Title: Residual Balancing Weights for Marginal Structural Models
Description: Residual balancing is a robust method of constructing weights for
marginal structural models, which can be used to estimate (a) the average treatment effect in
a cross-sectional observational study, (b) controlled direct/mediator effects in causal mediation
analysis, and (c) the effects of time-varying treatments in panel data (Zhou and Wodtke 2020
<doi:10.1017/pan.2020.2>). This package provides three functions, rbwATE(), rbwMed(), and rbwPanel(),
that produce residual balancing weights for estimating (a), (b), (c), respectively.
Author: Xiang Zhou [cre],
Derick da Silva Baum [aut]
Maintainer: Xiang Zhou <xiang_zhou@fas.harvard.edu>
Diff between rbw versions 0.2.0 dated 2020-04-15 and 0.3.0 dated 2021-09-22
rbw-0.2.0/rbw/data/education.rda |only rbw-0.2.0/rbw/man/education.Rd |only rbw-0.3.0/rbw/DESCRIPTION | 37 +++++------ rbw-0.3.0/rbw/MD5 | 36 ++++++----- rbw-0.3.0/rbw/NAMESPACE | 8 ++ rbw-0.3.0/rbw/NEWS.md | 7 -- rbw-0.3.0/rbw/R/data.R | 114 ++++++++++++++++++++++++----------- rbw-0.3.0/rbw/R/rbwATE.R |only rbw-0.3.0/rbw/R/rbwMed.R | 37 ++++++----- rbw-0.3.0/rbw/R/rbwPanel.R | 83 ++++++++++++++++++++----- rbw-0.3.0/rbw/R/utils.R | 2 rbw-0.3.0/rbw/README.md | 77 ++++++++++++----------- rbw-0.3.0/rbw/data/advertisement.rda |only rbw-0.3.0/rbw/data/campaign_long.rda |binary rbw-0.3.0/rbw/data/campaign_wide.rda |binary rbw-0.3.0/rbw/data/peace.rda |only rbw-0.3.0/rbw/man/advertisement.Rd |only rbw-0.3.0/rbw/man/campaign_long.Rd | 10 ++- rbw-0.3.0/rbw/man/campaign_wide.Rd | 24 ++++--- rbw-0.3.0/rbw/man/peace.Rd |only rbw-0.3.0/rbw/man/rbwATE.Rd |only rbw-0.3.0/rbw/man/rbwMed.Rd | 37 ++++++----- rbw-0.3.0/rbw/man/rbwPanel.Rd | 26 ++++--- 23 files changed, 317 insertions(+), 181 deletions(-)
Title: Parallel Runs of Reverse Depends
Description: Reverse depends for a given package are queued such that multiple
workers can run the tests in parallel.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between prrd versions 0.0.4 dated 2021-01-23 and 0.0.5 dated 2021-09-22
ChangeLog | 33 +++++++++++++++++++++++++++++++++ DESCRIPTION | 13 ++++++++----- MD5 | 32 ++++++++++++++++---------------- R/db.R | 2 +- R/dequeue.R | 6 ++++-- R/enqueue.R | 30 ++++++++++++++++++++++++++---- R/summarise.R | 2 +- build/partial.rdb |binary inst/NEWS.Rd | 12 ++++++++++++ inst/scripts/dequeueDepends.r | 2 +- inst/scripts/dequeueJobs.r | 5 +++-- inst/scripts/enqueueDepends.r | 2 +- inst/scripts/enqueueJobs.r | 10 +++++++--- inst/scripts/summariseJobs.r | 2 +- inst/scripts/xvfb-run-safe | 2 +- man/dequeueJobs.Rd | 5 ++++- man/enqueueJobs.Rd | 6 +++++- 17 files changed, 124 insertions(+), 40 deletions(-)
Title: A Test Environment for HTTP Requests
Description: Testing and documenting code that communicates with remote servers
can be painful. Dealing with authentication, server state,
and other complications can make testing seem too costly to
bother with. But it doesn't need to be that hard. This package enables one
to test all of the logic on the R sides of the API in your package without
requiring access to the remote service. Importantly, it provides three
contexts that mock the network connection in different ways, as well as
testing functions to assert that HTTP requests were---or were
not---made. It also allows one to safely record real API responses to use as
test fixtures. The ability to save responses and load them offline also
enables one to write vignettes and other dynamic documents that can be
distributed without access to a live server.
Author: Neal Richardson [aut, cre],
Jonathan Keane [ctb],
Maëlle Salmon [ctb] (<https://orcid.org/0000-0002-2815-0399>)
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httptest versions 4.0.0 dated 2021-02-01 and 4.1.0 dated 2021-09-22
DESCRIPTION | 8 MD5 | 22 - NAMESPACE | 1 NEWS.md | 2 R/mock-api.R | 7 build/vignette.rds |binary inst/doc/faq.html | 359 ++++++++------------ inst/doc/httptest.html | 690 ++++++++++++++++------------------------ inst/doc/redacting.html | 485 +++++++++++----------------- inst/doc/vignettes.html | 395 +++++++++------------- man/with_mock_api.Rd | 6 tests/testthat/test-fake-http.R | 16 12 files changed, 807 insertions(+), 1184 deletions(-)
Title: High Dimensional Bayesian Ridge Regression without MCMC
Description: The svd(singular value decomposition) or qr decomposition was using for the implementation, this avoid the recursion optimizing the time in the compute.
Author: Sergio Perez-Elizalde Developer [aut],
Blanca Monroy-Castillo Developer [aut, cre],
Paulino Perez-Rodriguez User [ctb],
Jose Crossa User [ctb]
Maintainer: Blanca Monroy-Castillo Developer <blancamonroy.96@gmail.com>
Diff between HDBRR versions 1.1.0 dated 2021-08-13 and 1.1.1 dated 2021-09-22
DESCRIPTION | 12 +++++---- MD5 | 12 ++++----- inst/doc/HDBRR.Rnw | 67 +++++++++++++++++++++++++++------------------------- inst/doc/HDBRR.pdf |binary man/HDBRR.Rd | 2 - man/pheno.Rd | 2 - vignettes/HDBRR.Rnw | 67 +++++++++++++++++++++++++++------------------------- 7 files changed, 87 insertions(+), 75 deletions(-)
Title: Interface Tools for LSD Simulation Results Files
Description: Interfaces R with LSD simulation models. Reads object-oriented data in results files (.res[.gz]) produced by LSD and creates appropriate multi-dimensional arrays in R. Supports multiple core parallel threads of multi-file data reading for increased performance. Also provides functions to extract basic information and statistics from data files. LSD (Laboratory for Simulation Development) is free software developed by Marco Valente (documentation and downloads available at <https://www.labsimdev.org/>).
Author: Marcelo C. Pereira [aut, cre] (<https://orcid.org/0000-0002-8069-2734>)
Maintainer: Marcelo C. Pereira <mcper@unicamp.br>
Diff between LSDinterface versions 1.0.1 dated 2021-08-18 and 1.1.0 dated 2021-09-22
DESCRIPTION | 9 MD5 | 47 - NAMESPACE | 2 R/LSDinterface.R | 1809 +++++++++++++++++++++++--------------------- build/partial.rdb |binary inst/extdata/Sim1.lsd | 60 - man/LSDinterface-package.Rd | 75 - man/info.details.lsd.Rd | 74 - man/info.dimensions.lsd.Rd | 85 +- man/info.init.lsd.Rd | 87 +- man/info.names.lsd.Rd | 77 - man/info.stats.lsd.Rd | 196 ++-- man/list.files.lsd.Rd |only man/name.check.lsd.Rd | 85 +- man/name.clean.lsd.Rd | 62 - man/name.nice.lsd.Rd | 66 - man/name.var.lsd.Rd | 68 - man/read.3d.lsd.Rd | 155 +-- man/read.4d.lsd.Rd | 167 ++-- man/read.list.lsd.Rd | 160 +-- man/read.multi.lsd.Rd | 129 +-- man/read.raw.lsd.Rd | 113 +- man/read.single.lsd.Rd | 141 +-- man/select.colattrs.lsd.Rd | 143 +-- man/select.colnames.lsd.Rd | 99 +- 25 files changed, 1999 insertions(+), 1910 deletions(-)
More information about vietnameseConverter at CRAN
Permanent link
Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are
cumulative probability distributions which are fitted to
toxicity concentrations for different species as described by
Posthuma et al.(2001) <isbn:9781566705783>.
The ssdtools package uses Maximum Likelihood to fit distributions
such as the log-normal, gamma, log-logistic,
log-Gumbel, Gompertz and Weibull.
The user can provide custom distributions.
Multiple distributions can be averaged using Information Criteria.
Confidence intervals on hazard concentrations and proportions are produced by
parametric bootstrapping.
Author: Joe Thorley [aut, cre, ctr] (<https://orcid.org/0000-0002-7683-4592>),
Carl Schwarz [aut, ctr],
Angeline Tillmanns [ctb],
Ali Azizishirazi [ctb],
Rebecca Fisher [ctb],
David Fox [ctb],
Kathleen McTavish [ctb],
Heather Thompson [ctb],
Andy Teucher [ctb],
Emilie Doussantousse [ctb],
Stephanie Hazlitt [ctb],
Nadine Hussein [ctb],
Nan-Hung Hsieh [ctb],
Sergio Ibarra Espinosa [ctb],
Province of British Columbia [cph]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between ssdtools versions 0.3.5 dated 2021-09-03 and 0.3.6 dated 2021-09-22
DESCRIPTION | 10 +-- MD5 | 50 +++++++++---------- NAMESPACE | 1 NEWS.md | 6 ++ R/fit.R | 9 ++- R/hc.R | 29 +++++++---- R/hp.R | 30 +++++++---- R/namespace.R | 1 R/predict.R | 12 +++- inst/doc/distributions.html | 4 - inst/doc/exposure-plots.html | 86 ++++++++++----------------------- inst/doc/faqs.html | 49 +----------------- inst/doc/small-sample-bias-ref.html | 4 - inst/doc/ssdtools.html | 38 +------------- tests/testthat/test-burrIII2.R | 6 +- tests/testthat/test-burrIII3.R | 2 tests/testthat/test-fit.R | 2 tests/testthat/test-gompertz.R | 6 +- tests/testthat/test-hc.R | 40 ++++++++++----- tests/testthat/test-hp.R | 65 ++++++++++++++++++------ tests/testthat/test-lgumbel.R | 7 +- tests/testthat/test-llog.R | 3 - tests/testthat/test-pareto.R | 7 +- tests/testthat/test-predict.R | 17 +++--- tests/testthat/test-schwarz-tillmans.R | 3 - tests/testthat/test-test-data.R | 4 - 26 files changed, 239 insertions(+), 252 deletions(-)
Title: Raw Data Quality Control Tool for LC-MS System
Description: Assess LC–MS system performance by visualizing instrument log files and monitoring raw quality control samples within a project.
Author: Yonghui Dong
Maintainer: Yonghui Dong <yonghui.dong@gmail.com>
Diff between RawHummus versions 0.1.5 dated 2021-07-30 and 0.1.8 dated 2021-09-22
DESCRIPTION | 6 MD5 | 14 README.md | 15 inst/shiny/Gui/Report.Rmd | 1052 ++++++++------- inst/shiny/Gui/rsconnect/shinyapps.io/dong/RawHummus.dcf | 6 inst/shiny/Gui/server.R | 52 inst/shiny/Gui/ui-tab-monitor.R | 166 +- inst/shiny/Gui/ui.R | 120 - 8 files changed, 789 insertions(+), 642 deletions(-)
Title: Estimates of Standard Errors for Risk and Performance Measures
Description: Estimates of standard errors of popular risk and performance
measures for asset or portfolio returns using methods as described in
Chen and Martin (2021) <doi:10.21314/JOR.2020.446>.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Xin Chen <chenx26@uw.edu>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RPESE versions 1.2.3 dated 2021-06-09 and 1.2.4 dated 2021-09-22
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 2 +- NEWS.md | 3 +++ README.md | 3 ++- build/vignette.rds |binary 6 files changed, 17 insertions(+), 13 deletions(-)
Title: Meta-Analysis of Significance Values
Description: The canonical way to perform meta-analysis involves using effect sizes.
When they are not available this package provides a number of methods for
meta-analysis of significance values including the methods of Edgington, Fisher,
Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results;
and a routine for graphical display.
Author: Michael Dewey [aut, cre] (<https://orcid.org/0000-0002-7522-3677>)
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between metap versions 1.4 dated 2020-07-12 and 1.5 dated 2021-09-22
metap-1.4/metap/data/beckerp.rda |only metap-1.4/metap/data/cholest.rda |only metap-1.4/metap/data/edgington.rda |only metap-1.4/metap/data/mourning.rda |only metap-1.4/metap/data/naep.rda |only metap-1.4/metap/data/rosenthal.rda |only metap-1.4/metap/data/teachexpect.rda |only metap-1.4/metap/data/validity.rda |only metap-1.4/metap/man/package-data.Rd |only metap-1.5/metap/DESCRIPTION | 9 ++- metap-1.5/metap/MD5 | 85 +++++++++++++++------------------- metap-1.5/metap/NEWS | 5 ++ metap-1.5/metap/R/invchisq.R | 6 +- metap-1.5/metap/R/invt.R | 5 +- metap-1.5/metap/R/logitp.R | 5 +- metap-1.5/metap/R/meanz.R | 6 +- metap-1.5/metap/R/sumlog.R | 5 +- metap-1.5/metap/R/sumz.R | 6 +- metap-1.5/metap/R/wilkinsonp.R | 22 ++++++-- metap-1.5/metap/build/metap.pdf |binary metap-1.5/metap/build/partial.rdb |binary metap-1.5/metap/build/vignette.rds |binary metap-1.5/metap/data/dat.metap.rda |only metap-1.5/metap/inst/doc/compare.R | 26 +++++++--- metap-1.5/metap/inst/doc/compare.Rnw | 49 +++++++++++++------ metap-1.5/metap/inst/doc/compare.pdf |binary metap-1.5/metap/inst/doc/metap.R | 9 ++- metap-1.5/metap/inst/doc/metap.Rnw | 6 ++ metap-1.5/metap/inst/doc/metap.pdf |binary metap-1.5/metap/man/allmetap.Rd | 3 - metap-1.5/metap/man/dat.metap.Rd |only metap-1.5/metap/man/invchisq.Rd | 7 ++ metap-1.5/metap/man/invt.Rd | 8 ++- metap-1.5/metap/man/logitp.Rd | 13 ++--- metap-1.5/metap/man/macros/macros.Rd | 1 metap-1.5/metap/man/meanp.Rd | 5 -- metap-1.5/metap/man/meanz.Rd | 7 ++ metap-1.5/metap/man/plotp.Rd | 3 - metap-1.5/metap/man/schweder.Rd | 3 - metap-1.5/metap/man/sumlog.Rd | 15 +++--- metap-1.5/metap/man/sump.Rd | 3 - metap-1.5/metap/man/sumz.Rd | 14 +++-- metap-1.5/metap/man/truncated.Rd | 3 - metap-1.5/metap/man/two2one.Rd | 3 - metap-1.5/metap/man/votep.Rd | 3 - metap-1.5/metap/man/wilkinsonp.Rd | 20 +++++--- metap-1.5/metap/vignettes/compare.Rnw | 49 +++++++++++++------ metap-1.5/metap/vignettes/metap.Rnw | 6 ++ metap-1.5/metap/vignettes/metap.bib | 2 49 files changed, 255 insertions(+), 157 deletions(-)
Title: Solvers for Initial Value Problems of Differential Equations
('ODE', 'DAE', 'DDE')
Description: Functions that solve initial value problems of a system
of first-order ordinary differential equations ('ODE'), of
partial differential equations ('PDE'), of differential
algebraic equations ('DAE'), and of delay differential
equations. The functions provide an interface to the FORTRAN
functions 'lsoda', 'lsodar', 'lsode', 'lsodes' of the 'ODEPACK'
collection, to the FORTRAN functions 'dvode', 'zvode' and 'daspk'
and a C-implementation of solvers of the 'Runge-Kutta' family with
fixed or variable time steps. The package contains routines
designed for solving 'ODEs' resulting from 1-D, 2-D and 3-D
partial differential equations ('PDE') that have been converted
to 'ODEs' by numerical differencing.
Author: Karline Soetaert [aut] (<https://orcid.org/0000-0003-4603-7100>),
Thomas Petzoldt [aut, cre] (<https://orcid.org/0000-0002-4951-6468>),
R. Woodrow Setzer [aut] (<https://orcid.org/0000-0002-6709-9186>),
Peter N. Brown [ctb] (files ddaspk.f, dvode.f, zvode.f),
George D. Byrne [ctb] (files dvode.f, zvode.f),
Ernst Hairer [ctb] (files radau5.f, radau5a),
Alan C. Hindmarsh [ctb] (files ddaspk.f, dlsode.f, dvode.f, zvode.f,
opdkmain.f, opdka1.f),
Cleve Moler [ctb] (file dlinpck.f),
Linda R. Petzold [ctb] (files ddaspk.f, dlsoda.f),
Youcef Saad [ctb] (file dsparsk.f),
Clement W. Ulrich [ctb] (file ddaspk.f)
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between deSolve versions 1.28 dated 2020-03-08 and 1.29 dated 2021-09-22
DESCRIPTION | 6 - MD5 | 48 ++++++------- NEWS | 5 + build/vignette.rds |binary data/ccl4data.rda |binary inst/CITATION | 2 inst/doc/compiledCode.R | 24 +++--- inst/doc/compiledCode.Rnw | 11 +-- inst/doc/compiledCode.pdf |binary inst/doc/deSolve.R | 156 ++++++++++++++++++++++----------------------- inst/doc/deSolve.Rnw | 9 +- inst/doc/deSolve.pdf |binary man/daspk.Rd | 2 man/deSolve.Rd | 2 man/lsoda.Rd | 2 man/lsodar.Rd | 2 man/rk4.Rd | 2 man/rkMethod.Rd | 4 - man/vode.Rd | 2 man/zvode.Rd | 2 src/deSolve_utils.c | 3 src/forcings.c | 3 src/rk_util.c | 18 ++++- vignettes/compiledCode.Rnw | 11 +-- vignettes/deSolve.Rnw | 9 +- 25 files changed, 166 insertions(+), 157 deletions(-)
Title: Trellis Graphics for R
Description: A powerful and elegant high-level data visualization
system inspired by Trellis graphics, with an emphasis on
multivariate data. Lattice is sufficient for typical graphics needs,
and is also flexible enough to handle most nonstandard requirements.
See ?Lattice for an introduction.
Author: Deepayan Sarkar [aut, cre] (<https://orcid.org/0000-0003-4107-1553>),
Felix Andrews [ctb],
Kevin Wright [ctb] (documentation),
Neil Klepeis [ctb],
Johan Larsson [ctb] (colorkey title),
Paul Murrell [ctb]
Maintainer: Deepayan Sarkar <deepayan.sarkar@r-project.org>
Diff between lattice versions 0.20-44 dated 2021-05-02 and 0.20-45 dated 2021-09-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ man/axis.default.Rd | 2 ++ man/latticeParseFormula.Rd | 5 +++-- man/make.groups.Rd | 4 ++++ man/oneway.Rd | 15 +++++++++------ man/trellis.par.get.Rd | 18 +++++++++++------- 7 files changed, 39 insertions(+), 25 deletions(-)
Title: Analysis of Single-Cell Chromatin Data
Description: A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2020) <doi:10.1101/2020.11.09.373613>.
Author: Tim Stuart [aut, cre] (<https://orcid.org/0000-0002-3044-0897>),
Avi Srivastava [aut] (<https://orcid.org/0000-0001-9798-2079>),
Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>),
Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)
Maintainer: Tim Stuart <tstuart@nygenome.org>
Diff between Signac versions 1.3.0 dated 2021-07-12 and 1.4.0 dated 2021-09-22
DESCRIPTION | 8 +-- MD5 | 48 +++++++++++------------ NAMESPACE | 1 NEWS.md | 20 +++++++++ R/data.R | 12 ++--- R/differential_accessibility.R | 1 R/fragments.R | 20 +++++++++ R/generics.R | 3 - R/motifs.R | 21 +++++++--- R/objects.R | 4 - R/peaks.R | 43 +++++++++++++++------ R/preprocessing.R | 14 ++++-- R/utilities.R | 75 ++++++++++++++++++++++++++++++++----- README.md | 83 +++++++++++++++++++++++++++++++++++------ build/partial.rdb |binary man/AddMotifs.Rd | 6 +- man/CallPeaks.Rd | 12 ++++- man/RunChromVAR.Rd | 3 - man/blacklist_ce10.Rd | 4 - man/blacklist_ce11.Rd | 4 - man/blacklist_dm3.Rd | 4 - man/blacklist_dm6.Rd | 4 - man/blacklist_hg19.Rd | 4 - man/blacklist_mm10.Rd | 4 - src/RcppExports.cpp | 5 ++ 25 files changed, 305 insertions(+), 98 deletions(-)
Title: Multiple Imputation in Cluster Analysis
Description: Implementation of a framework for cluster analysis with selection of the
final number of clusters and an optional variable selection procedure. The package
is designed to integrate the results of multiple imputed datasets while accounting
for the uncertainty that the imputations introduce in the final results. In addition,
the package can also be used for a cluster analysis of the complete cases of a single
dataset. The package also includes specific methods to summarize and plot the results.
The methods are described in Basagana et al. (2013) <doi:10.1093/aje/kws289>.
Author: Jose Barrera-Gomez [aut, cre] (<https://orcid.org/0000-0002-2688-6036>),
Xavier Basagana [aut] (<https://orcid.org/0000-0002-8457-1489>)
Maintainer: Jose Barrera-Gomez <jose.barrera@isglobal.org>
Diff between miclust versions 1.2.6 dated 2021-03-10 and 1.2.7 dated 2021-09-22
DESCRIPTION | 11 +++++------ MD5 | 8 +++++--- NEWS.md | 10 +++++++++- data/minhanes.RData |binary man/figures |only 5 files changed, 19 insertions(+), 10 deletions(-)
Title: Phylogenetic Tree Search Using Custom Optimality Criteria
Description: Search for phylogenetic trees that are optimal using a
user-defined criterion.
Contains a "shiny" user interface for interactive tree search and exploration
of results, including character visualization, rogue taxon detection,
tree space mapping, and cluster consensus trees.
Handles inapplicable data using the algorithm of Brazeau, Guillerme and
Smith (2019) <doi:10.1093/sysbio/syy083> using the "Morphy" library.
Implements Profile Parsimony (Faith and Trueman, 2001)
<doi:10.1080/10635150118627>, and Successive Approximations (Farris, 1969)
<doi:10.2307/2412182>.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Martin Brazeau [cph] (<https://orcid.org/0000-0002-0650-1282>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeSearch versions 0.4.3 dated 2020-07-09 and 1.0.0 dated 2021-09-22
TreeSearch-0.4.3/TreeSearch/R/Fitch.R |only TreeSearch-0.4.3/TreeSearch/R/TreeSearch.R |only TreeSearch-0.4.3/TreeSearch/R/mpl_prepare_data.R |only TreeSearch-0.4.3/TreeSearch/R/pp_ProfileScore.R |only TreeSearch-0.4.3/TreeSearch/inst/doc/inapplicable.R |only TreeSearch-0.4.3/TreeSearch/inst/doc/inapplicable.Rmd |only TreeSearch-0.4.3/TreeSearch/inst/doc/inapplicable.html |only TreeSearch-0.4.3/TreeSearch/man/AsBinary.Rd |only TreeSearch-0.4.3/TreeSearch/man/Evaluate.Rd |only TreeSearch-0.4.3/TreeSearch/man/Fitch.Rd |only TreeSearch-0.4.3/TreeSearch/man/ICPerStep.Rd |only TreeSearch-0.4.3/TreeSearch/man/ICSteps.Rd |only TreeSearch-0.4.3/TreeSearch/man/IWScore.Rd |only TreeSearch-0.4.3/TreeSearch/man/InfoAmounts.Rd |only TreeSearch-0.4.3/TreeSearch/man/LogisticPoints.Rd |only TreeSearch-0.4.3/TreeSearch/man/MorphyBootstrap.Rd |only TreeSearch-0.4.3/TreeSearch/man/ProfileScore.Rd |only TreeSearch-0.4.3/TreeSearch/man/SetMorphyWeights.Rd |only TreeSearch-0.4.3/TreeSearch/man/SuccessiveWeights.Rd |only TreeSearch-0.4.3/TreeSearch/man/TipsAreNames.Rd |only TreeSearch-0.4.3/TreeSearch/man/UniqueExceptHits.Rd |only TreeSearch-0.4.3/TreeSearch/src/from_ape.c |only TreeSearch-0.4.3/TreeSearch/tests/testthat/test-Fitch.R |only TreeSearch-0.4.3/TreeSearch/tests/testthat/test-TreeSearch.R |only TreeSearch-0.4.3/TreeSearch/tests/testthat/test-data-manipulation.R |only TreeSearch-0.4.3/TreeSearch/tests/testthat/test-pp-ICS.R |only TreeSearch-0.4.3/TreeSearch/vignettes/inapplicable.Rmd |only TreeSearch-1.0.0/TreeSearch/DESCRIPTION | 41 TreeSearch-1.0.0/TreeSearch/MD5 | 328 ++++-- TreeSearch-1.0.0/TreeSearch/NAMESPACE | 125 +- TreeSearch-1.0.0/TreeSearch/NEWS.md | 36 TreeSearch-1.0.0/TreeSearch/R/AdditionTree.R |only TreeSearch-1.0.0/TreeSearch/R/Bootstrap.R | 102 -- TreeSearch-1.0.0/TreeSearch/R/Concordance.R |only TreeSearch-1.0.0/TreeSearch/R/CustomSearch.R |only TreeSearch-1.0.0/TreeSearch/R/IWScore.R | 110 -- TreeSearch-1.0.0/TreeSearch/R/ImposeConstraint.R |only TreeSearch-1.0.0/TreeSearch/R/Jackknife.R | 103 +- TreeSearch-1.0.0/TreeSearch/R/MaximizeParsimony.R |only TreeSearch-1.0.0/TreeSearch/R/NNI.R | 86 + TreeSearch-1.0.0/TreeSearch/R/PlotCharacter.R |only TreeSearch-1.0.0/TreeSearch/R/RandomTreeScore.R | 35 TreeSearch-1.0.0/TreeSearch/R/Ratchet.R | 185 --- TreeSearch-1.0.0/TreeSearch/R/RcppExports.R |only TreeSearch-1.0.0/TreeSearch/R/SPR.R | 56 + TreeSearch-1.0.0/TreeSearch/R/Sectorial.R | 50 - TreeSearch-1.0.0/TreeSearch/R/SuccessiveApproximations.R | 56 - TreeSearch-1.0.0/TreeSearch/R/TBR.R | 107 -- TreeSearch-1.0.0/TreeSearch/R/TreeSearch_utilities.R |only TreeSearch-1.0.0/TreeSearch/R/ci-ri.R |only TreeSearch-1.0.0/TreeSearch/R/data.R | 74 - TreeSearch-1.0.0/TreeSearch/R/data_manipulation.R | 370 +++++-- TreeSearch-1.0.0/TreeSearch/R/mpl_morphy_objects.R | 211 +++- TreeSearch-1.0.0/TreeSearch/R/mpl_morphyex.R | 35 TreeSearch-1.0.0/TreeSearch/R/pp_info_extra_step.r | 496 +++++----- TreeSearch-1.0.0/TreeSearch/R/tree_length.R |only TreeSearch-1.0.0/TreeSearch/R/tree_rearrangement.R | 43 TreeSearch-1.0.0/TreeSearch/R/zzz.R | 25 TreeSearch-1.0.0/TreeSearch/build/partial.rdb |binary TreeSearch-1.0.0/TreeSearch/build/vignette.rds |binary TreeSearch-1.0.0/TreeSearch/data/profiles.rda |only TreeSearch-1.0.0/TreeSearch/inst/CITATION | 2 TreeSearch-1.0.0/TreeSearch/inst/Parsimony |only TreeSearch-1.0.0/TreeSearch/inst/REFERENCES.bib | 446 ++++++-- TreeSearch-1.0.0/TreeSearch/inst/WORDLIST | 14 TreeSearch-1.0.0/TreeSearch/inst/doc/custom.R |only TreeSearch-1.0.0/TreeSearch/inst/doc/custom.Rmd |only TreeSearch-1.0.0/TreeSearch/inst/doc/custom.html |only TreeSearch-1.0.0/TreeSearch/inst/doc/getting-started.Rmd | 50 - TreeSearch-1.0.0/TreeSearch/inst/doc/getting-started.html | 253 ----- TreeSearch-1.0.0/TreeSearch/inst/doc/profile-scores.Rmd | 4 TreeSearch-1.0.0/TreeSearch/inst/doc/profile-scores.html | 216 ---- TreeSearch-1.0.0/TreeSearch/inst/doc/profile.R | 199 ---- TreeSearch-1.0.0/TreeSearch/inst/doc/profile.Rmd | 241 ---- TreeSearch-1.0.0/TreeSearch/inst/doc/profile.html | 348 +------ TreeSearch-1.0.0/TreeSearch/inst/doc/tree-search.R |only TreeSearch-1.0.0/TreeSearch/inst/doc/tree-search.Rmd |only TreeSearch-1.0.0/TreeSearch/inst/doc/tree-search.html |only TreeSearch-1.0.0/TreeSearch/inst/tests/benchmark_timing.R | 7 TreeSearch-1.0.0/TreeSearch/man/AdditionTree.Rd |only TreeSearch-1.0.0/TreeSearch/man/Carter1.Rd |only TreeSearch-1.0.0/TreeSearch/man/CharacterLength.Rd | 22 TreeSearch-1.0.0/TreeSearch/man/ConcordantInformation.Rd |only TreeSearch-1.0.0/TreeSearch/man/Consistency.Rd |only TreeSearch-1.0.0/TreeSearch/man/GapHandler.Rd |only TreeSearch-1.0.0/TreeSearch/man/JackLabels.Rd | 24 TreeSearch-1.0.0/TreeSearch/man/Jackknife.Rd |only TreeSearch-1.0.0/TreeSearch/man/MaximizeParsimony.Rd |only TreeSearch-1.0.0/TreeSearch/man/MinimumLength.Rd | 85 + TreeSearch-1.0.0/TreeSearch/man/MorphyErrorCheck.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/MorphyTreeLength.Rd | 20 TreeSearch-1.0.0/TreeSearch/man/MorphyWeights.Rd | 44 TreeSearch-1.0.0/TreeSearch/man/NNI.Rd | 57 - TreeSearch-1.0.0/TreeSearch/man/PhyDat2Morphy.Rd | 32 TreeSearch-1.0.0/TreeSearch/man/PlotCharacter.Rd |only TreeSearch-1.0.0/TreeSearch/man/PrepareDataProfile.Rd | 41 TreeSearch-1.0.0/TreeSearch/man/RandomMorphyTree.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/RandomTreeScore.Rd | 20 TreeSearch-1.0.0/TreeSearch/man/Ratchet.Rd | 251 +---- TreeSearch-1.0.0/TreeSearch/man/RearrangeEdges.Rd | 9 TreeSearch-1.0.0/TreeSearch/man/SPR.Rd | 14 TreeSearch-1.0.0/TreeSearch/man/SingleCharMorphy.Rd | 20 TreeSearch-1.0.0/TreeSearch/man/SiteConcordance.Rd |only TreeSearch-1.0.0/TreeSearch/man/StepInformation.Rd |only TreeSearch-1.0.0/TreeSearch/man/SuccessiveApproximations.Rd | 24 TreeSearch-1.0.0/TreeSearch/man/TBR.Rd | 38 TreeSearch-1.0.0/TreeSearch/man/TreeLength.Rd |only TreeSearch-1.0.0/TreeSearch/man/TreeSearch.Rd | 147 +- TreeSearch-1.0.0/TreeSearch/man/UnloadMorphy.Rd | 6 TreeSearch-1.0.0/TreeSearch/man/WithOneExtraStep.Rd | 11 TreeSearch-1.0.0/TreeSearch/man/cSPR.Rd |only TreeSearch-1.0.0/TreeSearch/man/congreveLamsdellMatrices.Rd | 17 TreeSearch-1.0.0/TreeSearch/man/dot-CombineResults.Rd |only TreeSearch-1.0.0/TreeSearch/man/dot-GapHandler.Rd |only TreeSearch-1.0.0/TreeSearch/man/dot-UniqueExceptHits.Rd |only TreeSearch-1.0.0/TreeSearch/man/figures |only TreeSearch-1.0.0/TreeSearch/man/inapplicable.citations.Rd | 6 TreeSearch-1.0.0/TreeSearch/man/inapplicable.datasets.Rd | 10 TreeSearch-1.0.0/TreeSearch/man/inapplicable.phyData.Rd | 8 TreeSearch-1.0.0/TreeSearch/man/is.morphyPtr.Rd |only TreeSearch-1.0.0/TreeSearch/man/mpl_apply_tipdata.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_attach_rawdata.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_attach_symbols.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_delete_Morphy.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_delete_rawdata.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_first_down_recon.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_first_up_recon.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_get_charac_weight.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_get_gaphandl.Rd |only TreeSearch-1.0.0/TreeSearch/man/mpl_get_num_charac.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_get_num_internal_nodes.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_get_numtaxa.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_get_symbols.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_init_Morphy.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_new_Morphy.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_second_down_recon.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_second_up_recon.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_set_charac_weight.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_set_num_internal_nodes.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_set_parsim_t.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_translate_error.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_update_lower_root.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/mpl_update_tip.Rd | 4 TreeSearch-1.0.0/TreeSearch/man/profiles.Rd |only TreeSearch-1.0.0/TreeSearch/man/referenceTree.Rd | 10 TreeSearch-1.0.0/TreeSearch/man/summary.morphyPtr.Rd | 4 TreeSearch-1.0.0/TreeSearch/src/RMorphy.c | 116 +- TreeSearch-1.0.0/TreeSearch/src/RMorphy.h | 2 TreeSearch-1.0.0/TreeSearch/src/RcppExports.cpp |only TreeSearch-1.0.0/TreeSearch/src/TreeSearch-init.c | 23 TreeSearch-1.0.0/TreeSearch/src/build_postorder.h | 12 TreeSearch-1.0.0/TreeSearch/src/morphy.c | 4 TreeSearch-1.0.0/TreeSearch/src/morphy_score.cpp |only TreeSearch-1.0.0/TreeSearch/src/morphydefs.h | 4 TreeSearch-1.0.0/TreeSearch/src/mpl.c | 1 TreeSearch-1.0.0/TreeSearch/src/rearrange.cpp |only TreeSearch-1.0.0/TreeSearch/src/statedata.c | 9 TreeSearch-1.0.0/TreeSearch/tests/testthat/_snaps |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-AdditionTree.R |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-Concordance.R |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-CustomSearch.R |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-Jackknife.R | 36 TreeSearch-1.0.0/TreeSearch/tests/testthat/test-MaximizeParsimony.R |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-NNI.R |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-PlotCharacter.R |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-RMorphy.R | 14 TreeSearch-1.0.0/TreeSearch/tests/testthat/test-RandomTreeScore.R |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-TreeSearch_utilities.R |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-data_manipulation.R |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-iw-scoring.R |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-mpl_morphy_objects.R |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-pp-fitch.R | 97 + TreeSearch-1.0.0/TreeSearch/tests/testthat/test-pp-info_extra_step.R |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-pp-random-tree.R | 50 - TreeSearch-1.0.0/TreeSearch/tests/testthat/test-rearrange.cpp.R |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-tree_length.R |only TreeSearch-1.0.0/TreeSearch/tests/testthat/test-zzz-tree-rearrange.R | 220 ++-- TreeSearch-1.0.0/TreeSearch/vignettes/custom.Rmd |only TreeSearch-1.0.0/TreeSearch/vignettes/getting-started.Rmd | 50 - TreeSearch-1.0.0/TreeSearch/vignettes/gui_char.png |only TreeSearch-1.0.0/TreeSearch/vignettes/gui_rogue.png |only TreeSearch-1.0.0/TreeSearch/vignettes/gui_space.png |only TreeSearch-1.0.0/TreeSearch/vignettes/gui_start.png |only TreeSearch-1.0.0/TreeSearch/vignettes/profile-scores.Rmd | 4 TreeSearch-1.0.0/TreeSearch/vignettes/profile.Rmd | 241 ---- TreeSearch-1.0.0/TreeSearch/vignettes/tree-search.Rmd |only 186 files changed, 3219 insertions(+), 3134 deletions(-)
Title: Nonparametric Estimation of the Trend and Its Derivatives in TS
Description: The nonparametric trend and its derivatives in equidistant time
series (TS) with short-memory stationary errors can be estimated. The
estimation is conducted via local polynomial regression using an
automatically selected bandwidth obtained by a built-in iterative plug-in
algorithm or a bandwidth fixed by the user. A Nadaraya-Watson kernel
smoother is also built-in as a comparison. With version 1.1.0, a linearity
test for the trend function, forecasting methods and backtesting
approaches are implemented as well.
The smoothing methods of the package are described in Feng, Y., Gries, T.,
and Fritz, M. (2020) <doi:10.1080/10485252.2020.1759598>.
Author: Yuanhua Feng [aut] (Paderborn University, Germany),
Sebastian Letmathe [aut] (Paderborn University, Germany),
Dominik Schulz [aut, cre] (Paderborn University, Germany),
Thomas Gries [ctb] (Paderborn University, Germany),
Marlon Fritz [ctb] (Paderborn University, Germany)
Maintainer: Dominik Schulz <schulzd@mail.uni-paderborn.de>
Diff between smoots versions 1.1.0 dated 2021-05-11 and 1.1.1 dated 2021-09-22
DESCRIPTION | 52 ++++--- MD5 | 115 ++++++++-------- NAMESPACE | 33 +++- NEWS.md | 23 +++ R/RcppExports.R | 32 ---- R/bootCast.R | 254 +++++++++++++++++++++--------------- R/cf0.LW.est.R | 4 R/col.alpha.R | 4 R/color.name.R | 4 R/confBounds.R | 44 +++--- R/critMatrix.R | 4 R/dax.R | 2 R/dsmooth.R | 19 +- R/gdpUS.R | 3 R/gsmooth.R | 9 - R/knsmooth.R | 4 R/maInfty.R | 10 - R/modelCast.R | 74 ++++++---- R/msmooth.R | 15 +- R/normCast.R | 25 +-- R/plot.smoots.R | 4 R/rollCast.R | 87 +++++++----- R/smoots.R | 4 R/tempNH.R | 3 R/trendCast.R | 3 R/tsmooth.R | 17 +- R/tsmoothCalc.R | 10 - R/vix.R | 2 README.md | 129 ++++++++++-------- man/bootCast.Rd | 60 +++++--- man/confBounds.Rd | 20 +- man/critMatrix.Rd | 220 +++++++++++++++---------------- man/dax.Rd | 2 man/dsmooth.Rd | 15 +- man/figures/README-confbounds-1.png |binary man/figures/README-plot1-1.png |binary man/fitted.smoots.Rd | 52 +++---- man/gdpUS.Rd | 3 man/gsmooth.Rd | 3 man/modelCast.Rd | 54 +++++-- man/msmooth.Rd | 15 +- man/normCast.Rd | 4 man/optOrd.Rd | 144 ++++++++++---------- man/rescale.Rd | 128 +++++++++--------- man/residuals.smoots.Rd | 52 +++---- man/rollCast.Rd | 50 ++++--- man/smoots.Rd | 4 man/tempNH.Rd | 3 man/trendCast.Rd | 252 +++++++++++++++++------------------ man/tsmooth.Rd | 15 +- man/vix.Rd | 2 src/Makevars | 4 src/Makevars.win | 4 src/RcppExports.cpp | 155 +++++---------------- src/bootCast.cpp | 85 ++++-------- src/cf0.cpp | 43 ++---- src/gsmoothCpp.cpp | 160 +++++++++++++--------- tests |only 58 files changed, 1344 insertions(+), 1194 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive prebuilt widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre] (<https://orcid.org/0000-0002-1576-2126>),
Joe Cheng [aut],
JJ Allaire [aut],
Carson Sievert [aut] (<https://orcid.org/0000-0002-4958-2844>),
Barret Schloerke [aut] (<https://orcid.org/0000-0001-9986-114X>),
Yihui Xie [aut],
Jeff Allen [aut],
Jonathan McPherson [aut],
Alan Dipert [aut],
Barbara Borges [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/shared/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/shared/jqueryui/AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Prem Nawaz Khan [ctb] (Bootstrap accessibility plugin),
Victor Tsaran [ctb] (Bootstrap accessibility plugin),
Dennis Lembree [ctb] (Bootstrap accessibility plugin),
Srinivasu Chakravarthula [ctb] (Bootstrap accessibility plugin),
Cathy O'Connor [ctb] (Bootstrap accessibility plugin),
PayPal, Inc [cph] (Bootstrap accessibility plugin),
Stefan Petre [ctb, cph] (Bootstrap-datepicker library),
Andrew Rowls [ctb, cph] (Bootstrap-datepicker library),
Brian Reavis [ctb, cph] (selectize.js library),
Salmen Bejaoui [ctb, cph] (selectize-plugin-a11y library),
Denis Ineshin [ctb, cph] (ion.rangeSlider library),
Sami Samhuri [ctb, cph] (Javascript strftime library),
SpryMedia Limited [ctb, cph] (DataTables library),
John Fraser [ctb, cph] (showdown.js library),
John Gruber [ctb, cph] (showdown.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shiny versions 1.6.0 dated 2021-01-25 and 1.7.0 dated 2021-09-22
shiny-1.6.0/shiny/R/font-awesome.R |only shiny-1.6.0/shiny/R/stack.R |only shiny-1.6.0/shiny/inst/www/shared/fontawesome |only shiny-1.6.0/shiny/man/deprecatedReactives.Rd |only shiny-1.6.0/shiny/man/installExprFunction.Rd |only shiny-1.6.0/shiny/man/quoToFunction.Rd |only shiny-1.6.0/shiny/man/tableOutput.Rd |only shiny-1.6.0/shiny/tests/test-all.R |only shiny-1.6.0/shiny/tests/testthat/test-stack.R |only shiny-1.7.0/shiny/DESCRIPTION | 75 shiny-1.7.0/shiny/LICENSE | 444 shiny-1.7.0/shiny/MD5 | 347 shiny-1.7.0/shiny/NAMESPACE | 20 shiny-1.7.0/shiny/NEWS.md | 67 shiny-1.7.0/shiny/R/bind-cache.R | 51 shiny-1.7.0/shiny/R/bind-event.R | 21 shiny-1.7.0/shiny/R/bookmark-state.R | 15 shiny-1.7.0/shiny/R/bootstrap-layout.R | 24 shiny-1.7.0/shiny/R/bootstrap.R | 522 shiny-1.7.0/shiny/R/conditions.R | 113 shiny-1.7.0/shiny/R/deprecated.R | 29 shiny-1.7.0/shiny/R/devmode.R | 12 shiny-1.7.0/shiny/R/globals.R | 4 shiny-1.7.0/shiny/R/graph.R | 12 shiny-1.7.0/shiny/R/html-deps.R | 7 shiny-1.7.0/shiny/R/image-interact-opts.R | 1 shiny-1.7.0/shiny/R/image-interact.R | 34 shiny-1.7.0/shiny/R/input-date.R | 8 shiny-1.7.0/shiny/R/input-select.R | 13 shiny-1.7.0/shiny/R/input-slider.R | 81 shiny-1.7.0/shiny/R/insert-tab.R | 82 shiny-1.7.0/shiny/R/knitr.R | 1 shiny-1.7.0/shiny/R/map.R | 1 shiny-1.7.0/shiny/R/mock-session.R | 2 shiny-1.7.0/shiny/R/modal.R | 37 shiny-1.7.0/shiny/R/react.R | 2 shiny-1.7.0/shiny/R/reactives.R | 205 shiny-1.7.0/shiny/R/reexports.R | 16 shiny-1.7.0/shiny/R/render-cached-plot.R | 6 shiny-1.7.0/shiny/R/render-plot.R | 58 shiny-1.7.0/shiny/R/render-table.R | 34 shiny-1.7.0/shiny/R/runapp.R | 8 shiny-1.7.0/shiny/R/serializers.R | 1 shiny-1.7.0/shiny/R/server-input-handlers.R | 8 shiny-1.7.0/shiny/R/shiny-options.R | 6 shiny-1.7.0/shiny/R/shiny-package.R | 9 shiny-1.7.0/shiny/R/shiny.R | 46 shiny-1.7.0/shiny/R/shinyui.R | 48 shiny-1.7.0/shiny/R/shinywrappers.R | 258 shiny-1.7.0/shiny/R/showcase.R | 6 shiny-1.7.0/shiny/R/utils-lang.R | 239 shiny-1.7.0/shiny/R/utils.R | 347 shiny-1.7.0/shiny/R/version_bs_date_picker.R |only shiny-1.7.0/shiny/R/version_ion_range_slider.R |only shiny-1.7.0/shiny/R/version_jquery.R |only shiny-1.7.0/shiny/R/version_selectize.R |only shiny-1.7.0/shiny/R/version_strftime.R |only shiny-1.7.0/shiny/README.md | 4 shiny-1.7.0/shiny/build/shiny.pdf |binary shiny-1.7.0/shiny/inst/app_template/tests/testthat/test-examplemodule.R | 2 shiny-1.7.0/shiny/inst/app_template/tests/testthat/test-server.R | 2 shiny-1.7.0/shiny/inst/app_template/tests/testthat/test-sort.R | 2 shiny-1.7.0/shiny/inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js | 2 shiny-1.7.0/shiny/inst/www/shared/datepicker/js/bootstrap-datepicker.min.js | 7 shiny-1.7.0/shiny/inst/www/shared/ionrangeslider/css/ion.rangeSlider.css | 21 shiny-1.7.0/shiny/inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js | 2 shiny-1.7.0/shiny/inst/www/shared/ionrangeslider/scss/_base.scss | 10 shiny-1.7.0/shiny/inst/www/shared/ionrangeslider/scss/shiny.scss | 11 shiny-1.7.0/shiny/inst/www/shared/jquery.js | 227 shiny-1.7.0/shiny/inst/www/shared/jquery.min.js | 4 shiny-1.7.0/shiny/inst/www/shared/jquery.min.map | 2 shiny-1.7.0/shiny/inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js | 2 shiny-1.7.0/shiny/inst/www/shared/selectize/scss/selectize.bootstrap4.scss | 2 shiny-1.7.0/shiny/inst/www/shared/selectize/scss/selectize.bootstrap5.scss |only shiny-1.7.0/shiny/inst/www/shared/shiny-autoreload.js | 20 shiny-1.7.0/shiny/inst/www/shared/shiny-showcase.css | 89 shiny-1.7.0/shiny/inst/www/shared/shiny-showcase.js | 275 shiny-1.7.0/shiny/inst/www/shared/shiny-testmode.js | 11 shiny-1.7.0/shiny/inst/www/shared/shiny.js |18274 ++++++---- shiny-1.7.0/shiny/inst/www/shared/shiny.js.map | 8 shiny-1.7.0/shiny/inst/www/shared/shiny.min.css | 3 shiny-1.7.0/shiny/inst/www/shared/shiny.min.js | 7 shiny-1.7.0/shiny/inst/www/shared/shiny.min.js.map | 8 shiny-1.7.0/shiny/inst/www/shared/shiny_scss/shiny.scss | 9 shiny-1.7.0/shiny/man/bindCache.Rd | 54 shiny-1.7.0/shiny/man/bindEvent.Rd | 23 shiny-1.7.0/shiny/man/bootstrapPage.Rd | 11 shiny-1.7.0/shiny/man/clickOpts.Rd | 1 shiny-1.7.0/shiny/man/createRenderFunction.Rd | 136 shiny-1.7.0/shiny/man/devmode.Rd | 18 shiny-1.7.0/shiny/man/exprToFunction.Rd | 51 shiny-1.7.0/shiny/man/fillPage.Rd | 9 shiny-1.7.0/shiny/man/fixedPage.Rd | 22 shiny-1.7.0/shiny/man/fluidPage.Rd | 22 shiny-1.7.0/shiny/man/icon.Rd | 32 shiny-1.7.0/shiny/man/insertTab.Rd | 4 shiny-1.7.0/shiny/man/isTruthy.Rd |only shiny-1.7.0/shiny/man/knitr_methods.Rd | 1 shiny-1.7.0/shiny/man/markRenderFunction.Rd | 14 shiny-1.7.0/shiny/man/modalDialog.Rd | 2 shiny-1.7.0/shiny/man/navbarPage.Rd | 28 shiny-1.7.0/shiny/man/navlistPanel.Rd | 10 shiny-1.7.0/shiny/man/observe.Rd | 20 shiny-1.7.0/shiny/man/observeEvent.Rd | 77 shiny-1.7.0/shiny/man/onBookmark.Rd | 8 shiny-1.7.0/shiny/man/reactive.Rd | 40 shiny-1.7.0/shiny/man/reactlog.Rd | 5 shiny-1.7.0/shiny/man/reexports.Rd | 2 shiny-1.7.0/shiny/man/registerInputHandler.Rd | 8 shiny-1.7.0/shiny/man/renderCachedPlot.Rd | 20 shiny-1.7.0/shiny/man/renderDataTable.Rd | 75 shiny-1.7.0/shiny/man/renderImage.Rd | 11 shiny-1.7.0/shiny/man/renderPlot.Rd | 31 shiny-1.7.0/shiny/man/renderPrint.Rd | 11 shiny-1.7.0/shiny/man/renderTable.Rd | 50 shiny-1.7.0/shiny/man/renderUI.Rd | 11 shiny-1.7.0/shiny/man/req.Rd | 72 shiny-1.7.0/shiny/man/runApp.Rd | 5 shiny-1.7.0/shiny/man/runExample.Rd | 5 shiny-1.7.0/shiny/man/setSerializer.Rd | 1 shiny-1.7.0/shiny/man/shinyDeprecated.Rd | 8 shiny-1.7.0/shiny/man/shinyOptions.Rd | 2 shiny-1.7.0/shiny/man/sliderInput.Rd | 31 shiny-1.7.0/shiny/man/stacktrace.Rd | 28 shiny-1.7.0/shiny/man/tabsetPanel.Rd | 10 shiny-1.7.0/shiny/man/updateSliderInput.Rd | 20 shiny-1.7.0/shiny/man/validate.Rd | 75 shiny-1.7.0/shiny/tests/test-helpers/app7-port/app.R | 2 shiny-1.7.0/shiny/tests/test-helpers/app7-port/option-broken.R | 2 shiny-1.7.0/shiny/tests/test-helpers/app7-port/option.R | 2 shiny-1.7.0/shiny/tests/test-helpers/app7-port/wrapped2.R | 7 shiny-1.7.0/shiny/tests/test-modules/107_scatterplot/tests/testthat/test-linked-scatterplot-module.R | 3 shiny-1.7.0/shiny/tests/test-modules/107_scatterplot/tests/testthat/test-plot.R | 3 shiny-1.7.0/shiny/tests/test-modules/107_scatterplot/tests/testthat/test-server.R | 2 shiny-1.7.0/shiny/tests/test-modules/12_counter/tests/testthat/test-mymodule.R | 3 shiny-1.7.0/shiny/tests/test-modules/12_counter/tests/testthat/test-server.R | 2 shiny-1.7.0/shiny/tests/test-modules/12_counter/tests/testthat/test-utils.R | 2 shiny-1.7.0/shiny/tests/testthat.R |only shiny-1.7.0/shiny/tests/testthat/_snaps |only shiny-1.7.0/shiny/tests/testthat/test-actionButton.R | 2 shiny-1.7.0/shiny/tests/testthat/test-app.R | 78 shiny-1.7.0/shiny/tests/testthat/test-bind-cache.R | 55 shiny-1.7.0/shiny/tests/testthat/test-bookmarking.R | 16 shiny-1.7.0/shiny/tests/testthat/test-bootstrap.r | 2 shiny-1.7.0/shiny/tests/testthat/test-built-files.R | 16 shiny-1.7.0/shiny/tests/testthat/test-devmode.R | 48 shiny-1.7.0/shiny/tests/testthat/test-diagnostics.R | 2 shiny-1.7.0/shiny/tests/testthat/test-gc.r | 2 shiny-1.7.0/shiny/tests/testthat/test-get-extension.R | 2 shiny-1.7.0/shiny/tests/testthat/test-inline-markdown.R | 30 shiny-1.7.0/shiny/tests/testthat/test-input-handler.R | 2 shiny-1.7.0/shiny/tests/testthat/test-mock-session.R | 2 shiny-1.7.0/shiny/tests/testthat/test-modules.R | 54 shiny-1.7.0/shiny/tests/testthat/test-options.R | 11 shiny-1.7.0/shiny/tests/testthat/test-plot-coordmap.R | 1 shiny-1.7.0/shiny/tests/testthat/test-reactivity.r | 102 shiny-1.7.0/shiny/tests/testthat/test-reactlog.R | 25 shiny-1.7.0/shiny/tests/testthat/test-render-functions.R | 263 shiny-1.7.0/shiny/tests/testthat/test-shinywrappers.R | 2 shiny-1.7.0/shiny/tests/testthat/test-stacks-deep.R | 8 shiny-1.7.0/shiny/tests/testthat/test-stacks-pruning.R | 2 shiny-1.7.0/shiny/tests/testthat/test-stacks.R | 75 shiny-1.7.0/shiny/tests/testthat/test-stop-app.R | 2 shiny-1.7.0/shiny/tests/testthat/test-tabPanel.R | 99 shiny-1.7.0/shiny/tests/testthat/test-test-server-app.R | 2 shiny-1.7.0/shiny/tests/testthat/test-test-server-nesting.R | 2 shiny-1.7.0/shiny/tests/testthat/test-test-server-scope.R | 4 shiny-1.7.0/shiny/tests/testthat/test-test-server.R | 4 shiny-1.7.0/shiny/tests/testthat/test-test.R | 75 shiny-1.7.0/shiny/tests/testthat/test-text.R | 2 shiny-1.7.0/shiny/tests/testthat/test-timer.R | 2 shiny-1.7.0/shiny/tests/testthat/test-update-input.R | 2 shiny-1.7.0/shiny/tests/testthat/test-url.R | 2 shiny-1.7.0/shiny/tests/testthat/test-utils.R | 16 174 files changed, 15225 insertions(+), 9203 deletions(-)
Title: Relational Event Models
Description: Tools to fit relational event models.
Author: Carter T. Butts <buttsc@uci.edu>
Maintainer: Carter T. Butts <buttsc@uci.edu>
Diff between relevent versions 1.0-4 dated 2015-03-10 and 1.1 dated 2021-09-22
relevent-1.0-4/relevent/inst |only relevent-1.1/relevent/ChangeLog | 19 relevent-1.1/relevent/DESCRIPTION | 8 relevent-1.1/relevent/MD5 | 24 - relevent-1.1/relevent/NAMESPACE | 15 relevent-1.1/relevent/R/rem.R | 59 ++ relevent-1.1/relevent/R/rem.dyad.R | 549 ++++++++++++++++--------- relevent-1.1/relevent/man/relevent-internal.Rd | 24 - relevent-1.1/relevent/man/rem.dyad.Rd | 28 + relevent-1.1/relevent/src/init.c |only relevent-1.1/relevent/src/relevent.c | 311 +++++++++++--- relevent-1.1/relevent/src/relevent.h | 16 relevent-1.1/relevent/src/utils.c | 1 relevent-1.1/relevent/src/utils.h | 1 14 files changed, 781 insertions(+), 274 deletions(-)
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided. Furthermore, methods for the simulation of extreme value random fields are provided. Main geostatistical parts are based on the books by Christian Lantuejoul <doi:10.1007/978-3-662-04808-5>, Jean-Paul Chiles and Pierre Delfiner <doi:10.1002/9781118136188> and Noel A. Cressie <doi:10.1002/9781119115151>.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Paulo Ribeiro [ctb], Brian D. Ripley [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.3.8 dated 2020-02-06 and 3.3.10 dated 2021-09-22
DESCRIPTION | 13 +-- MD5 | 149 ++++++++++++++++++++--------------------- inst/CITATION | 4 - man/CoordinateSystems.Rd | 8 +- man/RandomFields.Rd | 4 - man/ca20.Rd | 2 man/macros/allg_defn.Rd | 7 + src/AutoRandomFields.h | 1 src/Brown.cc | 8 +- src/Coordinate_systems.cc | 9 +- src/D.H.cc | 4 - src/Error.cc | 3 src/Gneiting.cc | 5 + src/Huetchen.cc | 5 + src/InternalCov.cc | 4 + src/InternalCov.noncritical.cc | 10 +- src/KeyInfo.cc | 8 +- src/MLE.cc | 12 +-- src/MachineSchlather.h | 4 - src/NULL.cc | 9 +- src/Options.cc | 14 --- src/PoissonPolygon.cc | 5 - src/QMath.cc | 5 - src/RF.h | 4 - src/RMS.cc | 13 +-- src/RandomFields.h | 3 src/Specific.cc | 5 + src/auxiliary.cc | 7 + src/avltr_modified.cc | 11 +-- src/basic.h | 6 - src/bigdata.cc | 11 --- src/brownresnick.cc | 11 --- src/circulant.cc | 21 +++-- src/convhull2D.cc | 1 src/cubicsolver.cc | 4 - src/def.h | 1 src/direct.cc | 8 +- src/empvario.cc | 5 - src/extremes.cc | 5 + src/families.cc | 4 + src/fftVario.cc | 5 - src/gauss.cc | 5 + src/gausslikeli.cc | 5 + src/getNset.cc | 9 +- src/hyperplan.cc | 12 +-- src/init.cov.cc | 3 src/init.general.cc | 3 src/init.others.cc | 3 src/intrinsics.h | 2 src/kleinkram.cc | 6 + src/kleinkram.h | 3 src/metropolis.cc | 5 + src/nugget.cc | 6 + src/operator.cc | 7 + src/operator.extremes.cc | 4 + src/operator.gaussmethod.cc | 11 +-- src/plusmal.cc | 9 +- src/primitive.cov.cc | 5 + src/primitive.gauss.mix.cc | 5 + src/primitive.matern.cc | 5 + src/primitive.others.cc | 5 + src/questions.cc | 3 src/rf_interfaces.cc | 11 ++- src/sequential.cc | 6 + src/shape.cc | 10 +- src/spectral.cc | 5 + src/startGetNset.cc | 10 +- src/tbm.cc | 7 + src/trend.cc | 7 + src/userinterfaces.cc | 11 +-- src/variogramAndCo.cc | 4 - src/xport_import.cc | 3 src/xport_import.h | 3 src/xxx |only src/y.cc | 1 src/zzz.c | 2 76 files changed, 341 insertions(+), 273 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the <https://personality-project.org/r/> web page.
Author: William Revelle [aut, cre] (<https://orcid.org/0000-0003-4880-9610>)
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psych versions 2.1.6 dated 2021-06-18 and 2.1.9 dated 2021-09-22
DESCRIPTION | 8 +- MD5 | 95 +++++++++++++------------ NAMESPACE | 4 - R/ICC.R | 102 +++++++++++++++------------ R/bassAckward.R | 9 +- R/bassAckward.diagram.r | 61 +++++++++++----- R/bestScale.R | 2 R/cohen.d.R | 18 ++-- R/corr.test.R | 56 ++++++++++++++- R/diagram.R | 28 +++++-- R/error.dots.r | 8 +- R/fa.extension.R | 8 +- R/make.keys.R | 17 +++- R/misc.R | 2 R/multi.hist.R | 42 +++++------ R/plot.reliability.r |only R/print.psych.R | 9 ++ R/reliability.R | 156 +++++++++++++++--------------------------- R/scatter.hist.R | 40 ++++++---- R/scoreFast.r | 5 + R/spider.R | 56 ++++++++++----- R/splitHalf.R | 16 +++- R/validity.R |only build/partial.rdb |binary build/vignette.rds |binary data/GERAS.rda |only inst/CITATION | 4 - inst/News.Rd | 45 +++++++++++- inst/doc/intro.R | 63 +++++++++------- inst/doc/intro.Rnw | 63 +++++++++++++--- inst/doc/intro.pdf |binary inst/doc/scoring.pdf |binary man/00.psych-package.Rd | 11 +- man/GERAS.Rd |only man/ICC.Rd | 88 +++++++++++++++++++++-- man/alpha.Rd | 4 - man/bassAckward.Rd | 11 +- man/bifactor.Rd | 4 - man/cohen.d.Rd | 4 + man/corr.test.Rd | 12 ++- man/fa.extension.Rd | 6 + man/fa.lookup.Rd | 2 man/multilevel.reliability.Rd | 2 man/omega.Rd | 2 man/predicted.validity.Rd |only man/reliability.Rd | 34 ++++++--- man/scatter.hist.Rd | 7 + man/spider.Rd | 52 +++++++++++++- man/tetrachor.Rd | 6 + man/unidim.Rd | 4 - vignettes/intro.Rnw | 63 +++++++++++++--- 51 files changed, 832 insertions(+), 397 deletions(-)
Title: A Fast and Lightweight R6 Parameter Interface
Description: By making use of 'set6', alongside the S3 and R6 paradigms, this package provides a fast and lightweight R6 interface for parameters and parameter sets.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>)
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>
Diff between param6 versions 0.2.1 dated 2021-07-29 and 0.2.2 dated 2021-09-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/ParameterSet_methods.R | 3 ++- README.md | 25 ++++++++++++------------- 5 files changed, 25 insertions(+), 21 deletions(-)
Title: Lightweight Reproducible Reporting
Description: Order, create and store reports from R. By defining a
lightweight interface around the inputs and outputs of an
analysis, a lot of the repetitive work for reproducible research
can be automated. We define a simple format for organising and
describing work that facilitates collaborative reproducible
research and acknowledges that all analyses are run multiple
times over their lifespans.
Author: Rich FitzJohn [aut, cre],
Robert Ashton [aut],
Alex Hill [aut],
Martin Eden [aut],
Wes Hinsley [aut],
Emma Russell [aut],
James Thompson [aut],
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between orderly versions 1.3.0 dated 2021-06-17 and 1.4.3 dated 2021-09-22
DESCRIPTION | 15 +- MD5 | 157 +++++++++++---------- NAMESPACE | 1 NEWS.md | 16 ++ R/batch.R | 8 - R/bundle.R | 66 +++++---- R/cleanup.R | 6 R/db.R | 38 ++--- R/db2.R | 70 +++++++-- R/deduplicate.R | 18 +- R/dependencies.R | 48 +++--- R/develop.R | 40 ++--- R/helpers.R | 14 - R/init.R | 54 +++---- R/logging.R | 33 +--- R/migrate.R | 28 +++ R/new.R | 24 +-- R/orderly_recipe.R | 24 +++ R/orderly_recipe_artefacts.R | 11 - R/paths.R | 3 R/query.R | 87 ++++++++---- R/query_search.R | 52 +++---- R/recipe_commit.R | 8 - R/recipe_run.R | 68 ++++----- R/recipe_test.R | 18 +- R/remote.R | 250 +++++++++++++++++++++-------------- R/remote_path.R | 10 - R/testing.R | 3 R/util.R | 32 ++-- README.md | 4 build/vignette.rds |binary inst/doc/bundles.html | 84 +++++------ inst/doc/changelog.html | 4 inst/doc/orderly.Rmd | 4 inst/doc/orderly.html | 101 +++++++------- inst/doc/patterns.Rmd | 10 - inst/doc/patterns.html | 10 - inst/doc/remote.Rmd | 2 inst/doc/remote.html | 6 inst/init/gitignore | 1 man/orderly_batch.Rd | 6 man/orderly_bundle_pack.Rd | 50 +++---- man/orderly_bundle_pack_remote.Rd | 29 +--- man/orderly_cleanup.Rd | 6 man/orderly_commit.Rd | 4 man/orderly_config.Rd | 4 man/orderly_db.Rd | 25 +-- man/orderly_deduplicate.Rd | 14 - man/orderly_default_remote.Rd | 6 man/orderly_develop_start.Rd | 18 +- man/orderly_graph.Rd | 48 +++--- man/orderly_info.Rd | 2 man/orderly_init.Rd | 51 +++---- man/orderly_latest.Rd | 8 - man/orderly_list.Rd | 6 man/orderly_list_drafts.Rd | 12 - man/orderly_list_metadata.Rd |only man/orderly_log.Rd | 32 ---- man/orderly_migrate.Rd | 2 man/orderly_new.Rd | 7 man/orderly_pull_dependencies.Rd | 34 ++-- man/orderly_rebuild.Rd | 2 man/orderly_remote.Rd | 18 +- man/orderly_remote_path.Rd | 14 - man/orderly_remote_status.Rd | 2 man/orderly_run.Rd | 27 +-- man/orderly_run_info.Rd | 4 man/orderly_run_remote.Rd | 2 man/orderly_search.Rd | 23 --- man/orderly_test_start.Rd | 23 +-- man/orderly_use.Rd | 6 tests/testthat/helper-orderly.R | 7 tests/testthat/test-bundle.R | 52 +++++++ tests/testthat/test-orderly-recipe.R | 24 +++ tests/testthat/test-remote.R | 102 ++++++++++++++ tests/testthat/test-run.R | 67 ++++++++- tests/testthat/test-util.R | 45 ++++++ vignettes/orderly.Rmd | 4 vignettes/patterns.Rmd | 10 - vignettes/remote.Rmd | 2 80 files changed, 1323 insertions(+), 903 deletions(-)
Title: Algebraic and Statistical Functions for Genetics
Description: This is a collection of fast tools for application in quantitative genetics. For instance, the SNP matrix can be stored in a minimum of memory and the calculation of the genomic relationship matrix is based on a rapid algorithm. It also contains the window scanning approach by Kabluchko and Spodarev (2009), <doi:10.1239/aap/1240319575> to detect anomalous genomic areas <doi:10.1186/s12864-018-5009-y>. Furthermore, the package is used in the Modular Breeding Program Simulator (MoBPS, <https://github.com/tpook92/MoBPS>, <https://www.mobps.de/>). The tools are based on SIMD (Single Instruction Multiple Data, <https://en.wikipedia.org/wiki/SIMD>) and OMP (Open Multi-Processing, <https://de.wikipedia.org/wiki/OpenMP>).
Author: Martin Schlather [aut, cre], Malena Erbe [aut, cre], Florian Skene [aut], Alexander Freudenberg [ctr]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between miraculix versions 0.9.20 dated 2020-04-17 and 0.9.23 dated 2021-09-22
DESCRIPTION | 12 +++---- MD5 | 82 ++++++++++++++++++++++++------------------------ man/RFoptions.Rd | 4 -- man/macros/allg_defn.Rd | 5 +- man/macros/defn.Rd | 1 man/miraculix.Rd | 3 - src/2bit.cc | 10 +++++ src/3bit.cc | 10 +++++ src/Bit23.cc | 5 ++ src/Bit23.intern.h | 7 ---- src/Haplo.cc | 4 +- src/MX.cc | 6 +-- src/MX.h | 17 +++------ src/MoBPS.cc | 8 ++-- src/Scalar.cc | 7 ++-- src/Vector.matrix.cc | 7 ++-- src/error.h | 1 src/hamming.cc | 3 + src/hamming2.cc | 5 ++ src/hamming3.cc | 18 +++++++++- src/haplogeno.cc | 7 +++- src/haplogeno.h | 1 src/initNerror.cc | 7 ++-- src/intrinsics.h | 2 - src/kleinkram.cc | 4 +- src/kleinkram.h | 3 - src/miraculix.h | 4 -- src/multiply.cc | 4 ++ src/multiply256.cc | 3 + src/nocoding.cc | 6 +-- src/options.cc | 15 ++------ src/options.h | 2 - src/packed128.cc | 5 ++ src/packed256.cc | 7 ++++ src/packedDef.h | 1 src/scan.cc | 7 ++-- src/shuffle128.cc | 4 ++ src/shuffle256.cc | 4 ++ src/windower.cc | 4 +- src/xport_import.cc | 4 +- src/xport_import.h | 1 src/zzz.c | 2 - 42 files changed, 185 insertions(+), 127 deletions(-)
Title: Conditional Akaike Information Criterion for 'lme4' and 'nlme'
Description: Provides functions for the estimation of the conditional Akaike
information in generalized mixed-effect models fitted with (g)lmer()
from 'lme4', lme() from 'nlme' and gamm() from 'mgcv'.
For a manual on how to use 'cAIC4', see Saefken et al. (2021) <doi:10.18637/jss.v099.i08>.
Author: Benjamin Saefken, David Ruegamer, Philipp Baumann and Rene-Marcel Kruse, with contributions from Sonja
Greven and Thomas Kneib
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Diff between cAIC4 versions 0.9 dated 2019-12-18 and 1.0 dated 2021-09-22
DESCRIPTION | 11 +++++----- MD5 | 36 +++++++++++++++++------------------ NAMESPACE | 1 R/cAIC.R | 20 +++++++++++-------- R/datasets.R | 2 - R/getWeights.R | 25 ++++++++++++------------ R/helperfuns_stepcAIC.R | 19 +++++++++++++++--- R/modelAvg.R | 14 ++++++------- R/predictMA.R | 6 +++-- R/stepcAIC.R | 6 ++--- R/summaryMA.R | 3 +- build/partial.rdb |binary inst/CITATION | 49 ++++++++++++++++++++++-------------------------- man/Zambia.Rd | 2 - man/cAIC.Rd | 4 +-- man/getWeights.Rd | 19 +++++++++--------- man/modelAvg.Rd | 14 ++++++------- man/predictMA.Rd | 6 +++-- man/summaryMA.Rd | 3 +- 19 files changed, 132 insertions(+), 108 deletions(-)
Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting.
The package includes ADAM (Svetunkov, 2021, <https://openforecast.org/adam/>),
Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>),
SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>),
Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>),
Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>)
and several simulation functions. It also allows dealing with intermittent demand based on the
iETS framework (Svetunkov & Boylan, 2019, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics
and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between smooth versions 3.1.2 dated 2021-06-14 and 3.1.3 dated 2021-09-22
DESCRIPTION | 8 MD5 | 60 ++--- NEWS | 26 ++ R/adam.R | 336 ++++++++++++++++++++---------- R/adamGeneral.R | 60 ++++- R/autoadam.R | 27 +- R/ssfunctions.R | 17 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/adam.R | 2 inst/doc/adam.Rmd | 2 inst/doc/adam.html | 548 ++++++++++++++++++++++++------------------------- inst/doc/ces.html | 18 - inst/doc/es.R | 2 inst/doc/es.Rmd | 2 inst/doc/es.html | 103 ++++----- inst/doc/gum.html | 18 - inst/doc/oes.html | 143 ++++++------ inst/doc/simulate.html | 76 +++--- inst/doc/sma.html | 6 inst/doc/smooth.html | 4 inst/doc/ssarima.html | 30 +- man/adam.Rd | 3 man/forecast.smooth.Rd | 6 src/RcppExports.cpp | 5 src/adamGeneral.cpp | 29 +- src/adamGeneral.h | 12 - src/adamRefitter.cpp | 10 src/adamSimulator.cpp | 4 vignettes/adam.Rmd | 2 vignettes/es.Rmd | 2 31 files changed, 889 insertions(+), 672 deletions(-)
Title: Extract, Analyze and Visualize Mutational Signatures for Genomic
Variations
Description: Genomic alterations including single nucleotide
substitution, copy number alteration, etc. are the major force for
cancer initialization and development. Due to the specificity of
molecular lesions caused by genomic alterations, we can generate
characteristic alteration spectra, called 'signature' (Wang, Shixiang,
et al. (2020) <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil
B., et al. (2020) <DOI:10.1038/s41586-020-1943-3>). This package helps
users to extract, analyze and visualize signatures from genomic
alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Ziyu Tao [aut] (<https://orcid.org/0000-0003-3272-1227>),
Huimin Li [aut] (<https://orcid.org/0000-0003-1683-9057>),
Tao Wu [aut] (<https://orcid.org/0000-0002-8999-9628>),
Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>),
Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between sigminer versions 2.0.5 dated 2021-09-03 and 2.1.0 dated 2021-09-22
sigminer-2.0.5/sigminer/inst/extdata/toy_copynumber_signature_by_M.RData |only sigminer-2.0.5/sigminer/inst/extdata/toy_copynumber_tally_M.RData |only sigminer-2.1.0/sigminer/DESCRIPTION | 6 sigminer-2.1.0/sigminer/MD5 | 58 ++++----- sigminer-2.1.0/sigminer/NAMESPACE | 1 sigminer-2.1.0/sigminer/NEWS.md | 5 sigminer-2.1.0/sigminer/R/get_group_comparison.R | 2 sigminer-2.1.0/sigminer/R/get_pLOH_score.R | 1 sigminer-2.1.0/sigminer/R/hello.R | 2 sigminer-2.1.0/sigminer/R/show_cosmic_signature_profile.R | 2 sigminer-2.1.0/sigminer/R/show_group_comparison.R | 2 sigminer-2.1.0/sigminer/R/show_sig_exposure.R | 2 sigminer-2.1.0/sigminer/R/sig_auto_extract.R | 8 - sigminer-2.1.0/sigminer/R/sig_estimate.R | 4 sigminer-2.1.0/sigminer/R/sig_extract.R | 4 sigminer-2.1.0/sigminer/R/sig_unify_extract.R |only sigminer-2.1.0/sigminer/R/sigprofiler.R | 6 sigminer-2.1.0/sigminer/README.md | 64 +--------- sigminer-2.1.0/sigminer/build/partial.rdb |binary sigminer-2.1.0/sigminer/build/vignette.rds |binary sigminer-2.1.0/sigminer/inst/doc/sigminer.Rmd | 4 sigminer-2.1.0/sigminer/inst/doc/sigminer.html | 10 - sigminer-2.1.0/sigminer/inst/extdata/human_hg19_gene_info.rds |only sigminer-2.1.0/sigminer/inst/extdata/mouse_mm9_gene_info.rds |only sigminer-2.1.0/sigminer/man/get_group_comparison.Rd | 2 sigminer-2.1.0/sigminer/man/show_group_comparison.Rd | 2 sigminer-2.1.0/sigminer/man/show_sig_exposure.Rd | 2 sigminer-2.1.0/sigminer/man/sig_auto_extract.Rd | 4 sigminer-2.1.0/sigminer/man/sig_estimate.Rd | 4 sigminer-2.1.0/sigminer/man/sig_extract.Rd | 4 sigminer-2.1.0/sigminer/man/sig_unify_extract.Rd |only sigminer-2.1.0/sigminer/man/sigprofiler.Rd | 6 sigminer-2.1.0/sigminer/vignettes/sigminer.Rmd | 4 33 files changed, 87 insertions(+), 122 deletions(-)
Title: Single-Case Data Analyses for Single and Multiple Baseline
Designs
Description: A collection of procedures for analysing, visualising,
and managing single-case data. These include piecewise linear regression
models, multilevel models, overlap indices (PND, PEM, PAND, PET, tauU,
baseline corrected tau, CDC), and randomization tests. Data preparation functions
support outlier detection, handling missing values, scaling, truncating,
rank transformation, and smoothing. An exporting function helps to generate
html and latex tables in a publication friendly style. More details can be
found at <https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [cre, aut],
Timo Lueke [aut]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-potsdam.de>
Diff between scan versions 0.51 dated 2021-02-22 and 0.53 dated 2021-09-22
scan-0.51/scan/R/deprecated_estimateSC.R |only scan-0.51/scan/R/deprecated_makesingleSC.R |only scan-0.51/scan/R/deprecated_power.testSC.R |only scan-0.51/scan/R/describeSC.R |only scan-0.51/scan/R/longSCDF.R |only scan-0.51/scan/R/private_SCprepare.R |only scan-0.51/scan/R/smooth.R |only scan-0.51/scan/R/truncate.R |only scan-0.51/scan/man/describeSC.Rd |only scan-0.51/scan/man/estimateSC.Rd |only scan-0.51/scan/man/longSCDF.Rd |only scan-0.51/scan/man/makesingleSC.Rd |only scan-0.51/scan/man/power.testSC.Rd |only scan-0.53/scan/DESCRIPTION | 32 scan-0.53/scan/MD5 | 167 ++-- scan-0.53/scan/NAMESPACE | 195 +++-- scan-0.53/scan/NEWS.md | 172 ++++ scan-0.53/scan/R/add_l2.R |only scan-0.53/scan/R/as.data.frame.scdf.R |only scan-0.53/scan/R/autocorr.R | 59 - scan-0.53/scan/R/cdc.R |only scan-0.53/scan/R/check_scdf.R |only scan-0.53/scan/R/convert.R |only scan-0.53/scan/R/corrected_tau.R | 103 +- scan-0.53/scan/R/describe.R |only scan-0.53/scan/R/estimate_design.R | 51 - scan-0.53/scan/R/export.R | 880 +++++++++++++++---------- scan-0.53/scan/R/fill_missing.R | 22 scan-0.53/scan/R/hplm.R | 62 + scan-0.53/scan/R/mplm.R | 141 +--- scan-0.53/scan/R/nap.R | 28 scan-0.53/scan/R/outlier.R | 24 scan-0.53/scan/R/overlap.R | 113 ++- scan-0.53/scan/R/pand.R | 71 +- scan-0.53/scan/R/pem.R | 18 scan-0.53/scan/R/pet.R | 10 scan-0.53/scan/R/pipe.R |only scan-0.53/scan/R/pkg-package.R | 40 - scan-0.53/scan/R/plm.R | 4 scan-0.53/scan/R/plot.scdf.R | 717 ++++++++++++++------ scan-0.53/scan/R/pnd.R | 18 scan-0.53/scan/R/power_test.R | 2 scan-0.53/scan/R/print.sc.R | 1007 ++++++++++++++++------------- scan-0.53/scan/R/print.scdf.R | 24 scan-0.53/scan/R/private_keep_phases.R |only scan-0.53/scan/R/private_options.R | 113 ++- scan-0.53/scan/R/private_prepare_scdf.R |only scan-0.53/scan/R/private_utilities.R | 149 +--- scan-0.53/scan/R/rSC.R | 106 ++- scan-0.53/scan/R/rand_test.R | 46 + scan-0.53/scan/R/ranks.R | 2 scan-0.53/scan/R/rci.R | 36 - scan-0.53/scan/R/readSC.R | 225 +++--- scan-0.53/scan/R/sample_names.R |only scan-0.53/scan/R/scan-Data.R | 1 scan-0.53/scan/R/scan.R | 7 scan-0.53/scan/R/scdf-functions.R | 101 +- scan-0.53/scan/R/scdf.R | 43 - scan-0.53/scan/R/select_phases.R |only scan-0.53/scan/R/set_var.R |only scan-0.53/scan/R/smooth_cases.R |only scan-0.53/scan/R/standardize.R | 43 - scan-0.53/scan/R/style_plot.R | 13 scan-0.53/scan/R/subset.scdf.R | 21 scan-0.53/scan/R/summary.scdf.R | 15 scan-0.53/scan/R/tau_u.R | 981 +++++++++++----------------- scan-0.53/scan/R/trend.R | 80 +- scan-0.53/scan/R/truncate_phase.R |only scan-0.53/scan/R/writeSC.R | 23 scan-0.53/scan/data/scan-Data.RData |binary scan-0.53/scan/inst |only scan-0.53/scan/man/Beretvas2008.Rd | 1 scan-0.53/scan/man/add_l2.Rd |only scan-0.53/scan/man/as.data.frame.scdf.Rd |only scan-0.53/scan/man/cdc.Rd |only scan-0.53/scan/man/check_scdf.Rd |only scan-0.53/scan/man/combine.Rd | 14 scan-0.53/scan/man/convert.Rd |only scan-0.53/scan/man/corrected_tau.Rd | 27 scan-0.53/scan/man/describe.Rd |only scan-0.53/scan/man/export.Rd | 100 ++ scan-0.53/scan/man/fill_missing.Rd | 4 scan-0.53/scan/man/is.scdf.Rd |only scan-0.53/scan/man/mplm.Rd | 7 scan-0.53/scan/man/nap.Rd | 2 scan-0.53/scan/man/outlier.Rd | 2 scan-0.53/scan/man/overlap.Rd | 5 scan-0.53/scan/man/pipe.Rd |only scan-0.53/scan/man/plot.scdf.Rd | 34 scan-0.53/scan/man/print.sc.Rd | 70 +- scan-0.53/scan/man/ranks.Rd | 2 scan-0.53/scan/man/sample_names.Rd |only scan-0.53/scan/man/scdf.Rd | 14 scan-0.53/scan/man/select_phases.Rd |only scan-0.53/scan/man/set_vars.Rd |only scan-0.53/scan/man/shift.Rd | 2 scan-0.53/scan/man/smooth_cases.Rd | 4 scan-0.53/scan/man/standardize.Rd | 6 scan-0.53/scan/man/style_plot.Rd | 13 scan-0.53/scan/man/subset.scdf.Rd | 8 scan-0.53/scan/man/tau_u.Rd | 32 scan-0.53/scan/man/trend.Rd | 10 scan-0.53/scan/man/truncate_phase.Rd | 8 scan-0.53/scan/man/writeSC.Rd | 14 104 files changed, 3717 insertions(+), 2627 deletions(-)
Title: Interactive Graphics for Monitoring Clinical Trial Safety
Description: A framework for evaluation of clinical trial safety. Users can interactively explore their data using the included 'Shiny' application.
Author: Jeremy Wildfire [cre, aut],
Becca Krouse [aut],
Preston Burns [aut],
Xiao Ni [aut],
James Buchanan [aut],
Susan Duke [aut]
Maintainer: Jeremy Wildfire <jwildfire@gmail.com>
Diff between safetyGraphics versions 1.1.0 dated 2020-01-15 and 2.0.0 dated 2021-09-22
safetyGraphics-1.1.0/safetyGraphics/R/addChart.R |only safetyGraphics-1.1.0/safetyGraphics/R/addSetting.R |only safetyGraphics-1.1.0/safetyGraphics/R/adlbc.R |only safetyGraphics-1.1.0/safetyGraphics/R/chartRenderer.R |only safetyGraphics-1.1.0/safetyGraphics/R/chartsMetadata.R |only safetyGraphics-1.1.0/safetyGraphics/R/checkColumn.R |only safetyGraphics-1.1.0/safetyGraphics/R/checkField.R |only safetyGraphics-1.1.0/safetyGraphics/R/checkNumeric.R |only safetyGraphics-1.1.0/safetyGraphics/R/checkRequired.R |only safetyGraphics-1.1.0/safetyGraphics/R/createChart.R |only safetyGraphics-1.1.0/safetyGraphics/R/generateSettings.R |only safetyGraphics-1.1.0/safetyGraphics/R/generateShell.R |only safetyGraphics-1.1.0/safetyGraphics/R/getRequiredSettings.R |only safetyGraphics-1.1.0/safetyGraphics/R/getSettingKeys.R |only safetyGraphics-1.1.0/safetyGraphics/R/getSettingValue.R |only safetyGraphics-1.1.0/safetyGraphics/R/getSettingsMetadata.R |only safetyGraphics-1.1.0/safetyGraphics/R/removeCharts.R |only safetyGraphics-1.1.0/safetyGraphics/R/removeSettings.R |only safetyGraphics-1.1.0/safetyGraphics/R/setSettingsValue.R |only safetyGraphics-1.1.0/safetyGraphics/R/settingsMetadata.R |only safetyGraphics-1.1.0/safetyGraphics/R/standardsMetadata.R |only safetyGraphics-1.1.0/safetyGraphics/R/trimData.R |only safetyGraphics-1.1.0/safetyGraphics/R/trimSettings.R |only safetyGraphics-1.1.0/safetyGraphics/R/validateSettings.R |only safetyGraphics-1.1.0/safetyGraphics/data/adlbc.rda |only safetyGraphics-1.1.0/safetyGraphics/data/chartsMetadata.rda |only safetyGraphics-1.1.0/safetyGraphics/data/settingsMetadata.rda |only safetyGraphics-1.1.0/safetyGraphics/data/standardsMetadata.rda |only safetyGraphics-1.1.0/safetyGraphics/inst/doc/customWorkflows.R |only safetyGraphics-1.1.0/safetyGraphics/inst/doc/customWorkflows.Rmd |only safetyGraphics-1.1.0/safetyGraphics/inst/doc/customWorkflows.html |only safetyGraphics-1.1.0/safetyGraphics/inst/doc/shinyUserGuide.R |only safetyGraphics-1.1.0/safetyGraphics/inst/doc/shinyUserGuide.Rmd |only safetyGraphics-1.1.0/safetyGraphics/inst/doc/shinyUserGuide.html |only safetyGraphics-1.1.0/safetyGraphics/inst/examples |only safetyGraphics-1.1.0/safetyGraphics/inst/htmlwidgets |only safetyGraphics-1.1.0/safetyGraphics/inst/safetyGraphics_app |only safetyGraphics-1.1.0/safetyGraphics/man/addChart.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/addSetting.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/adlbc.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/chartRenderer-shiny.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/chartRenderer.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/chartsMetadata.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/checkColumn.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/checkField.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/checkNumeric.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/checkRequired.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/createChart.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/generateSettings.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/generateShell.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/getRequiredSettings.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/getSettingKeys.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/getSettingValue.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/getSettingsMetadata.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/removeCharts.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/removeSettings.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/setSettingsValue.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/settingsMetadata.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/standardsMetadata.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/trimData.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/trimSettings.Rd |only safetyGraphics-1.1.0/safetyGraphics/man/validateSettings.Rd |only safetyGraphics-1.1.0/safetyGraphics/tests/testthat/test_compareStandard.R |only safetyGraphics-1.1.0/safetyGraphics/tests/testthat/test_generateSettings.R |only safetyGraphics-1.1.0/safetyGraphics/tests/testthat/test_generateShell.R |only safetyGraphics-1.1.0/safetyGraphics/tests/testthat/test_getRequiredSettings.R |only safetyGraphics-1.1.0/safetyGraphics/tests/testthat/test_getSettingKeys.R |only safetyGraphics-1.1.0/safetyGraphics/tests/testthat/test_getSettingValue.R |only safetyGraphics-1.1.0/safetyGraphics/tests/testthat/test_getSettingsMetadata.R |only safetyGraphics-1.1.0/safetyGraphics/tests/testthat/test_setSettingsValue.R |only safetyGraphics-1.1.0/safetyGraphics/tests/testthat/test_textKeysToList.R |only safetyGraphics-1.1.0/safetyGraphics/tests/testthat/test_trimData.R |only safetyGraphics-1.1.0/safetyGraphics/tests/testthat/test_trimSettings.R |only safetyGraphics-1.1.0/safetyGraphics/tests/testthat/test_validateSettings.R |only safetyGraphics-1.1.0/safetyGraphics/vignettes/customWorkflows.Rmd |only safetyGraphics-1.1.0/safetyGraphics/vignettes/shinyUserGuide.Rmd |only safetyGraphics-2.0.0/safetyGraphics/DESCRIPTION | 40 - safetyGraphics-2.0.0/safetyGraphics/LICENSE | 4 safetyGraphics-2.0.0/safetyGraphics/MD5 | 268 +++++----- safetyGraphics-2.0.0/safetyGraphics/NAMESPACE | 103 ++- safetyGraphics-2.0.0/safetyGraphics/NEWS.md | 15 safetyGraphics-2.0.0/safetyGraphics/R/app_startup.R |only safetyGraphics-2.0.0/safetyGraphics/R/detectStandard.R | 71 +- safetyGraphics-2.0.0/safetyGraphics/R/evaluateStandard.R | 107 ++- safetyGraphics-2.0.0/safetyGraphics/R/generateMappingList.R |only safetyGraphics-2.0.0/safetyGraphics/R/hasColumn.R | 4 safetyGraphics-2.0.0/safetyGraphics/R/hasField.R | 15 safetyGraphics-2.0.0/safetyGraphics/R/makeChartConfig.R |only safetyGraphics-2.0.0/safetyGraphics/R/makeChartExport.R |only safetyGraphics-2.0.0/safetyGraphics/R/makeChartParams.R |only safetyGraphics-2.0.0/safetyGraphics/R/makeChartSummary.R |only safetyGraphics-2.0.0/safetyGraphics/R/makeMapping.R |only safetyGraphics-2.0.0/safetyGraphics/R/meta.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_chartsNav.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_chartsTab.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_filterTab.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_filterTabChecks.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_homeTab.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_loadCharts.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_loadData.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_mappingColumn.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_mappingDomain.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_mappingSelect.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_mappingTab.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_safetyGraphicsServer.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_safetyGraphicsUI.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_settingsCharts.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_settingsCode.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_settingsData.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_settingsMapping.R |only safetyGraphics-2.0.0/safetyGraphics/R/mod_settingsTab.R |only safetyGraphics-2.0.0/safetyGraphics/R/prepareChart.R |only safetyGraphics-2.0.0/safetyGraphics/R/safetyGraphics.R | 3 safetyGraphics-2.0.0/safetyGraphics/R/safetyGraphicsApp.R | 121 +--- safetyGraphics-2.0.0/safetyGraphics/R/safetyGraphicsInit.R |only safetyGraphics-2.0.0/safetyGraphics/R/setMappingListValue.R |only safetyGraphics-2.0.0/safetyGraphics/README.md | 53 - safetyGraphics-2.0.0/safetyGraphics/build/vignette.rds |binary safetyGraphics-2.0.0/safetyGraphics/data/meta.rda |only safetyGraphics-2.0.0/safetyGraphics/inst/doc/Cookbook.Rmd |only safetyGraphics-2.0.0/safetyGraphics/inst/doc/Cookbook.html |only safetyGraphics-2.0.0/safetyGraphics/inst/doc/TechnicalFAQ.Rmd |only safetyGraphics-2.0.0/safetyGraphics/inst/doc/TechnicalFAQ.html |only safetyGraphics-2.0.0/safetyGraphics/inst/doc/chartConfiguration.Rmd |only safetyGraphics-2.0.0/safetyGraphics/inst/doc/chartConfiguration.html |only safetyGraphics-2.0.0/safetyGraphics/inst/doc/intro.Rmd |only safetyGraphics-2.0.0/safetyGraphics/inst/doc/intro.html |only safetyGraphics-2.0.0/safetyGraphics/inst/report |only safetyGraphics-2.0.0/safetyGraphics/inst/rstudio |only safetyGraphics-2.0.0/safetyGraphics/inst/www |only safetyGraphics-2.0.0/safetyGraphics/man/SafetyGraphics.Rd | 3 safetyGraphics-2.0.0/safetyGraphics/man/app_startup.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/chartsNav.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/chartsTab.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/chartsTabUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/detectStandard.Rd | 20 safetyGraphics-2.0.0/safetyGraphics/man/evaluateStandard.Rd | 30 - safetyGraphics-2.0.0/safetyGraphics/man/filterTab.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/filterTabChecks.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/filterTabUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/generateMappingList.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/hasColumn.Rd | 4 safetyGraphics-2.0.0/safetyGraphics/man/hasField.Rd | 15 safetyGraphics-2.0.0/safetyGraphics/man/homeTab.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/homeTabUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/loadCharts.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/loadChartsUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/loadData.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/loadDataUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/makeChartConfig.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/makeChartExport.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/makeChartParams.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/makeChartSummary.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/makeMapping.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/mappingColumn.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/mappingColumnUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/mappingDomain.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/mappingDomainUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/mappingSelect.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/mappingSelectUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/mappingTab.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/mappingTabUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/meta.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/prepareChart.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/safetyGraphicsApp.Rd | 31 - safetyGraphics-2.0.0/safetyGraphics/man/safetyGraphicsInit.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/safetyGraphicsServer.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/safetyGraphicsUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/setMappingListValue.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/settingsCharts.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/settingsChartsUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/settingsCode.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/settingsCodeUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/settingsData.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/settingsDataUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/settingsMapping.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/settingsMappingUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/settingsTab.Rd |only safetyGraphics-2.0.0/safetyGraphics/man/settingsTabUI.Rd |only safetyGraphics-2.0.0/safetyGraphics/tests/testthat.R | 2 safetyGraphics-2.0.0/safetyGraphics/tests/testthat/module_examples |only safetyGraphics-2.0.0/safetyGraphics/tests/testthat/test_detectStandard.R | 52 + safetyGraphics-2.0.0/safetyGraphics/tests/testthat/test_evaluateStandard.R | 53 - safetyGraphics-2.0.0/safetyGraphics/tests/testthat/test_hasColumn.R | 20 safetyGraphics-2.0.0/safetyGraphics/tests/testthat/test_hasField.R | 26 safetyGraphics-2.0.0/safetyGraphics/tests/testthat/test_makeMapping.R |only safetyGraphics-2.0.0/safetyGraphics/tests/testthat/test_mod_filterTab.R |only safetyGraphics-2.0.0/safetyGraphics/tests/testthat/test_mod_mapping.R |only safetyGraphics-2.0.0/safetyGraphics/tests/testthat/test_mod_mappingColumn.R |only safetyGraphics-2.0.0/safetyGraphics/tests/testthat/test_mod_mappingDomain.R |only safetyGraphics-2.0.0/safetyGraphics/tests/testthat/test_mod_mappingSelect.R |only safetyGraphics-2.0.0/safetyGraphics/vignettes/Cookbook.Rmd |only safetyGraphics-2.0.0/safetyGraphics/vignettes/TechnicalFAQ.Rmd |only safetyGraphics-2.0.0/safetyGraphics/vignettes/chartConfiguration.Rmd |only safetyGraphics-2.0.0/safetyGraphics/vignettes/intro.Rmd |only 195 files changed, 560 insertions(+), 500 deletions(-)
More information about safetyGraphics at CRAN
Permanent link
Title: Interface to Geometry Engine - Open Source ('GEOS')
Description: Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. Please note that 'rgeos' will be retired by the end of 2023, plan transition to sf functions using 'GEOS' at your earliest convenience. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'. ('rgeos' >= 0.5-1): Up to and including 'GEOS' 3.7.1, topological operations succeeded with some invalid geometries for which the same operations fail from and including 'GEOS' 3.7.2. The 'checkValidity=' argument defaults and structure have been changed, from default FALSE to integer default '0L' for 'GEOS' < 3.7.2 (no check), '1L' 'GEOS' >= 3.7.2 (check and warn). A value of '2L' is also provided that may be used, assigned globally using 'set_RGEOS_CheckValidity(2L)', or locally using the 'checkValidity=2L' argument, to attempt zero-width buffer repair if invalid geometries are found. The previous default (FALSE, now '0L') is fastest and used for 'GEOS' < 3.7.2, but will not warn users of possible problems before the failure of topological operations that previously succeeded. From 'GEOS' 3.8.0, repair of geometries may also be attempted using 'gMakeValid()', which may, however, return a collection of geometries of different types.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Colin Rundel [aut],
Edzer Pebesma [ctb],
Rainer Stuetz [ctb],
Karl Ove Hufthammer [ctb],
Patrick Giraudoux [ctb],
Martin Davis [cph, ctb],
Sandro Santilli [cph, ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.5-7 dated 2021-09-07 and 0.5-8 dated 2021-09-22
ChangeLog | 1865 ++++++++++++++++++++++++++++--------------------------- DESCRIPTION | 8 MD5 | 14 NEWS.md | 6 configure | 18 configure.ac | 5 inst/ChangeLog | 1865 ++++++++++++++++++++++++++++--------------------------- inst/SVN_VERSION | 2 8 files changed, 1976 insertions(+), 1807 deletions(-)
Title: Random Ferns Classifier
Description: Provides the random ferns classifier by Ozuysal, Calonder, Lepetit and Fua (2009) <doi:10.1109/TPAMI.2009.23>, modified for generic and multi-label classification and featuring OOB error approximation and importance measure as introduced in Kursa (2014) <doi:10.18637/jss.v061.i10>.
Author: Miron Bartosz Kursa [aut, cre]
(<https://orcid.org/0000-0001-7672-648X>)
Maintainer: Miron Bartosz Kursa <M.Kursa@icm.edu.pl>
Diff between rFerns versions 4.0.0 dated 2020-08-17 and 5.0.0 dated 2021-09-22
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- inst/CITATION | 4 ++-- inst/NEWS | 4 ++++ src/ferns.c | 11 +---------- src/tools.h | 16 +++++++++++++--- 6 files changed, 30 insertions(+), 25 deletions(-)
Title: Bayesian and Classical Audit Sampling
Description: Implements the audit sampling workflow as discussed in Derks et al. (2019) <doi:10.31234/osf.io/9f6ub>. The package makes it easy for an auditor to plan a statistical sample, select the sample from the population, and evaluate the misstatement in the sample using various methods compliant with the International Standards on Auditing. Furthermore, the package implements Bayesian equivalents of these methods.
Author: Koen Derks [aut, cre] (<https://orcid.org/0000-0002-5533-9349>)
Maintainer: Koen Derks <k.derks@nyenrode.nl>
Diff between jfa versions 0.5.7 dated 2021-08-12 and 0.6.0 dated 2021-09-22
jfa-0.5.7/jfa/R/auditBF.R |only jfa-0.5.7/jfa/inst/doc/v4_testing_misstatement.R |only jfa-0.5.7/jfa/inst/doc/v4_testing_misstatement.Rmd |only jfa-0.5.7/jfa/inst/doc/v4_testing_misstatement.html |only jfa-0.5.7/jfa/inst/doc/v6_bayes_factors_summary_statistics.R |only jfa-0.5.7/jfa/inst/doc/v6_bayes_factors_summary_statistics.Rmd |only jfa-0.5.7/jfa/inst/doc/v6_bayes_factors_summary_statistics.html |only jfa-0.5.7/jfa/man/auditBF.Rd |only jfa-0.5.7/jfa/tests/testthat/test-consistency-auditBF.R |only jfa-0.5.7/jfa/vignettes/v4_testing_misstatement.Rmd |only jfa-0.5.7/jfa/vignettes/v6_bayes_factors_summary_statistics.Rmd |only jfa-0.6.0/jfa/DESCRIPTION | 10 jfa-0.6.0/jfa/MD5 | 141 jfa-0.6.0/jfa/NAMESPACE | 7 jfa-0.6.0/jfa/NEWS.md | 66 jfa-0.6.0/jfa/R/BuildIt-data.R | 4 jfa-0.6.0/jfa/R/auditPrior.R | 586 + jfa-0.6.0/jfa/R/carrier-data.R |only jfa-0.6.0/jfa/R/evaluation.R | 988 +-- jfa-0.6.0/jfa/R/jfa_internal.R | 84 jfa-0.6.0/jfa/R/jfa_methods.R | 951 +-- jfa-0.6.0/jfa/R/methods.R | 307 jfa-0.6.0/jfa/R/planning.R | 559 - jfa-0.6.0/jfa/R/report.R | 72 jfa-0.6.0/jfa/R/selection.R | 304 jfa-0.6.0/jfa/README.md | 273 jfa-0.6.0/jfa/build/vignette.rds |binary jfa-0.6.0/jfa/data/carrier.RData |only jfa-0.6.0/jfa/inst/CITATION | 4 jfa-0.6.0/jfa/inst/doc/jfa.R | 26 jfa-0.6.0/jfa/inst/doc/jfa.Rmd | 70 jfa-0.6.0/jfa/inst/doc/jfa.html | 324 - jfa-0.6.0/jfa/inst/doc/v1_sampling_workflow.R | 27 jfa-0.6.0/jfa/inst/doc/v1_sampling_workflow.Rmd | 45 jfa-0.6.0/jfa/inst/doc/v1_sampling_workflow.html | 160 jfa-0.6.0/jfa/inst/doc/v2_bayesian_sampling_workflow.R | 33 jfa-0.6.0/jfa/inst/doc/v2_bayesian_sampling_workflow.Rmd | 57 jfa-0.6.0/jfa/inst/doc/v2_bayesian_sampling_workflow.html | 232 jfa-0.6.0/jfa/inst/doc/v3_prior_distributions.R | 59 jfa-0.6.0/jfa/inst/doc/v3_prior_distributions.Rmd | 117 jfa-0.6.0/jfa/inst/doc/v3_prior_distributions.html | 523 - jfa-0.6.0/jfa/inst/doc/v4_selection_methodology.R |only jfa-0.6.0/jfa/inst/doc/v4_selection_methodology.Rmd |only jfa-0.6.0/jfa/inst/doc/v4_selection_methodology.html |only jfa-0.6.0/jfa/inst/doc/v5_estimating_misstatement.Rmd | 6 jfa-0.6.0/jfa/inst/doc/v5_estimating_misstatement.html | 6 jfa-0.6.0/jfa/inst/doc/v6_testing_misstatement.R |only jfa-0.6.0/jfa/inst/doc/v6_testing_misstatement.Rmd |only jfa-0.6.0/jfa/inst/doc/v6_testing_misstatement.html |only jfa-0.6.0/jfa/inst/doc/v7_bayes_factors_summary_statistics.R |only jfa-0.6.0/jfa/inst/doc/v7_bayes_factors_summary_statistics.Rmd |only jfa-0.6.0/jfa/inst/doc/v7_bayes_factors_summary_statistics.html |only jfa-0.6.0/jfa/inst/rmd/report.Rmd | 74 jfa-0.6.0/jfa/man/BuildIt.Rd | 2 jfa-0.6.0/jfa/man/auditPrior.Rd | 86 jfa-0.6.0/jfa/man/carrier.Rd |only jfa-0.6.0/jfa/man/evaluation.Rd | 134 jfa-0.6.0/jfa/man/jfa-methods.Rd | 60 jfa-0.6.0/jfa/man/jfa.Rd | 85 jfa-0.6.0/jfa/man/planning.Rd | 85 jfa-0.6.0/jfa/man/report.Rd | 24 jfa-0.6.0/jfa/man/selection.Rd | 72 jfa-0.6.0/jfa/tests/testthat/test-consistency-auditPrior.R | 144 jfa-0.6.0/jfa/tests/testthat/test-consistency-evaluation.R | 301 jfa-0.6.0/jfa/tests/testthat/test-consistency-other.R | 4 jfa-0.6.0/jfa/tests/testthat/test-consistency-planning.R | 301 jfa-0.6.0/jfa/tests/testthat/test-consistency-selection.R | 48 jfa-0.6.0/jfa/tests/testthat/test-consistency-statistical-tables.R | 3168 ++++------ jfa-0.6.0/jfa/tests/testthat/test-consistency-workflow.R | 53 jfa-0.6.0/jfa/tests/testthat/test-validation-MUS.R | 31 jfa-0.6.0/jfa/tests/testthat/test-validation-appendix-a.R | 274 jfa-0.6.0/jfa/tests/testthat/test-validation-appendix-c.R | 99 jfa-0.6.0/jfa/tests/testthat/test-validation-audit-sampler.R | 111 jfa-0.6.0/jfa/tests/testthat/test-validation-smash21.R | 101 jfa-0.6.0/jfa/tests/testthat/test-validation-touwhoogduin.R | 13 jfa-0.6.0/jfa/vignettes/img |only jfa-0.6.0/jfa/vignettes/jfa.Rmd | 70 jfa-0.6.0/jfa/vignettes/v1_sampling_workflow.Rmd | 45 jfa-0.6.0/jfa/vignettes/v2_bayesian_sampling_workflow.Rmd | 57 jfa-0.6.0/jfa/vignettes/v3_prior_distributions.Rmd | 117 jfa-0.6.0/jfa/vignettes/v4_selection_methodology.Rmd |only jfa-0.6.0/jfa/vignettes/v5_estimating_misstatement.Rmd | 6 jfa-0.6.0/jfa/vignettes/v6_testing_misstatement.Rmd |only jfa-0.6.0/jfa/vignettes/v7_bayes_factors_summary_statistics.Rmd |only 84 files changed, 5885 insertions(+), 5721 deletions(-)
Title: Optimal Test Design Approach to Fixed and Adaptive Test
Construction
Description: Use the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and
van der Linden (2018) <doi:10.1201/9781315117430> in constructing fixed and adaptive tests. Supports the following
mixed-integer programming (MIP) solver packages: 'lpsymphony', 'Rsymphony', 'gurobi', 'lpSolve', and 'Rglpk'. The 'gurobi' package
is not available from CRAN; see <https://www.gurobi.com/downloads/>.
Author: Seung W. Choi [aut, cre] (<https://orcid.org/0000-0003-4777-5420>),
Sangdon Lim [aut] (<https://orcid.org/0000-0002-2988-014X>)
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between TestDesign versions 1.2.5 dated 2021-07-12 and 1.2.6 dated 2021-09-22
DESCRIPTION | 15 MD5 | 65 +-- NEWS.md | 14 R/bayes_functions.R | 6 R/constraint_functions.R | 12 R/eligibility_functions.R | 279 +++++++++++---- R/exposure_control_functions.R | 184 ++++++++- R/other_functions.R | 69 ++- R/plot_functions.R | 115 ++++-- R/shadow_functions.R | 609 ++++++--------------------------- R/shadowtest_functions.R |only R/solver_functions.R | 4 R/summary_functions.R | 6 R/theta_functions.R | 350 ++++++++++++++++++ R/xdata_functions.R | 6 build/vignette.rds |binary inst/CITATION | 33 + man/Shadow-methods.Rd | 14 man/calcEscore-methods.Rd | 8 man/calcFisher-methods.Rd | 8 man/calcHessian-methods.Rd | 8 man/calcJacobian-methods.Rd | 8 man/calcLocation-methods.Rd | 8 man/calcLogLikelihood-methods.Rd | 8 man/calcProb-methods.Rd | 8 man/calc_info.Rd | 8 man/calc_likelihood.Rd | 8 man/info_item.Rd | 8 man/item-classes.Rd | 8 man/p_item.Rd | 8 man/plot-methods.Rd | 19 + man/simResp-methods.Rd | 8 man/theta_EB.Rd | 8 tests/testthat/test_exposure_methods.R | 15 34 files changed, 1156 insertions(+), 771 deletions(-)
Title: Univariate and Multivariate Spatial-Temporal Modeling
Description: Fits univariate and multivariate spatio-temporal
random effects models for point-referenced data using Markov chain Monte Carlo (MCMC). Details are given in Finley, Banerjee, and Gelfand (2015) <doi:10.18637/jss.v063.i13> and Finley, Banerjee, and Cook (2014) <doi:10.1111/2041-210X.12189>.
Author: Andrew Finley [aut, cre],
Sudipto Banerjee [aut]
Maintainer: Andrew Finley <finleya@msu.edu>
Diff between spBayes versions 0.4-4 dated 2021-09-20 and 0.4-5 dated 2021-09-22
DESCRIPTION | 8 ++-- MD5 | 84 +++++++++++++++++++++---------------------- inst/ChangeLog | 5 ++ src/Makevars | 1 src/adaptMetropGibbs.cpp | 5 +- src/mkSpCov.cpp | 12 ------ src/nonSpGLM_AMCMC.cpp | 10 +---- src/spDynLM.cpp | 11 +---- src/spGLM.cpp | 12 ++---- src/spGLM_AMCMC.cpp | 13 ++---- src/spLM.cpp | 7 +-- src/spLMPredict.cpp | 3 - src/spLMRecover.cpp | 7 +-- src/spMPPMvDIC.cpp | 7 --- src/spMisalign.cpp | 8 +--- src/spMisalignGLM.cpp | 16 ++------ src/spMisalignGLMPredict.cpp | 25 +++--------- src/spMisalignPredict.cpp | 16 ++------ src/spMisalignRecover.cpp | 8 +--- src/spMvGLM.cpp | 17 ++------ src/spMvGLMPredict.cpp | 10 +---- src/spMvGLM_AMCMC.cpp | 15 ++----- src/spMvLM.cpp | 8 +--- src/spMvLMPredict.cpp | 7 --- src/spMvLMRecover.cpp | 16 ++------ src/spPPDynLM.cpp | 9 +--- src/spPPGLM.cpp | 16 +++----- src/spPPGLM_AMCMC.cpp | 15 +++---- src/spPPLM.cpp | 9 +--- src/spPPLMPredict.cpp | 10 +---- src/spPPLMRecover.cpp | 12 +----- src/spPPMvGLM.cpp | 14 ++----- src/spPPMvGLMPredict.cpp | 16 ++------ src/spPPMvGLM_AMCMC.cpp | 10 +---- src/spPPMvLM.cpp | 9 +--- src/spPPMvLMPredict.cpp | 10 ----- src/spPPMvLMRecover.cpp | 11 +---- src/spSVC.cpp | 15 +++---- src/spSVCPredictJoint.cpp | 14 ++----- src/spSVCPredictMarg.cpp | 14 ++----- src/spSVCRecover.cpp | 14 ++----- src/util.cpp | 5 +- src/util.h | 5 -- 43 files changed, 172 insertions(+), 367 deletions(-)
Title: Stable Balancing Weights for Causal Inference and Missing Data
Description: Implements the Stable Balancing Weights by Zubizarreta (2015) <DOI:10.1080/01621459.2015.1023805>. These are the weights of minimum variance that approximately balance the empirical distribution of the observed covariates. For an overview, see Chattopadhyay, Hase and Zubizarreta (2020) <DOI:10.1002/(ISSN)1097-0258>. To solve the optimization problem in 'sbw', the default solver is 'quadprog', which is readily available through CRAN. The solver 'osqp' is also posted on CRAN. To enhance the performance of 'sbw', users are encouraged to install other solvers such as 'gurobi' and 'Rmosek', which require special installation. For the installation of gurobi and pogs, please follow the instructions at <https://www.gurobi.com/documentation/9.1/quickstart_mac/r_ins_the_r_package.html> and <http://foges.github.io/pogs/stp/r>.
Author: Jose R. Zubizarreta [aut, cre],
Yige Li [aut],
Kwangho Kim [aut],
Amine Allouah [ctb],
Noah Greifer [ctb]
Maintainer: Jose R. Zubizarreta <zubizarreta@hcp.med.harvard.edu>
Diff between sbw versions 1.1.3 dated 2021-06-18 and 1.1.5 dated 2021-09-22
DESCRIPTION | 17 ++++++---- MD5 | 10 +++--- R/sbw.R | 4 +- R/sbwauxfix.R | 6 +++ R/sbwpri.R | 94 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++- man/sbw.Rd | 4 +- 6 files changed, 118 insertions(+), 17 deletions(-)
Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb], Brian D. Ripley [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFieldsUtils versions 0.5.3 dated 2019-03-04 and 0.5.4 dated 2021-09-22
DESCRIPTION | 9 +--- MD5 | 67 +++++++++++++++--------------- R/internal_use.R | 2 inst/include/AutoRandomFieldsUtilsLocal.h | 2 inst/include/Basic_utils.h | 46 ++++++++++---------- inst/include/General_utils.h | 9 ---- inst/include/Options_utils.h | 5 -- inst/include/RandomFieldsUtils.h |only inst/include/intrinsics.h | 16 ++++--- inst/include/kleinkram.h | 4 - inst/include/own.h |only inst/include/zzz_calls.h | 2 man/internal.Rd |only man/macros/allg_defn.Rd | 4 - src/AutoRandomFieldsUtilsLocal.h | 2 src/Basic_utils.h | 42 +++++++++--------- src/General_utils.h | 9 ---- src/Options_utils.h | 5 -- src/RFoptions.cc | 5 +- src/RandomFieldsUtils.h | 5 -- src/brdomain.cc | 1 src/cholmodified.f | 4 + src/intrinsics.h | 16 ++++--- src/kleinkram.cc | 8 +-- src/kleinkram.h | 4 - src/linear.cc | 13 ++++- src/maths.cc | 6 +- src/options.cc | 6 +- src/own.cc | 6 -- src/scalar.cc | 10 +--- src/solve.cc | 10 ++-- src/sort.cc | 1 src/utils.cc | 9 +--- src/win_linux_aux.cc | 17 +------ src/zzz.c | 1 src/zzz_calls.h | 2 36 files changed, 163 insertions(+), 185 deletions(-)
More information about RandomFieldsUtils at CRAN
Permanent link
Title: Toolbox for Model Building and Forecasting
Description: Implements functions and instruments for regression model building and its
application to forecasting. The main scope of the package is in variables selection
and models specification for cases of time series data. This includes promotional
modelling, selection between different dynamic regressions with non-standard
distributions of errors, selection based on cross validation, solutions to the fat
regression model problem and more. Models developed in the package are tailored
specifically for forecasting purposes. So as a results there are several methods
that allow producing forecasts from these models and visualising them.
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics
and Forecasting, Lancaster University, UK),
Yves R. Sagaert [ctb] (Visiting Research at Centre for Marketing
Analytics and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between greybox versions 1.0.0 dated 2021-06-27 and 1.0.1 dated 2021-09-22
DESCRIPTION | 10 +- MD5 | 34 ++++----- NAMESPACE | 6 - NEWS | 14 ++++ R/alm.R | 2 R/error-measures.R | 148 ++++++++++++++++++++----------------------- R/graphmaker.R | 4 - R/temporaldummy.R | 7 -- R/zzz.R | 6 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/alm.html | 118 +++++++++++++++++----------------- inst/doc/greybox.html | 118 +++++++++++++++++----------------- inst/doc/maUsingGreybox.html | 4 - inst/doc/ro.html | 14 ++-- man/error-measures.Rd | 54 +++++++-------- man/pinball.Rd | 4 - src/RcppExports.cpp | 5 + 18 files changed, 278 insertions(+), 270 deletions(-)
Title: Offline 'Google' Fonts for 'Markdown' and 'Shiny'
Description: Download 'Google' fonts and generate 'CSS' to use in 'rmarkdown' documents and
'shiny' applications. Some popular fonts are included and ready to use.
Author: Victor Perrier [aut, cre],
Fanny Meyer [aut],
Mario Ranftl [ctb, cph] (google-webfonts-helper)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between gfonts versions 0.1.2 dated 2021-01-11 and 0.1.3 dated 2021-09-22
DESCRIPTION | 8 MD5 | 117 +-- NAMESPACE | 47 - NEWS.md | 7 R/api.R | 8 R/css.R | 19 R/data.R | 28 R/gfonts-package.R | 40 - R/onLoad.R | 16 R/setup_font.R | 23 R/sysdata.rda |binary R/tag_example.R | 134 +-- R/use_font.R | 110 +- R/use_pkg_gfont.R | 6 R/utils.R | 8 README.md | 14 build/vignette.rds |binary inst/assets/css/alegreya.css | 48 - inst/assets/css/baloo.css | 24 inst/assets/css/happy-monkey.css | 24 inst/assets/css/henny-penny.css | 24 inst/assets/css/lato.css | 72 - inst/assets/css/montserrat.css | 72 - inst/assets/css/nunito-sans.css | 72 - inst/assets/css/open-sans.css | 72 - inst/assets/css/oswald.css |only inst/assets/css/poppins.css |only inst/assets/css/roboto.css | 72 - inst/assets/fonts/oswald |only inst/assets/fonts/poppins |only inst/assets/templates/css_best.txt | 26 inst/assets/templates/css_modern.txt |only inst/doc/gfonts.R | 4 inst/doc/gfonts.Rmd | 4 inst/doc/gfonts.html | 330 +------- man/generate_css.Rd | 96 +- man/get_all_fonts.Rd | 52 - man/gfonts.Rd | 50 - man/setup_font.Rd | 122 +-- man/tag_example.Rd | 40 - man/use_pkg_gfont.Rd | 2 tests/testthat.R | 8 tests/testthat/download_font.yml | 64 - tests/testthat/generate_css.yml | 90 +- tests/testthat/get_all_fonts.yml | 1042 ++++++++++++++-------------- tests/testthat/get_font_info_montserrat.yml | 104 +- tests/testthat/get_font_info_roboto.yml | 90 +- tests/testthat/helper-gfonts.R | 6 tests/testthat/setup_font.yml | 152 ++-- tests/testthat/test-api.R | 20 tests/testthat/test-css.R | 72 - tests/testthat/test-setup_font.R | 25 tests/testthat/test-tag_example.R | 12 tests/testthat/test-use_font.R | 36 tests/testthat/test-use_pkg_gfont.R | 18 vignettes/articles/included-fonts.Rmd | 26 vignettes/gfonts.Rmd | 4 57 files changed, 1730 insertions(+), 1830 deletions(-)
Title: A C++11 Interface for R's C Interface
Description: Provides a header only, C++11 interface to R's C
interface. Compared to other approaches 'cpp11' strives to be safe
against long jumps from the C API as well as C++ exceptions, conform
to normal R function semantics and supports interaction with 'ALTREP'
vectors.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>),
Romain François [ctb],
Benjamin Kietzman [ctb],
RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between cpp11 versions 0.3.1 dated 2021-06-25 and 0.4.0 dated 2021-09-22
DESCRIPTION | 8 MD5 | 82 ++++---- NEWS.md | 31 +++ R/register.R | 40 +++- R/source.R | 69 +++---- README.md | 8 build/vignette.rds |binary inst/doc/FAQ.R |only inst/doc/FAQ.Rmd |only inst/doc/FAQ.html |only inst/doc/converting.Rmd | 33 +-- inst/doc/converting.html | 8 inst/doc/cpp11.Rmd | 10 - inst/doc/cpp11.html | 40 ++-- inst/doc/motivations.html | 20 -- inst/include/cpp11/as.hpp | 17 - inst/include/cpp11/declarations.hpp | 4 inst/include/cpp11/doubles.hpp | 23 ++ inst/include/cpp11/environment.hpp | 3 inst/include/cpp11/external_pointer.hpp | 3 inst/include/cpp11/function.hpp | 40 ++++ inst/include/cpp11/integers.hpp | 28 ++ inst/include/cpp11/list.hpp | 3 inst/include/cpp11/logicals.hpp | 4 inst/include/cpp11/matrix.hpp | 207 +++++++++++++++++----- inst/include/cpp11/protect.hpp | 121 +++++++++--- inst/include/cpp11/r_bool.hpp | 2 inst/include/cpp11/r_vector.hpp | 82 +++++--- inst/include/cpp11/raws.hpp | 3 inst/include/cpp11/strings.hpp | 11 - inst/include/fmt |only man/cpp11-package.Rd | 1 man/cpp_register.Rd | 3 man/cpp_source.Rd | 8 tests/testthat/helper.R | 9 tests/testthat/linking_to_incorrect_registers.cpp |only tests/testthat/linking_to_registers.cpp |only tests/testthat/multiple_incorrect.cpp | 6 tests/testthat/single_error.cpp |only tests/testthat/single_incorrect.cpp | 2 tests/testthat/test-register.R | 93 ++++++++- tests/testthat/test-source.R | 72 +++++++ vignettes/FAQ.Rmd |only vignettes/converting.Rmd | 33 +-- vignettes/cpp11.Rmd | 10 - 45 files changed, 821 insertions(+), 316 deletions(-)
Title: General Utility Functions for Analysis of Clinical Data
Description: Utility functions to facilitate the import,
the reporting and analysis of clinical data.
Example datasets in 'SDTM' and 'ADaM' format, containing a subset of patients/domains
from the 'CDISC Pilot 01 study' are also available as R datasets to demonstrate
the package functionalities.
Author: Laure Cougnaud [aut, cre],
Michela Pasetto [aut],
Arne De Roeck [rev] (tests),
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between clinUtils versions 0.0.4 dated 2021-07-21 and 0.1.0 dated 2021-09-22
clinUtils-0.0.4/clinUtils/inst/doc/clinUtils-vignette.R |only clinUtils-0.0.4/clinUtils/tests/testthat/test_plots-palettesCDISC.R |only clinUtils-0.1.0/clinUtils/DESCRIPTION | 15 clinUtils-0.1.0/clinUtils/MD5 | 58 clinUtils-0.1.0/clinUtils/NAMESPACE | 1 clinUtils-0.1.0/clinUtils/R/compareTables.R | 15 clinUtils-0.1.0/clinUtils/R/knitPrintListObjects.R | 29 clinUtils-0.1.0/clinUtils/R/knitPrintListPlots.R | 22 clinUtils-0.1.0/clinUtils/R/table-getClinDT.R | 143 clinUtils-0.1.0/clinUtils/build/vignette.rds |binary clinUtils-0.1.0/clinUtils/inst/NEWS | 6 clinUtils-0.1.0/clinUtils/inst/doc/clinUtils-vignette.Rmd | 10 clinUtils-0.1.0/clinUtils/inst/doc/clinUtils-vignette.html |56070 +++++++++- clinUtils-0.1.0/clinUtils/inst/examples/getClinDT-example.R | 78 clinUtils-0.1.0/clinUtils/inst/examples/knitPrintListObjects-example.R | 10 clinUtils-0.1.0/clinUtils/inst/examples/knitPrintListPlots-example.R | 52 clinUtils-0.1.0/clinUtils/man/clinColors.Rd | 24 clinUtils-0.1.0/clinUtils/man/getClinDT.Rd | 104 clinUtils-0.1.0/clinUtils/man/getClinDTButtons.Rd |only clinUtils-0.1.0/clinUtils/man/knitPrintListObjects.Rd | 88 clinUtils-0.1.0/clinUtils/man/knitPrintListPlots.Rd | 86 clinUtils-0.1.0/clinUtils/tests/testthat/test_compareTables.R | 40 clinUtils-0.1.0/clinUtils/tests/testthat/test_getClinDT.R | 67 clinUtils-0.1.0/clinUtils/tests/testthat/test_knitPrintListPlots.R | 46 clinUtils-0.1.0/clinUtils/tests/testthat/test_label.R | 10 clinUtils-0.1.0/clinUtils/tests/testthat/test_loadDataADaMSDTM.R | 84 clinUtils-0.1.0/clinUtils/tests/testthat/test_miscellaneous.R | 38 clinUtils-0.1.0/clinUtils/tests/testthat/test_palettes.R | 12 clinUtils-0.1.0/clinUtils/tests/testthat/test_palettesCDISC.R |only clinUtils-0.1.0/clinUtils/tests/testthat/test_plots-utility.R | 157 clinUtils-0.1.0/clinUtils/tests/testthat/test_roundHalfUp.R | 67 clinUtils-0.1.0/clinUtils/vignettes/clinUtils-vignette.Rmd | 10 32 files changed, 56793 insertions(+), 549 deletions(-)
Title: Adaptive Approaches for Signal Detection in Pharmacovigilance
Description: A collection of several pharmacovigilance signal detection methods based on adaptive lasso. Additional lasso-based and propensity score-based signal detection approaches are also supplied.
Author: Emeline Courtois [cre],
Ismaïl Ahmed [aut],
Hervé Perdry [ctb]
Maintainer: Emeline Courtois <emeline.courtois@inserm.fr>
Diff between adapt4pv versions 0.2-0 dated 2021-08-05 and 0.2-1 dated 2021-09-22
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/adapt_cisl.R | 4 ++-- R/internals.R | 2 +- build/partial.rdb |binary man/adapt_cisl.Rd | 4 ++-- 7 files changed, 19 insertions(+), 14 deletions(-)
Title: Time-Varying Coefficient for Single and Multi-Equation
Regressions
Description: Fitting time-varying coefficient models for single and multi-equation regressions, using kernel smoothing techniques.
Author: Isabel Casas [aut, cre],
Ruben Fernandez-Casal [aut]
Maintainer: Isabel Casas <casasis@gmail.com>
Diff between tvReg versions 0.5.4 dated 2021-03-09 and 0.5.6 dated 2021-09-22
tvReg-0.5.4/tvReg/R/data.R |only tvReg-0.5.4/tvReg/data/CEES.rdata |only tvReg-0.5.4/tvReg/data/FF5F.rdata |only tvReg-0.5.4/tvReg/data/RV.rdata |only tvReg-0.5.6/tvReg/DESCRIPTION | 10 tvReg-0.5.6/tvReg/MD5 | 67 - tvReg-0.5.6/tvReg/NAMESPACE | 1 tvReg-0.5.6/tvReg/NEWS.md | 46 - tvReg-0.5.6/tvReg/R/bw.R | 891 +++++++++++------------ tvReg-0.5.6/tvReg/R/forecast_tvReg.R | 14 tvReg-0.5.6/tvReg/R/predict_tvReg.R | 661 ++++++++--------- tvReg-0.5.6/tvReg/R/print_tvReg.R | 317 ++++---- tvReg-0.5.6/tvReg/R/summary_tvReg.R | 365 ++++----- tvReg-0.5.6/tvReg/R/tvAR.R | 322 ++++---- tvReg-0.5.6/tvReg/R/tvBOOT.R | 328 ++++---- tvReg-0.5.6/tvReg/R/tvCov.R | 385 +++++----- tvReg-0.5.6/tvReg/R/tvFE.R | 319 ++++---- tvReg-0.5.6/tvReg/R/tvGLS.R | 18 tvReg-0.5.6/tvReg/R/tvIRF.R | 295 +++---- tvReg-0.5.6/tvReg/R/tvOLS.R | 26 tvReg-0.5.6/tvReg/R/tvPLM.R | 377 ++++----- tvReg-0.5.6/tvReg/R/tvPsi.R | 108 +- tvReg-0.5.6/tvReg/R/tvRE.R | 333 ++++---- tvReg-0.5.6/tvReg/R/tvReg-package.R |only tvReg-0.5.6/tvReg/R/tvSURE.R | 673 ++++++++--------- tvReg-0.5.6/tvReg/R/tvVAR.R | 40 - tvReg-0.5.6/tvReg/R/update.R | 182 ++-- tvReg-0.5.6/tvReg/build/vignette.rds |binary tvReg-0.5.6/tvReg/data/CEES.rda |only tvReg-0.5.6/tvReg/data/FF5F.rda |only tvReg-0.5.6/tvReg/data/RV.rda |only tvReg-0.5.6/tvReg/inst/doc/tvReg.html | 1228 ++++++++++++-------------------- tvReg-0.5.6/tvReg/man/CEES.Rd | 2 tvReg-0.5.6/tvReg/man/FF5F.Rd | 2 tvReg-0.5.6/tvReg/man/OECD.Rd | 2 tvReg-0.5.6/tvReg/man/RV.Rd | 14 tvReg-0.5.6/tvReg/man/forecast-tvReg.Rd | 8 tvReg-0.5.6/tvReg/man/predict-tvReg.Rd | 3 tvReg-0.5.6/tvReg/man/tvReg-package.Rd |only 39 files changed, 3397 insertions(+), 3640 deletions(-)
Title: Single Tree Simulator
Description: Framework to build an individual tree simulator.
Author: Clara Anton Fernandez [aut, cre]
Maintainer: Clara Anton Fernandez <caf@nibio.no>
Diff between sitree versions 0.1-9 dated 2021-08-04 and 0.1-10 dated 2021-09-22
DESCRIPTION | 8 ++-- MD5 | 10 +++--- R/sitreesummary.R | 23 +++++++++----- R/zzz.R | 2 - inst/doc/SiTree.html | 72 ++++++++++++++++++++++---------------------- inst/doc/TestEquations.html | 4 +- 6 files changed, 63 insertions(+), 56 deletions(-)
Title: Use Open Data from the Czech Statistical Office in R
Description: Get programmatic access to the open data provided by the
Czech Statistical Office (CZSO, <https://czso.cz>).
Author: Petr Bouchal [aut, cre] (<https://orcid.org/0000-0002-0471-716X>),
Jindra Lacko [ctb]
Maintainer: Petr Bouchal <pbouchal@gmail.com>
Diff between czso versions 0.3.4 dated 2021-03-01 and 0.3.5 dated 2021-09-22
DESCRIPTION | 9 +-- MD5 | 12 ++--- NEWS.md | 13 +++++ R/core.R | 105 ++++++++-------------------------------------- build/czso.pdf |binary man/czso-package.Rd | 4 - man/czso_get_catalogue.Rd | 4 + 7 files changed, 47 insertions(+), 100 deletions(-)
Title: Data & Functions for Working with US ZIP Codes
Description: Make working with ZIP codes in R painless with an integrated dataset of U.S. ZIP codes and functions for working with them.
Search ZIP codes by multiple geographies, including state, county, city & across time zones. Also included are functions for relating
ZIP codes to Census data, geocoding & distance calculations.
Author: Gavin Rozzi [aut, cre] (<https://orcid.org/0000-0002-9969-8175>)
Maintainer: Gavin Rozzi <gr@gavinrozzi.com>
Diff between zipcodeR versions 0.3.2 dated 2021-09-02 and 0.3.3 dated 2021-09-22
DESCRIPTION | 8 - MD5 | 18 ++-- NEWS.md | 4 R/download_data.r | 4 R/zip_helper_functions.R | 51 +++++++++-- README.md | 150 +++++++++++++++++++---------------- inst/doc/geographic.html | 3 inst/doc/zipcodeR.html | 55 ++++++------ man/zip_distance.Rd | 11 +- tests/testthat/test-01-zip-lookups.R | 7 - 10 files changed, 179 insertions(+), 132 deletions(-)
Title: The Self-Updating Process Clustering Algorithms
Description: Implements the self-updating process clustering algorithms proposed
in Shiu and Chen (2016) <doi:10.1080/00949655.2015.1049605>.
Author: Wush Wu [aut, cre],
Shang-Ying Shiu [aut, ctb]
Maintainer: Wush Wu <wush978@gmail.com>
Diff between supc versions 0.2.2 dated 2019-11-27 and 0.2.3 dated 2021-09-22
DESCRIPTION | 6 MD5 | 23 + R/supc1.R | 4 build/partial.rdb |only build/vignette.rds |binary inst/doc/supc.html | 553 +++++++++++++++++++++++++++++++++++------------- inst/doc/supc_demo.html | 465 +++++++++++++++++++++++++++++++--------- man/supc.random.Rd | 21 + man/supc1.Rd | 18 + src/Makevars.in | 2 src/Makevars.win | 2 src/clusterize.cpp | 3 src/supc1.cpp | 1 13 files changed, 814 insertions(+), 284 deletions(-)
Title: Multiple Sequence Alignment for R Shiny
Description: Visualizes multiple sequence alignments dynamically within the
Shiny web application framework.
Author: Benedikt Rauscher [aut, cph],
Zachary Charlop-Powers [cre, aut]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>
Diff between msaR versions 0.5.0 dated 2021-01-05 and 0.6.0 dated 2021-09-22
DESCRIPTION | 11 +++++------ MD5 | 10 +++++----- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/msaR.html | 29 ++++++++++++++++++----------- inst/htmlwidgets/lib/msa.js | 2 +- 6 files changed, 33 insertions(+), 23 deletions(-)
Title: Lioness Algorithm (LA)
Description: Contains Lioness Algorithm (LA) for finding optimal designs over continuous design space, optimal Latin hypercube designs, and optimal order-of-addition designs. LA is a brand new nature-inspired meta-heuristic optimization algorithm. Detailed methodologies of LA and its implementation on numerical simulations can be found at Hongzhi Wang, Qian Xiao and Abhyuday Mandal (2021) <arXiv:2010.09154>.
Author: Hongzhi Wang [aut, cre],
Qian Xiao [aut],
Abhyuday Mandal [aut]
Maintainer: Hongzhi Wang <hw34508@uga.edu>
Diff between LA versions 0.1.1 dated 2021-04-20 and 0.1.2 dated 2021-09-22
DESCRIPTION | 10 - MD5 | 14 - NEWS.md | 8 R/LA_opt.R | 341 +++++++++++++++++++++--------------------- R/rOofA.R | 44 +++++ build/vignette.rds |binary inst/doc/Vignette_for_LA.html | 154 +++++++++--------- man/LA_opt.Rd | 9 - 8 files changed, 322 insertions(+), 258 deletions(-)
Title: Bayesian Screening and Variable Selection
Description: Performs Bayesian variable screening and selection for ultra-high dimensional linear regression models.
Author: Dongjin Li [aut, cre], Somak Dutta [aut], Vivekananda Roy [ctb]
Maintainer: Dongjin Li <dongjl@iastate.edu>
Diff between bravo versions 2.0.0 dated 2021-07-20 and 2.0.1 dated 2021-09-22
DESCRIPTION | 8 +-- MD5 | 6 +- R/bits.r | 125 +++++++++++++++++++++++++++++------------------------------- man/bits.Rd | 3 + 4 files changed, 71 insertions(+), 71 deletions(-)
Title: Decorate a 'ggplot' with Associated Information
Description: For many times, we are not just aligning plots as what 'cowplot' and 'patchwork' did. Users would like to align associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. This package provides utilities to aligns associated subplots to a main plot at different sides (left, right, top and bottom) with axes exactly matched.
Author: Guangchuang Yu [aut, cre, cph]
(<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between aplot versions 0.1.0 dated 2021-09-03 and 0.1.1 dated 2021-09-22
aplot-0.1.0/aplot/man/is.ggtree.Rd |only aplot-0.1.1/aplot/DESCRIPTION | 11 - aplot-0.1.1/aplot/MD5 | 25 +- aplot-0.1.1/aplot/NAMESPACE | 91 ++++----- aplot-0.1.1/aplot/NEWS.md | 112 ++++++------ aplot-0.1.1/aplot/R/aplot.R | 158 +++++++++-------- aplot-0.1.1/aplot/R/axis.R | 270 ++++++++++++++--------------- aplot-0.1.1/aplot/R/insertion.R | 337 ++++++++++++++++++------------------- aplot-0.1.1/aplot/R/plot-list.R | 202 ++++++++++++---------- aplot-0.1.1/aplot/R/re-export.R | 14 - aplot-0.1.1/aplot/R/utilities.R | 73 ++------ aplot-0.1.1/aplot/man/ggrange.Rd | 46 ++--- aplot-0.1.1/aplot/man/plot_list.Rd | 107 ++++++----- aplot-0.1.1/aplot/man/reexports.Rd | 38 ++-- 14 files changed, 750 insertions(+), 734 deletions(-)