | 2 man/get_chebiid.Rd | 2 man/get_cid.Rd | 2 man/get_etoxid.Rd | 5 man/is.inchikey_cs.Rd | 2 man/is.inchikey_format.Rd | 2 man/opsin_query.Rd | 2 man/pc_prop.Rd | 2 man/pc_sect.Rd | 2 man/pc_synonyms.Rd | 2 man/srs_query.Rd | 2 tests/testthat/test-bcpc.R | 26 +++- tests/testthat/test-chemspider.R | 14 +- tests/testthat/test-cir.R | 29 +++- tests/testthat/test-cts.R | 10 - tests/testthat/test-etox.R | 4 tests/testthat/test-pubchem.R | 19 +++ 41 files changed, 465 insertions(+), 162 deletions(-)
Title: Quality Control for RNA-Seq Data
Description: Functions for semi-automated quality control of bulk RNA-seq data.
Author: Frederik Ziebell [aut, cre] ,
GlaxoSmithKline Research & Development Limited [cph]
Maintainer: Frederik Ziebell <frederik.x.ziebell@gsk.com>
Diff between RNAseqQC versions 0.1.3 dated 2022-05-27 and 0.1.4 dated 2022-06-15
DESCRIPTION | 6 +- MD5 | 28 ++++----- NEWS.md | 10 +++ R/other.R | 39 ++++++++----- R/pca.R | 38 +++++++----- R/preprocessing.R | 2 inst/doc/introduction.R | 5 + inst/doc/introduction.Rmd | 5 + inst/doc/introduction.html | 124 ++++++++++++++++++++++-------------------- man/mean_sd_plot.Rd | 2 man/plot_chromosome.Rd | 6 +- man/plot_pca.Rd | 5 + man/plot_pca_scatters.Rd | 3 - man/plot_sample_clustering.Rd | 17 ++++- vignettes/introduction.Rmd | 5 + 15 files changed, 176 insertions(+), 119 deletions(-)
Title: A Collection of Models that Employ a Product Partition
Distribution as a Prior on Partitions
Description: Provides a suite of functions that fit models that use PPM type priors for partitions.
Models include hierarchical Gaussian and probit ordinal models with a (covariate
dependent) PPM. If a covariate dependent product partition model is selected,
then all the options detailed in Page, G.L.; Quintana, F.A. (2018)
<doi:10.1007/s11222-017-9777-z> are available. If covariate values are missing,
then the approach detailed in Page, G.L.; Quintana, F.A.; Mueller, P (2020)
<doi:10.1080/10618600.2021.1999824> is employed. Also included in the package is
a function that fits a Gaussian likelihood spatial product partition model that is
detailed in Page, G.L.; Quintana, F.A. (2016) <doi:10.1214/15-BA971>, and
multivariate PPM change point models that are detailed in Quinlan, J.J.; Page, G.L.;
Castro, L.M. (2021) <arXiv:2201.07830>.
Author: Garritt L. Page [aut, cre, cph],
Jose J. Quinlan [aut, cph],
S. McKay Curtis [ctb, cph],
Radford M. Neal [ctb, cph]
Maintainer: Garritt L. Page <page@stat.byu.edu>
Diff between ppmSuite versions 0.2.3 dated 2022-06-13 and 0.2.4 dated 2022-06-15
DESCRIPTION | 8 +-- MD5 | 12 ++-- src/Rutil.c | 112 ++++++++++++++++++++++---------------------- src/gaussian.ppmx.c | 2 src/gaussian.ppmx.missing.c | 4 - src/ordinal.ppmx.c | 4 - src/ordinal.ppmx.missing.c | 4 - 7 files changed, 74 insertions(+), 72 deletions(-)
Title: Dots and Their Connections in Polar Coordinate System
Description: Provides basic graphing functions to fully demonstrate
point-to-point connections in a polar coordinate space.
Author: Shixiang Wang [aut, cre]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between ggpolar versions 0.2.0 dated 2021-11-10 and 0.2.1 dated 2022-06-15
DESCRIPTION | 18 ++++++++---------- MD5 | 11 ++++++++--- README.md | 10 ++++++++-- build |only inst |only man/figures/README-unnamed-chunk-2-2.png |binary vignettes |only 7 files changed, 24 insertions(+), 15 deletions(-)
Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean,
extreme-value and other copula families, as well as their rotations,
mixtures and asymmetrizations. Nested Archimedean copulas, related
tools and special functions. Methods for density, distribution, random
number generation, bivariate dependence measures, Rosenblatt transform,
Kendall distribution function, perspective and contour plots. Fitting of
copula models with potentially partly fixed parameters, including
standard errors. Serial independence tests, copula specification tests
(independence, exchangeability, radial symmetry, extreme-value
dependence, goodness-of-fit) and model selection based on
cross-validation. Empirical copula, smoothed versions, and
non-parametric estimators of the Pickands dependence function.
Author: Marius Hofert [aut] ,
Ivan Kojadinovic [aut] ,
Martin Maechler [aut, cre] ,
Jun Yan [aut] ,
Johanna G. Neslehova [ctb] ,
<https://orcid.org/0000-0001-9634-4796>),
Rebecca Morger [ctb] : code for free mixCopula weight
parameters)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between copula versions 1.0-1 dated 2020-12-12 and 1.1-0 dated 2022-06-15
DESCRIPTION | 31 +++--- MD5 | 157 ++++++++++++++++---------------- NAMESPACE | 12 +- R/AllClass.R | 5 - R/AllGeneric.R | 6 - R/Auxiliaries.R | 13 +- R/Classes.R | 3 R/Copula.R | 2 R/asymCopula.R | 6 - R/aux-acopula.R | 31 ++++-- R/dC-dc.R | 19 ++- R/ellipCopula.R | 35 +++++++ R/empCopula.R | 61 ++++++++++-- R/estimation.R | 26 ----- R/fitCopula.R | 146 +++++++++++++++++++++-------- R/fitLambda.R | 81 +++++++++++----- R/fitMvdc.R | 2 R/fixedPar.R | 6 - R/frankCopula.R | 8 - R/frankExpr.R | 2 R/graphics.R | 8 + R/matrix_tools.R | 13 +- R/mixCopula.R | 1 R/normalCopula.R | 22 +--- R/obs.R |only R/rotCopula.R | 4 R/sysdata.rda |binary R/tCopula.R | 17 +-- R/varianceReduction.R | 6 + R/xvCopula.R | 8 - build/partial.rdb |binary build/vignette.rds |binary data/SMI.12.rda |binary data/gasoil.rda |binary data/rdj.rda |binary demo/gof_graph.R | 11 +- inst/NEWS.Rd | 46 +++++++++ inst/doc/AC_Liouville.html | 60 +++--------- inst/doc/AR_Clayton.html | 59 +++--------- inst/doc/Frank-Rmpfr.pdf |binary inst/doc/GIG.html | 70 ++++---------- inst/doc/HAXC.html | 78 ++++----------- inst/doc/NALC.html | 66 +++---------- inst/doc/copula_GARCH.html | 66 +++---------- inst/doc/dNAC.html | 58 ++--------- inst/doc/empiricial_copulas.html | 58 ++--------- inst/doc/logL_visualization.html | 142 +++++++++++----------------- inst/doc/nacopula-pkg.Rnw | 7 - inst/doc/nacopula-pkg.pdf |binary inst/doc/qrng.html | 66 +++---------- inst/doc/rhoAMH-dilog.pdf |binary inst/doc/wild_animals.html | 138 +++++++++++----------------- man/Bernoulli.Rd | 2 man/Copula.Rd | 2 man/Sibuya.Rd | 2 man/contourplot2-methods.Rd | 2 man/copula-class.Rd | 8 + man/copula-package.Rd | 2 man/describeCop.Rd | 2 man/ellipCopula.Rd | 108 ++++++++++++++++++---- man/emle.Rd | 4 man/empCopula.Rd | 35 +++++-- man/fitCopula.Rd | 21 +++- man/fitLambda.Rd | 20 +++- man/getTheta.Rd | 4 man/gofTstat.Rd | 2 man/interval-class.Rd | 2 man/matrix_tools.Rd | 14 +- man/pobs.Rd | 8 - man/polylog.Rd | 2 man/polynEval.Rd | 2 man/setTheta.Rd | 4 man/splom2-methods.Rd | 2 man/varianceReduction.Rd | 7 - src/init.c | 78 +++++++-------- tests/fitting-ex.R | 191 ++++++++++++++++++++++++++++----------- tests/pdf.R | 9 + tests/tail-pcopula.R | 8 + tests/tail-pcopula.Rout.save | 30 +++--- vignettes/nacopula-pkg.Rnw | 7 - 80 files changed, 1163 insertions(+), 1071 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]
Maintainer: James Pustejovsky <jepusto@gmail.com>
Diff between clubSandwich versions 0.5.6 dated 2022-04-23 and 0.5.7 dated 2022-06-15
DESCRIPTION | 10 MD5 | 146 ++-- NEWS.md | 5 R/Wald_test.R | 12 R/coef_test.R | 13 R/conf_int.R | 56 + R/glm.R | 14 R/gls.R | 20 R/ivreg.R | 28 R/lm.R | 29 R/lme.R | 139 +--- R/lmer.R | 15 R/mlm.R | 1 R/plm.R | 71 +- R/rma-mv.R | 54 + R/rma-uni.R | 18 R/robu.R | 4 R/utilities.R | 1 build/partial.rdb |binary inst/doc/Wald-tests-in-clubSandwich.R | 9 inst/doc/Wald-tests-in-clubSandwich.Rmd | 12 inst/doc/Wald-tests-in-clubSandwich.html | 640 +++++++++++++++++---- inst/doc/meta-analysis-with-CRVE.R | 9 inst/doc/meta-analysis-with-CRVE.Rmd | 10 inst/doc/meta-analysis-with-CRVE.html | 350 +++++++++-- inst/doc/panel-data-CRVE.R | 16 inst/doc/panel-data-CRVE.Rmd | 17 inst/doc/panel-data-CRVE.html | 506 ++++++++++++++-- man/Wald_test.Rd | 5 man/coef_test.Rd | 13 man/conf_int.Rd | 13 man/constraint_matrices.Rd | 4 man/findCluster.rma.mv.Rd | 60 + man/impute_covariance_matrix.Rd | 5 man/linear_contrast.Rd | 181 +++-- man/pattern_covariance_matrix.Rd | 10 man/vcovCR.glm.Rd | 14 man/vcovCR.gls.Rd | 16 man/vcovCR.ivreg.Rd | 28 man/vcovCR.lm.Rd | 27 man/vcovCR.lme.Rd | 35 - man/vcovCR.lmerMod.Rd | 15 man/vcovCR.mlm.Rd | 1 man/vcovCR.plm.Rd | 67 +- man/vcovCR.rma.mv.Rd | 21 man/vcovCR.rma.uni.Rd | 18 man/vcovCR.robu.Rd | 4 tests/testthat/test_Wald.R | 4 tests/testthat/test_conf_int.R | 2 tests/testthat/test_estfun.R | 5 tests/testthat/test_glm_logit.R | 2 tests/testthat/test_gls.R | 6 tests/testthat/test_ignore_absorption.R | 2 tests/testthat/test_impute_covariance_matrix.R | 9 tests/testthat/test_ivreg.R | 3 tests/testthat/test_linear_contrast.R | 4 tests/testthat/test_lm.R | 4 tests/testthat/test_lme_2level.R | 6 tests/testthat/test_lme_3level.R | 9 tests/testthat/test_lme_MVML.R | 41 - tests/testthat/test_lmerMod.R | 4 tests/testthat/test_mlm.R | 2 tests/testthat/test_plm-ID-variables.R | 1 tests/testthat/test_plm-first-differences.R | 3 tests/testthat/test_plm-fixed-effects.R | 1 tests/testthat/test_plm-random-effects.R | 7 tests/testthat/test_plm-unbalanced-fixed-effects.R | 1 tests/testthat/test_plm_overspecified_problem.R | 1 tests/testthat/test_rma-mv.R | 2 tests/testthat/test_rma-uni.R | 3 tests/testthat/test_robu.R | 2 vignettes/Wald-tests-in-clubSandwich.Rmd | 12 vignettes/meta-analysis-with-CRVE.Rmd | 10 vignettes/panel-data-CRVE.Rmd | 17 74 files changed, 2132 insertions(+), 773 deletions(-)
Title: Testbench for Univariate Time Series Cleaning
Description: A reliable and efficient tool for cleaning univariate time
series data. It implements reliable and efficient procedures for
automating the process of cleaning univariate time series data.
The package provides integration with already developed and deployed
tools for missing value imputation and outlier detection. It also
provides a way of visualizing large time-series data in different
resolutions.
Author: Mayur Shende [aut, cre] ,
Neeraj Bokde [aut] ,
Andres E. Feijoo-Lorenzo [aut]
Maintainer: Mayur Shende <mayur.k.shende@gmail.com>
Diff between cleanTS versions 0.1.0 dated 2021-08-26 and 0.1.1 dated 2022-06-15
DESCRIPTION | 8 ++++---- MD5 | 33 +++++++++++++++++---------------- R/animate_interval.R | 25 +++++++++++++++++++++++-- R/cleanTS.R | 34 +++++++++++++++++++++++++++++++++- R/gen_report.R | 4 ++-- R/interact_plot.R | 12 ++++++++++++ R/mergecsv.R | 6 ++++++ R/missing_values.R | 2 +- R/util.R | 33 +++++++++++++++++++++++---------- README.md | 15 +++++---------- inst |only man/animate_interval.Rd | 19 ++++++++++++++++++- man/cleanTS.Rd | 35 ++++++++++++++++++++++++++++++++++- man/figures/README-Example-1.gif |binary man/gen.animation.Rd | 7 ++++++- man/gen.report.Rd | 4 ++-- man/interact_plot.Rd | 13 +++++++++++++ man/mergecsv.Rd | 7 +++++++ 18 files changed, 206 insertions(+), 51 deletions(-)
Title: Representation of Archaeological Data
Description: A collection of classes that represent
archaeological data. This package provides a set of S4 classes that
represent different special types of matrix (absolute/relative
frequency, presence/absence data, co-occurrence matrix, etc.) upon
which package developers can build subclasses. It also provides a set
of generic methods (mutators and coercion mechanisms) and functions
(e.g. summary statistics, predicates). In addition, a few classes of
general interest (e.g. that represent stratigraphic relationships)
are implemented.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb]
Maintainer: Nicolas Frerebeau
<nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between arkhe versions 0.4.0 dated 2021-09-18 and 0.5.0 dated 2022-06-15
arkhe-0.4.0/arkhe/R/clean.R |only arkhe-0.5.0/arkhe/DESCRIPTION | 29 - arkhe-0.5.0/arkhe/MD5 | 59 ++- arkhe-0.5.0/arkhe/NAMESPACE | 8 arkhe-0.5.0/arkhe/NEWS.md | 22 - arkhe-0.5.0/arkhe/R/AllGenerics.R | 184 +++++++++- arkhe-0.5.0/arkhe/R/arkhe-package.R | 2 arkhe-0.5.0/arkhe/R/assign.R |only arkhe-0.5.0/arkhe/R/check.R | 11 arkhe-0.5.0/arkhe/R/coerce.R | 4 arkhe-0.5.0/arkhe/R/compact.R |only arkhe-0.5.0/arkhe/R/detect.R |only arkhe-0.5.0/arkhe/R/replace.R |only arkhe-0.5.0/arkhe/R/statistics.R |only arkhe-0.5.0/arkhe/R/utilities.R | 24 - arkhe-0.5.0/arkhe/R/validate.R | 2 arkhe-0.5.0/arkhe/README.md | 85 ++-- arkhe-0.5.0/arkhe/build/partial.rdb |binary arkhe-0.5.0/arkhe/build/vignette.rds |binary arkhe-0.5.0/arkhe/inst/CITATION | 7 arkhe-0.5.0/arkhe/inst/doc/arkhe.html | 319 +++++++++++++++--- arkhe-0.5.0/arkhe/inst/examples/ex-clean.R | 34 + arkhe-0.5.0/arkhe/inst/examples/ex-resample.R |only arkhe-0.5.0/arkhe/man/arkhe-package.Rd | 14 arkhe-0.5.0/arkhe/man/assign.Rd |only arkhe-0.5.0/arkhe/man/check-numeric.Rd | 3 arkhe-0.5.0/arkhe/man/confidence.Rd |only arkhe-0.5.0/arkhe/man/count.Rd |only arkhe-0.5.0/arkhe/man/detect.Rd |only arkhe-0.5.0/arkhe/man/jackknife.Rd |only arkhe-0.5.0/arkhe/man/remove.Rd | 104 +++-- arkhe-0.5.0/arkhe/man/replace.Rd | 43 +- arkhe-0.5.0/arkhe/tests/testthat/_snaps/statistics.md |only arkhe-0.5.0/arkhe/tests/testthat/test-assign.R |only arkhe-0.5.0/arkhe/tests/testthat/test-check.R | 8 arkhe-0.5.0/arkhe/tests/testthat/test-clean.R | 197 ++++++----- arkhe-0.5.0/arkhe/tests/testthat/test-statistics.R |only arkhe-0.5.0/arkhe/tests/testthat/test-utilities.R | 13 38 files changed, 829 insertions(+), 343 deletions(-)
Title: Model Wrappers for Poisson Regression
Description: Bindings for Poisson regression models for use with the
'parsnip' package. Models include simple generalized linear models,
Bayesian models, and zero-inflated Poisson models (Zeileis, Kleiber,
and Jackman (2008) <doi:10.18637/jss.v027.i08>).
Author: Max Kuhn [aut] ,
Hannah Frick [aut, cre] ,
RStudio [cph, fnd]
Maintainer: Hannah Frick <hannah@rstudio.com>
Diff between poissonreg versions 0.2.0 dated 2022-03-09 and 1.0.0 dated 2022-06-15
DESCRIPTION | 35 ++--- MD5 | 33 ++--- NEWS.md | 4 R/0_imports.R | 1 R/poisson_reg.R | 25 ++-- R/poisson_reg_data.R | 14 +- R/zzz.R | 1 README.md | 10 - inst/WORDLIST | 3 man/poissonreg-package.Rd | 2 tests/spelling.R | 9 - tests/testthat/_snaps |only tests/testthat/helper-objects.R | 5 tests/testthat/helpers.R | 5 tests/testthat/test-poisson-reg-hurdle.R | 29 +--- tests/testthat/test-poisson-reg-zeroinfl.R | 29 +--- tests/testthat/test-poisson-reg.R | 177 +---------------------------- tests/testthat/test-tidy.R | 9 - 18 files changed, 117 insertions(+), 274 deletions(-)
Title: Fit Models Derived from Point Processes to Species Distributions
using 'inlabru'
Description: Integrated species distribution modeling is a rising field in quantitative ecology thanks to significant rises in the quantity of data available, increases in computational speed and the proven benefits of using such models.
Despite this, the general software to help ecologists construct such models in an easy-to-use framework is lacking.
We therefore introduce the R package 'PointedSDMs': which provides the tools to help ecologists set up integrated models and perform inference on them.
There are also functions within the package to help run spatial cross-validation for model selection, as well as generic plotting and predicting functions.
An introduction to these methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.
Author: Philip Mostert [aut, cre],
Bob O'hara [aut]
Maintainer: Philip Mostert <philip.s.mostert@ntnu.no>
Diff between PointedSDMs versions 1.0.5 dated 2022-06-14 and 1.0.6 dated 2022-06-15
DESCRIPTION | 6 +++--- MD5 | 27 ++++++++++++++------------- NEWS.md |only R/data2ENV.R | 2 +- R/dataSDM.R | 9 ++++++++- R/dataSet.R | 12 ++++++------ R/intModel.R | 2 +- R/runModel.R | 15 +++++++++++++-- inst/doc/Setophaga.html | 4 ++-- man/data2ENV.Rd | 2 +- man/dataSDM.Rd | 16 ++++++++++++++-- man/dataSet.Rd | 2 +- man/intModel.Rd | 2 +- tests/testthat/testthat_dataOrganize.R | 2 +- tests/testthat/testthat_dataSDM.R | 4 ++-- 15 files changed, 68 insertions(+), 37 deletions(-)
Title: Permutation Tests for Time Series Data
Description: Helps you determine the analysis window to use when analyzing densely-sampled
time-series data, such as EEG data, using permutation testing (Maris & Oostenveld, 2007)
<doi:10.1016/j.jneumeth.2007.03.024>. These permutation tests can help identify the timepoints
where significance of an effect begins and ends, and the results can be plotted in various
types of heatmap for reporting. Mixed-effects models are supported using an implementation of
the approach by Lee & Braun (2012) <doi:10.1111/j.1541-0420.2011.01675.x>.
Author: Cesko C. Voeten [aut, cre]
Maintainer: Cesko C. Voeten <cvoeten@gmail.com>
Diff between permutes versions 2.4 dated 2022-05-20 and 2.5 dated 2022-06-15
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/buildmer.R | 27 +++++++++++++-------------- R/pkgcheck.R | 4 ++-- inst/doc/buildmer.pdf |binary inst/doc/permutes.pdf |binary man/clusterperm.glmmTMB.Rd | 2 +- 7 files changed, 26 insertions(+), 27 deletions(-)
Title: Functional Control Charts
Description: Provides functional control charts
for statistical process monitoring of functional data,
using the methods of Capezza et al. (2020) <doi:10.1002/asmb.2507> and
Centofanti et al. (2020) <doi:10.1080/00401706.2020.1753581>.
Author: Christian Capezza [cre, aut],
Fabio Centofanti [aut],
Antonio Lepore [aut],
Alessandra Menafoglio [aut],
Biagio Palumbo [aut],
Simone Vantini [aut]
Maintainer: Christian Capezza <christian.capezza@unina.it>
Diff between funcharts versions 1.1.0 dated 2021-10-01 and 1.2.0 dated 2022-06-15
funcharts-1.1.0/funcharts/inst/doc/centofanti2020.Rmd |only funcharts-1.1.0/funcharts/inst/doc/centofanti2020.html |only funcharts-1.1.0/funcharts/vignettes/centofanti2020-plot_bifd-1.png |only funcharts-1.1.0/funcharts/vignettes/centofanti2020-plot_control_charts-1.png |only funcharts-1.1.0/funcharts/vignettes/centofanti2020-plot_control_charts_real_time-1.png |only funcharts-1.1.0/funcharts/vignettes/centofanti2020-plot_mon-1.png |only funcharts-1.1.0/funcharts/vignettes/centofanti2020.Rmd |only funcharts-1.2.0/funcharts/DESCRIPTION | 12 funcharts-1.2.0/funcharts/MD5 | 117 +-- funcharts-1.2.0/funcharts/NAMESPACE | 2 funcharts-1.2.0/funcharts/NEWS.md | 12 funcharts-1.2.0/funcharts/R/00_mfd.R | 351 ++++++--- funcharts-1.2.0/funcharts/R/01_pca.mfd.R | 145 +++ funcharts-1.2.0/funcharts/R/02_fof_pc.R | 85 +- funcharts-1.2.0/funcharts/R/02_sof_pc.R | 33 funcharts-1.2.0/funcharts/R/03_phaseI_training.R | 22 funcharts-1.2.0/funcharts/R/04_phaseII.R | 112 ++ funcharts-1.2.0/funcharts/R/05_fault_detection.R | 2 funcharts-1.2.0/funcharts/R/funcharts.R | 7 funcharts-1.2.0/funcharts/R/real_time_00_mfd.R | 12 funcharts-1.2.0/funcharts/R/real_time_04_phaseII.R | 104 +- funcharts-1.2.0/funcharts/R/simulate.R | 96 ++ funcharts-1.2.0/funcharts/README.md | 16 funcharts-1.2.0/funcharts/build/vignette.rds |binary funcharts-1.2.0/funcharts/inst/doc/capezza2020.Rmd | 22 funcharts-1.2.0/funcharts/inst/doc/capezza2020.html | 374 ++++++++-- funcharts-1.2.0/funcharts/inst/doc/centofanti2021.Rmd |only funcharts-1.2.0/funcharts/inst/doc/centofanti2021.html |only funcharts-1.2.0/funcharts/inst/doc/mfd.html | 280 ++++++- funcharts-1.2.0/funcharts/man/cbind_mfd.Rd | 4 funcharts-1.2.0/funcharts/man/control_charts_pca.Rd | 54 - funcharts-1.2.0/funcharts/man/control_charts_pca_mfd_real_time.Rd | 17 funcharts-1.2.0/funcharts/man/control_charts_sof_pc.Rd | 20 funcharts-1.2.0/funcharts/man/control_charts_sof_pc_real_time.Rd | 11 funcharts-1.2.0/funcharts/man/data_sim_mfd.Rd | 5 funcharts-1.2.0/funcharts/man/fof_pc.Rd | 12 funcharts-1.2.0/funcharts/man/funcharts.Rd | 6 funcharts-1.2.0/funcharts/man/get_mfd_array.Rd | 2 funcharts-1.2.0/funcharts/man/get_mfd_fd.Rd | 4 funcharts-1.2.0/funcharts/man/get_mfd_list.Rd | 3 funcharts-1.2.0/funcharts/man/get_mfd_list_real_time.Rd | 4 funcharts-1.2.0/funcharts/man/inprod_mfd.Rd | 5 funcharts-1.2.0/funcharts/man/mfd.Rd | 8 funcharts-1.2.0/funcharts/man/predict_fof_pc.Rd | 4 funcharts-1.2.0/funcharts/man/rbind_mfd.Rd | 4 funcharts-1.2.0/funcharts/man/regr_cc_fof.Rd | 15 funcharts-1.2.0/funcharts/man/regr_cc_fof_real_time.Rd | 7 funcharts-1.2.0/funcharts/man/sim_funcharts.Rd |only funcharts-1.2.0/funcharts/man/simulate_mfd.Rd | 25 funcharts-1.2.0/funcharts/tests/testthat/test_mfd.R | 18 funcharts-1.2.0/funcharts/vignettes/capezza2020-cont_plot-1.png |binary funcharts-1.2.0/funcharts/vignettes/capezza2020-plot_beta-1.png |binary funcharts-1.2.0/funcharts/vignettes/capezza2020-plot_bootstrap_sof_pc-1.png |binary funcharts-1.2.0/funcharts/vignettes/capezza2020-plot_control_charts_pca-1.png |binary funcharts-1.2.0/funcharts/vignettes/capezza2020-plot_control_charts_real_time-1.png |binary funcharts-1.2.0/funcharts/vignettes/capezza2020-plot_control_charts_sof_pc-1.png |binary funcharts-1.2.0/funcharts/vignettes/capezza2020-plot_mon-1.png |binary funcharts-1.2.0/funcharts/vignettes/capezza2020.Rmd | 22 funcharts-1.2.0/funcharts/vignettes/centofanti2021-plot_bifd-1.png |only funcharts-1.2.0/funcharts/vignettes/centofanti2021-plot_control_charts-1.png |only funcharts-1.2.0/funcharts/vignettes/centofanti2021-plot_control_charts_real_time-1.png |only funcharts-1.2.0/funcharts/vignettes/centofanti2021-plot_mon-1.png |only funcharts-1.2.0/funcharts/vignettes/centofanti2021.Rmd |only funcharts-1.2.0/funcharts/vignettes/mfd-geom_mfd-1.png |binary funcharts-1.2.0/funcharts/vignettes/mfd-plot_mfd-1.png |binary funcharts-1.2.0/funcharts/vignettes/mfd-plot_mfd-2.png |binary funcharts-1.2.0/funcharts/vignettes/mfd-plot_pca_mfd-1.png |binary 67 files changed, 1495 insertions(+), 559 deletions(-)
Title: Functions for 'Ecdat'
Description: Functions and vignettes to update
data sets in 'Ecdat' and to create, manipulate,
plot, and analyze those and similar data sets.
Author: Spencer Graves <spencer.graves@effectivedefense.org>
Maintainer: Spencer Graves <spencer.graves@effectivedefense.org>
Diff between Ecfun versions 0.2-5 dated 2021-06-30 and 0.2-6 dated 2022-06-15
DESCRIPTION | 11 MD5 | 40 +- NEWS.md | 3 R/asNumericChar.R | 13 R/asNumericDF.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/UpdatingUSGDPpresidents.R | 134 ++++++- inst/doc/UpdatingUSGDPpresidents.Rmd | 210 ++++++++++- inst/doc/UpdatingUSGDPpresidents.html | 432 +++++++++++++++++++++-- inst/doc/nuclearArmageddon.Rmd | 4 inst/doc/nuclearArmageddon.html | 559 ++++++++++++++++++++++++------- inst/doc/updateOCC1950.Rmd | 2 inst/doc/updateOCC1950.html | 2 inst/doc/update_nuclearWeaponStates.html | 254 +++++++++++++- man/asNumericDF.Rd | 11 man/simulate.bic.glm.Rd | 2 man/simulate.glm.Rd | 2 vignettes/UpdatingUSGDPpresidents.Rmd | 210 ++++++++++- vignettes/nuclearArmageddon.Rmd | 4 vignettes/updateOCC1950.Rmd | 2 21 files changed, 1645 insertions(+), 254 deletions(-)
Title: Call 'BEAST2'
Description: 'BEAST2' (<https://www.beast2.org>) is a widely used
Bayesian phylogenetic tool, that uses DNA/RNA/protein data
and many model priors to create a posterior of jointly estimated
phylogenies and parameters.
'BEAST2' is a command-line tool.
This package provides a way to call 'BEAST2'
from an 'R' function call.
Author: Richel J.C. Bilderbeek [aut, cre]
,
Joelle Barido-Sottani [rev] ,
David Winter [rev] ,
Jason Griffiths [ctb] ,
Thijs Janzen [ctb]
Maintainer: Richel J.C. Bilderbeek <richel@richelbilderbeek.nl>
Diff between beastier versions 2.4.9 dated 2022-06-03 and 2.4.10 dated 2022-06-15
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/create_beautier_tempfolder.R | 16 +++++----------- R/remove_beaustier_folders.R | 2 +- R/remove_beautier_folder.R | 14 +++++++------- R/run_beast2_from_options.R | 2 +- inst/WORDLIST | 1 + inst/doc/demo.html | 36 ++++++++++++++++++------------------ man/create_beautier_tempfolder.Rd | 10 +--------- man/remove_beautier_folder.Rd | 8 ++++---- 10 files changed, 51 insertions(+), 64 deletions(-)
Title: Agricultural Datasets
Description: Datasets from books, papers, and websites related to agriculture.
Example graphics and analyses are included. Data come from small-plot trials,
multi-environment trials, uniformity trials, yield monitors, and more.
Author: Kevin Wright [aut, cre]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between agridat versions 1.20 dated 2021-12-20 and 1.21 dated 2022-06-15
DESCRIPTION | 8 MD5 | 190 ++-- NEWS.md | 14 R/libs.R | 5 build/vignette.rds |binary data/bachmaier.nitrogen.txt |only data/ducker.groundnut.uniformity.txt |only data/kling.augmented.txt |only data/sharma.met.txt |only inst/doc/agridat_data.Rmd | 169 ++- inst/doc/agridat_data.html | 780 +++++++++++++---- inst/doc/agridat_examples.Rmd | 4 inst/doc/agridat_examples.html | 486 +++++++++-- inst/doc/agridat_intro.Rmd | 7 inst/doc/agridat_intro.html | 274 +++++- inst/doc/agridat_uniformity.Rmd | 119 ++ inst/doc/agridat_uniformity.html | 1519 +++++++++++++++++++++++++++-------- man/agridat.Rd | 3 man/australia.soybean.Rd | 23 man/bachmaier.nitrogen.Rd |only man/barrero.maize.Rd | 7 man/besag.checks.Rd | 2 man/buntaran.wheat.Rd | 2 man/byers.apple.Rd | 17 man/caribbean.maize.Rd | 11 man/cate.potassium.Rd | 3 man/cleveland.soil.Rd | 5 man/cochran.beets.Rd | 2 man/cochran.bib.Rd | 2 man/cochran.latin.Rd | 3 man/crowder.seeds.Rd | 9 man/damesa.maize.Rd | 1 man/darwin.maize.Rd | 5 man/depalluel.sheep.Rd | 2 man/ducker.groundnut.uniformity.Rd |only man/eden.nonnormal.Rd | 5 man/eden.potato.Rd | 3 man/engelstad.nitro.Rd | 1 man/fisher.barley.Rd | 60 - man/fox.wheat.Rd | 2 man/gomez.multilocsplitplot.Rd | 3 man/grover.diallel.Rd | 2 man/hadasch.lettuce.Rd | 18 man/harris.wateruse.Rd | 10 man/heady.fertilizer.Rd | 5 man/hunter.corn.Rd | 2 man/ivins.herbs.Rd | 3 man/jansen.carrot.Rd | 2 man/jayaraman.bamboo.Rd | 7 man/jenkyn.mildew.Rd | 3 man/johnson.blight.Rd | 3 man/johnson.douglasfir.Rd | 2 man/kang.maize.Rd | 4 man/karcher.turfgrass.Rd | 3 man/kling.augmented.Rd |only man/kreusler.maize.Rd | 25 man/lambert.soiltemp.Rd | 2 man/lehner.soybeanmold.Rd | 2 man/libs.Rd | 13 man/lillemo.wheat.Rd | 4 man/linder.wheat.Rd | 3 man/lucas.switchback.Rd | 2 man/lyons.wheat.Rd | 3 man/mcleod.barley.Rd | 2 man/mead.germination.Rd | 2 man/minnesota.barley.yield.Rd | 2 man/moore.uniformity.Rd | 6 man/nair.turmeric.uniformity.Rd | 2 man/nass.corn.Rd | 3 man/obsi.potato.uniformity.Rd | 3 man/omer.sorghum.Rd | 3 man/onofri.winterwheat.Rd | 2 man/pearl.kernels.Rd | 2 man/pederson.lettuce.repeated.Rd | 2 man/petersen.sorghum.cowpea.Rd | 3 man/sharma.met.Rd |only man/shaw.oats.Rd | 2 man/sinclair.clover.Rd | 3 man/snijders.fusarium.Rd | 3 man/steptoe.morex.pheno.Rd | 6 man/stickler.sorghum.uniformity.Rd | 6 man/stroup.nin.Rd | 3 man/stroup.splitplot.Rd | 35 man/tai.potato.Rd | 3 man/theobald.barley.Rd | 2 man/theobald.covariate.Rd | 73 - man/thompson.cornsoy.Rd | 2 man/vaneeuwijk.nematodes.Rd | 2 man/vargas.wheat1.Rd | 12 man/walsh.cottonprice.Rd | 2 man/wassom.brome.uniformity.Rd | 7 man/wedderburn.barley.Rd | 2 man/wheatley.carrot.Rd | 3 man/williams.trees.Rd | 4 man/wyatt.multi.uniformity.Rd | 2 man/zuidhof.broiler.Rd | 5 vignettes/agridat_data.Rmd | 169 ++- vignettes/agridat_examples.Rmd | 4 vignettes/agridat_intro.Rmd | 7 vignettes/agridat_uniformity.Rmd | 119 ++ 100 files changed, 3263 insertions(+), 1109 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-04 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-19 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-08-23 0.1.3
2012-02-16 0.1
2011-10-18 0.0.9
2011-01-17 0.0.8
2009-11-08 0.0.7
2009-07-02 0.0.6
2009-05-06 0.0.5
2009-03-04 0.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-09-18 2.1
2012-02-27 2.0
2011-02-14 1.3
2009-12-30 1.2
2009-10-15 1.1
2009-09-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-06 1.0-1
2011-01-24 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-05-19 1.0
2013-05-19 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-05-18 0.46.0
2015-04-10 0.45.0
2014-06-18 0.39.4
2014-06-09 0.39.1
2014-04-23 0.38.3
2014-04-03 0.38.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-05-10 0.1.7
2013-04-08 0.1.6
2013-01-07 0.1.5
2012-11-26 0.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-15 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-02-10 2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-31 0.1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-22 1.0.1
2015-05-31 1.0
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 3.0-1 dated 2021-05-18 and 3.0-2 dated 2022-06-15
DESCRIPTION | 10 - MD5 | 74 ++++---- NEWS.md | 38 ++++ R/vcovBS.lm.R | 15 - R/vcovCL.R | 40 +++- R/vcovHAC.R | 4 R/vcovHC.R | 40 +++- R/vcovPL.R | 35 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/sandwich-CL.R | 178 ++++++++++++++++---- inst/doc/sandwich-CL.Rnw | 155 ++++++++++++++--- inst/doc/sandwich-CL.pdf |binary inst/doc/sandwich-OOP.R | 29 ++- inst/doc/sandwich-OOP.Rnw | 22 ++ inst/doc/sandwich-OOP.pdf |binary inst/doc/sandwich.R | 89 +++++++--- inst/doc/sandwich.Rnw | 62 ++++++- inst/doc/sandwich.pdf |binary man/NeweyWest.Rd | 3 man/PublicSchools.Rd | 7 man/vcovBS.Rd | 10 + man/vcovHC.Rd | 6 man/vcovPL.Rd | 9 - man/weightsAndrews.Rd | 3 tests/Examples/sandwich-Ex.Rout.save | 9 - tests/vcovCL.R | 4 tests/vcovCL.Rout.save | 307 +++++++++++++++++------------------ tests/vcovPC.R | 1 tests/vcovPC.Rout.save | 15 + tests/vcovPL.R | 1 tests/vcovPL.Rout.save | 8 vignettes/sandwich-CL.Rnw | 155 ++++++++++++++--- vignettes/sandwich-CL.Rout.save | 119 ++++++++----- vignettes/sandwich-OOP.Rnw | 22 ++ vignettes/sandwich-OOP.Rout.save | 50 ++--- vignettes/sandwich.Rnw | 62 ++++++- vignettes/sandwich.Rout.save | 51 +++-- 38 files changed, 1154 insertions(+), 479 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Armadillo requires a C++11 compiler.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.11.1.1.0 dated 2022-05-15 and 0.11.2.0.0 dated 2022-06-15
RcppArmadillo-0.11.1.1.0/RcppArmadillo/inst/include/armadillo_bits/GenSpecialiser.hpp |only RcppArmadillo-0.11.2.0.0/RcppArmadillo/ChangeLog | 17 RcppArmadillo-0.11.2.0.0/RcppArmadillo/DESCRIPTION | 8 RcppArmadillo-0.11.2.0.0/RcppArmadillo/MD5 | 85 +-- RcppArmadillo-0.11.2.0.0/RcppArmadillo/configure.ac | 2 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/NEWS.Rd | 13 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/doc/RcppArmadillo-sparseMatrix.pdf |binary RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo | 34 + RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/Cube_meat.hpp | 4 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/GenCube_bones.hpp | 11 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/GenCube_meat.hpp | 104 --- RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/Gen_bones.hpp | 11 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/Gen_meat.hpp | 161 +----- RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp | 8 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/Proxy.hpp | 96 --- RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/ProxyCube.hpp | 92 --- RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp | 8 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/SpProxy.hpp | 10 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/arma_forward.hpp | 2 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/arma_rng.hpp | 128 ++++ RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 6 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/distr_param.hpp | 55 +- RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/eop_aux.hpp | 4 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_accu.hpp | 33 - RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_as_scalar.hpp | 34 - RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_eye.hpp | 22 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_norm.hpp | 26 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_ones.hpp | 23 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_randg.hpp | 50 - RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_randi.hpp | 50 - RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_randn.hpp | 262 ++++++++- RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_randu.hpp | 258 +++++++-- RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_speye.hpp | 11 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/fn_zeros.hpp | 34 - RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/glue_kron_meat.hpp | 19 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/glue_solve_meat.hpp | 2 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/include_hdf5.hpp | 35 + RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/include_superlu.hpp | 265 +++++----- RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/memory.hpp | 2 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/newarp_SparseGenRealShiftSolve_meat.hpp | 3 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/op_nonzeros_meat.hpp | 36 - RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/spop_norm_bones.hpp | 2 RcppArmadillo-0.11.2.0.0/RcppArmadillo/inst/include/armadillo_bits/spop_norm_meat.hpp | 22 44 files changed, 1111 insertions(+), 937 deletions(-)
Title: Pre-Commit Hooks
Description: Useful git hooks for R building on top of the multi-language
framework 'pre-commit' for hook management. This package provides git
hooks for common tasks like formatting files with 'styler' or spell
checking as well as wrapper functions to access the 'pre-commit'
executable.
Author: Lorenz Walthert
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Diff between precommit versions 0.3.0 dated 2022-05-20 and 0.3.1 dated 2022-06-15
DESCRIPTION | 6 - MD5 | 50 ++++++++-------- NEWS.md | 29 ++++++++- R/assert.R | 2 R/release.R | 2 R/setup.R | 3 R/utils.R | 18 +++++ R/zzz.R | 4 + README.md | 1 inst/doc/FAQ.Rmd | 14 ++++ inst/doc/FAQ.html | 11 +++ inst/doc/available-hooks.Rmd | 11 +-- inst/doc/available-hooks.html | 4 - inst/doc/ci.Rmd | 5 + inst/doc/precommit.Rmd | 2 inst/doc/why-use-hooks.Rmd | 7 +- inst/pre-commit-config-pkg.yaml | 9 ++ inst/pre-commit-config-proj.yaml | 9 ++ tests/testthat/reference-objects/pre-commit-config.yaml | 2 tests/testthat/test-conda.R | 8 ++ tests/testthat/test-utils.R | 7 ++ vignettes/FAQ.Rmd | 14 ++++ vignettes/available-hooks.Rmd | 11 +-- vignettes/ci.Rmd | 5 + vignettes/precommit.Rmd | 2 vignettes/why-use-hooks.Rmd | 7 +- 26 files changed, 187 insertions(+), 56 deletions(-)
More information about MissingPlotRBD at CRAN
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Title: Testing, Monitoring, and Dating Structural Changes
Description: Testing, monitoring and dating structural changes in (linear)
regression models. strucchange features tests/methods from
the generalized fluctuation test framework as well as from
the F test (Chow test) framework. This includes methods to
fit, plot and test fluctuation processes (e.g., CUSUM, MOSUM,
recursive/moving estimates) and F statistics, respectively.
It is possible to monitor incoming data online using
fluctuation processes.
Finally, the breakpoints in regression models with structural
changes can be estimated together with confidence intervals.
Emphasis is always given to methods for visualizing the data.
Author: Achim Zeileis [aut, cre] ,
Friedrich Leisch [aut],
Kurt Hornik [aut],
Christian Kleiber [aut],
Bruce Hansen [ctb],
Edgar C. Merkle [ctb],
Nikolaus Umlauf [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between strucchange versions 1.5-2 dated 2019-10-12 and 1.5-3 dated 2022-06-15
DESCRIPTION | 14 +++++---- MD5 | 59 ++++++++++++++++++++-------------------- NEWS | 15 +++++++++- R/breakpoints.R | 10 ++++-- R/efp.R | 4 +- build/partial.rdb |only build/vignette.rds |binary data/BostonHomicide.rda |binary data/DJIA.rda |binary data/GermanM1.rda |binary data/Grossarl.rda |binary data/PhillipsCurve.rda |binary data/RealInt.rda |binary data/SP2001.rda |binary data/USIncExp.rda |binary data/durab.rda |binary data/scPublications.rda |binary inst/CITATION | 58 ++++++++++++++------------------------- inst/doc/strucchange-intro.Rnw | 23 ++++++--------- inst/doc/strucchange-intro.pdf |binary man/SP2001.Rd | 8 ++--- man/USIncExp.Rd | 2 - man/breakpoints.Rd | 5 ++- man/efp.Rd | 8 ++--- man/plot.efp.Rd | 2 - man/scPublications.Rd | 2 - man/sctest.Rd | 4 +- man/sctest.efp.Rd | 2 - src/strucchange_functions.c | 7 +++- vignettes/strucchange-intro.Rnw | 23 ++++++--------- vignettes/strucchange.bib | 2 - 31 files changed, 123 insertions(+), 125 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Data
Description: Conduct a noncompartmental analysis with industrial strength.
Some features are
1) Use of CDISC SDTM terms
2) Automatic or manual slope selection
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between NonCompart versions 0.5.0 dated 2022-02-26 and 0.5.1 dated 2022-06-15
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- R/BestSlope.R | 2 +- inst/NEWS.Rd | 5 +++++ inst/doc/NCA-formula.pdf |only inst/doc/NonCompart-manual.pdf |binary 6 files changed, 15 insertions(+), 9 deletions(-)
Title: Multi-Way Component Analysis
Description: For single tensor data, any matrix factorization method can be specified the matricised tensor in each dimension by Multi-way Component Analysis (MWCA). An originally extended MWCA is also implemented to specify and decompose multiple matrices and tensors simultaneously (CoupledMWCA). See the reference section of GitHub README.md <https://github.com/rikenbit/mwTensor>, for details of the methods.
Author: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between mwTensor versions 0.99.5 dated 2021-10-12 and 0.99.6 dated 2022-06-15
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/myICA.R | 4 ++-- build/partial.rdb |binary inst/NEWS | 4 ++++ tests/testthat.R | 2 +- 7 files changed, 19 insertions(+), 15 deletions(-)
Title: Multiple Empirical Likelihood Tests
Description: Performs multiple empirical likelihood tests for linear and
generalized linear models. The core computational routines are
implemented using the 'Eigen' C++ library and 'RcppEigen' interface,
with OpenMP for parallel computation. Details of multiple testing
procedures are given in Kim et al. (2021) <arxiv:2112.09206>.
Author: Eunseop Kim [aut, cre],
Steven MacEachern [aut, ths],
Mario Peruggia [aut, ths]
Maintainer: Eunseop Kim <kim.7302@osu.edu>
Diff between melt versions 1.5.1 dated 2022-05-06 and 1.5.2 dated 2022-06-15
melt-1.5.1/melt/R/deprecated.R |only melt-1.5.1/melt/man/coef-method.Rd |only melt-1.5.1/melt/man/el_test.Rd |only melt-1.5.1/melt/man/print-method.Rd |only melt-1.5.1/melt/man/summary-method.Rd |only melt-1.5.1/melt/src/deprecated.cpp |only melt-1.5.1/melt/tests/testthat/test-deprecated.R |only melt-1.5.1/melt/tests/testthat/test-el_pairwise.R |only melt-1.5.2/melt/DESCRIPTION | 46 ++-- melt-1.5.2/melt/MD5 | 99 +++++----- melt-1.5.2/melt/NAMESPACE | 1 melt-1.5.2/melt/NEWS.md | 41 ++-- melt-1.5.2/melt/R/AllClasses.R | 21 -- melt-1.5.2/melt/R/AllGenerics.R | 12 - melt-1.5.2/melt/R/RcppExports.R | 8 melt-1.5.2/melt/R/checker.R | 208 +++++++++++++++++++--- melt-1.5.2/melt/R/coef-methods.R | 9 melt-1.5.2/melt/R/confint-methods.R | 7 melt-1.5.2/melt/R/confreg-methods.R | 4 melt-1.5.2/melt/R/el_glm.R | 206 ++++++++++++++++++++- melt-1.5.2/melt/R/el_lm.R | 36 +-- melt-1.5.2/melt/R/el_mean.R | 2 melt-1.5.2/melt/R/el_pairwise.R | 5 melt-1.5.2/melt/R/eld-methods.R | 2 melt-1.5.2/melt/R/lht.R | 27 +- melt-1.5.2/melt/R/logLik-methods.R | 3 melt-1.5.2/melt/R/mht.R |only melt-1.5.2/melt/R/print-methods.R | 12 - melt-1.5.2/melt/R/summary-methods.R | 8 melt-1.5.2/melt/README.md | 12 - melt-1.5.2/melt/inst/WORDLIST | 1 melt-1.5.2/melt/man/CEL-class.Rd | 2 melt-1.5.2/melt/man/ControlEL-class.Rd | 1 melt-1.5.2/melt/man/EL-class.Rd | 4 melt-1.5.2/melt/man/coef.Rd |only melt-1.5.2/melt/man/el_lm.Rd | 12 - melt-1.5.2/melt/man/el_pairwise.Rd | 1 melt-1.5.2/melt/man/lht.Rd | 21 +- melt-1.5.2/melt/man/print.Rd |only melt-1.5.2/melt/man/summary.Rd |only melt-1.5.2/melt/src/EL.cpp | 60 ++---- melt-1.5.2/melt/src/EL.h | 42 +--- melt-1.5.2/melt/src/RcppExports.cpp | 33 --- melt-1.5.2/melt/src/confint.cpp | 34 +-- melt-1.5.2/melt/src/confreg.cpp | 6 melt-1.5.2/melt/src/eld.cpp | 1 melt-1.5.2/melt/src/eval.cpp | 2 melt-1.5.2/melt/src/glm.cpp | 158 +++++++++++++++- melt-1.5.2/melt/src/lht.cpp | 26 +- melt-1.5.2/melt/src/lm.cpp | 11 - melt-1.5.2/melt/src/mht-utils.cpp |only melt-1.5.2/melt/src/mht-utils.h |only melt-1.5.2/melt/src/mht.cpp |only melt-1.5.2/melt/src/utils.cpp | 43 ++-- melt-1.5.2/melt/src/utils.h | 18 + melt-1.5.2/melt/tests/testthat/test-confint.R | 13 + melt-1.5.2/melt/tests/testthat/test-el_mean.R | 26 ++ melt-1.5.2/melt/tests/testthat/test-lht.R | 14 + 58 files changed, 906 insertions(+), 392 deletions(-)
More information about IIProductionUnknown at CRAN
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Title: Experimental Statistics and Graphics for Agricultural Sciences
Description: Performs the analysis of completely randomized experimental designs (CRD), randomized blocks (RBD) and Latin square (LSD), experiments in double and triple factorial scheme (in CRD and RBD), experiments in subdivided plot scheme (in CRD and RBD), subdivided and joint analysis of experiments in CRD and RBD, linear regression analysis, test for two samples. The package performs analysis of variance, ANOVA assumptions and multiple comparison test of means or regression, according to Pimentel-Gomes (2009, ISBN: 978-85-7133-055-9), nonparametric test (Conover, 1999, ISBN: 0471160687), test for two samples, joint analysis of experiments according to Ferreira (2018, ISBN: 978-85-7269-566-4) and generalized linear model (glm) for binomial and Poisson family in CRD and RBD (Carvalho, FJ (2019), <doi:10.14393/ufu.te.2019.1244>). It can also be used to obtain descriptive measures and graphics, in addition to correlations and creative graphics used in agricultural sciences (Agronomy, Zootechnics, Food Science and related areas).
Author: Gabriel Danilo Shimizu [aut, cre]
,
Rodrigo Yudi Palhaci Marubayashi [aut, ctb]
,
Leandro Simoes Azeredo Goncalves [aut, ctb]
Maintainer: Gabriel Danilo Shimizu <shimizu@uel.br>
Diff between AgroR versions 1.2.9 dated 2022-04-06 and 1.3.0 dated 2022-06-15
DESCRIPTION | 12 ++++++------ MD5 | 45 ++++++++++++++++++++++++++------------------- NAMESPACE | 4 ++++ NEWS.md | 12 ++++++++++++ R/bar_dunnett.R |only R/bargraph2_function.R |only R/croqui_function.R | 24 ++++++++++++------------ R/dbct_function.R | 1 - R/dic_function.R | 1 + R/dict_function.R | 1 - R/dqlt_function.R | 1 - R/dunnet_function.R | 45 ++++++++++++++++++++++++++++++++++----------- R/ibarplot_double.R |only R/logistic_function.R | 4 +++- R/plotjitter_function.R | 9 +++++---- R/sk_graph_function.R | 2 +- build |only man/AgroR-package.Rd | 4 ++-- man/DBCT.Rd | 2 -- man/DICT.Rd | 2 -- man/DQLT.Rd | 2 -- man/bar_dunnett.Rd |only man/bar_graph2.Rd |only man/dunnett.Rd | 26 +++++++++++++++++++++++++- man/ibarplot.double.Rd |only man/logistic.Rd | 2 +- man/sketch.Rd | 2 +- 27 files changed, 133 insertions(+), 68 deletions(-)
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