Title: An Efficient Swiss Army Knife for Population Genomic Analyses
Description: Provides efficient tools for population genomics data analysis,
able to process individual loci, large sets of loci, or whole genomes. PopGenome <DOI:10.1093/molbev/msu136> not only
implements a wide range of population genetics statistics, but also facilitates the easy
implementation of new algorithms by other researchers. PopGenome is optimized for speed via
the seamless integration of C code.
Author: Bastian Pfeifer [aut, cre],
Ulrich Wittelsbuerger [ctb],
Heng Li [ctb],
Bob Handsaker [ctb]
Maintainer: Bastian Pfeifer <bastianxpfeifer@gmail.com>
Diff between PopGenome versions 2.6.1 dated 2018-05-20 and 2.7.1 dated 2019-05-11
PopGenome-2.6.1/PopGenome/R/calc_BDF.R |only PopGenome-2.6.1/PopGenome/README.md |only PopGenome-2.7.1/PopGenome/DESCRIPTION | 8 PopGenome-2.7.1/PopGenome/MD5 | 47 ++--- PopGenome-2.7.1/PopGenome/NEWS | 6 PopGenome-2.7.1/PopGenome/R/GEN.R | 6 PopGenome-2.7.1/PopGenome/R/GENOME.R | 10 - PopGenome-2.7.1/PopGenome/R/calc_df.R |only PopGenome-2.7.1/PopGenome/R/introgression.stats.R | 58 +++--- PopGenome-2.7.1/PopGenome/R/readData.R | 7 PopGenome-2.7.1/PopGenome/R/set.synnonsyn.R | 9 - PopGenome-2.7.1/PopGenome/R/splitting.data.sep.R | 8 PopGenome-2.7.1/PopGenome/R/weighted.jackknife.R | 78 ++++----- PopGenome-2.7.1/PopGenome/build/vignette.rds |binary PopGenome-2.7.1/PopGenome/inst/doc/An_introduction_to_the_PopGenome_package.pdf |binary PopGenome-2.7.1/PopGenome/inst/doc/Integration_of_new_Methods.Rnw | 1 PopGenome-2.7.1/PopGenome/inst/doc/Integration_of_new_Methods.pdf |binary PopGenome-2.7.1/PopGenome/inst/doc/Whole_genome_analyses_using_VCF_files.Rnw | 2 PopGenome-2.7.1/PopGenome/inst/doc/Whole_genome_analyses_using_VCF_files.pdf |binary PopGenome-2.7.1/PopGenome/man/GENOME-class.Rd | 10 - PopGenome-2.7.1/PopGenome/man/introgression.stats.Rd | 18 +- PopGenome-2.7.1/PopGenome/man/weighted.jackknife.Rd | 86 ++++++---- PopGenome-2.7.1/PopGenome/src/whopgenome/whoptbi_info.cpp | 4 PopGenome-2.7.1/PopGenome/src/whopgenome/whoptbi_region.cpp | 6 PopGenome-2.7.1/PopGenome/vignettes/Integration_of_new_Methods.Rnw | 1 PopGenome-2.7.1/PopGenome/vignettes/Whole_genome_analyses_using_VCF_files.Rnw | 2 26 files changed, 206 insertions(+), 161 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 0.8.2 dated 2019-05-11 and 0.8.3 dated 2019-05-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ R/ggpairs.R | 4 ++-- R/kaplan.R | 2 +- R/timeroc.R | 9 +++++++-- inst/doc/jsmodule.html | 4 ++-- 7 files changed, 30 insertions(+), 17 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent access to
information contained in various R models, like model formulas, model terms,
information about random effects, data that was used to fit the model or
data from response variables. 'insight' mainly revolves around two types
of functions: Functions that find (the names of) information, starting with
'find_', and functions that get the underlying data, starting with 'get_'.
The package has a consistent syntax and works with many different model
objects, where otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between insight versions 0.2.0 dated 2019-03-29 and 0.3.0 dated 2019-05-11
insight-0.2.0/insight/man/dot-get_variance_beta_family.Rd |only insight-0.2.0/insight/man/dot-get_variance_default.Rd |only insight-0.2.0/insight/man/dot-get_variance_dist.Rd |only insight-0.2.0/insight/man/dot-get_variance_nbinom_family.Rd |only insight-0.2.0/insight/man/dot-get_variance_tweedie_family.Rd |only insight-0.3.0/insight/DESCRIPTION | 22 insight-0.3.0/insight/MD5 | 166 +++--- insight-0.3.0/insight/NAMESPACE | 60 ++ insight-0.3.0/insight/NEWS.md | 41 + insight-0.3.0/insight/R/clean_names.R | 17 insight-0.3.0/insight/R/compute_variances.R | 211 ++++++-- insight-0.3.0/insight/R/find_algorithm.R | 30 + insight-0.3.0/insight/R/find_formula.R | 111 +++- insight-0.3.0/insight/R/find_parameters.R | 280 ++++++++--- insight-0.3.0/insight/R/find_predictors.R | 7 insight-0.3.0/insight/R/find_random.R | 45 + insight-0.3.0/insight/R/find_variables.R | 49 + insight-0.3.0/insight/R/get_data.R | 222 +++++++- insight-0.3.0/insight/R/get_parameters.R | 89 +++ insight-0.3.0/insight/R/get_predictors.R | 9 insight-0.3.0/insight/R/get_priors.R | 71 ++ insight-0.3.0/insight/R/get_variances.R | 3 insight-0.3.0/insight/R/has_intercept.R |only insight-0.3.0/insight/R/helper_functions.R | 64 ++ insight-0.3.0/insight/R/is_model.R | 20 insight-0.3.0/insight/R/is_nullmodel.R |only insight-0.3.0/insight/R/link_function.R | 90 +++ insight-0.3.0/insight/R/link_inverse.R | 84 +++ insight-0.3.0/insight/R/model_info.R | 151 +++++ insight-0.3.0/insight/R/n_obs.R | 41 + insight-0.3.0/insight/README.md |only insight-0.3.0/insight/build/partial.rdb |binary insight-0.3.0/insight/build/vignette.rds |only insight-0.3.0/insight/inst |only insight-0.3.0/insight/man/dot-badlink.Rd | 4 insight-0.3.0/insight/man/dot-between_subject_variance.Rd |only insight-0.3.0/insight/man/dot-collapse_cond.Rd | 6 insight-0.3.0/insight/man/dot-null_model.Rd | 4 insight-0.3.0/insight/man/dot-random_slope_intercept_corr.Rd |only insight-0.3.0/insight/man/dot-random_slope_variance.Rd |only insight-0.3.0/insight/man/dot-variance_distributional.Rd |only insight-0.3.0/insight/man/dot-variance_family_beta.Rd |only insight-0.3.0/insight/man/dot-variance_family_default.Rd |only insight-0.3.0/insight/man/dot-variance_family_nbinom.Rd |only insight-0.3.0/insight/man/dot-variance_family_poisson.Rd |only insight-0.3.0/insight/man/dot-variance_family_tweedie.Rd |only insight-0.3.0/insight/man/dot-variance_zinb.Rd |only insight-0.3.0/insight/man/dot-variance_zip.Rd |only insight-0.3.0/insight/man/find_formula.Rd | 1 insight-0.3.0/insight/man/find_parameters.Rd | 14 insight-0.3.0/insight/man/find_predictors.Rd | 2 insight-0.3.0/insight/man/find_random.Rd | 2 insight-0.3.0/insight/man/find_terms.Rd | 2 insight-0.3.0/insight/man/find_variables.Rd | 5 insight-0.3.0/insight/man/get_data.Rd | 8 insight-0.3.0/insight/man/get_parameters.Rd | 8 insight-0.3.0/insight/man/get_variance.Rd | 3 insight-0.3.0/insight/man/has_intercept.Rd |only insight-0.3.0/insight/man/is_nullmodel.Rd |only insight-0.3.0/insight/man/n_obs.Rd | 5 insight-0.3.0/insight/tests/testthat/test-BayesFactorBF.R |only insight-0.3.0/insight/tests/testthat/test-GLMMadaptive.R | 12 insight-0.3.0/insight/tests/testthat/test-Gam2.R | 4 insight-0.3.0/insight/tests/testthat/test-LORgee.R |only insight-0.3.0/insight/tests/testthat/test-all_models_equal.R |only insight-0.3.0/insight/tests/testthat/test-aovlist.R | 2 insight-0.3.0/insight/tests/testthat/test-betareg.R | 2 insight-0.3.0/insight/tests/testthat/test-bigglm.R |only insight-0.3.0/insight/tests/testthat/test-blmer.R | 2 insight-0.3.0/insight/tests/testthat/test-brms.R | 122 ++-- insight-0.3.0/insight/tests/testthat/test-censReg.R |only insight-0.3.0/insight/tests/testthat/test-clm.R | 2 insight-0.3.0/insight/tests/testthat/test-clm2.R | 2 insight-0.3.0/insight/tests/testthat/test-clmm.R | 2 insight-0.3.0/insight/tests/testthat/test-data.frame.R |only insight-0.3.0/insight/tests/testthat/test-feis.R |only insight-0.3.0/insight/tests/testthat/test-felm.R | 4 insight-0.3.0/insight/tests/testthat/test-gbm.R |only insight-0.3.0/insight/tests/testthat/test-glm.R | 10 insight-0.3.0/insight/tests/testthat/test-glmmTMB.R | 49 + insight-0.3.0/insight/tests/testthat/test-gmnl.R | 2 insight-0.3.0/insight/tests/testthat/test-has_intercept.R |only insight-0.3.0/insight/tests/testthat/test-is_nullmodel.R |only insight-0.3.0/insight/tests/testthat/test-lm.R | 41 + insight-0.3.0/insight/tests/testthat/test-lme.R | 38 + insight-0.3.0/insight/tests/testthat/test-lmer.R | 111 +++- insight-0.3.0/insight/tests/testthat/test-mixed.R | 25 insight-0.3.0/insight/tests/testthat/test-namespace.R |only insight-0.3.0/insight/tests/testthat/test-ols.R |only insight-0.3.0/insight/tests/testthat/test-plm.R | 159 +++--- insight-0.3.0/insight/tests/testthat/test-polr.R | 2 insight-0.3.0/insight/tests/testthat/test-psm.R |only insight-0.3.0/insight/tests/testthat/test-rlmer.R | 1 insight-0.3.0/insight/tests/testthat/test-rstanarm.R | 34 - insight-0.3.0/insight/tests/testthat/test-speedglm.R |only insight-0.3.0/insight/tests/testthat/test-speedlm.R |only insight-0.3.0/insight/tests/testthat/test-survey.R | 2 insight-0.3.0/insight/tests/testthat/test-tobit.R | 6 insight-0.3.0/insight/tests/testthat/test-truncreg.R | 2 insight-0.3.0/insight/tests/testthat/test-vgam.R | 235 ++++----- insight-0.3.0/insight/vignettes |only 101 files changed, 2175 insertions(+), 643 deletions(-)
Title: Interactive Cluster Heat Maps Using 'plotly'
Description: Create interactive cluster 'heatmaps' that can be saved as a stand-
alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and
available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to
show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical
method for visualizing high-dimensional data, in which a table of numbers
are encoded as a grid of colored cells. The rows and columns of the matrix
are ordered to highlight patterns and are often accompanied by 'dendrograms'.
'Heatmaps' are used in many fields for visualizing observations, correlations,
missing values patterns, and more. Interactive 'heatmaps' allow the inspection
of specific value by hovering the mouse over a cell, as well as zooming into
a region of the 'heatmap' by dragging a rectangle around the relevant area.
This work is based on the 'ggplot2' and 'plotly.js' engine. It produces
similar 'heatmaps' as 'heatmap.2' or 'd3heatmap', with the advantage of speed
('plotly.js' is able to handle larger size matrix), the ability to zoom from
the 'dendrogram' panes, and the placing of factor variables in the sides of the
'heatmap'.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Alan O'Callaghan [aut] (https://github.com/Alanocallaghan),
Jonathan Sidi [ctb] (https://github.com/yonicd),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between heatmaply versions 0.15.2 dated 2018-07-06 and 0.16.0 dated 2019-05-11
ChangeLog | 167 ++++++++++++++++++++++++-------- DESCRIPTION | 24 ++-- MD5 | 24 ++-- NAMESPACE | 1 NEWS | 25 ++++ NEWS.md | 27 ++++- R/heatmaply.R | 84 ++++++++++------ R/plots.R | 141 +++++++++++++++++++-------- build/vignette.rds |binary inst/doc/heatmaply.html | 233 ++++++++++++++++++++++++++++----------------- man/heatmaply.Rd | 86 +++++++++------- man/heatmapr.Rd | 17 +-- tests/testthat/test_misc.R | 2 13 files changed, 559 insertions(+), 272 deletions(-)
Title: Analogue and Weighted Averaging Methods for Palaeoecology
Description: Fits Modern Analogue Technique and Weighted Averaging transfer
function models for prediction of environmental data from species
data, and related methods used in palaeoecology.
Author: Gavin L. Simpson [aut, cre] (<https://orcid.org/0000-0002-9084-8413>),
Jari Oksanen [aut]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between analogue versions 0.17-1 dated 2018-10-23 and 0.17-3 dated 2019-05-11
DESCRIPTION | 10 MD5 | 42 build/vignette.rds |binary data/Biome.rda |binary data/Climate.rda |binary data/ImbrieKipp.rda |binary data/Location.rda |binary data/Pollen.rda |binary data/Salinity.rda |binary data/SumSST.rda |binary data/V12.122.rda |binary data/WinSST.rda |binary data/abernethy.rda |binary data/rlgh.rda |binary data/swapdiat.rda |binary data/swappH.rda |binary inst/NEWS | 8 inst/doc/analogue_methods.pdf |binary man/cma.Rd | 4 man/predict.wa.Rd | 1 man/weightedCor.Rd | 3 tests/Examples/analogue-Ex.Rout.save | 3319 +++++++++++++++++------------------ 22 files changed, 1736 insertions(+), 1651 deletions(-)
Title: Welch-James Statistic for Robust Hypothesis Testing under
Heterocedasticity and Non-Normality
Description: Implementation of Johansen's general formulation of Welch-James's statistic with Approximate Degrees of Freedom, which makes it suitable for testing
any linear hypothesis concerning cell means in univariate and multivariate mixed model designs when the data pose non-normality and non-homogeneous variance. Some
improvements, namely trimmed means and Winsorized variances, and bootstrapping for calculating an empirical critical value, have been added to the classical formulation.
The code departs from a previous SAS implementation by L.M. Lix and H.J. Keselman, available at <http://supp.apa.org/psycarticles/supplemental/met_13_2_110/SAS_Program.pdf> and
published in Keselman, H.J., Wilcox, R.R., and Lix, L.M. (2003) <DOI:10.1111/1469-8986.00060>.
Author: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Maintainer: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Diff between welchADF versions 0.3 dated 2018-06-01 and 0.3.1 dated 2019-05-11
DESCRIPTION | 8 ++--- MD5 | 22 ++++++++++----- R/compute-omnibus.R | 7 ++--- R/robust-interaction.R | 1 R/welch-james-statistic.R | 2 - R/welch-wrapper.R | 6 ++-- R/wrapper-aux.R | 64 +++++++++++++++++++++++++--------------------- build |only inst |only man/perceptionData.Rd | 1 man/welchADF.test.Rd | 17 +++++++----- vignettes |only 12 files changed, 72 insertions(+), 56 deletions(-)
Title: Co-Correspondence Analysis Methods
Description: Fits predictive and symmetric co-correspondence analysis (CoCA) models to relate one data matrix to another data matrix. More specifically, CoCA maximises the weighted covariance between the weighted averaged species scores of one community and the weighted averaged species scores of another community. CoCA attempts to find patterns that are common to both communities.
Author: Original Matlab routines by C.J.F. ter Braak and A.P. Schaffers. R port by Gavin L. Simpson.
Function simpls based on simpls.fit (package pls) by Ron Wehrens and Bjorn-Helge Mevik.
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between cocorresp versions 0.3-0 dated 2016-02-28 and 0.4-0 dated 2019-05-11
cocorresp-0.3-0/cocorresp/R/eigenvals.coca.R |only cocorresp-0.4-0/cocorresp/DESCRIPTION | 15 cocorresp-0.4-0/cocorresp/MD5 | 103 +- cocorresp-0.4-0/cocorresp/NAMESPACE | 13 cocorresp-0.4-0/cocorresp/R/biplots.R |only cocorresp-0.4-0/cocorresp/R/coca.default.R | 42 - cocorresp-0.4-0/cocorresp/R/coca.formula.R | 73 - cocorresp-0.4-0/cocorresp/R/corAxis.R | 9 cocorresp-0.4-0/cocorresp/R/eigenvals.R |only cocorresp-0.4-0/cocorresp/R/fitted.symcoca.R | 48 - cocorresp-0.4-0/cocorresp/R/loadings.R |only cocorresp-0.4-0/cocorresp/R/plot.predcoca.R | 26 cocorresp-0.4-0/cocorresp/R/plot.symcoca.R | 21 cocorresp-0.4-0/cocorresp/R/print.coinertia.R | 2 cocorresp-0.4-0/cocorresp/R/print.fitted.symcoca.R | 20 cocorresp-0.4-0/cocorresp/R/print.predcoca.R | 35 cocorresp-0.4-0/cocorresp/R/print.summary.coinertia.R | 2 cocorresp-0.4-0/cocorresp/R/print.summary.predcoca.R | 49 - cocorresp-0.4-0/cocorresp/R/print.summary.symcoca.R | 56 - cocorresp-0.4-0/cocorresp/R/print.symcoca.R | 8 cocorresp-0.4-0/cocorresp/R/rescale.symcoca.R | 35 cocorresp-0.4-0/cocorresp/R/scores.symcoca.R | 17 cocorresp-0.4-0/cocorresp/R/summary.predcoca.R | 13 cocorresp-0.4-0/cocorresp/R/summary.symcoca.R | 23 cocorresp-0.4-0/cocorresp/R/which-selector.R |only cocorresp-0.4-0/cocorresp/README.md | 28 cocorresp-0.4-0/cocorresp/build/vignette.rds |binary cocorresp-0.4-0/cocorresp/data/beetles.rda |binary cocorresp-0.4-0/cocorresp/data/bryophyte.rda |binary cocorresp-0.4-0/cocorresp/data/plants.rda |binary cocorresp-0.4-0/cocorresp/data/vascular.rda |binary cocorresp-0.4-0/cocorresp/inst/CITATION | 2 cocorresp-0.4-0/cocorresp/inst/doc/cocorresp-intro.R | 6 cocorresp-0.4-0/cocorresp/inst/doc/cocorresp-intro.Rmd | 22 cocorresp-0.4-0/cocorresp/inst/doc/cocorresp-intro.html | 49 - cocorresp-0.4-0/cocorresp/man/biplots.Rd |only cocorresp-0.4-0/cocorresp/man/coca.Rd | 42 - cocorresp-0.4-0/cocorresp/man/cocorresp-package.Rd | 26 cocorresp-0.4-0/cocorresp/man/corAxis.Rd | 10 cocorresp-0.4-0/cocorresp/man/envfit.coca.Rd | 2 cocorresp-0.4-0/cocorresp/man/fitted.symcoca.Rd | 16 cocorresp-0.4-0/cocorresp/man/loadings.Rd |only cocorresp-0.4-0/cocorresp/man/permutest.coca.Rd | 22 cocorresp-0.4-0/cocorresp/man/plot.predcoca.Rd | 10 cocorresp-0.4-0/cocorresp/man/plot.symcoca.Rd | 10 cocorresp-0.4-0/cocorresp/man/points.coca.Rd | 2 cocorresp-0.4-0/cocorresp/man/rescale.Rd | 16 cocorresp-0.4-0/cocorresp/man/scores.predcoca.Rd | 8 cocorresp-0.4-0/cocorresp/man/screeplot.symcoca.Rd | 2 cocorresp-0.4-0/cocorresp/man/summary.predcoca.Rd | 29 cocorresp-0.4-0/cocorresp/tests/Examples/cocorresp-Ex.Rout.save | 409 ++++++---- cocorresp-0.4-0/cocorresp/tests/testthat/test-coca.R | 2 cocorresp-0.4-0/cocorresp/tests/testthat/test-eigenvals.R |only cocorresp-0.4-0/cocorresp/tests/testthat/test-fitted.R |only cocorresp-0.4-0/cocorresp/tests/testthat/test-permutest.R | 4 cocorresp-0.4-0/cocorresp/tests/testthat/test-summary-methods.R |only cocorresp-0.4-0/cocorresp/tests/testthat/test-utils.R |only cocorresp-0.4-0/cocorresp/vignettes/cocorresp-intro.Rmd | 22 58 files changed, 760 insertions(+), 589 deletions(-)
Title: Composable Preprocessing Operators and Pipelines for Machine
Learning
Description: Toolset that enriches 'mlr' with a diverse set of preprocessing
operators. Composable Preprocessing Operators ("CPO"s) are first-class
R objects that can be applied to data.frames and 'mlr' "Task"s to modify
data, can be attached to 'mlr' "Learner"s to add preprocessing to machine
learning algorithms, and can be composed to form preprocessing pipelines.
Author: Martin Binder [aut, cre],
Bernd Bischl [ctb],
Michel Lang [ctb],
Lars Kotthoff [ctb]
Maintainer: Martin Binder <developer.mb706@doublecaret.com>
Diff between mlrCPO versions 0.3.4-2 dated 2019-01-10 and 0.3.4-3 dated 2019-05-11
DESCRIPTION | 6 ++--- MD5 | 38 ++++++++++++++++---------------- NAMESPACE | 1 R/CPO_encode.R | 15 ++++++++++-- R/CPO_filterFeatures.R | 11 +++++---- R/CPO_scale.R | 4 +++ R/FormatCheck.R | 7 ++++- R/learner.R | 14 ++++++++++- build/vignette.rds |binary inst/doc/a_1_getting_started.html | 35 +++++++++++++++++++++++++---- inst/doc/a_2_mlrCPO_core.html | 33 ++++++++++++++++++++++++--- inst/doc/a_3_all_CPOs.html | 37 ++++++++++++++++++++++++++----- inst/doc/a_4_custom_CPOs.html | 35 +++++++++++++++++++++++++---- inst/doc/z_1_getting_started_terse.html | 33 ++++++++++++++++++++++++--- inst/doc/z_2_mlrCPO_core_terse.html | 33 ++++++++++++++++++++++++--- inst/doc/z_3_all_CPOs_terse.html | 33 ++++++++++++++++++++++++--- inst/doc/z_4_custom_CPOs_terse.html | 33 ++++++++++++++++++++++++--- man/cpoDummyEncode.Rd | 15 ++++++++---- tests/testthat/test_cpo_concrete.R | 18 +++++++++++++++ tests/testthat/test_cpo_filter.R | 19 ++++++++-------- 20 files changed, 338 insertions(+), 82 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description: Contains functions for multiple imputation which
complements existing functionality in R.
In particular, several imputation methods for the
mice package (van Buuren & Groothuis-Oudshoorn, 2011,
<doi:10.18637/jss.v045.i03>) are included.
Main features of the miceadds package include
plausible value imputation (Mislevy, 1991,
<doi:10.1007/BF02294457>), multilevel imputation for
variables at any level or with any number of hierarchical
and non-hierarchical levels (Grund, Luedtke & Robitzsch,
2018, <doi:10.1177/1094428117703686>; van Buuren, 2018,
Ch.7, <doi:10.1201/9780429492259>), imputation using
partial least squares (PLS) for high dimensional
predictors (Robitzsch, Pham & Yanagida, 2016),
nested multiple imputation (Rubin, 2003,
<doi:10.1111/1467-9574.00217>) and substantive model
compatible imputation (Bartlett et al., 2015,
<doi:10.1177/0962280214521348>).
Author: Alexander Robitzsch [aut, cre], Simon Grund [aut],
Thorsten Henke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 3.2-48 dated 2019-04-15 and 3.3-33 dated 2019-05-11
miceadds-3.2-48/miceadds/R/mice_imputation_draw_bootstrap_sample.R |only miceadds-3.2-48/miceadds/R/sub.micombine.cor.R |only miceadds-3.2-48/miceadds/R/sub.micombine.cov.R |only miceadds-3.3-33/miceadds/DESCRIPTION | 17 miceadds-3.3-33/miceadds/MD5 | 177 +++--- miceadds-3.3-33/miceadds/NAMESPACE | 67 +- miceadds-3.3-33/miceadds/R/GroupMean.R | 14 miceadds-3.3-33/miceadds/R/GroupMean_extend_data.R |only miceadds-3.3-33/miceadds/R/GroupMean_group_indices.R |only miceadds-3.3-33/miceadds/R/GroupSD.R | 12 miceadds-3.3-33/miceadds/R/GroupSum.R | 14 miceadds-3.3-33/miceadds/R/RcppExports.R | 2 miceadds-3.3-33/miceadds/R/VariableNames2String.R | 9 miceadds-3.3-33/miceadds/R/cxxfunction.copy.R | 4 miceadds-3.3-33/miceadds/R/datlist2nested.datlist.R |only miceadds-3.3-33/miceadds/R/draw.pv.ctt.R | 4 miceadds-3.3-33/miceadds/R/glm.cluster.R | 45 - miceadds-3.3-33/miceadds/R/latent_regression_em_sampling.R | 6 miceadds-3.3-33/miceadds/R/lm.cluster.R | 43 - miceadds-3.3-33/miceadds/R/lm_cluster_compute_vcov.R |only miceadds-3.3-33/miceadds/R/lm_cluster_subset.R |only miceadds-3.3-33/miceadds/R/lmer_extract_sd_random_effects.R | 3 miceadds-3.3-33/miceadds/R/lmer_vcov.R | 9 miceadds-3.3-33/miceadds/R/lmer_vcov2.R | 7 miceadds-3.3-33/miceadds/R/load.data.R | 6 miceadds-3.3-33/miceadds/R/ma.wtd.quantileNA.R | 3 miceadds-3.3-33/miceadds/R/ma_wtd_stat_prepare_data.R | 4 miceadds-3.3-33/miceadds/R/mi.anova.R | 4 miceadds-3.3-33/miceadds/R/mice.impute.2l.latentgroupmean.mcmc.R | 4 miceadds-3.3-33/miceadds/R/mice.impute.2l.latentgroupmean.ml.R | 3 miceadds-3.3-33/miceadds/R/mice.impute.2l.pmm.R | 4 miceadds-3.3-33/miceadds/R/mice.impute.grouped.R | 4 miceadds-3.3-33/miceadds/R/mice.impute.hotDeck.R | 8 miceadds-3.3-33/miceadds/R/mice.impute.lm.R |only miceadds-3.3-33/miceadds/R/mice.impute.lm_fun.R |only miceadds-3.3-33/miceadds/R/mice.impute.lqs.R |only miceadds-3.3-33/miceadds/R/mice.impute.ml.lmer.R | 7 miceadds-3.3-33/miceadds/R/mice.impute.plausible.values.R | 5 miceadds-3.3-33/miceadds/R/mice.impute.pls.R | 15 miceadds-3.3-33/miceadds/R/mice.impute.pmm3.R | 3 miceadds-3.3-33/miceadds/R/mice.impute.rlm.R |only miceadds-3.3-33/miceadds/R/mice.impute.smcfcs.R | 20 miceadds-3.3-33/miceadds/R/mice_imputation_2l_lmer.R | 5 miceadds-3.3-33/miceadds/R/mice_imputation_extract_list_arguments.R | 10 miceadds-3.3-33/miceadds/R/mice_imputation_input_data_frame.R |only miceadds-3.3-33/miceadds/R/mice_imputation_linear_model_main.R |only miceadds-3.3-33/miceadds/R/mice_imputation_multilevel_lmerControl_define_optimizer.R | 3 miceadds-3.3-33/miceadds/R/mice_imputation_pls_do_impute.R | 107 +-- miceadds-3.3-33/miceadds/R/mice_imputation_pls_draw_bootstrap_sample.R |only miceadds-3.3-33/miceadds/R/mice_imputation_pls_estimate_pls_regression.R | 6 miceadds-3.3-33/miceadds/R/mice_imputation_pls_pmm_match.R |only miceadds-3.3-33/miceadds/R/mice_imputation_prepare_2l_functions.R | 16 miceadds-3.3-33/miceadds/R/mice_imputation_refresh_update_factor.R | 2 miceadds-3.3-33/miceadds/R/mice_imputation_smcfcs_clean_input.R | 22 miceadds-3.3-33/miceadds/R/mice_imputation_smcfcs_draw_bootstrap_sample.R |only miceadds-3.3-33/miceadds/R/mice_imputation_transformation.R |only miceadds-3.3-33/miceadds/R/mice_ml_lmer_define_lmer_function.R | 6 miceadds-3.3-33/miceadds/R/mice_multilevel_imputation_pmm5.R | 4 miceadds-3.3-33/miceadds/R/miceadds_import_CDM_CDM_rmvnorm.R |only miceadds-3.3-33/miceadds/R/miceadds_import_mitools_MIcombine.R |only miceadds-3.3-33/miceadds/R/miceadds_import_mitools_imputationList.R |only miceadds-3.3-33/miceadds/R/miceadds_matrix2.R |only miceadds-3.3-33/miceadds/R/miceadds_weighted_centering.R | 3 miceadds-3.3-33/miceadds/R/miceadds_weighted_scaling_y.R | 3 miceadds-3.3-33/miceadds/R/micombine.chisquare.R | 18 miceadds-3.3-33/miceadds/R/micombine.cor.R | 28 - miceadds-3.3-33/miceadds/R/micombine.cov.R | 4 miceadds-3.3-33/miceadds/R/micombine_cor_compute.R |only miceadds-3.3-33/miceadds/R/micombine_cov_compute.R |only miceadds-3.3-33/miceadds/R/mids2datlist.R | 14 miceadds-3.3-33/miceadds/R/ml_mcmc_initial_values.R | 3 miceadds-3.3-33/miceadds/R/nested.datlist2datlist.R | 99 +-- miceadds-3.3-33/miceadds/R/nnig_coef.R | 3 miceadds-3.3-33/miceadds/R/require_namespace.R |only miceadds-3.3-33/miceadds/R/save.data.R | 4 miceadds-3.3-33/miceadds/R/scale_datlist.R | 10 miceadds-3.3-33/miceadds/R/sirt_subset_object.R |only miceadds-3.3-33/miceadds/R/stats0.R | 6 miceadds-3.3-33/miceadds/R/string_to_matrix.R | 31 - miceadds-3.3-33/miceadds/R/subset_datlist.R | 18 miceadds-3.3-33/miceadds/R/subset_nested.datlist.R | 276 ++++------ miceadds-3.3-33/miceadds/R/summary.MIwaldtest.R | 6 miceadds-3.3-33/miceadds/R/summary.NMIwaldtest.R | 6 miceadds-3.3-33/miceadds/R/summary.lmer_pool.R | 6 miceadds-3.3-33/miceadds/R/summary.lmer_vcov.R | 4 miceadds-3.3-33/miceadds/R/summary.ml_mcmc.R | 5 miceadds-3.3-33/miceadds/R/summaryMIwaldtest_linear_hyp.R | 6 miceadds-3.3-33/miceadds/R/systime.R | 7 miceadds-3.3-33/miceadds/R/var0.R | 5 miceadds-3.3-33/miceadds/R/vector2matrix.R | 6 miceadds-3.3-33/miceadds/R/with.datlist.R | 6 miceadds-3.3-33/miceadds/README.md | 4 miceadds-3.3-33/miceadds/build/partial.rdb |binary miceadds-3.3-33/miceadds/inst/NEWS | 24 miceadds-3.3-33/miceadds/man/filename_split.Rd | 20 miceadds-3.3-33/miceadds/man/fleishman_sim.Rd | 5 miceadds-3.3-33/miceadds/man/lm.cluster.Rd | 16 miceadds-3.3-33/miceadds/man/mice.impute.ml.lmer.Rd | 4 miceadds-3.3-33/miceadds/man/mice.impute.pls.Rd | 12 miceadds-3.3-33/miceadds/man/mice.impute.rlm.Rd |only miceadds-3.3-33/miceadds/man/mice.impute.tricube.pmm.Rd | 4 miceadds-3.3-33/miceadds/man/nnig_sim.Rd | 4 miceadds-3.3-33/miceadds/src/RcppExports.cpp | 2 103 files changed, 714 insertions(+), 662 deletions(-)
Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed for formatting columns
of data using the full range of colours provided by modern terminals.
Author: Kirill Müller [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between pillar versions 1.3.1 dated 2018-12-15 and 1.4.0 dated 2019-05-11
DESCRIPTION | 27 +- MD5 | 213 ++++++++++--------- NAMESPACE | 25 -- NEWS.md | 23 ++ R/compat-lifecycle.R |only R/compat-purrr.R | 2 R/dim.R | 2 R/empty-data.R |only R/lengths.R |only R/multi.R | 42 ++- R/ornament.R | 4 R/pillar-package.R | 16 + R/pillar.R | 18 + R/rowid-data.R | 15 - R/rowid-title.R | 4 R/rowid-type.R | 4 R/shaft-simple.R | 2 R/shaft.R | 43 +++ R/sigfig.R | 52 ++-- R/spark-bar.R | 7 R/spark-line.R | 7 R/strrep.R | 23 -- R/styles.R | 117 ++++++++-- R/testthat.R | 7 R/type-sum.R | 88 ++++--- R/type.R | 2 R/zzz.R | 21 + README.md | 139 +++++++----- build |only man/colonnade.Rd | 12 - man/expect_known_display.Rd | 2 man/extra_cols.Rd | 4 man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-soft-deprecated.svg |only man/figures/lifecycle-stable.svg |only man/new_pillar_shaft.Rd | 23 +- man/pillar-package.Rd | 15 + man/pillar.Rd | 18 + man/pillar_shaft.Rd | 2 man/type_sum.Rd | 12 + tests/testthat/bw-out/asis-list.txt | 2 tests/testthat/bw-out/asis-number.txt | 2 tests/testthat/bw-out/basic.txt | 24 +- tests/testthat/bw-out/decimal-insignif.txt | 22 - tests/testthat/bw-out/difftime.txt | 2 tests/testthat/bw-out/list-narrow.txt | 2 tests/testthat/bw-out/lubridate.txt | 8 tests/testthat/bw-out/matrix-col-empty.txt |only tests/testthat/bw-out/multi-extra-10.txt | 6 tests/testthat/bw-out/multi-extra-20.txt | 6 tests/testthat/bw-out/multi-extra-30.txt | 4 tests/testthat/bw-out/multi-extra-35.txt | 2 tests/testthat/bw-out/style-bold-false.txt | 20 - tests/testthat/bw-out/style-neg-false.txt | 20 - tests/testthat/bw-out/style-regular.txt | 20 - tests/testthat/bw-out/style-subtle-false.txt | 20 - tests/testthat/bw-out/style-subtle-neg-false.txt | 20 - tests/testthat/bw-out/style-subtle-num-true.txt | 20 - tests/testthat/bw-out/tibble-col-empty.txt |only tests/testthat/bw-out/time-digits-secs.txt | 2 tests/testthat/bw-out/time-posix.txt | 2 tests/testthat/bw-out/title-crayon.txt | 22 - tests/testthat/bw-out/title-none.txt | 20 - tests/testthat/bw-out/title-short.txt | 22 - tests/testthat/helper-output.R | 17 + tests/testthat/out-native/asis-list.txt | 2 tests/testthat/out-native/asis-number.txt | 2 tests/testthat/out-native/basic.txt | 24 +- tests/testthat/out-native/decimal-insignif.txt | 22 - tests/testthat/out-native/difftime.txt | 2 tests/testthat/out-native/list-narrow.txt | 2 tests/testthat/out-native/lubridate.txt | 8 tests/testthat/out-native/matrix-col-empty.txt |only tests/testthat/out-native/style-bold-false.txt | 20 - tests/testthat/out-native/style-neg-false.txt | 20 - tests/testthat/out-native/style-regular.txt | 20 - tests/testthat/out-native/style-subtle-false.txt | 20 - tests/testthat/out-native/style-subtle-neg-false.txt | 20 - tests/testthat/out-native/style-subtle-num-true.txt | 20 - tests/testthat/out-native/tibble-col-empty.txt |only tests/testthat/out-native/time-digits-secs.txt | 2 tests/testthat/out-native/time-posix.txt | 2 tests/testthat/out-native/title-crayon.txt | 22 - tests/testthat/out-native/title-none.txt | 20 - tests/testthat/out-native/title-short.txt | 22 - tests/testthat/out/asis-list.txt | 2 tests/testthat/out/asis-number.txt | 2 tests/testthat/out/basic.txt | 24 +- tests/testthat/out/decimal-insignif.txt | 22 - tests/testthat/out/difftime.txt | 2 tests/testthat/out/list-narrow.txt | 2 tests/testthat/out/lubridate.txt | 8 tests/testthat/out/matrix-col-empty.txt |only tests/testthat/out/style-bold-false.txt | 20 - tests/testthat/out/style-neg-false.txt | 20 - tests/testthat/out/style-regular.txt | 20 - tests/testthat/out/style-subtle-false.txt | 20 - tests/testthat/out/style-subtle-neg-false.txt | 20 - tests/testthat/out/style-subtle-num-true.txt | 20 - tests/testthat/out/tibble-col-empty.txt |only tests/testthat/out/time-digits-secs.txt | 2 tests/testthat/out/time-posix.txt | 2 tests/testthat/out/title-crayon.txt | 22 - tests/testthat/out/title-none.txt | 20 - tests/testthat/out/title-short.txt | 22 - tests/testthat/test-aaa.R |only tests/testthat/test-format_character.R | 4 tests/testthat/test-format_decimal.R | 38 ++- tests/testthat/test-format_list.R | 2 tests/testthat/test-format_multi.R | 27 ++ tests/testthat/test-format_scientific.R | 50 +++- tests/testthat/test-obj-sum.R | 38 +-- 117 files changed, 1163 insertions(+), 772 deletions(-)
Title: Identify Sudden Gains in Longitudinal Data
Description: Identify sudden gains based on the three criteria outlined by Tang and DeRubeis (1999) <doi:10.1037/0022-006X.67.6.894> to a selection of repeated measures.
Sudden losses, defined as the opposite of sudden gains can also be identified.
Two different datasets can be created, one including all sudden gains/losses and one including one selected sudden gain/loss for each case.
It can extract scores around sudden gains/losses.
It can plot the average change around sudden gains/losses and trajectories of individual cases.
Author: Milan Wiedemann [aut, cre] (<https://orcid.org/0000-0003-1991-282X>),
Graham M Thew [ctb] (<https://orcid.org/0000-0003-2851-1315>),
Richard Stott [ctb] (<https://orcid.org/0000-0003-2533-5504>),
Anke Ehlers [ctb, ths] (<https://orcid.org/0000-0002-8742-0192>)
Maintainer: Milan Wiedemann <milan.wiedemann@gmail.com>
Diff between suddengains versions 0.1.0 dated 2019-05-03 and 0.2.0 dated 2019-05-11
suddengains-0.1.0/suddengains/inst/doc/suddengains-functions.R |only suddengains-0.1.0/suddengains/inst/doc/suddengains-functions.Rmd |only suddengains-0.1.0/suddengains/inst/doc/suddengains-functions.html |only suddengains-0.1.0/suddengains/vignettes/suddengains-functions.Rmd |only suddengains-0.2.0/suddengains/DESCRIPTION | 22 suddengains-0.2.0/suddengains/MD5 | 88 +- suddengains-0.2.0/suddengains/NAMESPACE | 1 suddengains-0.2.0/suddengains/NEWS.md | 13 suddengains-0.2.0/suddengains/R/count_intervals.R | 87 +- suddengains-0.2.0/suddengains/R/create_byperson.R | 117 +-- suddengains-0.2.0/suddengains/R/create_bysg.R | 95 +- suddengains-0.2.0/suddengains/R/define_crit1_cutoff.R | 21 suddengains-0.2.0/suddengains/R/describe_sg.R | 6 suddengains-0.2.0/suddengains/R/extract_values.R | 9 suddengains-0.2.0/suddengains/R/identify_sg.R | 16 suddengains-0.2.0/suddengains/R/identify_sl.R | 18 suddengains-0.2.0/suddengains/R/plot_sg.R | 384 ++++++---- suddengains-0.2.0/suddengains/R/plot_sg_trajectories.R |only suddengains-0.2.0/suddengains/R/rename_sg_vars.R | 14 suddengains-0.2.0/suddengains/R/select_cases.R | 26 suddengains-0.2.0/suddengains/R/sgdata.R | 12 suddengains-0.2.0/suddengains/R/sgdata_bad.R | 12 suddengains-0.2.0/suddengains/R/suddengains.R | 3 suddengains-0.2.0/suddengains/R/write_byperson.R | 7 suddengains-0.2.0/suddengains/R/write_bysg.R | 8 suddengains-0.2.0/suddengains/README.md | 92 +- suddengains-0.2.0/suddengains/build/vignette.rds |binary suddengains-0.2.0/suddengains/data/sgdata.RData |binary suddengains-0.2.0/suddengains/data/sgdata_bad.RData |binary suddengains-0.2.0/suddengains/inst/CITATION | 4 suddengains-0.2.0/suddengains/inst/doc/suddengains-tutorial.R |only suddengains-0.2.0/suddengains/inst/doc/suddengains-tutorial.Rmd |only suddengains-0.2.0/suddengains/inst/doc/suddengains-tutorial.html |only suddengains-0.2.0/suddengains/man/count_intervals.Rd | 12 suddengains-0.2.0/suddengains/man/create_byperson.Rd | 7 suddengains-0.2.0/suddengains/man/create_bysg.Rd | 7 suddengains-0.2.0/suddengains/man/define_crit1_cutoff.Rd | 5 suddengains-0.2.0/suddengains/man/describe_sg.Rd | 6 suddengains-0.2.0/suddengains/man/extract_values.Rd | 11 suddengains-0.2.0/suddengains/man/identify_sg.Rd | 3 suddengains-0.2.0/suddengains/man/identify_sl.Rd | 3 suddengains-0.2.0/suddengains/man/plot_sg.Rd | 30 suddengains-0.2.0/suddengains/man/plot_sg_trajectories.Rd |only suddengains-0.2.0/suddengains/man/rename_sg_vars.Rd | 14 suddengains-0.2.0/suddengains/man/select_cases.Rd | 23 suddengains-0.2.0/suddengains/man/sgdata.Rd | 6 suddengains-0.2.0/suddengains/man/sgdata_bad.Rd | 6 suddengains-0.2.0/suddengains/man/write_byperson.Rd | 9 suddengains-0.2.0/suddengains/man/write_bysg.Rd | 9 suddengains-0.2.0/suddengains/vignettes/suddengains-tutorial.Rmd |only 50 files changed, 755 insertions(+), 451 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'. Note that
Armadillo requires a fairly recent compiler; for the g++ family at least
version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.9.400.2.0 dated 2019-04-29 and 0.9.400.3.0 dated 2019-05-11
ChangeLog | 9 + DESCRIPTION | 8 - MD5 | 44 ++--- build/vignette.rds |binary inst/NEWS.Rd | 17 ++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo_bits/BaseCube_bones.hpp | 7 inst/include/armadillo_bits/BaseCube_meat.hpp | 81 +++++++++++ inst/include/armadillo_bits/SpBase_bones.hpp | 14 - inst/include/armadillo_bits/SpBase_meat.hpp | 147 ++++++++++++++++++++ inst/include/armadillo_bits/SpMat_bones.hpp | 3 inst/include/armadillo_bits/SpMat_meat.hpp | 59 +++++++- inst/include/armadillo_bits/arma_static_check.hpp | 6 inst/include/armadillo_bits/arma_version.hpp | 2 inst/include/armadillo_bits/auxlib_meat.hpp | 26 ++- inst/include/armadillo_bits/fn_accu.hpp | 27 +++ inst/include/armadillo_bits/fn_misc.hpp | 18 -- inst/include/armadillo_bits/fn_vectorise.hpp | 2 inst/include/armadillo_bits/op_diagmat_bones.hpp | 2 inst/include/armadillo_bits/spop_mean_bones.hpp | 3 inst/include/armadillo_bits/spop_mean_meat.hpp | 26 +++ inst/include/armadillo_bits/spop_vectorise_meat.hpp | 6 23 files changed, 443 insertions(+), 64 deletions(-)
Title: Analysis of fMRI Experiments
Description: Contains R-functions to perform an fMRI analysis as described in
Tabelow et al. (2006) <DOI:10.1016/j.neuroimage.2006.06.029>,
Polzehl et al. (2010) <DOI:10.1016/j.neuroimage.2010.04.241>,
Tabelow and Polzehl (2011) <DOI:10.18637/jss.v044.i11>.
Author: Karsten Tabelow [aut, cre],
Joerg Polzehl [aut],
Brandon Whitcher [ctb],
Dames Sibylle [ctb]
Maintainer: Karsten Tabelow <tabelow@wias-berlin.de>
Diff between fmri versions 1.7-2 dated 2016-09-15 and 1.9 dated 2019-05-11
fmri-1.7-2/fmri/R/fmriGUI.r |only fmri-1.7-2/fmri/R/lm.R |only fmri-1.7-2/fmri/R/ngca.r |only fmri-1.7-2/fmri/R/segmkrv.r |only fmri-1.7-2/fmri/man/extract.data.Rd |only fmri-1.7-2/fmri/man/fmri.gui.Rd |only fmri-1.7-2/fmri/man/fmriica.Rd |only fmri-1.7-2/fmri/man/ngca.Rd |only fmri-1.7-2/fmri/src/ngca.f |only fmri-1.7-2/fmri/src/segm3Dkrv.f |only fmri-1.9/fmri/ChangeLog | 54 +- fmri-1.9/fmri/DESCRIPTION | 18 fmri-1.9/fmri/MD5 | 99 ++-- fmri-1.9/fmri/NAMESPACE | 33 - fmri-1.9/fmri/R/aws.r | 131 ++--- fmri-1.9/fmri/R/cluster.R |only fmri-1.9/fmri/R/detrend.R | 42 + fmri-1.9/fmri/R/fmri.R | 120 ++--- fmri-1.9/fmri/R/fmrisICA.R |only fmri-1.9/fmri/R/gen_fmridata.R |only fmri-1.9/fmri/R/io.R | 159 +++---- fmri-1.9/fmri/R/lmGroup.R | 16 fmri-1.9/fmri/R/lmslicetime.R |only fmri-1.9/fmri/R/misc.r | 221 ++++------ fmri-1.9/fmri/R/oro2fmri.R | 21 fmri-1.9/fmri/R/plot.r | 530 ++++++++++++++++++++++-- fmri-1.9/fmri/R/randomfield.R | 18 fmri-1.9/fmri/R/searchlight.r |only fmri-1.9/fmri/R/segm.r | 33 - fmri-1.9/fmri/R/sysdata.rda |binary fmri-1.9/fmri/R/utilities.r | 8 fmri-1.9/fmri/R/view23D.r | 637 ++++++++++++++--------------- fmri-1.9/fmri/demo/fmri.r | 4 fmri-1.9/fmri/man/ICAfingerprint.Rd |only fmri-1.9/fmri/man/extractData.Rd |only fmri-1.9/fmri/man/fmri.cluster.Rd |only fmri-1.9/fmri/man/fmri.design.Rd | 10 fmri-1.9/fmri/man/fmri.detrend.Rd | 5 fmri-1.9/fmri/man/fmri.lm.Rd | 59 +- fmri-1.9/fmri/man/fmri.lmePar.Rd | 82 +-- fmri-1.9/fmri/man/fmri.metaPar.Rd | 32 - fmri-1.9/fmri/man/fmri.pvalue.Rd | 26 - fmri-1.9/fmri/man/fmri.sICA.Rd |only fmri-1.9/fmri/man/fmri.searchlight.Rd |only fmri-1.9/fmri/man/fmri.sgroupICA.Rd |only fmri-1.9/fmri/man/fmri.stimulus.Rd | 41 + fmri-1.9/fmri/man/gen_fmridata.Rd |only fmri-1.9/fmri/man/getSearchlightPattern.Rd |only fmri-1.9/fmri/man/niftiImage2fmri.Rd |only fmri-1.9/fmri/man/oro2fmri.Rd | 6 fmri-1.9/fmri/man/plot.fmriICA.Rd |only fmri-1.9/fmri/man/plot.fmridata.Rd | 16 fmri-1.9/fmri/man/plot.fmripvalue.Rd |only fmri-1.9/fmri/man/read.AFNI.Rd | 8 fmri-1.9/fmri/man/read.ANALYZE.Rd | 6 fmri-1.9/fmri/man/read.NIFTI.Rd | 4 fmri-1.9/fmri/man/setmask.Rd |only fmri-1.9/fmri/man/sincfilter.Rd |only fmri-1.9/fmri/man/slicetiming.Rd |only fmri-1.9/fmri/man/write.AFNI.Rd | 4 fmri-1.9/fmri/src/clusterthresh.f |only fmri-1.9/fmri/src/init.c |only fmri-1.9/fmri/src/misc.f | 218 +-------- fmri-1.9/fmri/src/segm3D.f | 18 fmri-1.9/fmri/src/slicetime.f |only fmri-1.9/fmri/src/slight.f |only fmri-1.9/fmri/src/vaws3D.f | 77 +-- 67 files changed, 1536 insertions(+), 1220 deletions(-)
Title: Distances on Directed Graphs
Description: Distances on dual-weighted directed graphs using priority-queue
shortest paths (Padgham (2019) <doi:10.32866/6945>). Weighted directed
graphs have weights from A to B which may differ from those from B to A.
Dual-weighted directed graphs have two sets of such weights. A canonical
example is a street network to be used for routing in which routes are
calculated by weighting distances according to the type of way and mode of
transport, yet lengths of routes must be calculated from direct distances.
Author: Mark Padgham [aut, cre],
Andreas Petutschnig [aut],
Robin Lovelace [ctb],
Andrew Smith [ctb],
Malcolm Morgan [ctb],
Shane Saunders [cph] (Original author of included code for priority
heaps)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between dodgr versions 0.1.3 dated 2019-03-20 and 0.1.4 dated 2019-05-11
dodgr-0.1.3/dodgr/R/streetnet-fns.R |only dodgr-0.1.3/dodgr/src/dijkstra.cpp |only dodgr-0.1.3/dodgr/src/dijkstra.h |only dodgr-0.1.4/dodgr/DESCRIPTION | 11 dodgr-0.1.4/dodgr/MD5 | 151 +++--- dodgr-0.1.4/dodgr/NAMESPACE | 3 dodgr-0.1.4/dodgr/NEWS.md | 24 + dodgr-0.1.4/dodgr/R/RcppExports.R | 53 +- dodgr-0.1.4/dodgr/R/compare-heaps.R | 10 dodgr-0.1.4/dodgr/R/dists.R | 150 ++++-- dodgr-0.1.4/dodgr/R/dodgr-package.r | 8 dodgr-0.1.4/dodgr/R/dodgr-streetnet.R |only dodgr-0.1.4/dodgr/R/flows.R | 21 dodgr-0.1.4/dodgr/R/fund-cycles.R | 11 dodgr-0.1.4/dodgr/R/graph-contraction.R | 52 +- dodgr-0.1.4/dodgr/R/graph-conversion.R | 45 +- dodgr-0.1.4/dodgr/R/graph-functions-misc.R | 43 + dodgr-0.1.4/dodgr/R/graph-functions.R | 143 ++++-- dodgr-0.1.4/dodgr/R/paths.R | 11 dodgr-0.1.4/dodgr/R/times.R |only dodgr-0.1.4/dodgr/R/weight-streetnet-times.R |only dodgr-0.1.4/dodgr/R/weight-streetnet.R |only dodgr-0.1.4/dodgr/R/weighting_profiles.R |only dodgr-0.1.4/dodgr/README.md | 333 +++++++++++---- dodgr-0.1.4/dodgr/build/vignette.rds |binary dodgr-0.1.4/dodgr/data/weighting_profiles.rda |binary dodgr-0.1.4/dodgr/inst/doc/benchmark.R | 2 dodgr-0.1.4/dodgr/inst/doc/benchmark.Rmd | 4 dodgr-0.1.4/dodgr/inst/doc/benchmark.html | 4 dodgr-0.1.4/dodgr/inst/doc/dodgr.R | 11 dodgr-0.1.4/dodgr/inst/doc/dodgr.Rmd | 26 - dodgr-0.1.4/dodgr/inst/doc/dodgr.html | 327 +++++++------- dodgr-0.1.4/dodgr/inst/doc/times.R |only dodgr-0.1.4/dodgr/inst/doc/times.Rmd |only dodgr-0.1.4/dodgr/inst/doc/times.html |only dodgr-0.1.4/dodgr/man/compare_heaps.Rd | 2 dodgr-0.1.4/dodgr/man/dodgr_distances.Rd | 18 dodgr-0.1.4/dodgr/man/dodgr_dists.Rd | 43 + dodgr-0.1.4/dodgr/man/dodgr_flows_aggregate.Rd | 9 dodgr-0.1.4/dodgr/man/dodgr_flows_disperse.Rd | 7 dodgr-0.1.4/dodgr/man/dodgr_paths.Rd | 9 dodgr-0.1.4/dodgr/man/dodgr_streetnet.Rd | 2 dodgr-0.1.4/dodgr/man/dodgr_streetnet_sc.Rd |only dodgr-0.1.4/dodgr/man/dodgr_times.Rd |only dodgr-0.1.4/dodgr/man/dodgr_to_igraph.Rd | 5 dodgr-0.1.4/dodgr/man/dodgr_to_sf.Rd | 4 dodgr-0.1.4/dodgr/man/dodgr_to_sfc.Rd | 4 dodgr-0.1.4/dodgr/man/weight_railway.Rd | 2 dodgr-0.1.4/dodgr/man/weight_streetnet.Rd | 84 ++- dodgr-0.1.4/dodgr/man/weighting_profiles.Rd | 8 dodgr-0.1.4/dodgr/man/write_dodgr_wt_profile.Rd |only dodgr-0.1.4/dodgr/src/Makevars | 5 dodgr-0.1.4/dodgr/src/Makevars.win | 5 dodgr-0.1.4/dodgr/src/RcppExports.cpp | 63 +- dodgr-0.1.4/dodgr/src/fund-cycles.cpp | 6 dodgr-0.1.4/dodgr/src/graph-contract.cpp | 65 ++ dodgr-0.1.4/dodgr/src/graph-sample.cpp | 5 dodgr-0.1.4/dodgr/src/graph.cpp | 24 - dodgr-0.1.4/dodgr/src/graph.h | 21 dodgr-0.1.4/dodgr/src/heaps/bheap.cpp | 5 dodgr-0.1.4/dodgr/src/heaps/bheap.h | 2 dodgr-0.1.4/dodgr/src/heaps/fheap.h | 4 dodgr-0.1.4/dodgr/src/heaps/heap.h | 2 dodgr-0.1.4/dodgr/src/heaps/heap23.h | 4 dodgr-0.1.4/dodgr/src/heaps/heap23_2.h | 4 dodgr-0.1.4/dodgr/src/heaps/radixheap.h | 4 dodgr-0.1.4/dodgr/src/heaps/triheap.h | 4 dodgr-0.1.4/dodgr/src/heaps/triheap_ext.h | 4 dodgr-0.1.4/dodgr/src/pathfinders.cpp |only dodgr-0.1.4/dodgr/src/pathfinders.h |only dodgr-0.1.4/dodgr/src/run_sp.cpp | 161 ++++--- dodgr-0.1.4/dodgr/src/run_sp.h | 19 dodgr-0.1.4/dodgr/src/sc-as-network.cpp |only dodgr-0.1.4/dodgr/src/sc-as-network.h |only dodgr-0.1.4/dodgr/src/sf-as-network.cpp | 180 +++----- dodgr-0.1.4/dodgr/src/sf-as-network.h | 14 dodgr-0.1.4/dodgr/src/turn_penalty.cpp |only dodgr-0.1.4/dodgr/src/turn_penalty.h |only dodgr-0.1.4/dodgr/tests/testthat/test-cycles.R | 8 dodgr-0.1.4/dodgr/tests/testthat/test-dists.R | 16 dodgr-0.1.4/dodgr/tests/testthat/test-graph-conversion.R | 14 dodgr-0.1.4/dodgr/tests/testthat/test-graph-fns.R | 111 +++-- dodgr-0.1.4/dodgr/tests/testthat/test-sc.R |only dodgr-0.1.4/dodgr/tests/testthat/test-streetnet.R |only dodgr-0.1.4/dodgr/tests/testthat/test-wt-profiles.R |only dodgr-0.1.4/dodgr/vignettes/benchmark.Rmd | 4 dodgr-0.1.4/dodgr/vignettes/dodgr.Rmd | 26 - dodgr-0.1.4/dodgr/vignettes/times-fig1.tex |only dodgr-0.1.4/dodgr/vignettes/times.Rmd |only 89 files changed, 1511 insertions(+), 909 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)
<http://www.statcan.gc.ca/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'), robu() (from 'robumeta'), and rma.uni() and rma.mv()
(from 'metafor').
Author: James Pustejovsky [aut, cre] (<https://orcid.org/0000-0003-0591-9465>)
Maintainer: James Pustejovsky <jepusto@gmail.com>
Diff between clubSandwich versions 0.3.3 dated 2019-01-24 and 0.3.4 dated 2019-05-11
DESCRIPTION | 12 MD5 | 59 - NEWS | 5 R/coef_test.R | 28 R/conf_int.R | 3 R/data-documentation.R | 8 R/plm.R | 15 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Robust-Variance-Estimation-with-clubSandwich.html | 193 +++++ inst/doc/meta-analysis-with-CRVE.html | 399 ++++++++--- inst/doc/panel-data-CRVE.html | 445 +++++++++---- man/AchievementAwardsRCT.Rd | 4 man/MortalityRates.Rd | 2 man/SATcoaching.Rd | 2 man/coef_test.Rd | 5 tests/testthat.R | 1 tests/testthat/test_coef.R | 8 tests/testthat/test_glm_logit.R | 17 tests/testthat/test_gls.R | 10 tests/testthat/test_ignore_absorption.R | 14 tests/testthat/test_ivreg.R | 12 tests/testthat/test_lm.R | 14 tests/testthat/test_lme_2level.R | 15 tests/testthat/test_lme_3level.R | 20 tests/testthat/test_mlm.R | 26 tests/testthat/test_plm-ID-variables.R |only tests/testthat/test_plm-random-effects.R | 8 tests/testthat/test_rma-mv.R | 22 tests/testthat/test_rma-uni.R | 14 tests/testthat/test_robu.R | 14 31 files changed, 1006 insertions(+), 369 deletions(-)
Title: Critical Line Algorithm in Pure R
Description: Implements 'Markovitz' Critical Line Algorithm ('CLA') for classical
mean-variance portfolio optimization, see Markovitz (1952) <doi:10.2307/2975974>.
Care has been taken for correctness in light of previous buggy implementations.
Author: Yanhao Shi <syhelena@163.com>,
Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between CLA versions 0.95-0 dated 2019-03-13 and 0.95-1 dated 2019-05-11
DESCRIPTION | 8 ++--- MD5 | 9 +++--- build/partial.rdb |binary inst/NEWS.Rd | 19 ++++++++++++ inst/xtraR/platform-sessionInfo.R |only tests/SP500-ex.R | 57 ++++---------------------------------- 6 files changed, 35 insertions(+), 58 deletions(-)
Title: Extending 'dendrogram' Functionality in R
Description: Offers a set of functions for extending
'dendrogram' objects in R, letting you visualize and compare trees of
'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different 'dendrograms' to one another.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Yoav Benjamini [ths],
Gavin Simpson [ctb],
Gregory Jefferis [aut, ctb] (imported code from his dendroextras
package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
The R Core Team [ctb] (Thanks for the Infastructure, and code in the
examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),
Andrie de Vries [ctb] (ggdendro author),
Zuguang Gu [ctb] (circlize author),
Cath [ctb] (https://github.com/CathG),
John Ma [ctb] (https://github.com/JohnMCMa),
Krzysiek G [ctb] (https://github.com/storaged),
Manuela Hummel [ctb] (https://github.com/hummelma),
Chase Clark [ctb] (https://github.com/chasemc),
Lucas Graybuck [ctb] (https://github.com/hypercompetent),
jdetribol [ctb] (https://github.com/jdetribol),
Ben Ho [ctb] (https://github.com/SplitInf),
Samuel Perreault [ctb] (https://github.com/samperochkin),
Christian Hennig [ctb] (http://www.homepages.ucl.ac.uk/~ucakche/)
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between dendextend versions 1.10.0 dated 2019-03-15 and 1.12.0 dated 2019-05-11
dendextend-1.10.0/dendextend/R/d3dendrogram.R |only dendextend-1.10.0/dendextend/man/d3dendro_options.Rd |only dendextend-1.10.0/dendextend/man/d3dendrogram.Rd |only dendextend-1.12.0/dendextend/ChangeLog | 1143 +++++----- dendextend-1.12.0/dendextend/DESCRIPTION | 25 dendextend-1.12.0/dendextend/MD5 | 95 dendextend-1.12.0/dendextend/NAMESPACE | 2 dendextend-1.12.0/dendextend/NEWS | 21 dendextend-1.12.0/dendextend/NEWS.md | 53 dendextend-1.12.0/dendextend/R/dendextend-package.R | 1 dendextend-1.12.0/dendextend/R/find_k.R | 341 ++ dendextend-1.12.0/dendextend/R/unbranch.R | 17 dendextend-1.12.0/dendextend/R/untangle.R | 3 dendextend-1.12.0/dendextend/R/zzz.R | 6 dendextend-1.12.0/dendextend/README.md | 4 dendextend-1.12.0/dendextend/build/vignette.rds |binary dendextend-1.12.0/dendextend/inst/doc/Cluster_Analysis.html | 43 dendextend-1.12.0/dendextend/inst/doc/FAQ.html | 33 dendextend-1.12.0/dendextend/inst/doc/Quick_Introduction.html | 33 dendextend-1.12.0/dendextend/inst/doc/introduction.R | 4 dendextend-1.12.0/dendextend/inst/doc/introduction.Rmd | 20 dendextend-1.12.0/dendextend/inst/doc/introduction.html | 237 +- dendextend-1.12.0/dendextend/man/Bk.Rd | 4 dendextend-1.12.0/dendextend/man/Bk_plot.Rd | 9 dendextend-1.12.0/dendextend/man/FM_index.Rd | 3 dendextend-1.12.0/dendextend/man/all.equal.dendrogram.Rd | 5 dendextend-1.12.0/dendextend/man/assign_values_to_branches_edgePar.Rd | 4 dendextend-1.12.0/dendextend/man/assign_values_to_nodes_nodePar.Rd | 4 dendextend-1.12.0/dendextend/man/bakers_gamma_for_2_k_matrix.Rd | 3 dendextend-1.12.0/dendextend/man/branches_attr_by_labels.Rd | 4 dendextend-1.12.0/dendextend/man/branches_attr_by_lists.Rd | 4 dendextend-1.12.0/dendextend/man/circlize_dendrogram.Rd | 5 dendextend-1.12.0/dendextend/man/cor_bakers_gamma.Rd | 8 dendextend-1.12.0/dendextend/man/cut_lower_fun.Rd | 3 dendextend-1.12.0/dendextend/man/cutree-methods.Rd | 1 dendextend-1.12.0/dendextend/man/find_dend.Rd | 6 dendextend-1.12.0/dendextend/man/get_root_branches_attr.Rd | 3 dendextend-1.12.0/dendextend/man/plot_horiz.dendrogram.Rd | 11 dendextend-1.12.0/dendextend/man/pvclust_show_signif.Rd | 3 dendextend-1.12.0/dendextend/man/pvclust_show_signif_gradient.Rd | 5 dendextend-1.12.0/dendextend/man/rect.dendrogram.Rd | 6 dendextend-1.12.0/dendextend/man/set.Rd | 16 dendextend-1.12.0/dendextend/man/sort_2_clusters_vectors.Rd | 3 dendextend-1.12.0/dendextend/man/tanglegram.Rd | 49 dendextend-1.12.0/dendextend/man/unbranch.Rd | 8 dendextend-1.12.0/dendextend/man/untangle.Rd | 8 dendextend-1.12.0/dendextend/man/untangle_step_rotate_1side.Rd | 4 dendextend-1.12.0/dendextend/man/untangle_step_rotate_2side.Rd | 4 dendextend-1.12.0/dendextend/tests/testthat/test-unbranch.R | 2 dendextend-1.12.0/dendextend/vignettes/introduction.Rmd | 20 50 files changed, 1401 insertions(+), 885 deletions(-)
Title: Sparse Multi-Type Regularized Feature Modeling
Description: Implementation of the SMuRF algorithm of Devriendt et al. (2018) <arXiv:1810.03136> to fit generalized linear models (GLMs) with multiple types of predictors via regularized maximum likelihood.
Author: Tom Reynkens [aut, cre] (<https://orcid.org/0000-0002-5516-5107>),
Sander Devriendt [aut],
Katrien Antonio [aut]
Maintainer: Tom Reynkens <tomreynkens@hotmail.com>
Diff between smurf versions 1.0.0 dated 2018-12-09 and 1.0.1 dated 2019-05-11
DESCRIPTION | 8 MD5 | 14 - R/glmsmurf.R | 89 ++++++---- build/vignette.rds |binary inst/NEWS.Rd | 15 + inst/Rent_example2.R | 3 inst/doc/smurf.html | 425 +++++++++++++++++++++++++++++++++++++++++++-------- man/plot_lambda.Rd | 3 8 files changed, 443 insertions(+), 114 deletions(-)
Title: Bradley-Terry Models
Description: Specify and fit the Bradley-Terry model, including structured versions in which the parameters are related to explanatory variables through a linear predictor and versions with contest-specific effects, such as a home advantage.
Author: Heather Turner [aut, cre],
David Firth [aut]
Maintainer: Heather Turner <ht@heatherturner.net>
Diff between BradleyTerry2 versions 1.0-9 dated 2019-02-25 and 1.1-0 dated 2019-05-11
BradleyTerry2-1.0-9/BradleyTerry2/R/coef.BTm.R |only BradleyTerry2-1.0-9/BradleyTerry2/R/vcov.BTm.R |only BradleyTerry2-1.0-9/BradleyTerry2/TODO |only BradleyTerry2-1.0-9/BradleyTerry2/data/icehockey.rda |only BradleyTerry2-1.0-9/BradleyTerry2/data/springall.rda |only BradleyTerry2-1.1-0/BradleyTerry2/DESCRIPTION | 6 BradleyTerry2-1.1-0/BradleyTerry2/MD5 | 94 - BradleyTerry2-1.1-0/BradleyTerry2/NAMESPACE | 154 +- BradleyTerry2-1.1-0/BradleyTerry2/NEWS.md | 8 BradleyTerry2-1.1-0/BradleyTerry2/R/BTabilities.R | 2 BradleyTerry2-1.1-0/BradleyTerry2/R/anova.BTm.R | 3 BradleyTerry2-1.1-0/BradleyTerry2/R/anova.BTmlist.R | 3 BradleyTerry2-1.1-0/BradleyTerry2/R/glmmPQL.R | 2 BradleyTerry2-1.1-0/BradleyTerry2/R/icehockey.R | 2 BradleyTerry2-1.1-0/BradleyTerry2/R/print.summary.glmmPQL.R | 4 BradleyTerry2-1.1-0/BradleyTerry2/R/summary.BTglmmPQL.R | 6 BradleyTerry2-1.1-0/BradleyTerry2/README.md | 60 - BradleyTerry2-1.1-0/BradleyTerry2/build/vignette.rds |binary BradleyTerry2-1.1-0/BradleyTerry2/inst/WORDLIST | 20 BradleyTerry2-1.1-0/BradleyTerry2/inst/doc/BradleyTerry.R | 526 +++++----- BradleyTerry2-1.1-0/BradleyTerry2/inst/doc/BradleyTerry.pdf |binary BradleyTerry2-1.1-0/BradleyTerry2/man/BTabilities.Rd | 168 +-- BradleyTerry2-1.1-0/BradleyTerry2/man/BTm.Rd | 438 ++++---- BradleyTerry2-1.1-0/BradleyTerry2/man/CEMS.Rd | 340 +++--- BradleyTerry2-1.1-0/BradleyTerry2/man/GenDavidson.Rd | 416 +++---- BradleyTerry2-1.1-0/BradleyTerry2/man/add1.BTm.Rd | 166 +-- BradleyTerry2-1.1-0/BradleyTerry2/man/anova.BTm.Rd | 156 +- BradleyTerry2-1.1-0/BradleyTerry2/man/baseball.Rd | 120 +- BradleyTerry2-1.1-0/BradleyTerry2/man/chameleons.Rd | 184 +-- BradleyTerry2-1.1-0/BradleyTerry2/man/citations.Rd | 110 +- BradleyTerry2-1.1-0/BradleyTerry2/man/countsToBinomial.Rd | 86 - BradleyTerry2-1.1-0/BradleyTerry2/man/flatlizards.Rd | 324 +++--- BradleyTerry2-1.1-0/BradleyTerry2/man/football.Rd | 134 +- BradleyTerry2-1.1-0/BradleyTerry2/man/glmmPQL.Rd | 302 ++--- BradleyTerry2-1.1-0/BradleyTerry2/man/glmmPQL.control.Rd | 136 +- BradleyTerry2-1.1-0/BradleyTerry2/man/icehockey.Rd | 244 ++-- BradleyTerry2-1.1-0/BradleyTerry2/man/plotProportions.Rd | 430 ++++---- BradleyTerry2-1.1-0/BradleyTerry2/man/predict.BTglmmPQL.Rd | 180 +-- BradleyTerry2-1.1-0/BradleyTerry2/man/predict.BTm.Rd | 376 +++---- BradleyTerry2-1.1-0/BradleyTerry2/man/qvcalc.BTabilities.Rd | 168 +-- BradleyTerry2-1.1-0/BradleyTerry2/man/reexports.Rd | 32 BradleyTerry2-1.1-0/BradleyTerry2/man/residuals.BTm.Rd | 150 +- BradleyTerry2-1.1-0/BradleyTerry2/man/seeds.Rd | 84 - BradleyTerry2-1.1-0/BradleyTerry2/man/sound.fields.Rd | 188 +-- BradleyTerry2-1.1-0/BradleyTerry2/man/springall.Rd | 166 +-- BradleyTerry2-1.1-0/BradleyTerry2/tests/BTabilities.Rout.save | 9 BradleyTerry2-1.1-0/BradleyTerry2/tests/flatlizards.R | 3 BradleyTerry2-1.1-0/BradleyTerry2/tests/flatlizards.Rout.save | 168 +-- BradleyTerry2-1.1-0/BradleyTerry2/tests/predict.R | 37 BradleyTerry2-1.1-0/BradleyTerry2/tests/predict.Rout.save | 67 - BradleyTerry2-1.1-0/BradleyTerry2/vignettes/BradleyTerry-concordance.tex |only 51 files changed, 3127 insertions(+), 3145 deletions(-)
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
some of which were ported from S-plus in the 1990's.
For graphics, have pretty (Log-scale) axes, an enhanced Tukey-Anscombe
plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()',
pretty arrows, etc.
For robustness, have a robust F test and robust range().
For system support, notably on Linux, provides 'Sys.*()' functions with
more access to system and CPU information.
Finally, miscellaneous utilities such as simple efficient prime numbers,
integer codes, Duplicated(), toLatex.numeric() and is.whole().
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Werner Stahel [ctb] (Functions: compresid2way(), f.robftest(), last(),
p.scales(), p.dnorm()),
Andreas Ruckstuhl [ctb] (Functions: p.arrows(), p.profileTraces(),
p.res.2x()),
Christian Keller [ctb] (Functions: histBxp(), p.tachoPlot()),
Kjetil Halvorsen [ctb] (Functions: KSd(), ecdf.ksCI()),
Alain Hauser [ctb] (Functions: cairoSwd(), is.whole(),
toLatex.numeric()*),
Christoph Buser [ctb] (to function Duplicated()),
Lorenz Gygax [ctb] (to function p.res.2fact()),
Bill Venables [ctb] (Functions: empty.dimnames(), primes()),
Tony Plate [ctb] (to inv.seq()),
Isabelle Flückiger [ctb],
Marcel Wolbers [ctb],
Markus Keller [ctb],
Sandrine Dudoit [ctb],
Jane Fridlyand [ctb],
Greg Snow [ctb] (to loessDemo()),
Henrik Aa. Nielsen [ctb] (to loessDemo()),
Vincent Carey [ctb],
Ben Bolker [ctb],
Philippe Grosjean [ctb],
Frédéric Ibanez [ctb],
Caterina Savi [ctb],
Charles Geyer [ctb],
Jens Oehlschlägel [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.1-3 dated 2018-11-27 and 1.1-4 dated 2019-05-11
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 2 +- R/TA.plot.R | 9 +++++---- R/prettylab.R | 22 +++++++++++----------- R/sessionInfo-ext.R | 17 +++++++++++++---- inst/NEWS.Rd | 18 +++++++++++++++++- man/eaxis.Rd | 9 ++++++++- man/roundfixS.Rd | 2 +- tests/dDA.R | 1 + tests/dDA.Rout.save | 16 ++++++++++++---- 11 files changed, 83 insertions(+), 41 deletions(-)
Title: Measuring Spatial Segregation
Description: Measuring spatial segregation. The methods implemented in this
package include White's P index (1983) <doi:10.1086/227768>,
Morrill's D(adj) (1991), Wong's D(w) and D(s) (1993)
<doi:10.1080/00420989320080551>, and Reardon and O'Sullivan's set of
spatial segregation measures (2004)
<doi:10.1111/j.0081-1750.2004.00150.x>.
Author: Seong-Yun Hong <syhong@khu.ac.kr> and
David O'Sullivan <david.osullivan@vuw.ac.nz>, with code contributions by
Benjamin Jarvis and Changlock Choi
Maintainer: Seong-Yun Hong <syhong@khu.ac.kr>
Diff between seg versions 0.5-5 dated 2018-09-25 and 0.5-6 dated 2019-05-11
DESCRIPTION | 14 ++++++---- MD5 | 6 ++-- R/localenv.R | 70 ++++++++++++++++++++++++++++++++--------------------- src/envconstruct.c | 12 ++++----- 4 files changed, 60 insertions(+), 42 deletions(-)
Title: An R Interface to the 'Tiingo' Stock Price API
Description: Functionality to download stock prices, cryptocurrency data, and
more from the 'Tiingo' API <https://api.tiingo.com/>.
Author: Davis Vaughan [aut, cre],
Matt Dancho [aut]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between riingo versions 0.1.0 dated 2018-04-16 and 0.2.0 dated 2019-05-11
DESCRIPTION | 19 ++-- MD5 | 36 ++++--- NAMESPACE | 1 NEWS.md | 12 ++ R/assertions.R | 25 +++-- R/latest.R | 30 +++++- R/meta.R | 26 +++++ R/news.R | 6 - R/prices.R | 38 +++++++- R/quote.R | 18 ++- R/safety.R |only R/url_constructor.R | 2 R/utils.R | 11 ++ README.md | 160 ++++++++++++++++++----------------- man/riingo_crypto_prices.Rd | 4 tests/testthat/helper-maybe-closed.R |only tests/testthat/test-latest.R | 79 +++++++++++++++++ tests/testthat/test-meta.R | 75 ++++++++++++++++ tests/testthat/test-prices.R | 75 +++++++++++++++- tests/testthat/test-quote.R | 38 ++++++++ 20 files changed, 517 insertions(+), 138 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 0.8.1 dated 2019-04-19 and 0.8.2 dated 2019-05-11
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NAMESPACE | 1 - NEWS.md | 4 ++++ R/ggpairs.R | 26 ++++++++++++++++++++------ R/kaplan.R | 11 +++++++++-- R/timeroc.R | 12 ++++++++++-- inst/doc/jsmodule.html | 4 ++-- 8 files changed, 58 insertions(+), 25 deletions(-)
Title: Wrapper Package for Design of Experiments Functionality
Description: Various kinds of designs for
(industrial) experiments can be created. The package uses, and sometimes enhances,
design generation routines from other packages.
So far, response surface designs from package rsm, latin hypercube
samples from packages lhs and DiceDesign, and
D-optimal designs from package AlgDesign have been implemented.
Author: Ulrike Groemping [aut, cre],
Lenth Russ [ctb]
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>
Diff between DoE.wrapper versions 0.9 dated 2017-09-15 and 0.10 dated 2019-05-11
DESCRIPTION | 10 ++++---- MD5 | 32 +++++++++++++-------------- inst/NEWS | 15 +++++++++++- man/Dopt.augment.Rd | 20 +++++++++++++++- man/Dopt.design.Rd | 20 +++++++++++++++- man/bbd.design.Rd | 18 ++++++++++++++- man/ccd.augment.Rd | 20 +++++++++++++++- man/ccd.design.Rd | 18 ++++++++++++++- man/lhs.design.Rd | 28 +++++++++++++++++++++-- tests/Dopt.test.R | 4 +++ tests/Dopt.test.Rout.save | 40 ++++++++++++++++++--------------- tests/bbd.test.R | 4 +++ tests/bbd.test.Rout.save | 46 +++++++++++++++++++++------------------ tests/ccd.augment.test.R | 3 ++ tests/ccd.augment.test.Rout.save | 39 +++++++++++++++++---------------- tests/qua.design.test.R | 4 +++ tests/qua.design.test.Rout.save | 40 ++++++++++++++++++--------------- 17 files changed, 252 insertions(+), 109 deletions(-)