Title: A Grammar of Clinical Data Summary
Description: A tool created to simplify the data manipulation necessary to create clinical reports.
Author: Eli Miller [aut] (<https://orcid.org/0000-0002-2127-9456>),
Mike Stackhouse [aut, cre] (<https://orcid.org/0000-0001-6030-723X>),
Ashley Tarasiewicz [aut],
Nathan Kosiba [aut] (<https://orcid.org/0000-0001-5359-4234>),
Atorus Research LLC [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between Tplyr versions 0.2.1 dated 2020-11-10 and 0.2.2 dated 2020-11-30
DESCRIPTION | 6 MD5 | 78 +++++--- NAMESPACE | 1 NEWS.md | 8 R/count.R | 30 ++- R/count_bindings.R | 146 ++++++++++------ R/shift.R | 7 R/shift_bindings.R | 18 +- R/sort.R | 6 R/zzz.R | 5 README.md | 16 + build/vignette.rds |binary inst/doc/Tplyr.Rmd | 15 - inst/doc/Tplyr.html | 27 +-- inst/doc/count.R |only inst/doc/count.Rmd |only inst/doc/count.html |only inst/doc/denom.R |only inst/doc/denom.Rmd |only inst/doc/denom.html |only inst/doc/shift.R |only inst/doc/shift.Rmd |only inst/doc/shift.html |only inst/doc/table.Rmd | 3 inst/doc/table.html | 3 man/add_total_row.Rd | 38 ++-- man/ordering.Rd | 2 man/set_denom_ignore.Rd | 10 - man/set_denom_where.Rd | 11 - man/set_denoms_by.Rd | 4 man/set_distinct_by.Rd | 2 man/set_indentation.Rd | 2 man/set_missing_count.Rd | 20 +- man/set_nest_count.Rd | 2 man/set_outer_sort_position.Rd | 2 tests/testthat/count_t3 | 6 tests/testthat/count_t6 | 4 tests/testthat/count_t7 | 6 tests/testthat/test-count.R | 53 ++++-- tests/testthat/test-shift.R | 14 + vignettes/Tplyr.Rmd | 15 - vignettes/count.Rmd |only vignettes/denom.Rmd |only vignettes/shift.Rmd |only vignettes/styled_example.rtf | 362 ++++++++++++++++++++--------------------- vignettes/table.Rmd | 3 46 files changed, 536 insertions(+), 389 deletions(-)
Title: Fitting Semi-Parametric Generalized log-Gamma Regression Models
Description: Set of tools to fit a linear multiple or semi-parametric regression
models and non-informative right-censoring may be considered. Under this setup, the localization parameter of the response variable distribution is modeled by using linear multiple regression
or semi-parametric functions, whose non-parametric components may be approximated
by natural cubic spline or P-splines. The supported distribution for the model error is a generalized log-gamma distribution which includes
the generalized extreme value and standard normal distributions as important special cases.
Author: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com> and G. Paula and L. Vanegas
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between sglg versions 0.1.7 dated 2020-09-19 and 0.1.8 dated 2020-11-30
DESCRIPTION | 8 ++-- MD5 | 31 ++++++++-------- NAMESPACE | 1 R/aux_fs.R |only R/bootglg.R | 55 +++++++++++++++++++++------- R/deviance_residuals.R | 3 - R/glg.R | 94 ++++++++----------------------------------------- R/influence.sglg.R | 4 -- R/quantile_residuals.R | 8 ++++ R/sglg2.R | 82 ++++++++---------------------------------- R/ssurvglg.R | 7 --- R/survglg.R | 8 ---- R/survival_glg.R |only man/bootglg.Rd | 25 +++++++++---- man/glg.Rd | 16 ++++---- man/sglg.Rd | 2 - man/survglg.Rd | 1 man/survival_gg.Rd |only 18 files changed, 133 insertions(+), 212 deletions(-)
Title: Converts Between R Objects and Simple Feature Objects
Description: Converts between R and Simple Feature 'sf' objects, without depending
on the Simple Feature library. Conversion functions are available at both the R level,
and through 'Rcpp'.
Author: David Cooley [aut, cre],
Michael Sumner [ctb]
Maintainer: David Cooley <david.cooley.au@gmail.com>
Diff between sfheaders versions 0.3.0 dated 2020-10-31 and 0.4.0 dated 2020-11-30
DESCRIPTION | 12 MD5 | 40 +- NEWS.md | 8 R/df.R | 8 R/sfc.R | 2 README.md | 8 inst/include/sfheaders/df/sf.hpp | 2 inst/include/sfheaders/sf/multipolygon/sf_multipolygon.hpp | 22 - inst/include/sfheaders/sf/polygon/sf_polygon.hpp | 26 - inst/include/sfheaders/sf/sf.hpp | 6 inst/include/sfheaders/sf/sf_utils.hpp | 168 ++++++++++- inst/include/sfheaders/sfc/multipolygon/sfc_multipolygon.hpp | 5 inst/include/sfheaders/sfc/polygon/sfc_polygon.hpp | 18 + inst/include/sfheaders/sfc/sfc_attributes.hpp | 9 man/sf_to_df.Rd | 6 man/sfc_linestring.Rd | 2 man/sfc_to_df.Rd | 2 tests/testthat/test-bbox.R | 39 -- tests/testthat/test-lists.R | 75 ++-- tests/testthat/test-sf_polygon.R | 85 +++++ tests/testthat/test-sfc_polygon.R | 1 21 files changed, 403 insertions(+), 141 deletions(-)
Title: Estimating Hierarchical Linear Models for Single-Case Designs
Description: Provides a set of tools for estimating hierarchical linear
models and effect sizes based on data from single-case designs.
Functions are provided for calculating standardized mean difference effect sizes that
are directly comparable to standardized mean differences estimated from between-subjects randomized experiments,
as described in Hedges, Pustejovsky, and Shadish (2012) <DOI:10.1002/jrsm.1052>;
Hedges, Pustejovsky, and Shadish (2013) <DOI:10.1002/jrsm.1086>; and
Pustejovsky, Hedges, and Shadish (2014) <DOI:10.3102/1076998614547577>.
Includes an interactive web interface.
Author: James Pustejovsky [aut, cre],
Man Chen [aut],
Bethany Hamilton [aut]
Maintainer: James Pustejovsky <jepusto@gmail.com>
Diff between scdhlm versions 0.5.0 dated 2020-11-08 and 0.5.1 dated 2020-11-30
scdhlm-0.5.0/scdhlm/inst/shiny-examples/scdhlm/code-chunks/Graph.R |only scdhlm-0.5.1/scdhlm/DESCRIPTION | 6 scdhlm-0.5.1/scdhlm/MD5 | 44 +- scdhlm-0.5.1/scdhlm/NEWS.md | 6 scdhlm-0.5.1/scdhlm/R/graphing-functions.R | 1 scdhlm-0.5.1/scdhlm/R/preprocess-function.R | 2 scdhlm-0.5.1/scdhlm/R/scdhlm-package.r | 3 scdhlm-0.5.1/scdhlm/R/simulation-functions.R | 14 scdhlm-0.5.1/scdhlm/data/Schutte.RData |binary scdhlm-0.5.1/scdhlm/inst/CITATION | 13 scdhlm-0.5.1/scdhlm/inst/doc/Estimating-effect-sizes.R | 49 +- scdhlm-0.5.1/scdhlm/inst/doc/Estimating-effect-sizes.Rmd | 67 +-- scdhlm-0.5.1/scdhlm/inst/doc/Estimating-effect-sizes.html | 191 ++++------ scdhlm-0.5.1/scdhlm/inst/shiny-examples/scdhlm/code-chunks/es-RML-MB.R | 2 scdhlm-0.5.1/scdhlm/inst/shiny-examples/scdhlm/code-chunks/graph-scd.R |only scdhlm-0.5.1/scdhlm/inst/shiny-examples/scdhlm/lme-fit.R | 2 scdhlm-0.5.1/scdhlm/inst/shiny-examples/scdhlm/markdown/scdhlm.md | 4 scdhlm-0.5.1/scdhlm/inst/shiny-examples/scdhlm/rsconnect/shinyapps.io/jepusto/scdhlm.dcf | 4 scdhlm-0.5.1/scdhlm/inst/shiny-examples/scdhlm/server.R | 12 scdhlm-0.5.1/scdhlm/man/Schutte.Rd | 3 scdhlm-0.5.1/scdhlm/man/simulate_MB2.Rd | 7 scdhlm-0.5.1/scdhlm/man/simulate_MB4.Rd | 7 scdhlm-0.5.1/scdhlm/tests/testthat/test-g_mlm.R | 4 scdhlm-0.5.1/scdhlm/vignettes/Estimating-effect-sizes.Rmd | 67 +-- 24 files changed, 257 insertions(+), 251 deletions(-)
Title: Power and Sample Size for Health Researchers via Shiny
Description: Power and Sample Size for Health Researchers is a Shiny application that brings together a
series of functions related to sample size and power calculations for common analysis in the healthcare
field. There are functionalities to calculate the power, sample size to estimate or test hypotheses for means and
proportions (including test for equivalence, non-inferiority and superiority), association, Pearson's correlation coefficient,
regression coefficients (linear, logistic and Cox), linear mixed model,
Cronbach's alpha, interobserver agreement, intraclass correlation coefficients,
limit of agreement on Bland-Altman plots,
area under the curve, sensitivity and specificity incorporating the prevalence of disease.
Author: Rogério Boff Borges [aut, cre]
(<https://orcid.org/0000-0002-2548-1889>),
Guilherme Serpa Azambuja [aut]
(<https://orcid.org/0000-0001-6246-4538>),
Aline Castello Branco Mancuso [aut]
(<https://orcid.org/0000-0001-6033-8335>),
Vanessa Bielefeldt Leotti [aut]
(<https://orcid.org/0000-0003-3860-9367>),
Vânia Naomi Hirakata [aut] (<https://orcid.org/0000-0003-4645-2080>),
Suzi Alves Camey [aut] (<https://orcid.org/0000-0002-5564-081X>),
Stela Maris de Jezus Castro [aut]
(<https://orcid.org/0000-0001-5862-6709>),
Hospital de Clínicas de Porto Alegre [fnd]
Maintainer: Rogério Boff Borges <roborges@hcpa.edu.br>
Diff between PSS.Health versions 0.1.4 dated 2020-11-12 and 0.1.5 dated 2020-11-30
DESCRIPTION | 61 - MD5 | 10 NAMESPACE | 1 R/PSS_Health.R | 1 inst/PSS.Health/server.R | 2584 ++++++++++++++++++++++++++++++++++++++++------- inst/PSS.Health/ui.R | 733 ++++++------- 6 files changed, 2617 insertions(+), 773 deletions(-)
Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript
library 'paged.js' to split the content of an HTML document into discrete
pages. Each page can have its page size, page numbers, margin boxes, and
running headers, etc. Applications of this package include books, letters,
reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Romain Lesur [aut, cph] (<https://orcid.org/0000-0002-0721-5595>),
Brent Thorne [aut] (<https://orcid.org/0000-0002-1099-3857>),
Xianying Tan [aut] (<https://orcid.org/0000-0002-6072-3521>),
Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>),
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
RStudio, PBC [cph],
Adam Hyde [ctb] (paged.js in resources/js/),
Min-Zhong Lu [ctb] (resume.css in resources/css/),
Zulko [ctb] (poster-relaxed.css in resources/css/)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between pagedown versions 0.12 dated 2020-10-13 and 0.13 dated 2020-11-30
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 12 ++++++++++++ R/chrome.R | 2 +- R/paged.R | 4 ++-- inst/resources/js/hooks.js | 2 +- 6 files changed, 24 insertions(+), 12 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] (<https://orcid.org/0000-0001-8316-9503>),
Martin Maechler [aut] (<https://orcid.org/0000-0002-8685-9910>),
Ben Bolker [aut, cre] (<https://orcid.org/0000-0002-2127-0443>),
Steven Walker [aut] (<https://orcid.org/0000-0002-4394-9078>),
Rune Haubo Bojesen Christensen [ctb]
(<https://orcid.org/0000-0002-4494-3399>),
Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>),
Bin Dai [ctb],
Fabian Scheipl [ctb] (<https://orcid.org/0000-0001-8172-3603>),
Gabor Grothendieck [ctb],
Peter Green [ctb] (<https://orcid.org/0000-0002-0238-9852>),
John Fox [ctb],
Alexander Bauer [ctb],
Pavel N. Krivitsky [ctb, cph] (<https://orcid.org/0000-0002-9101-3362>,
shared copyright on simulate.formula)
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-25 dated 2020-10-23 and 1.1-26 dated 2020-11-30
DESCRIPTION | 6 MD5 | 131 ++++----- NAMESPACE | 1 R/lmer.R | 1 R/predict.R | 1 R/profile.R | 76 +++-- build/partial.rdb |binary inst/NEWS.Rd | 20 + inst/doc/PLSvGLS.pdf |binary inst/doc/Theory.pdf |binary inst/doc/lmer.pdf |binary inst/doc/lmerperf.html | 45 ++- inst/testdata/harmel_density.R |only inst/testdata/harmel_profile.rds |only inst/testdata/strip_env.R |only man/VerbAgg.Rd | 14 man/allFit.Rd | 4 man/bootMer.Rd | 4 man/confint.merMod.Rd | 4 man/convergence.Rd | 4 man/grouseticks.Rd | 2 man/influence.merMod.Rd | 4 man/plots.thpr.Rd | 5 man/profile-methods.Rd | 4 tests/HSAURtrees.R | 100 +++--- tests/agridat_gotway.R | 2 tests/bootMer.R | 163 +++++------ tests/boundary.R | 322 +++++++++++----------- tests/confint.R | 69 ++-- tests/devCritFun.R | 34 +- tests/drop.R | 35 +- tests/drop1contrasts.R | 28 + tests/elston.R | 107 +++---- tests/evalCall.R | 16 - tests/falsezero_dorie.R | 58 ++- tests/getME.R | 122 ++++---- tests/glmer-1.R | 515 +++++++++++++++++------------------ tests/glmerControlPass.R | 33 +- tests/glmerWarn.R | 86 +++-- tests/glmmExt.R | 2 tests/glmmWeights.R | 3 tests/hatvalues.R | 54 +-- tests/is.R | 48 +-- tests/lme4_nlme.R | 67 ++-- tests/lmer-0.R | 228 +++++++-------- tests/lmer-1.R | 2 tests/lmer-1.Rout.save | 566 +++++++++++++-------------------------- tests/lmer-conv.R | 22 - tests/methods.R | 34 +- tests/minval.R | 52 +-- tests/modFormula.R | 115 ++++--- tests/nbinom.R | 278 +++++++++---------- tests/offset.R | 3 tests/optimizer.R | 2 tests/predsim.R | 2 tests/priorWeights.R | 2 tests/priorWeightsModComp.R | 8 tests/respiratory.R | 2 tests/simulate.R | 4 tests/testcolonizer.R | 3 tests/testcrab.R | 2 tests/testthat/test-glmer.R | 12 tests/testthat/test-methods.R | 8 tests/testthat/test-nbinom.R | 5 tests/testthat/test-predict.R | 10 tests/testthat/test-utils.R | 2 tests/throw.R | 2 tests/varcorr.R | 3 68 files changed, 1791 insertions(+), 1766 deletions(-)
Title: Landscape Epidemiology and Evolution
Description: A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution
of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies.
It is based on a spatial geometry for describing the landscape and allocation of different cultivars,
a dispersal kernel for the dissemination of the pathogen, and a SEIR
('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step.
It provides a useful tool to assess the performance of a wide range of deployment options with
respect to their epidemiological, evolutionary and economic outcomes.
Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett,
Peter H Thrall (2018) <doi:10.1371/journal.pcbi.1006067>.
Author: Loup Rimbaud [aut],
Julien Papaix [aut],
Jean-Francois Rey [cre],
Jean-Loup Gaussen [ctb]
Maintainer: Jean-Francois Rey <jean-francois.rey@inrae.fr>
Diff between landsepi versions 1.0.1 dated 2020-07-02 and 1.0.2 dated 2020-11-30
landsepi-1.0.1/landsepi/R/catch-routine-registration.R |only landsepi-1.0.1/landsepi/src/test-runner.cpp |only landsepi-1.0.1/landsepi/tests/testthat/test-cpp.R |only landsepi-1.0.1/landsepi/tests/testthat/test.dbf |only landsepi-1.0.1/landsepi/tests/testthat/test.gpkg |only landsepi-1.0.2/landsepi/DESCRIPTION | 17 landsepi-1.0.2/landsepi/MD5 | 23 landsepi-1.0.2/landsepi/R/landsepi.R | 4 landsepi-1.0.2/landsepi/build/vignette.rds |binary landsepi-1.0.2/landsepi/inst/doc/landscape_dispersal.html | 300 ++-- landsepi-1.0.2/landsepi/inst/doc/list_of_parameters.pdf |binary landsepi-1.0.2/landsepi/inst/doc/run_exp_design.html | 508 ++++--- landsepi-1.0.2/landsepi/inst/doc/run_simple_simul.html | 944 +++++++------- landsepi-1.0.2/landsepi/man/landsepi-package.Rd | 8 landsepi-1.0.2/landsepi/src/RcppExports.cpp | 3 15 files changed, 1016 insertions(+), 791 deletions(-)
Title: Joint Change Point Detection
Description: Procedures for joint detection of changes in both expectation and variance in univariate sequences. Performs a statistical test of the null hypothesis of the absence of change points. In case of rejection performs an algorithm for change point detection. References - Bivariate change point detection (2019+), Michael Messer.
Author: Michael Messer
Maintainer: Michael Messer <michael.messer@tuwien.ac.at>
Diff between jcp versions 1.0 dated 2019-03-22 and 1.1 dated 2020-11-30
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/jcp.r | 1 + man/jcp.Rd | 3 +-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Functions to Inline C, C++, Fortran Function Calls from R
Description: Functionality to dynamically define R functions and S4 methods
with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling
conventions.
Author: Oleg Sklyar, Duncan Murdoch, Mike Smith, Dirk Eddelbuettel,
Romain Francois, Karline Soetaert, Johannes Ranke
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between inline versions 0.3.16 dated 2020-09-06 and 0.3.17 dated 2020-11-30
DESCRIPTION | 13 -- MD5 | 28 ++-- NAMESPACE | 5 R/cfunction.R | 43 +++---- R/cxxfunction.R | 290 +++++++++++++++++++++++------------------------- R/utilities.R | 169 +++++++++++++-------------- README.md | 14 +- build/partial.rdb |binary inst/NEWS.Rd | 17 ++ inst/tinytest |only man/cfunction.Rd | 112 ++++++++++-------- man/cxxfunction.Rd | 60 +++------ man/package.skeleton.Rd | 21 +-- man/utilities.Rd | 148 +++++++++++++----------- tests |only 15 files changed, 471 insertions(+), 449 deletions(-)
Title: Idiograms with Marks and Karyotype Indices
Description: Plot idiograms of karyotypes, plasmids, circular chr. having a set of data.frames for chromosome data and optionally mark data. Two styles of chromosomes can be used: without or with visible chromatids (when not circular). Supports micrometers, cM and Mb or any unit. Two styles of centromeres are available: triangular and rounded; and six styles of marks: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow, downArrow; its legend (label) can be drawn inline or to the right of karyotypes. Idiograms can also be plotted in concentric circles. It is possible to calculate chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x>, karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).
Author: Fernando Roa [aut, cre],
Mariana PC Telles [ctb]
Maintainer: Fernando Roa <froao@unal.edu.co>
Diff between idiogramFISH versions 1.16.7 dated 2020-10-15 and 1.16.8 dated 2020-11-30
DESCRIPTION | 19 -- MD5 | 38 ++-- NEWS.md | 14 + R/addNotes.R | 294 +++++++++++++++++++----------------- R/mapGGChr.R | 127 ++++++++++++--- R/mapXY.R | 16 + R/plotIdiograms.R | 176 ++++++++++++--------- README.md | 2 inst/doc/index.html | 19 +- man/figures/cranmanualbookdown.svg | 2 man/figures/cranversion.svg | 4 man/figures/develmanualvignette.svg | 2 man/figures/ggplot.svg | 20 +- man/figures/gitbadge.svg | 2 man/figures/manual.svg | 2 man/figures/pkgdownver.svg | 2 man/idiogramFISH-package.Rd | 11 - man/mapGGChr.Rd | 8 man/mapXY.Rd | 4 man/plotIdiograms.Rd | 18 +- 20 files changed, 462 insertions(+), 318 deletions(-)
Title: Some Empiric and Nonparametric Copula Models
Description: Provides S4 classes and methods to fit several copula models: The classic empirical checkerboard copula and the empirical checkerboard copula with known margins, see Cuberos, Masiello and Maume-Deschamps (2019) <doi:10.1080/03610926.2019.1586936> are proposed. These two models allow to fit copulas in high dimension with a small number of observations, and they are always proper copulas. Some flexibility is added via a possibility to differentiate the checkerboard parameter by dimension. The last model consist of the implementation of the Copula Recursive Tree algorithm proposed by Laverny, Maume-Deschamps, Masiello and Rullière (2020) <arXiv:2005.02912>, including the localised dimension reduction, which fits a copula by recursive splitting of the copula domain. We also provide an efficient way of mixing copulas, allowing to bag the algorithm into a forest, and a generic way of measuring d-dimensional boxes with a copula.
Author: Oskar Laverny [aut, cre] (<https://orcid.org/0000-0002-7508-999X>)
Maintainer: Oskar Laverny <oskar.laverny@gmail.com>
Diff between cort versions 0.3.1 dated 2020-05-13 and 0.3.2 dated 2020-11-30
DESCRIPTION | 10 MD5 | 96 +++---- NAMESPACE | 2 NEWS.md | 11 R/ConvexCombCopula.R | 6 R/Cort.R | 40 ++- R/CortForest.R | 31 ++ R/cbCopula.R | 2 R/cbkmCopula.R | 8 R/data.R | 60 ++++ R/generics.R | 71 +++-- R/utils.R | 2 README.md | 14 + build/partial.rdb |binary inst/WORDLIST | 82 +++--- inst/doc/vignette01_ecb.R | 2 inst/doc/vignette01_ecb.Rmd | 2 inst/doc/vignette01_ecb.html | 128 +++++++--- inst/doc/vignette02_cort_clayton.R | 13 - inst/doc/vignette02_cort_clayton.Rmd | 16 - inst/doc/vignette02_cort_clayton.html | 184 +++++++++----- inst/doc/vignette03_ecbkm.html | 172 +++++++++---- inst/doc/vignette04_bootstrap_varying_m.R | 10 inst/doc/vignette04_bootstrap_varying_m.Rmd | 10 inst/doc/vignette04_bootstrap_varying_m.html | 338 +++++++++++++++------------ man/ConvexCombCopula-Class.Rd | 4 man/Cort-Class.Rd | 37 ++ man/CortForest-Class.Rd | 22 + man/biv_tau-methods.Rd | 2 man/cbCopula-Class.Rd | 2 man/cbkmCopula-Class.Rd | 8 man/clayton_data.Rd | 21 + man/constraint_infl-methods.Rd | 5 man/dCopula-methods.Rd | 10 man/funcdep_data.Rd | 14 + man/impossible_data.Rd | 22 + man/kendall_func-methods.Rd | 5 man/loss-methods.Rd | 7 man/pCopula-methods.Rd | 12 man/project_on_dims-methods.Rd | 5 man/quad_norm-methods.Rd | 5 man/quad_prod-methods.Rd | 5 man/quad_prod_with_data-methods.Rd | 3 man/rCopula-methods.Rd | 8 man/recoveryourself_data.Rd | 23 + man/vCopula-methods.Rd | 4 vignettes/vignette01_ecb.Rmd | 2 vignettes/vignette02_cort_clayton.Rmd | 16 - vignettes/vignette04_bootstrap_varying_m.Rmd | 10 49 files changed, 1007 insertions(+), 555 deletions(-)
Title: Biological Risk Assessment
Description: A spatio-temporal exposure-hazard model for assessing biological
risk and impact. The model is based on stochastic geometry for describing
the landscape and the exposed individuals, a dispersal kernel for the
dissemination of contaminants, a set of tools to handle spatio-temporal dataframe
and ecotoxicological equations.
Walker E, Leclerc M, Rey JF, Beaudouin R, Soubeyrand S, and Messean A, (2017),
A Spatio-Temporal Exposure-Hazard Model for Assessing Biological Risk and Impact,
Risk Analysis, <doi:10.1111/risa.12941>.
Leclerc M, Walker E, Messean A, Soubeyrand S (2018),
Spatial exposure-hazard and landscape models for assessing the impact of GM crops on non-target organisms,
Science of the Total Environment, 624, 470-479.
Author: Virgile Baudrot [aut],
Emily Walker [aut],
Jean-Francois Rey [aut, cre],
Melen Leclerc [aut],
Samuel Soubeyrand [ctb],
Marc Bourotte [ctb]
Maintainer: Jean-Francois Rey <jean-francois.rey@inrae.fr>
Diff between briskaR versions 1.0.0 dated 2020-09-15 and 1.0.1 dated 2020-11-30
DESCRIPTION | 14 ++++---- MD5 | 14 ++++---- R/0briskaR.R | 6 +-- R/catch-routine-registration.R |only build/vignette.rds |binary inst/doc/demonstrations.html | 68 ++++++++++++++++++++++++++++++++++------- src/RcppExports.cpp | 4 +- src/test-try.cpp |only tests/testthat/test-cpp.R | 5 --- 9 files changed, 79 insertions(+), 32 deletions(-)
Title: Rapid Realistic Routing with 'R5'
Description: Rapid realistic routing on multimodal transport networks (walk,
bike, public transport and car) using 'R5', the Rapid Realistic
Routing on Real-world and Reimagined networks
<https://github.com/conveyal/r5>. The package allows users to
generate detailed routing analysis or calculate travel time matrices
using seamless parallel computing on top of the R5 Java machine.
Author: Marcus Saraiva [aut] (<https://orcid.org/0000-0001-6218-2338>),
Rafael H. M. Pereira [aut, cre]
(<https://orcid.org/0000-0003-2125-7465>),
Daniel Herszenhut [aut] (<https://orcid.org/0000-0001-8066-1105>),
Carlos Kaue Vieira Braga [aut]
(<https://orcid.org/0000-0002-6104-7297>),
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between r5r versions 0.2-0 dated 2020-10-20 and 0.2-1 dated 2020-11-30
DESCRIPTION | 8 MD5 | 46 +-- NAMESPACE | 1 NEWS.md | 87 +++-- R/detailed_itineraries.R | 8 R/download_r5.R | 188 ++++++------ R/setup_r5.R | 231 +++++++-------- R/street_network_to_sf.R | 2 R/travel_time_matrix.R | 429 ++++++++++++++--------------- R/zzz.R | 71 ++-- inst/doc/intro_to_r5r.R | 4 inst/doc/intro_to_r5r.Rmd | 4 inst/doc/intro_to_r5r.html | 133 +++----- inst/extdata/poa/poa.zip |binary man/detailed_itineraries.Rd | 4 man/setup_r5.Rd | 1 man/street_network_to_sf.Rd | 2 man/travel_time_matrix.Rd | 4 tests/testthat.R | 2 tests/testthat/test-detailed_itineraries.R | 6 tests/testthat/test-street_network_to_sf.R | 5 tests/testthat/test-travel_time_matrix.R | 7 tests/testthat/test-utils.R | 4 vignettes/intro_to_r5r.Rmd | 4 24 files changed, 636 insertions(+), 615 deletions(-)
Title: Data and Functions for the Book Modern Statistical Graphics
Description: A companion to the Chinese book ``Modern Statistical Graphics''.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Lijia Yu [ctb],
Xiangyun Huang [ctb],
Peng Zhao [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between MSG versions 0.5 dated 2020-09-09 and 0.6 dated 2020-11-30
MSG-0.5/MSG/inst/examples/pay-rating-points-tikz.R |only MSG-0.5/MSG/inst/examples/quake6-bubbles-tikz.R |only MSG-0.6/MSG/DESCRIPTION | 6 MSG-0.6/MSG/MD5 | 144 ++++++++++----------- MSG-0.6/MSG/NEWS.md | 4 MSG-0.6/MSG/inst/examples/PlantCounts2.R | 6 MSG-0.6/MSG/inst/examples/assocplot.R | 4 MSG-0.6/MSG/inst/examples/assocplot2.R | 9 + MSG-0.6/MSG/inst/examples/axis-demo.R | 6 MSG-0.6/MSG/inst/examples/bagplot2.R | 3 MSG-0.6/MSG/inst/examples/basketball-fourfold.R | 26 +-- MSG-0.6/MSG/inst/examples/canabalt-boxplot.R | 3 MSG-0.6/MSG/inst/examples/cdplot2.R | 5 MSG-0.6/MSG/inst/examples/cn-us-redraw.R | 19 ++ MSG-0.6/MSG/inst/examples/coplot.R | 4 MSG-0.6/MSG/inst/examples/coplot2.R | 3 MSG-0.6/MSG/inst/examples/covidcountries.R | 4 MSG-0.6/MSG/inst/examples/diamonds-carat.R | 3 MSG-0.6/MSG/inst/examples/diamonds-cut.R | 4 MSG-0.6/MSG/inst/examples/diamonds-hex.R | 2 MSG-0.6/MSG/inst/examples/diamonds-polar.R | 5 MSG-0.6/MSG/inst/examples/dotchart.R | 4 MSG-0.6/MSG/inst/examples/dotchart2.R | 7 - MSG-0.6/MSG/inst/examples/filled-contour.R | 16 ++ MSG-0.6/MSG/inst/examples/fourfoldplot.R | 3 MSG-0.6/MSG/inst/examples/geom-jitter-demo.R | 3 MSG-0.6/MSG/inst/examples/ggparcoord.R | 4 MSG-0.6/MSG/inst/examples/ggplot2-layers.R | 3 MSG-0.6/MSG/inst/examples/ggplot2-minard.R | 2 MSG-0.6/MSG/inst/examples/ggplot2-violin.R | 3 MSG-0.6/MSG/inst/examples/gov-cn-pct2.R | 5 MSG-0.6/MSG/inst/examples/grad-color.R | 2 MSG-0.6/MSG/inst/examples/hist-density2.R | 1 MSG-0.6/MSG/inst/examples/hist-geyser2.R | 3 MSG-0.6/MSG/inst/examples/image2.R | 4 MSG-0.6/MSG/inst/examples/insects-boxplot2.R | 1 MSG-0.6/MSG/inst/examples/install-packages.R | 14 +- MSG-0.6/MSG/inst/examples/interaction-plot.R | 4 MSG-0.6/MSG/inst/examples/iris-ggplot2.R | 4 MSG-0.6/MSG/inst/examples/lattice-data-par-tikz.R | 2 MSG-0.6/MSG/inst/examples/lattice-iris-hist.R | 3 MSG-0.6/MSG/inst/examples/lattice-panel-function.R | 2 MSG-0.6/MSG/inst/examples/lattice-vadeaths.R | 4 MSG-0.6/MSG/inst/examples/map2.R | 2 MSG-0.6/MSG/inst/examples/mtcars-smooth.R | 3 MSG-0.6/MSG/inst/examples/murcia-ternary.R | 3 MSG-0.6/MSG/inst/examples/music-3d-pcp.R | 7 - MSG-0.6/MSG/inst/examples/pairs.R | 2 MSG-0.6/MSG/inst/examples/pairs2.R | 4 MSG-0.6/MSG/inst/examples/pay-rating-log.R | 4 MSG-0.6/MSG/inst/examples/pay-rating-points.R | 8 - MSG-0.6/MSG/inst/examples/pie-chart.R | 4 MSG-0.6/MSG/inst/examples/pie-chart2.R | 4 MSG-0.6/MSG/inst/examples/plot-design.R | 11 + MSG-0.6/MSG/inst/examples/point-iris.R | 3 MSG-0.6/MSG/inst/examples/pork-price2.R | 3 MSG-0.6/MSG/inst/examples/qplot.R | 2 MSG-0.6/MSG/inst/examples/qqnorm2.R | 4 MSG-0.6/MSG/inst/examples/quake6-bubbles.R | 5 MSG-0.6/MSG/inst/examples/rpart.R | 6 MSG-0.6/MSG/inst/examples/rug.R | 2 MSG-0.6/MSG/inst/examples/rug2.R | 4 MSG-0.6/MSG/inst/examples/song-words-hclust.R | 2 MSG-0.6/MSG/inst/examples/spineplot.R | 3 MSG-0.6/MSG/inst/examples/stem-islands.R | 1 MSG-0.6/MSG/inst/examples/stem-poisson.R | 1 MSG-0.6/MSG/inst/examples/stripchart.R | 6 MSG-0.6/MSG/inst/examples/stripchart2.R | 1 MSG-0.6/MSG/inst/examples/sunflowerplot.R | 3 MSG-0.6/MSG/inst/examples/sunspots-asp.R | 4 MSG-0.6/MSG/inst/examples/survival2.R | 3 MSG-0.6/MSG/inst/examples/tufte1997.R | 6 MSG-0.6/MSG/inst/examples/tvearn.R | 4 MSG-0.6/MSG/inst/examples/vadeaths-barplot2.R | 5 74 files changed, 297 insertions(+), 177 deletions(-)
Title: PARAFAC Analysis of Fluorescence Excitation-Emission Matrices
Description: Perform parallel factor analysis (PARAFAC: Hitchcock, 1927)
<doi:10.1002/sapm192761164> on fluorescence excitation-emission
matrices (FEEMs): handle scattering signal and inner filter
effect, scale the dataset, fit the model; perform split-half
validation or jack-knifing. A modified approach called
"randomised split-half" is also available. The package has a low
dependency footprint (only two direct dependencies not in core
or recommended; four total non-core/recommended dependencies)
and has been tested on a wide range of R versions (including R
as old as 3.3.3 from Debian Stretch).
Author: Ivan Krylov [aut, cre],
Timur Labutin [ths]
Maintainer: Ivan Krylov <ikrylov@laser.chem.msu.ru>
Diff between albatross versions 0.1-2 dated 2020-10-02 and 0.2-0 dated 2020-11-30
DESCRIPTION | 10 ++-- MD5 | 63 +++++++++++++------------- NAMESPACE | 6 ++ R/bootstrap.R | 20 ++++++-- R/cubeapply.R |only R/feem.R | 4 - R/feemcube.R | 20 ++++++-- R/feemife.R | 33 +++++-------- R/feemscale.R | 5 -- R/feemscatter.R | 27 +++++++++-- R/jackknife.R | 11 ++-- R/parafac.R | 110 ++++++++++++++++++++++++++-------------------- R/splithalf.R | 16 ++++-- build/partial.rdb |binary inst/CITATION |only inst/NEWS.Rd | 48 ++++++++++++++++---- man/as.data.frame.feem.Rd | 9 ++- man/feem.Rd | 3 - man/feemife.Rd | 33 ++++++++----- man/feemjackknife.Rd | 10 ++-- man/feemparafac.Rd | 39 +++++++++++++++- man/feems.Rd | 3 - man/feemscale.Rd | 8 ++- man/feemscatter.Rd | 36 ++++++++++++--- man/feemsplithalf.Rd | 12 +++-- man/marine.colours.Rd | 15 +++--- tests/feem.R | 3 - tests/feemcube.R | 5 +- tests/feemife.R | 20 +++++++- tests/feemscale.R | 2 tests/feemscatter.R | 6 ++ tests/jackknife.R |only tests/parafac.R | 22 +++++++++ tests/splithalf.R | 11 ++++ 34 files changed, 423 insertions(+), 187 deletions(-)
Title: A Collection of R Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive, with millions of observations, data) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include a) Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). An elliptically symmetric angular Gaussian distribution. Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). Comparison of discriminant analysis methods on the sphere. Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2020). Spherical regression models with general covariates and anisotropic errors. Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872-2>.
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 4.4 dated 2020-07-13 and 4.5 dated 2020-11-30
DESCRIPTION | 10 +-- MD5 | 113 ++++++++++++++++++++++++--------------------- R/ESAG.da.R | 4 - R/ESAGda.pred.R | 4 - R/ESAGsim.R | 2 R/bic.mixvmf.R | 2 R/circ.summary.R | 2 R/dirda.cv.R | 8 +-- R/embed.aov.R | 4 - R/embed.boot.R | 14 +++-- R/embed.perm.R |only R/embedcirc.boot.R |only R/embedcirc.perm.R | 33 +++---------- R/euclid.inv.R | 1 R/eul2rot.R | 1 R/fb.saddle.R | 2 R/fishkent.R | 2 R/group.gof.R | 15 ++--- R/group.vm.R | 2 R/habeck.rot.R | 5 - R/hcf.aov.R | 4 - R/hcf.boot.R | 20 +++---- R/hcf.perm.R |only R/hcfcirc.boot.R |only R/het.aov.R | 2 R/het.boot.R | 4 - R/het.perm.R |only R/hetcirc.boot.R |only R/hetcirc.perm.R | 7 +- R/kent.density.R | 2 R/knn.reg.R | 16 +----- R/knnreg.tune.R | 14 ++--- R/lambert.R | 4 - R/lambert.inv.R | 4 - R/lr.aov.R | 20 ++----- R/lr.boot.R | 2 R/lr.perm.R |only R/lrcirc.boot.R |only R/lrcirc.perm.R | 25 +++++++++ R/makefolds.R | 4 - R/matrixfisher.mle.R | 2 R/meandir.test.R | 4 - R/rfb.R | 2 R/rkent.R | 2 R/rmatrixfisher.R | 5 - R/rot2eul.R | 4 - R/rsop.R | 3 - R/rspml.R |only R/rwrapcauchy.R | 1 R/sphereplot.R | 1 R/vm.kde.R | 4 - R/vmf.kde.R | 2 R/vmf.kerncontour.R | 2 man/Directional-package.Rd | 6 +- man/hcf.boot.Rd | 2 man/hcf.perm.Rd |only man/hcfcirc.boot.Rd |only man/hcfcirc.perm.Rd | 4 - man/knn.reg.Rd | 18 +------ man/knnreg.tune.Rd | 10 +-- man/matrixfisher.mle.Rd | 4 - man/rvonmises.Rd | 7 ++ man/spml.reg.Rd | 1 63 files changed, 213 insertions(+), 223 deletions(-)
Title: Installing and Loading R Packages for Reproducible Workflows
Description: A single key function, 'Require' that wraps 'install.packages',
'remotes::install_github', 'versions::install.versions', and 'base::require'
that allows for reproducible workflows. As with other functions in a
reproducible workflow, this package emphasizes functions that return the
same result whether it is the first or subsequent times running the function.
Maturing.
Author: Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>),
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between Require versions 0.0.8 dated 2020-09-10 and 0.0.9 dated 2020-11-30
DESCRIPTION | 8 MD5 | 32 ++- NAMESPACE | 3 NEWS.md | 19 ++ R/Require-helpers.R | 200 +++++++++++++---------- R/Require.R | 80 +++++++-- R/helpers.R | 51 ++++-- R/pkgDep.R | 34 +++- README.md | 1 man/Require.Rd | 18 +- man/messageDF.Rd | 34 ++-- man/modifyList2.Rd |only man/normPath.Rd | 112 ++++++------- man/pkgDepIfDepRemoved.Rd |only tests/testit/packageVersions.txt | 331 ++++++++++++++++++++++----------------- tests/testit/test-1packages.R | 6 tests/testit/test-helpers.R | 10 + tests/testit/test-other.R | 2 18 files changed, 596 insertions(+), 345 deletions(-)
Title: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
Description: Estimates statistically significant marker combination values within
which one immunologically distinctive group (i.e., disease case) is more associated than
another group (i.e., healthy control), successively, using various combinations (i.e.,
"gates") of markers to examine features of cells that may be different between
groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk
function that is estimated using the 'sparr' package. Details about the 'sparr' package
methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details
about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>.
More information about relative risk functions using kernel density estimation can be
found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] (<https://orcid.org/0000-0001-9477-8582>),
Elena Hsieh [ctb] (<https://orcid.org/0000-0003-3969-6597>),
Debashis Ghosh [ctb] (<https://orcid.org/0000-0001-6618-1316>),
Lance A. Waller [ctb] (<https://orcid.org/0000-0001-5002-8886>),
NCI [cph]
Maintainer: Ian D. Buller <ian.buller@nih.gov>
Diff between gateR versions 0.1.3 dated 2020-11-17 and 0.1.4 dated 2020-11-30
DESCRIPTION | 8 +- MD5 | 26 ++++---- NAMESPACE | 1 NEWS.md | 5 + R/gating.R | 9 ++ R/lotrrs.R | 153 ++++++++++++++++++++++++++----------------------- R/package.R | 2 R/rrs.R | 10 ++- README.md | 16 ++--- inst/doc/vignette.html | 23 ++++--- man/gating.Rd | 8 ++ man/lotrrs.Rd | 8 ++ man/rrs.Rd | 5 + vignettes/vignette.Rmd | 7 +- 14 files changed, 171 insertions(+), 110 deletions(-)
Title: Single Cell Mapper
Description: Description of scMappR R package adapted from pre-print. The single cell mapper (scMappR) R package contains a suite of bioinformatic tools that provide experimentally relevant cell-type specific information to a list of differentially expressed genes (DEG). The function "scMappR_and_pathway_analysis" reranks DEGs to generate cell-type specificity scores called cell-weighted fold-changes. Users input a list of DEGs, normalized counts, and a signature matrix into this function. scMappR then re-weights bulk DEGs by cell-type specific expression from the signature matrix, cell-type proportions from RNA-seq deconvolution and the ratio of cell-type proportions between the two conditions to account for changes in cell-type proportion. With cwFold-changes calculated, scMappR uses two approaches to utilize cwFold-changes to complete cell-type specific pathway analysis. The "process_dgTMatrix_lists" function in the scMappR package contains an automated scRNA-seq processing pipeline where users input scRNA-seq count data, which is made compatible for scMappR and other R packages that analyze scRNA-seq data. We further used this to store hundreds up regularly updating signature matrices. The functions "tissue_by_celltype_enrichment", "tissue_scMappR_internal", and "tissue_scMappR_custom" combine these consistently processed scRNAseq count data with gene-set enrichment tools to allow for cell-type marker enrichment of a generic gene list (e.g. GWAS hits). Reference: Sokolowski,D.J., Faykoo-Martinez,M., Erdman,L., Hou,H., Chan,C., Zhu,H., Holmes,M.M., Goldenberg,A. and Wilson,M.D. (2020) Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes. BioRxiv, 10.1101/2020.08.24.265298.
Author: Dustin Sokolowski [aut, cre],
Mariela Faykoo-Martinez [aut],
Lauren Erdman [aut],
Houyun Hou [aut],
Cadia Chan [aut],
Helen Zhu [aut],
Melissa Holmes [aut],
Anna Goldenberg [aut],
Michael Wilson [aut]
Maintainer: Dustin Sokolowski <dustin.sokolowski@sickkids.ca>
Diff between scMappR versions 0.1.4 dated 2020-09-02 and 0.1.5 dated 2020-11-30
DESCRIPTION | 8 MD5 | 130 +-- NAMESPACE | 14 R/DeconRNAseq_CRAN.R | 8 R/PBMC_example.R | 4 R/POA_example.R | 2 R/cellmarker_enrich.R | 6 R/coEnrich.R | 6 R/compare_deconvolution_methods.R |only R/cwFoldChange_evaluate.R |only R/deconvolute_and_contextualize.R | 134 ++- R/extract_genes_cell.R | 8 R/gProfiler_cellWeighted_Foldchange.R | 17 R/generes_to_heatmap.R | 8 R/get_gene_symbol.R | 8 R/get_signature_matrices.R | 10 R/gsva_cellIdentify.R | 16 R/heatmap_generation.R | 10 R/human_mouse_ct_marker_enrich.R | 6 R/make_TF_barplot.R | 16 R/pathway_enrich_internal.R | 18 R/plotBP.R | 14 R/process_dgTMatrix_lists.R | 21 R/process_from_count.R | 16 R/scMappR_and_pathway_analysis.R | 205 ++--- R/scMappR_tissues.R | 4 R/seurat_to_generes.R | 12 R/single_gene_preferences.R | 6 R/sm.R | 2 R/tissue_by_celltype_enirchment.R | 10 R/tissue_scMappR_custom.R | 14 R/tissue_scMappR_internal.R | 10 R/toNum.R | 6 R/tochr.R | 8 R/topgenes_extract.R | 8 R/two_method_pathway_enrichment.R | 39 README.md | 155 ++- inst/doc/scMappR_Vignette.R | 110 +- inst/doc/scMappR_Vignette.Rmd | 310 ++++--- inst/doc/scMappR_Vignette.html | 1217 +++++++++++++++++-------------- man/PBMC_example.Rd | 4 man/POA_example.Rd | 2 man/compare_deconvolution_methods.Rd |only man/cwFoldChange_evaluate.Rd |only man/deconvolute_and_contextualize.Rd | 34 man/extract_genes_cell.Rd | 2 man/gProfiler_cellWeighted_Foldchange.Rd | 2 man/generes_to_heatmap.Rd | 2 man/get_gene_symbol.Rd | 2 man/get_signature_matrices.Rd | 4 man/gsva_cellIdentify.Rd | 10 man/heatmap_generation.Rd | 4 man/make_TF_barplot.Rd | 8 man/pathway_enrich_internal.Rd | 6 man/plotBP.Rd | 6 man/process_dgTMatrix_lists.Rd | 14 man/process_from_count.Rd | 10 man/scMappR_and_pathway_analysis.Rd | 31 man/scMappR_tissues.Rd | 4 man/seurat_to_generes.Rd | 6 man/sm.Rd | 2 man/tissue_by_celltype_enrichment.Rd | 4 man/tissue_scMappR_custom.Rd | 4 man/tissue_scMappR_internal.Rd | 4 man/tochr.Rd | 2 man/topgenes_extract.Rd | 2 man/two_method_pathway_enrichment.Rd | 14 vignettes/scMappR_Vignette.Rmd | 310 ++++--- 68 files changed, 1714 insertions(+), 1375 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Extended
Description: For one-way layout experiments the one-way ANOVA can
be performed as an omnibus test. All-pairs multiple comparisons
tests (Tukey-Kramer test, Scheffe test, LSD-test)
and many-to-one tests (Dunnett test) for normally distributed
residuals and equal within variance are available. Furthermore,
all-pairs tests (Games-Howell test, Tamhane's T2 test,
Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one
(Tamhane-Dunnett Test) for normally distributed residuals
and heterogeneous variances are provided. Van der Waerden's normal
scores test for omnibus, all-pairs and many-to-one tests is
provided for non-normally distributed residuals and homogeneous
variances. The Kruskal-Wallis, BWS and Anderson-Darling
omnibus test and all-pairs tests
(Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow-
Fligner test) as well as many-to-one (Nemenyi test, Dunn test,
U-test) are given for the analysis of variance by ranks.
Non-parametric trend tests (Jonckheere test, Cuzick test,
Johnson-Mehrotra test, Spearman test) are included.
In addition, a Friedman-test for one-way ANOVA with repeated
measures on ranks (CRBD) and Skillings-Mack test for unbalanced
CRBD is provided with consequent all-pairs tests (Nemenyi test,
Siegel test, Miller test, Conover test, Exact test)
and many-to-one tests (Nemenyi test, Demsar test, Exact test).
A trend can be tested with Pages's test. Durbin's test
for a two-way balanced incomplete block design (BIBD) is given
in this package as well as Gore's test for CRBD with multiple
observations per cell is given. Outlier tests, Mandel's k- and
h statistic as well as functions for Type I error and Power
analysis as well as generic summary, print and plot methods
are provided.
Author: Thorsten Pohlert [aut, cre] (<https://orcid.org/0000-0003-3855-3025>)
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMRplus versions 1.7.0 dated 2020-10-30 and 1.7.1 dated 2020-11-30
DESCRIPTION | 8 +- MD5 | 102 +++++++++++++++++++------------------- NAMESPACE | 1 R/GSTTest.R | 16 ++--- R/HStat.R |only R/chaAllPairsNashimotoTest.R | 13 ++-- R/chackoTest.R | 30 ++++++++--- R/duncanTest.R | 40 ++++++++++++-- R/dunnettT3Test.R | 48 ++++++++++++++--- R/dunnettTest.R | 56 ++++++++++++++------ R/flignerWolfeTest.R | 26 ++++----- R/friedmanTest.R | 8 +- R/gamesHowellTest.R | 47 ++++++++++++++--- R/gettiesDunn.R |only R/gettiesFW.R |only R/gettiesKruskal.R |only R/kruskalTest.R | 88 +++++++++++++++++++++++--------- R/kwAllPairsConoverTest.R | 26 ++------- R/kwAllPairsDunnTest.R | 22 ++------ R/kwAllPairsNemenyiTest.R | 80 ++++++++++++++++++++--------- R/kwManyOneConoverTest.R | 37 ++----------- R/kwManyOneDunnTest.R | 11 +--- R/kwManyOneNdwTest.R | 11 ---- R/lsdTest.R | 37 +++++++++---- R/scheffeTest.R | 27 +++++++--- R/shirleyWilliamsTest.R | 34 +++++++++++- R/tamhaneDunnettTest.R | 46 ++++++++++++++--- R/tamhaneT2Test.R | 72 +++++++++++++++++++++----- R/toTidy.R | 12 +++- R/tukeyTest.R | 27 +++++++--- R/uryWigginsHochbergTest.R | 55 ++++++++++++++++---- R/williamsTest.R | 51 +++++++++++++++++-- README.md | 14 +---- demo/algae.R | 29 +++++----- inst/NEWS.Rd | 21 +++++++ inst/doc/QuickReferenceGuide.html | 4 - man/chaAllPairsNashimotoTest.Rd | 13 ++-- man/chackoTest.Rd | 30 ++++++++--- man/duncanTest.Rd | 39 ++++++++++++-- man/dunnettT3Test.Rd | 47 ++++++++++++++--- man/dunnettTest.Rd | 54 ++++++++++++++------ man/flignerWolfeTest.Rd | 2 man/friedmanTest.Rd | 8 +- man/gamesHowellTest.Rd | 46 ++++++++++++++--- man/kruskalTest.Rd | 73 +++++++++++++++++++++------ man/kwAllPairsNemenyiTest.Rd | 56 ++++++++++++++++++-- man/lsdTest.Rd | 37 +++++++++---- man/scheffeTest.Rd | 27 +++++++--- man/shirleyWilliamsTest.Rd | 34 +++++++++++- man/tamhaneDunnettTest.Rd | 46 ++++++++++++++--- man/tamhaneT2Test.Rd | 68 ++++++++++++++++++++----- man/tukeyTest.Rd | 27 +++++++--- man/uryWigginsHochbergTest.Rd | 51 +++++++++++++++---- man/williamsTest.Rd | 34 +++++++++++- 54 files changed, 1311 insertions(+), 480 deletions(-)
Title: Simulate Dynamic Networks using Exponential Random Graph Models
(ERGM) Family
Description: Functions are provided to fit temporal lag models to dynamic
networks. The models are build on top of exponential random graph models (ERGM) framework. There are
functions for simulating or forecasting networks for future time points.
Abhirup Mallik & Zack W. Almquist (2019) Stable Multiple Time Step Simulation/Prediction From Lagged Dynamic Network Regression Models, Journal of Computational and Graphical Statistics, 28:4, 967-979, <DOI: 10.1080/10618600.2019.1594834>.
Author: Abhirup Mallik [aut, cre],
Zack Almquist [aut]
Maintainer: Abhirup Mallik <abhirupkgp@gmail.com>
Diff between dnr versions 0.3.4 dated 2018-07-26 and 0.3.5 dated 2020-11-30
dnr-0.3.4/dnr/R/engineEdgeExperimental.R |only dnr-0.3.4/dnr/TODO |only dnr-0.3.4/dnr/data/datalist |only dnr-0.3.4/dnr/man/engineEdgeExperimental.Rd |only dnr-0.3.4/dnr/vignettes/bibliography.bib |only dnr-0.3.5/dnr/DESCRIPTION | 14 - dnr-0.3.5/dnr/MD5 | 67 +++---- dnr-0.3.5/dnr/NAMESPACE | 1 dnr-0.3.5/dnr/NEWS.md | 4 dnr-0.3.5/dnr/R/compareMetrics.R | 2 dnr-0.3.5/dnr/R/dnr.R | 8 dnr-0.3.5/dnr/R/paramVertex.R | 252 +++++++++++++++------------- dnr-0.3.5/dnr/R/paramVertexOnly.R | 2 dnr-0.3.5/dnr/R/paramest.R | 9 - dnr-0.3.5/dnr/R/simEdgesSmooth.R | 40 ++-- dnr-0.3.5/dnr/R/simVertexNonSmooth.R | 2 dnr-0.3.5/dnr/R/simulateVertex.R | 4 dnr-0.3.5/dnr/R/utilities.R | 234 +++++++++++++------------- dnr-0.3.5/dnr/README.md | 2 dnr-0.3.5/dnr/build/vignette.rds |binary dnr-0.3.5/dnr/inst/doc/dnr_vignette.Rnw | 9 - dnr-0.3.5/dnr/inst/doc/dnr_vignette.pdf |binary dnr-0.3.5/dnr/man/beach.Rd | 4 dnr-0.3.5/dnr/man/dnr.Rd | 15 + dnr-0.3.5/dnr/man/engineEdge.Rd | 21 ++ dnr-0.3.5/dnr/man/engineEdgeBayes.Rd | 22 ++ dnr-0.3.5/dnr/man/engineEdgeNS.Rd | 21 ++ dnr-0.3.5/dnr/man/engineVertex.Rd | 32 ++- dnr-0.3.5/dnr/man/engineVertexNS.Rd | 32 ++- dnr-0.3.5/dnr/man/expdeg.Rd | 2 dnr-0.3.5/dnr/man/paramEdge.Rd | 27 ++- dnr-0.3.5/dnr/man/paramVertex.Rd | 31 ++- dnr-0.3.5/dnr/man/paramVertexOnly.Rd | 14 + dnr-0.3.5/dnr/man/paramVertexOnlyGroup.Rd | 14 + dnr-0.3.5/dnr/man/rdNets.Rd | 4 dnr-0.3.5/dnr/man/regEngine.Rd | 9 - dnr-0.3.5/dnr/vignettes/dnr_vignette.Rnw | 9 - 37 files changed, 524 insertions(+), 383 deletions(-)
Title: Bayesian Copula Regression
Description: Tools for Bayesian copula generalized linear models (GLMs).
The sampling scheme is based on Pitt, Chan, and Kohn (2006) <doi:10.1093/biomet/93.3.537>.
Regression parameters (including coefficients and dispersion parameters) are
estimated via the adaptive random walk Metropolis approach developed by
Haario, Saksman, and Tamminen (1999) <doi:10.1007/s001800050022>.
The prior for the correlation matrix is based on Hoff (2007) <doi:10.1214/07-AOAS107>.
Author: Ethan Alt [aut, cre],
Yash Bhosale [aut]
Maintainer: Ethan Alt <ethanalt@live.unc.edu>
Diff between bayescopulareg versions 0.1.2 dated 2020-05-28 and 0.1.3 dated 2020-11-30
DESCRIPTION | 12 ++--- MD5 | 19 ++++----- NEWS.md | 10 ++++ R/RcppExports.R | 11 ++++- src/RcppExports.cpp | 24 +++++++++++ src/bayescopulareg.h | 53 ++++++++++++++++++++++++++ src/cdf.cpp | 41 +++++++++++++++++++- src/cholesky.cpp |only src/loglik_pointer.cpp | 99 ++++++++++++++++++++++++++++++++++++++++++++++--- src/sample_copula.cpp | 23 ++++++++++- src/update_params.cpp | 11 ++--- 11 files changed, 272 insertions(+), 31 deletions(-)
More information about bayescopulareg at CRAN
Permanent link
Title: Graph-Constrained Functional Pruning Optimal Partitioning
Description: Penalized parametric change-point detection by functional pruning dynamic programming algorithm.
The successive means are constrained using a graph structure with edges of types null, up, down, std or abs. To each edge we can associate some additional properties: a minimal gap size, a penalty, some robust parameters (K,a). The user can also constrain the inferred means to lie between some minimal and maximal values. Data is modeled by a quadratic cost with possible use of a robust loss, biweight and Huber (see edge parameters K and a). Other losses are also available with log-linear representation or a log-log representation.
Author: Vincent Runge [aut, cre],
Toby Hocking [aut],
Guillem Rigaill [aut],
Gaetano Romano [aut],
Fatemeh Afghah [aut],
Paul Fearnhead [aut],
Michel Koskas [ctb],
Arnaud Liehrmann [ctb]
Maintainer: Vincent Runge <vincent.runge@univ-evry.fr>
Diff between gfpop versions 1.0.0 dated 2020-11-25 and 1.0.1 dated 2020-11-30
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ src/Cost.cpp | 2 +- src/Data.cpp | 2 +- src/ListPiece.cpp | 4 ++-- src/Omega.cpp | 10 +++++----- src/Piece.cpp | 4 ++-- 7 files changed, 20 insertions(+), 20 deletions(-)
Title: Funnel Plots for Comparing Institutional Performance
Description: An implementation of methods presented by Spiegelhalter (2005) <doi:10.1002/sim.1970> Funnel plots for comparing institutional performance, for standardised ratios, ratios of counts and proportions with additive overdispersion adjustment.
Author: Chris Mainey [aut, cre] (<https://orcid.org/0000-0002-3018-6171>),
Matthew Bass [ctb]
Maintainer: Chris Mainey <chris.mainey@uhb.nhs.uk>
Diff between FunnelPlotR versions 0.3.1 dated 2020-09-16 and 0.3.2 dated 2020-11-30
DESCRIPTION | 8 LICENSE | 4 MD5 | 68 - NAMESPACE | 78 +- NEWS.md | 68 - R/aggregate_func.R | 44 - R/build_limits_lookup.R | 214 ++--- R/classes_methods.R | 396 +++++----- R/draw_plot.R | 314 ++++---- R/funnel_plot.R | 536 +++++++------- R/funnel_themes.R | 72 - R/od_adjustment.R | 349 ++++----- R/od_limits.R | 104 +- R/outliers_func.R | 91 +- R/poisson_limits.R | 42 - README.md | 372 ++++----- build/vignette.rds |binary inst/CITATION | 30 inst/doc/changing_funnel_plot_options.R | 170 ++-- inst/doc/changing_funnel_plot_options.Rmd | 276 +++---- inst/doc/changing_funnel_plot_options.html | 942 +++++++++++++----------- inst/doc/funnel_plots.R | 158 ++-- inst/doc/funnel_plots.Rmd | 386 +++++----- inst/doc/funnel_plots.html | 1096 +++++++++++++++-------------- man/phi_func.Rd | 2 tests/testthat.R | 8 tests/testthat/test-aggregate_fun.R | 18 tests/testthat/test-build_limits_lookup.R | 22 tests/testthat/test-funnel_plot.R | 104 +- tests/testthat/test-funnel_themes.R | 6 tests/testthat/test-poisson_limits.R | 20 vignettes/changing_funnel_plot_options.Rmd | 276 +++---- vignettes/funnel_plots.Rmd | 386 +++++----- vignettes/harvard.csl | 614 ++++++++-------- vignettes/references.bib | 252 +++--- 35 files changed, 3838 insertions(+), 3688 deletions(-)
Title: Flexible Bayes Factor Testing of Scientific Expectations
Description: Implementation of various default Bayes factors
for testing statistical hypotheses. The package is
intended for applied quantitative researchers in the
social and behavioral sciences, medical research,
and related fields. The Bayes factor tests can be
executed for statistical models such as
univariate and multivariate normal linear models,
generalized linear models, special cases of
linear mixed models, survival models, relational
event models. Parameters that can be tested are
location parameters (e.g., regression coefficients),
variances (e.g., group variances), and measures of
association (e.g,. bivariate correlations).
The statistical underpinnings are
described in
Mulder, Hoijtink, and Xin (2019) <arXiv:1904.00679>,
Mulder and Gelissen (2019) <arXiv:1807.05819>,
Mulder (2016) <DOI:10.1016/j.jmp.2014.09.004>,
Mulder and Fox (2019) <DOI:10.1214/18-BA1115>,
Mulder and Fox (2013) <DOI:10.1007/s11222-011-9295-3>,
Boeing-Messing, van Assen, Hofman, Hoijtink, and Mulder <DOI:10.1037/met0000116>,
Hoijtink, Mulder, van Lissa, and Gu, (2018) <DOI:10.31234/osf.io/v3shc>,
Gu, Mulder, and Hoijtink, (2018) <DOI:10.1111/bmsp.12110>,
Hoijtink, Gu, and Mulder, (2018) <DOI:10.1111/bmsp.12145>, and
Hoijtink, Gu, Mulder, and Rosseel, (2018) <DOI:10.1037/met0000187>.
Author: Joris Mulder [aut, cre],
Caspar van Lissa [aut, ctb],
Donald R. Williams [aut, ctb],
Xin Gu [aut],
Anton Olsson-Collentine [aut, ctb],
Florian Boeing-Messing [aut, ctb],
Jean-Paul Fox [aut, ctb],
Janosch Menke [ctb],
Robbie van Aert [ctb],
Barry Brown [ctb],
James Lovato [ctb],
Kathy Russell [ctb],
Lapack 3.8 [ctb],
Jack Dongarra [ctb],
Jim Bunch [ctb],
Cleve Moler [ctb],
Gilbert Stewart [ctb],
John Burkandt [ctb],
Ashwith Rego [ctb],
Alexander Godunov [ctb],
Alan Miller [ctb],
Jean-Pierre Moreau [ctb],
The R Core Team [cph]
Maintainer: Joris Mulder <j.mulder3@tilburguniversity.edu>
Diff between BFpack versions 0.2.1 dated 2020-05-11 and 0.3.1 dated 2020-11-30
BFpack-0.2.1/BFpack/data/datalist |only BFpack-0.3.1/BFpack/DESCRIPTION | 30 BFpack-0.3.1/BFpack/MD5 | 67 + BFpack-0.3.1/BFpack/NAMESPACE | 2 BFpack-0.3.1/BFpack/NEWS.md | 8 BFpack-0.3.1/BFpack/R/BF.lm.R | 32 BFpack-0.3.1/BFpack/R/BF.print.R | 19 BFpack-0.3.1/BFpack/R/BF.summary.R | 160 ++-- BFpack-0.3.1/BFpack/R/BF_methods.R | 72 -- BFpack-0.3.1/BFpack/R/BFicc.R | 66 + BFpack-0.3.1/BFpack/R/BFmeta.R |only BFpack-0.3.1/BFpack/R/BFpack-package.R | 72 ++ BFpack-0.3.1/BFpack/R/get_estimates_unique_to_BFpack.R | 4 BFpack-0.3.1/BFpack/README.md | 353 +++++++--- BFpack-0.3.1/BFpack/build |only BFpack-0.3.1/BFpack/inst |only BFpack-0.3.1/BFpack/man/BF.Rd | 74 +- BFpack-0.3.1/BFpack/man/BFpack-package.Rd |only BFpack-0.3.1/BFpack/man/actors.Rd | 6 BFpack-0.3.1/BFpack/man/attention.Rd | 4 BFpack-0.3.1/BFpack/man/figures |only BFpack-0.3.1/BFpack/man/fmri.Rd | 4 BFpack-0.3.1/BFpack/man/memory.Rd | 4 BFpack-0.3.1/BFpack/man/relevents.Rd | 6 BFpack-0.3.1/BFpack/man/same_building.Rd | 6 BFpack-0.3.1/BFpack/man/same_division.Rd | 6 BFpack-0.3.1/BFpack/man/same_hierarchy.Rd | 6 BFpack-0.3.1/BFpack/man/sivan.Rd | 4 BFpack-0.3.1/BFpack/man/therapeutic.Rd | 4 BFpack-0.3.1/BFpack/man/timssICC.Rd | 4 BFpack-0.3.1/BFpack/man/tvprices.Rd | 4 BFpack-0.3.1/BFpack/man/wilson.Rd | 4 BFpack-0.3.1/BFpack/tests/testthat/test_BFmeta.R |only BFpack-0.3.1/BFpack/tests/testthat/test_application2_BF.lm.R | 24 BFpack-0.3.1/BFpack/tests/testthat/test_application7_BF.lmerMod.R | 19 BFpack-0.3.1/BFpack/tests/testthat/test_metafor.R |only BFpack-0.3.1/BFpack/tests/testthat/test_paper_fmri.R |only BFpack-0.3.1/BFpack/vignettes |only 38 files changed, 663 insertions(+), 401 deletions(-)
Title: Bessel and Beta Regressions via Expectation-Maximization
Algorithm for Continuous Bounded Data
Description: Functions to fit, via Expectation-Maximization (EM) algorithm, the Bessel and Beta regressions to a data set with a bounded continuous response variable. The Bessel regression is a new and robust approach proposed in the literature. The EM version for the well known Beta regression is another major contribution of this package. See the reference Barreto-Souza, Mayrink and Simas (2020) <arXiv:2003.05157> for details.
Author: Vinicius Mayrink [cre, aut] (<https://orcid.org/0000-0002-5683-8326>),
Alexandre B. Simas [aut] (<https://orcid.org/0000-0003-2562-2829>),
Wagner Barreto-Souza [aut] (<https://orcid.org/0000-0003-0831-7881>)
Maintainer: Vinicius Mayrink <vdinizm@gmail.com>
Diff between bbreg versions 2.0.0 dated 2020-11-30 and 2.0.1 dated 2020-11-30
DESCRIPTION | 6 +- MD5 | 97 +++++++++++++++++++++---------------------- R/EM_Bes.R | 22 ++++----- R/EM_Bet.R | 22 ++++----- R/EM_DBB.R | 14 +++--- R/EM_bbreg.R | 8 +-- R/explore_functions.R | 28 ++++++------ build/vignette.rds |binary data/SA.RData |binary inst/doc/intro-bbreg.Rmd | 4 - inst/doc/intro-bbreg.html | 6 +- man/D2Q_Obs_Fisher_bes.Rd | 2 man/D2Q_Obs_Fisher_bet.Rd | 2 man/DQ2_Obs_Fisher_bes.Rd | 2 man/DQ2_Obs_Fisher_bet.Rd | 2 man/EMrun_bes.Rd | 2 man/EMrun_bes_dbb.Rd | 2 man/EMrun_bet.Rd | 2 man/EMrun_bet_dbb.Rd | 2 man/Qf_bes.Rd | 2 man/Qf_bes_dbb.Rd | 2 man/Qf_bet.Rd | 2 man/Qf_bet_dbb.Rd | 2 man/bbreg.Rd | 6 +- man/coef.bbreg.Rd | 2 man/d2phideta2.Rd | 2 man/dbbtest.Rd | 2 man/envelope_bes.Rd | 2 man/envelope_bet.Rd | 2 man/fitted.bbreg.Rd | 2 man/gradlam_bes_dbb.Rd | 2 man/gradlam_bet_dbb.Rd | 2 man/gradtheta_bes.Rd | 2 man/gradtheta_bet.Rd | 2 man/infmat_bes.Rd | 2 man/infmat_bet.Rd | 2 man/plot.bbreg.Rd | 9 ++- man/pred_accuracy_bes.Rd | 2 man/pred_accuracy_bet.Rd | 2 man/predict.bbreg.Rd | 2 man/print.bbreg.Rd | 2 man/quantile_residual_bes.Rd | 2 man/quantile_residual_bet.Rd | 2 man/score_residual_bes.Rd | 2 man/score_residual_bet.Rd | 2 man/simdata_bes.Rd | 2 man/simdata_bet.Rd | 2 man/summary.bbreg.Rd | 2 vignettes/intro-bbreg.Rmd | 4 - vignettes/rsconnect |only 50 files changed, 149 insertions(+), 147 deletions(-)
Title: Functions to Make Surveys Processing Easier
Description: Set of functions to make the processing and analysis of
surveys easier : interactive shiny apps and addins for data recoding,
contingency tables, dataset metadata handling, and several convenience
functions.
Author: Julien Barnier [aut, cre],
François Briatte [aut],
Joseph Larmarange [aut]
Maintainer: Julien Barnier <julien.barnier@cnrs.fr>
Diff between questionr versions 0.7.3 dated 2020-10-05 and 0.7.4 dated 2020-11-30
DESCRIPTION | 12 ++--- MD5 | 46 ++++++++++---------- NAMESPACE | 2 NEWS.md | 11 ++++ R/ggsurvey.R |only R/icut.R | 7 +-- R/iorder.R | 52 ++++++++++++++++++++-- R/weighting.R | 51 +++++++++++++++------- build/vignette.rds |binary data/fecondite.RData |binary data/fertility.RData |binary data/happy.RData |binary data/hdv2003.RData |binary data/rp2012.RData |binary data/rp99.RData |binary inst/doc/recoding_addins.html | 52 +++++++++++++++++++++- inst/po/en@quot/LC_MESSAGES/R-questionr.mo |binary inst/po/fr/LC_MESSAGES/R-questionr.mo |binary man/ggsurvey.Rd |only man/wtd.mean.Rd | 5 -- man/wtd.table.Rd | 7 ++- po/R-fr.mo |binary po/R-fr.po | 66 +++++++++++++++++------------ po/R-questionr.pot | 36 ++++++++++----- tests/testthat/test_ggsurvey.R |only tests/testthat/test_weighting.R |only 26 files changed, 247 insertions(+), 100 deletions(-)
Title: The Integration Between 'IBM COGNOS TM1' and R
Description: Useful functions to connect to 'TM1' <https://www.ibm.com/uk-en/products/planning-and-analytics> instance from R via REST API. With the functions in the package, data can be imported from 'TM1' via mdx view or native view, data can be sent to 'TM1', processes and chores can be executed, and cube and dimension metadata information can be taken.
Author: Muhammed Ali Onder
Maintainer: Muhammed Ali Onder <muhammedalionder@gmail.com>
Diff between tm1r versions 1.1.6 dated 2020-11-14 and 1.1.7 dated 2020-11-30
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/tm1_connection.R | 9 ++++++--- R/tm1_create_element.R | 9 ++++++--- 4 files changed, 18 insertions(+), 12 deletions(-)
Title: An IMAP Client for R
Description: An easy-to-use IMAP client that provides tools for message searching,
selective fetching of message attributes, mailbox management, attachment extraction,
and several other IMAP features, paving the way for e-mail data analysis.
Author: Allan Quadros [aut, cre] (<https://orcid.org/0000-0003-3250-5380>)
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between mRpostman versions 0.9.0.0 dated 2020-09-16 and 1.0.0 dated 2020-11-30
mRpostman-0.9.0.0/mRpostman/R/configure_imap.R |only mRpostman-0.9.0.0/mRpostman/man/execute_attachment_fetch.Rd |only mRpostman-0.9.0.0/mRpostman/man/execute_complementary_operations.Rd |only mRpostman-0.9.0.0/mRpostman/man/execute_fetch_loop.Rd |only mRpostman-1.0.0/mRpostman/DESCRIPTION | 16 mRpostman-1.0.0/mRpostman/MD5 | 128 +++--- mRpostman-1.0.0/mRpostman/NAMESPACE | 2 mRpostman-1.0.0/mRpostman/R/R6.R | 197 +++++----- mRpostman-1.0.0/mRpostman/R/before.R | 2 mRpostman-1.0.0/mRpostman/R/check-args.R | 16 mRpostman-1.0.0/mRpostman/R/clean-fetch-results.R | 38 + mRpostman-1.0.0/mRpostman/R/clean-msg-text.R |only mRpostman-1.0.0/mRpostman/R/config-con-handle-and-params.R | 21 - mRpostman-1.0.0/mRpostman/R/configure-imap.R |only mRpostman-1.0.0/mRpostman/R/decode-mime-header.R |only mRpostman-1.0.0/mRpostman/R/decode-mime-text.R |only mRpostman-1.0.0/mRpostman/R/decode-quoted-printable-text.R |only mRpostman-1.0.0/mRpostman/R/decode-quoted-printable.R |only mRpostman-1.0.0/mRpostman/R/examine-folder-int.R | 2 mRpostman-1.0.0/mRpostman/R/execute-attachment-fetch.R | 153 ++++--- mRpostman-1.0.0/mRpostman/R/execute-complementary-operations.R | 2 mRpostman-1.0.0/mRpostman/R/execute-fetch-loop.R | 28 - mRpostman-1.0.0/mRpostman/R/execute-search.R | 9 mRpostman-1.0.0/mRpostman/R/extract-MIME-level-and-filenames.R | 29 - mRpostman-1.0.0/mRpostman/R/fetch-attachments-int.R | 25 - mRpostman-1.0.0/mRpostman/R/fetch-attachments-list-int.R | 43 +- mRpostman-1.0.0/mRpostman/R/fetch-body-int.R | 22 - mRpostman-1.0.0/mRpostman/R/fetch-metadata-int.R | 20 - mRpostman-1.0.0/mRpostman/R/get-attachments-int.R | 91 ++-- mRpostman-1.0.0/mRpostman/R/has-attachment.R | 2 mRpostman-1.0.0/mRpostman/R/list-attachments.R | 28 - mRpostman-1.0.0/mRpostman/R/list-flags-int.R | 2 mRpostman-1.0.0/mRpostman/R/list-mail-folders-int.R | 6 mRpostman-1.0.0/mRpostman/R/list-server-capabilities-int.R | 2 mRpostman-1.0.0/mRpostman/R/rename-folder-int.R | 23 + mRpostman-1.0.0/mRpostman/R/search-before-int.R | 2 mRpostman-1.0.0/mRpostman/R/search-on-int.R | 2 mRpostman-1.0.0/mRpostman/R/search-period-int.R | 4 mRpostman-1.0.0/mRpostman/R/search-sent-before-int.R | 4 mRpostman-1.0.0/mRpostman/R/search-sent-on-int.R | 4 mRpostman-1.0.0/mRpostman/R/search-sent-period-int.R | 6 mRpostman-1.0.0/mRpostman/R/search-sent-since-int.R | 4 mRpostman-1.0.0/mRpostman/R/search-since-int.R | 2 mRpostman-1.0.0/mRpostman/R/select-folder-int.R | 2 mRpostman-1.0.0/mRpostman/R/zzz.R | 4 mRpostman-1.0.0/mRpostman/README.md | 96 ++-- mRpostman-1.0.0/mRpostman/build/partial.rdb |binary mRpostman-1.0.0/mRpostman/build/vignette.rds |binary mRpostman-1.0.0/mRpostman/inst/doc/basics.R | 6 mRpostman-1.0.0/mRpostman/inst/doc/basics.Rmd | 22 - mRpostman-1.0.0/mRpostman/inst/doc/basics.html | 74 +++ mRpostman-1.0.0/mRpostman/inst/doc/code_migration.R | 2 mRpostman-1.0.0/mRpostman/inst/doc/code_migration.Rmd | 10 mRpostman-1.0.0/mRpostman/inst/doc/code_migration.html | 58 ++ mRpostman-1.0.0/mRpostman/inst/doc/xoauth2.0.R | 5 mRpostman-1.0.0/mRpostman/inst/doc/xoauth2.0.Rmd | 7 mRpostman-1.0.0/mRpostman/inst/doc/xoauth2.0.html | 65 ++- mRpostman-1.0.0/mRpostman/man/ImapCon.Rd | 161 ++++---- mRpostman-1.0.0/mRpostman/man/before.Rd | 2 mRpostman-1.0.0/mRpostman/man/clean_msg_text.Rd |only mRpostman-1.0.0/mRpostman/man/configure_imap.Rd | 26 + mRpostman-1.0.0/mRpostman/man/decode_mime_header.Rd |only mRpostman-1.0.0/mRpostman/man/mRpostman-package.Rd | 8 mRpostman-1.0.0/mRpostman/man/on.Rd | 2 mRpostman-1.0.0/mRpostman/man/sent_before.Rd | 2 mRpostman-1.0.0/mRpostman/man/sent_on.Rd | 2 mRpostman-1.0.0/mRpostman/man/sent_since.Rd | 2 mRpostman-1.0.0/mRpostman/man/since.Rd | 2 mRpostman-1.0.0/mRpostman/vignettes/basics.Rmd | 22 - mRpostman-1.0.0/mRpostman/vignettes/code_migration.Rmd | 10 mRpostman-1.0.0/mRpostman/vignettes/xoauth2.0.Rmd | 7 71 files changed, 913 insertions(+), 619 deletions(-)
Title: Tools for Fast Computing and Plotting Euclidean Minimum Spanning
Trees
Description: Fast and easily computes an Euclidean Minimum Spanning Tree (EMST) from data.
This package relies on 'RcppMLPACK' to provide an R interface to the Dual-Tree Boruvka
algorithm (March, Ram, Gray, 2010, <doi:10.1145/1835804.1835882>) implemented in
'mlpack', the C++ Machine Learning Library (Curtin et. al., 2013). The Dual-Tree
Boruvka is theoretically and empirically the fastest algorithm for computing an EMST.
This package also provides functions and an S3 method for readily plotting Minimum
Spanning Trees (MST) using either the style of the 'base', 'scatterplot3d', or
'ggplot2' libraries.
Author: Allan Quadros [aut, cre]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between emstreeR versions 2.2.0 dated 2019-05-08 and 2.2.2 dated 2020-11-30
emstreeR-2.2.0/emstreeR/NEWS.md |only emstreeR-2.2.0/emstreeR/man/data_check.Rd |only emstreeR-2.2.0/emstreeR/man/figures |only emstreeR-2.2.0/emstreeR/man/mlpack_mst.Rd |only emstreeR-2.2.2/emstreeR/DESCRIPTION | 36 ++++----- emstreeR-2.2.2/emstreeR/MD5 | 37 ++++----- emstreeR-2.2.2/emstreeR/NAMESPACE | 6 + emstreeR-2.2.2/emstreeR/R/ComputeMST.R | 2 emstreeR-2.2.2/emstreeR/R/RcppExports.R | 1 emstreeR-2.2.2/emstreeR/R/data-check.R | 6 + emstreeR-2.2.2/emstreeR/R/zzz.R |only emstreeR-2.2.2/emstreeR/README.md | 93 ++++++++++++------------ emstreeR-2.2.2/emstreeR/man/ComputeMST.Rd | 2 emstreeR-2.2.2/emstreeR/man/README-figures |only emstreeR-2.2.2/emstreeR/man/emstreeR-package.Rd | 12 --- emstreeR-2.2.2/emstreeR/man/plot.MST.Rd | 3 emstreeR-2.2.2/emstreeR/man/plotMST3D.Rd | 12 ++- emstreeR-2.2.2/emstreeR/man/stat_MST.Rd | 14 ++- emstreeR-2.2.2/emstreeR/src/mlpack_mst.cpp | 8 +- 19 files changed, 127 insertions(+), 105 deletions(-)
Title: Broken Adaptive Ridge AFT Model with Censored Data
Description: Broken adaptive ridge estimator for censored data is used to
select variables and estimate their coefficients in the semi-parametric
accelerated failure time model for right-censored survival data.
Author: Zhihua Sun [aut, cre],
Chunyu Yu [aut],
Gang Li [aut],
Kani Chen [ctb],
Yi Liu [ctb]
Maintainer: Zhihua Sun <zhihuasun@ouc.edu.cn>
Diff between CenBAR versions 0.1.0 dated 2020-02-26 and 0.1.1 dated 2020-11-30
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Execute and Control System Processes
Description: Tools to run system processes in the background.
It can check if a background process is running; wait on a background
process to finish; get the exit status of finished processes; kill
background processes. It can read the standard output and error of
the processes, using non-blocking connections. 'processx' can poll
a process for standard output or error, with a timeout. It can also
poll several processes at once.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>),
Winston Chang [aut],
RStudio [cph, fnd],
Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between processx versions 3.4.4 dated 2020-09-03 and 3.4.5 dated 2020-11-30
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 8 ++++++++ R/errors.R | 19 ++++++++++++++----- R/initialize.R | 2 ++ R/process.R | 8 +++++++- README.md | 3 +-- man/default_pty_options.Rd | 2 ++ src/processx-connection.c | 2 +- src/processx.h | 2 ++ src/unix/processx.c | 14 +++++++++++++- tests/testthat/test-err.R | 17 +++++++++++++++++ tests/testthat/test-utf8.R | 2 ++ 13 files changed, 84 insertions(+), 25 deletions(-)
Title: Bessel and Beta Regressions via Expectation-Maximization
Algorithm for Continuous Bounded Data
Description: Functions to fit, via Expectation-Maximization (EM) algorithm, the Bessel and Beta regressions to a data set with a bounded continuous response variable. The Bessel regression is a new and robust approach proposed in the literature. The EM version for the well known Beta regression is another major contribution of this package. See the reference Barreto-Souza, Mayrink and Simas (2020) <arXiv:2003.05157> for details.
Author: Vinicius Mayrink [cre, aut] (<https://orcid.org/0000-0002-5683-8326>),
Alexandre B. Simas [aut] (<https://orcid.org/0000-0003-2562-2829>),
Wagner Barreto-Souza [aut] (<https://orcid.org/0000-0003-0831-7881>)
Maintainer: Vinicius Mayrink <vdinizm@gmail.com>
Diff between bbreg versions 1.0.0 dated 2020-03-20 and 2.0.0 dated 2020-11-30
bbreg-1.0.0/bbreg/inst/CITATION |only bbreg-1.0.0/bbreg/man/bbsummary.Rd |only bbreg-1.0.0/bbreg/man/eplot.Rd |only bbreg-2.0.0/bbreg/DESCRIPTION | 37 bbreg-2.0.0/bbreg/MD5 | 99 +- bbreg-2.0.0/bbreg/NAMESPACE | 31 bbreg-2.0.0/bbreg/R/EM_Bes.R | 1025 +++++++++++++------------ bbreg-2.0.0/bbreg/R/EM_Bet.R | 892 ++++++++++++--------- bbreg-2.0.0/bbreg/R/EM_DBB.R | 501 ++++++------ bbreg-2.0.0/bbreg/R/EM_bbreg.R | 677 +++++++++------- bbreg-2.0.0/bbreg/R/explore_functions.R | 730 +++++++++++++---- bbreg-2.0.0/bbreg/build |only bbreg-2.0.0/bbreg/inst/doc |only bbreg-2.0.0/bbreg/man/BF.Rd | 28 bbreg-2.0.0/bbreg/man/D2Q_Obs_Fisher_bes.Rd |only bbreg-2.0.0/bbreg/man/D2Q_Obs_Fisher_bet.Rd |only bbreg-2.0.0/bbreg/man/DQ2_Obs_Fisher_bes.Rd |only bbreg-2.0.0/bbreg/man/DQ2_Obs_Fisher_bet.Rd |only bbreg-2.0.0/bbreg/man/EMrun_bes.Rd | 8 bbreg-2.0.0/bbreg/man/EMrun_bes_dbb.Rd | 7 bbreg-2.0.0/bbreg/man/EMrun_bet.Rd | 14 bbreg-2.0.0/bbreg/man/EMrun_bet_dbb.Rd | 7 bbreg-2.0.0/bbreg/man/Ew1z.Rd | 6 bbreg-2.0.0/bbreg/man/Ew2z.Rd | 4 bbreg-2.0.0/bbreg/man/Qf_bes.Rd | 14 bbreg-2.0.0/bbreg/man/Qf_bes_dbb.Rd | 11 bbreg-2.0.0/bbreg/man/Qf_bet.Rd | 12 bbreg-2.0.0/bbreg/man/Qf_bet_dbb.Rd | 9 bbreg-2.0.0/bbreg/man/SA.Rd | 4 bbreg-2.0.0/bbreg/man/WT.Rd | 6 bbreg-2.0.0/bbreg/man/bbreg.Rd | 93 +- bbreg-2.0.0/bbreg/man/coef.bbreg.Rd |only bbreg-2.0.0/bbreg/man/d2mudeta2.Rd |only bbreg-2.0.0/bbreg/man/d2phideta2.Rd |only bbreg-2.0.0/bbreg/man/dbbtest.Rd | 13 bbreg-2.0.0/bbreg/man/envelope_bes.Rd | 20 bbreg-2.0.0/bbreg/man/envelope_bet.Rd | 27 bbreg-2.0.0/bbreg/man/fitted.bbreg.Rd |only bbreg-2.0.0/bbreg/man/gradlam_bes_dbb.Rd | 11 bbreg-2.0.0/bbreg/man/gradlam_bet_dbb.Rd | 9 bbreg-2.0.0/bbreg/man/gradtheta_bes.Rd | 16 bbreg-2.0.0/bbreg/man/gradtheta_bet.Rd | 12 bbreg-2.0.0/bbreg/man/infmat_bes.Rd | 13 bbreg-2.0.0/bbreg/man/infmat_bet.Rd | 15 bbreg-2.0.0/bbreg/man/plot.bbreg.Rd |only bbreg-2.0.0/bbreg/man/pred_accuracy_bes.Rd | 24 bbreg-2.0.0/bbreg/man/pred_accuracy_bet.Rd | 33 bbreg-2.0.0/bbreg/man/predict.bbreg.Rd |only bbreg-2.0.0/bbreg/man/print.bbreg.Rd |only bbreg-2.0.0/bbreg/man/quantile_residual_bes.Rd | 13 bbreg-2.0.0/bbreg/man/quantile_residual_bet.Rd | 13 bbreg-2.0.0/bbreg/man/score_residual_bes.Rd | 22 bbreg-2.0.0/bbreg/man/score_residual_bet.Rd | 26 bbreg-2.0.0/bbreg/man/simdata_bes.Rd | 18 bbreg-2.0.0/bbreg/man/simdata_bet.Rd | 16 bbreg-2.0.0/bbreg/man/startvalues.Rd | 7 bbreg-2.0.0/bbreg/man/summary.bbreg.Rd |only bbreg-2.0.0/bbreg/man/vcov.bbreg.Rd |only bbreg-2.0.0/bbreg/vignettes |only 59 files changed, 2752 insertions(+), 1771 deletions(-)
Title: Access WHO Global Health Observatory Data from R
Description: Access WHO Global Health Observatory
(<https://www.who.int/data/gho/>)
data from R via the Athena web service
(<https://apps.who.int/gho/data/node.resources.api>),
an application program interface providing
a simple query interface to the World
Health Organization's data and statistics content.
Author: Antoine Filipovic-Pierucci [aut,cre]
Maintainer: Kevin Zarca <kevin.zarca@gmail.com>
Diff between rgho versions 2.0.0 dated 2020-04-07 and 2.0.1 dated 2020-11-30
DESCRIPTION | 14 MD5 | 60 NAMESPACE | 5 NEWS.md | 6 R/build_url.R | 2 R/filter.R | 13 R/get_data.R | 5 R/get_gho.R | 9 R/get_object.R | 6 R/rgho.R | 5 R/utils.R | 7 README.md | 6 build/vignette.rds |binary inst/doc/a-intro.R | 18 inst/doc/a-intro.Rmd | 4 inst/doc/a-intro.html | 380 +- inst/doc/b-dimensions.R | 4 inst/doc/b-dimensions.html | 347 +- inst/doc/c-codes-gho.R | 4 inst/doc/c-codes-gho.html | 5889 +++++++++++++++------------------------- inst/doc/d-codes-country.R | 4 inst/doc/d-codes-country.html | 139 inst/doc/e-details.R | 2 inst/doc/e-details.html | 79 man/build_gho_url.Rd | 9 man/get_gho_.Rd | 6 man/get_gho_data.Rd | 5 man/rgho.Rd | 1 tests/testthat/test-build_gho.R | 2 tests/testthat/test-build_url.R | 30 vignettes/a-intro.Rmd | 4 31 files changed, 3080 insertions(+), 3985 deletions(-)
Title: Bayesian Network Learning with the PCHC and Related Algorithms
Description: Bayesian network learning using the PCHC algorithm. PCHC stands for PC Hill-Climbing. It is a new hybrid algorithm that used PC to construct the skeleton of the BN and then utilizes the Hill-Climbing greedy search. The relevant paper is: Tsagris M. (2021). "A new scalable Bayesian network learning algorithm with applications to economics". Computational Economics (Accepted for publication). <doi:10.1007/s10614-020-10065-7>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between pchc versions 0.2 dated 2020-08-28 and 0.3 dated 2020-11-30
DESCRIPTION | 15 ++++----- MD5 | 74 +++++++++++++++++++++++++++++++++++++-------- NAMESPACE | 17 ++++++++-- R/auc.R |only R/big_cor.R |only R/big_read.R |only R/bn.skel.utils.R |only R/bn.skel.utils2.R |only R/bnmat.R |only R/bnplot.R | 2 - R/chi2test_univariate.R |only R/conf.edge.lower.R |only R/cor.fbed.R |only R/correls.R |only R/fedhc.R |only R/fedhc.skel.R |only R/fedhc.skel.boot.R |only R/g2test_univariate.R |only R/g2test_univariate_perm.R |only R/is.dag.R |only R/mb.R |only R/mmhc.R |only R/mmhc.skel.R |only R/mmhc.skel.boot.R |only R/mmpc.R |only R/pc.sel.R |only R/pchc.R | 24 ++++++++++++-- R/pchc.skel.R | 32 +++++++++++++++++-- R/pchc.skel.boot.R |only R/pi0est.R |only R/rbn2.R |only R/rbn3.R |only R/rmcd.R |only man/auc.Rd |only man/big_cor.Rd |only man/big_read.Rd |only man/bn.skel.utils.Rd |only man/bnmat.Rd |only man/bnplot.Rd | 4 +- man/cat.tests.Rd | 9 +++-- man/conf.edge.lower.Rd |only man/cor.fbed.Rd |only man/correls.Rd |only man/cortest.Rd | 12 +++---- man/fedhc.Rd |only man/fedhc.skel.Rd |only man/g2test.Rd | 27 +++++++++------- man/g2test_univariate.Rd |only man/is.dag.Rd |only man/mb.Rd |only man/mmhc.Rd |only man/mmhc.skel.Rd |only man/mmpc.Rd |only man/pc.sel.Rd |only man/pchc-package.Rd | 11 ++++-- man/pchc.Rd | 44 ++++++++++++++------------ man/pchc.skel.Rd | 33 +++++++++++--------- man/pchc.skel.boot.Rd |only man/pcor.Rd | 4 +- man/pi0est.Rd |only man/rbn2.Rd |only man/rmcd.Rd |only 62 files changed, 214 insertions(+), 94 deletions(-)
Title: Estimation Methods for Markets in Disequilibrium
Description: Provides estimation methods for markets in equilibrium and
disequilibrium. Specifically, it supports the estimation of an equilibrium and
four disequilibrium models with both correlated and independent shocks.
It also provides post-estimation analysis tools, such as aggregation and
marginal effects calculations. The estimation methods are based on full
information maximum likelihood techniques given in Maddala and Nelson (1974)
<doi:10.2307/1914215>. They are implemented using the analytic derivative
expressions calculated in Karapanagiotis (2020) <doi:10.2139/ssrn.3525622>.
The equilibrium estimation constitutes a special case of
a system of simultaneous equations. The disequilibrium models, instead, replace
the market clearing condition with a short side rule and
allow for different specifications of price dynamics.
Author: Pantelis Karapanagiotis [aut, cre]
(<https://orcid.org/0000-0001-9871-1908>)
Maintainer: Pantelis Karapanagiotis <pikappa.devel@gmail.com>
Diff between diseq versions 0.0.13 dated 2020-09-21 and 0.0.14 dated 2020-11-30
DESCRIPTION | 8 MD5 | 73 +-- NAMESPACE | 1 NEWS.md | 17 R/derivatives_deterministic_adjustment.R | 24 - R/derivatives_directional.R | 38 - R/derivatives_fiml.R | 10 R/derivatives_stochastic_adjustment.R | 18 R/diseq.R | 2 R/diseq_base.R | 16 R/diseq_basic.R | 16 R/diseq_deterministic_adjustment.R | 9 R/diseq_directional.R | 32 + R/diseq_stochastic_adjustment.R | 9 R/eq_fiml.R | 78 ++- R/model_base.R | 97 ++++ R/system_base.R | 4 R/system_deterministic_adjustment.R | 48 ++ R/system_stochastic_adjustment.R | 56 ++ README.md | 525 +++++++++++++------------ build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/basic_usage.R | 22 - inst/doc/basic_usage.Rmd | 24 - inst/doc/basic_usage.html | 204 +++++---- inst/doc/market_clearing_assessment.Rmd | 2 inst/doc/market_clearing_assessment.html | 12 man/diseq.Rd | 2 man/estimate.Rd | 16 man/scores.Rd |only tests/testthat/helper-common.R | 9 tests/testthat/test-basic.R | 4 tests/testthat/test-deterministic_adjustment.R | 4 tests/testthat/test-directional.R | 4 tests/testthat/test-fiml.R | 4 tests/testthat/test-stochastic_adjustment.R | 4 vignettes/basic_usage.Rmd | 24 - vignettes/market_clearing_assessment.Rmd | 2 38 files changed, 928 insertions(+), 493 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearization of several non-linear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, Sample Survey Methods And Theory, vol. I: Methods and Applications; vol. II: Theory. 1953, New York: John Wiley and Sons), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y. G., 2015, <doi:10.1111/rssa.12116>). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut],
Martins Liberts [aut, cre],
Santa Ivanova [aut],
Aleksis Jursevskis [ctb],
Anthony Damico [ctb],
Central Statistical Bureau of Latvia [cph, fnd]
Maintainer: Martins Liberts <martins.liberts@csb.gov.lv>
Diff between vardpoor versions 0.20.0 dated 2020-05-20 and 0.20.1 dated 2020-11-30
vardpoor-0.20.0/vardpoor/R/vardbootstr.R |only vardpoor-0.20.0/vardpoor/README |only vardpoor-0.20.0/vardpoor/inst/NEWS |only vardpoor-0.20.0/vardpoor/inst/README |only vardpoor-0.20.0/vardpoor/man/vardbootstr.Rd |only vardpoor-0.20.1/vardpoor/DESCRIPTION | 42 vardpoor-0.20.1/vardpoor/LICENSE |only vardpoor-0.20.1/vardpoor/MD5 | 122 - vardpoor-0.20.1/vardpoor/NAMESPACE | 74 vardpoor-0.20.1/vardpoor/NEWS.md |only vardpoor-0.20.1/vardpoor/R/domain.R | 4 vardpoor-0.20.1/vardpoor/R/incPercentile.R | 2 vardpoor-0.20.1/vardpoor/R/lin.ratio.R | 2 vardpoor-0.20.1/vardpoor/R/linarpr.R | 6 vardpoor-0.20.1/vardpoor/R/linarpt.R | 10 vardpoor-0.20.1/vardpoor/R/linarr.R | 2 vardpoor-0.20.1/vardpoor/R/lingini.R | 10 vardpoor-0.20.1/vardpoor/R/lingini2.R | 12 vardpoor-0.20.1/vardpoor/R/lingpg.R | 20 vardpoor-0.20.1/vardpoor/R/linpoormed.R | 4 vardpoor-0.20.1/vardpoor/R/linqsr.R | 12 vardpoor-0.20.1/vardpoor/R/linrmir.R | 2 vardpoor-0.20.1/vardpoor/R/linrmpg.R | 6 vardpoor-0.20.1/vardpoor/R/residual_est.R | 2 vardpoor-0.20.1/vardpoor/R/vardannual.R | 1035 +++++----- vardpoor-0.20.1/vardpoor/R/vardchangstrs.R | 38 vardpoor-0.20.1/vardpoor/R/vardcros.R | 15 vardpoor-0.20.1/vardpoor/R/vardom.R | 14 vardpoor-0.20.1/vardpoor/R/vardom_othstr.R | 4 vardpoor-0.20.1/vardpoor/R/vardomh.R | 8 vardpoor-0.20.1/vardpoor/R/variance_est.R | 4 vardpoor-0.20.1/vardpoor/R/variance_othstr.R | 4 vardpoor-0.20.1/vardpoor/R/varpoord.R | 16 vardpoor-0.20.1/vardpoor/README.md |only vardpoor-0.20.1/vardpoor/inst/BUGS | 2 vardpoor-0.20.1/vardpoor/inst/COPYING | 2 vardpoor-0.20.1/vardpoor/man/domain.Rd | 136 - vardpoor-0.20.1/vardpoor/man/incPercentile.Rd | 106 - vardpoor-0.20.1/vardpoor/man/lin.ratio.Rd | 120 - vardpoor-0.20.1/vardpoor/man/linarpr.Rd | 204 - vardpoor-0.20.1/vardpoor/man/linarpt.Rd | 188 - vardpoor-0.20.1/vardpoor/man/linarr.Rd | 206 - vardpoor-0.20.1/vardpoor/man/lingini.Rd | 152 - vardpoor-0.20.1/vardpoor/man/lingini2.Rd | 162 - vardpoor-0.20.1/vardpoor/man/lingpg.Rd | 210 +- vardpoor-0.20.1/vardpoor/man/linpoormed.Rd | 174 - vardpoor-0.20.1/vardpoor/man/linqsr.Rd | 164 - vardpoor-0.20.1/vardpoor/man/linrmir.Rd | 174 - vardpoor-0.20.1/vardpoor/man/linrmpg.Rd | 186 - vardpoor-0.20.1/vardpoor/man/residual_est.Rd | 128 - vardpoor-0.20.1/vardpoor/man/var_srs.Rd | 76 vardpoor-0.20.1/vardpoor/man/vardannual.Rd | 641 +++--- vardpoor-0.20.1/vardpoor/man/vardchanges.Rd | 514 ++-- vardpoor-0.20.1/vardpoor/man/vardchangespoor.Rd | 420 ++-- vardpoor-0.20.1/vardpoor/man/vardchangstrs.Rd | 235 -- vardpoor-0.20.1/vardpoor/man/vardcros.Rd | 665 +++--- vardpoor-0.20.1/vardpoor/man/vardcrospoor.Rd | 434 ++-- vardpoor-0.20.1/vardpoor/man/vardom.Rd | 292 +- vardpoor-0.20.1/vardpoor/man/vardom_othstr.Rd | 300 +- vardpoor-0.20.1/vardpoor/man/vardomh.Rd | 400 +-- vardpoor-0.20.1/vardpoor/man/variance_est.Rd | 236 +- vardpoor-0.20.1/vardpoor/man/variance_othstr.Rd | 248 +- vardpoor-0.20.1/vardpoor/man/varpoord.Rd | 454 ++-- vardpoor-0.20.1/vardpoor/tests/testthat/test_random_household_order.R | 7 vardpoor-0.20.1/vardpoor/tests/testthat/test_same_domains.R | 5 vardpoor-0.20.1/vardpoor/tests/testthat/test_vardom_vardomh_same.R | 9 66 files changed, 4402 insertions(+), 4318 deletions(-)
More information about modeltime.gluonts at CRAN
Permanent link
More information about leaflet.multiopacity at CRAN
Permanent link
Title: Create Reports Using R and 'asciidoc'
Description: Inspired by Karl Broman`s reader on using 'knitr'
with 'asciidoc'
(<http://kbroman.org/knitr_knutshell/pages/asciidoc.html>), this is
merely a wrapper to 'knitr' and 'asciidoc'.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between rasciidoc versions 2.2.2 dated 2020-11-25 and 3.0.0 dated 2020-11-30
DESCRIPTION | 6 MD5 | 17 - NEWS.md | 13 R/internals.R | 4 R/render.R | 96 ++++-- inst/doc/An_Introduction_to_rasciidoc.html | 178 ++--------- inst/files/default.asciidoc |only inst/files/default.html | 5 inst/runit_tests/runit-render.R | 432 ++++++++++++++--------------- man/rasciidoc.Rd | 12 10 files changed, 357 insertions(+), 406 deletions(-)
More information about ellipticalsymmetry at CRAN
Permanent link
Title: Genetics and Independence Testing of Mixed Genetic Panels
Description: Developed to deal with multi-locus genotype data, this package is especially designed for those panel which include different type of markers. Basic genetic parameters like allele frequency, genotype frequency, heterozygosity and Hardy-Weinberg test of mixed genetic data can be obtained. In addition, a new test for mutual independence which is compatible for mixed genetic data is developed in this package.
Author: Bing Song
Maintainer: Bing Song <bingsong@my.unthsc.edu>
Diff between mixIndependR versions 0.4.2 dated 2020-11-26 and 0.4.3 dated 2020-11-30
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NAMESPACE | 2 ++ NEWS.md | 4 ++++ R/mixIndependK.R | 12 +++--------- R/mixIndependX.R | 12 +++--------- R/read_vcf_gt.R | 1 + R/splitGenotype.R | 1 + inst/doc/DistributionBuildingNComparison.html | 2 +- inst/doc/HypothesisTest.html | 2 +- 10 files changed, 28 insertions(+), 32 deletions(-)
Title: Nonparametric Regression via Smoothing Splines
Description: Multiple and generalized nonparametric regression using smoothing spline ANOVA models and generalized additive models, as described in Helwig (2020) <doi:10.4135/9781526421036885885>. Includes support for Gaussian and non-Gaussian responses, smoothers for multiple types of predictors, interactions between smoothers of mixed types, and eight different methods for smoothing parameter selection.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between npreg versions 1.0-4 dated 2020-08-10 and 1.0-5 dated 2020-11-30
npreg-1.0-4/npreg/R/tune.theta.R |only npreg-1.0-5/npreg/ChangeLog | 36 ++++++++++++ npreg-1.0-5/npreg/DESCRIPTION | 8 +- npreg-1.0-5/npreg/MD5 | 45 +++++++-------- npreg-1.0-5/npreg/R/basis_poly.R | 92 +++++++++++++++++++++++++++---- npreg-1.0-5/npreg/R/fit_gsm.R | 24 +++----- npreg-1.0-5/npreg/R/fit_sm.R | 17 ++++- npreg-1.0-5/npreg/R/penalty_poly.R | 5 + npreg-1.0-5/npreg/R/penalty_tps.R | 4 - npreg-1.0-5/npreg/R/predict.ss.R | 4 - npreg-1.0-5/npreg/R/psolve.R | 4 - npreg-1.0-5/npreg/R/sm.R | 16 ++++- npreg-1.0-5/npreg/R/ss.R | 12 ++-- npreg-1.0-5/npreg/R/summary.gsm.R | 62 ++++++++++++-------- npreg-1.0-5/npreg/R/summary.sm.R | 5 + npreg-1.0-5/npreg/R/summary.ss.R | 5 + npreg-1.0-5/npreg/R/theta.mle.R |only npreg-1.0-5/npreg/man/NegBin.Rd | 4 + npreg-1.0-5/npreg/man/gsm.Rd | 2 npreg-1.0-5/npreg/man/npreg-internals.Rd | 12 +++- npreg-1.0-5/npreg/man/polynomial.Rd | 11 +++ npreg-1.0-5/npreg/man/sm.Rd | 7 +- npreg-1.0-5/npreg/man/ss.Rd | 10 ++- npreg-1.0-5/npreg/man/summary.Rd | 1 npreg-1.0-5/npreg/man/theta.mle.Rd |only 25 files changed, 275 insertions(+), 111 deletions(-)
Title: Creating Flexible, Reproducible 'PDF' Reports
Description: A tool which allows users the ability to intuitively create
flexible, reproducible portable document format reports comprised of
aesthetically pleasing tables, images, plots and/or text.
Author: Calvin Floyd [aut, cre, cph]
Maintainer: Calvin Floyd <calvin.michael.floyd@gmail.com>
Diff between grobblR versions 0.1.1 dated 2020-08-28 and 0.2.0 dated 2020-11-30
DESCRIPTION | 6 MD5 | 35 ++-- NAMESPACE | 1 NEWS.md | 9 + R/alter.R | 6 R/headings.R | 229 ++++++++++++++++++++++++++++++-- README.md | 4 inst/doc/grob_layout.html | 4 inst/doc/grob_matrix.R | 22 +++ inst/doc/grob_matrix.Rmd | 31 ++++ inst/doc/grob_matrix.html | 181 ++++++++++++++----------- inst/doc/grobblR.html | 4 man/add_column_headings.Rd | 10 - man/alter_at.Rd | 5 man/alter_column_names.Rd |only tests/testthat/test_grob_image.R | 3 tests/testthat/test_grob_matrix.R | 199 +++++++++++++++++++++++++-- tests/testthat/test_matrix_aesthetics.R | 4 vignettes/grob_matrix.Rmd | 31 ++++ 19 files changed, 636 insertions(+), 148 deletions(-)
Title: R-Squared and Related Measures
Description: Calculate generalized R-squared, partial R-squared, and partial correlation coefficients for generalized linear (mixed) models (including quasi models with well defined variance functions).
Author: Dabao Zhang
Maintainer: Dabao Zhang <zhangdb@stat.purdue.edu>
Diff between rsq versions 2.0 dated 2020-05-09 and 2.1 dated 2020-11-30
DESCRIPTION | 10 +- MD5 | 16 ++-- NAMESPACE | 4 - R/rsq.R | 190 +++++++++++++++++++++++++++++-------------------------- man/hschool.Rd | 2 man/rsq.glmm.Rd | 5 - man/rsq.lmm.Rd | 2 man/rsq.v.Rd | 7 -- man/vresidual.Rd | 14 ++-- 9 files changed, 132 insertions(+), 118 deletions(-)