Title: Disciplined Convex Optimization
Description: An object-oriented modeling language for disciplined convex
programming (DCP). It allows the user to formulate convex optimization problems
in a natural way following mathematical convention and DCP rules. The system
analyzes the problem, verifies its convexity, converts it into a canonical form,
and hands it off to an appropriate solver to obtain the solution.
Author: Anqi Fu [aut, cre],
Balasubramanian Narasimhan [aut],
Steven Diamond [aut],
John Miller [aut],
Stephen Boyd [ctb],
Paul Kunsberg Rosenfield [ctb]
Maintainer: Anqi Fu <anqif@stanford.edu>
Diff between CVXR versions 0.99-5 dated 2019-05-13 and 0.99-6 dated 2019-06-01
DESCRIPTION | 6 - MD5 | 18 +-- NEWS.md | 7 + R/constraints.R | 24 +++- inst/doc/cvxr_intro.html | 209 ++++++++++++++++++++++++++++++++++--- inst/python/mosekglue.py | 19 ++- src/RcppExports.cpp | 1 tests/testthat/test-g02-examples.R | 10 - tests/testthat/test-g03-test_ls.R | 8 - tests/testthat/test-g04-scs.R | 8 - 10 files changed, 260 insertions(+), 50 deletions(-)
Title: Univariate Feature Selection and Compound Covariate for
Predicting Survival
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (e.g., gene expressions).
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>,
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al. (2019)<DOI:10.1016/j.cmpb.2018.10.020>.
Algorithms for generating correlated gene expressions are also available.
Author: Takeshi Emura, Hsuan-Yu Chen, Shigeyuki Matsui, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.16 dated 2019-05-31 and 3.17 dated 2019-06-01
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/compound.Cox-package.Rd | 4 ++-- man/dependCox.reg.Rd | 35 +++++++++++++++-------------------- 4 files changed, 24 insertions(+), 29 deletions(-)
Title: Call 'BEAST2'
Description: 'BEAST2' (<http://www.beast2.org>) is a widely used
Bayesian phylogenetic tool, that uses DNA/RNA/protein data
and many model priors to create a posterior of jointly estimated
phylogenies and parameters.
'BEAST2' is a command-line tool.
This package provides a way to call 'BEAST2'
from an 'R' function call.
Author: Richèl J.C. Bilderbeek [aut, cre]
(<https://orcid.org/0000-0003-1107-7049>),
Joëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci,
see https://github.com/ropensci/onboarding/issues/209),
David Winter [rev] (David reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/209)
Maintainer: Richèl J.C. Bilderbeek <richel@richelbilderbeek.nl>
Diff between beastier versions 2.0.14 dated 2019-05-31 and 2.0.15 dated 2019-06-01
DESCRIPTION | 6 MD5 | 18 +- R/get_default_beast2_bin_path.R | 2 R/get_default_beast2_folder.R | 11 - R/get_default_beast2_jar_path.R | 2 R/run_beast2.R | 262 ++++++++++++++++++++++--------------- man/get_default_beast2_bin_path.Rd | 2 man/get_default_beast2_folder.Rd | 11 - man/get_default_beast2_jar_path.Rd | 2 man/run_beast2.Rd | 38 ++--- 10 files changed, 193 insertions(+), 161 deletions(-)
Title: 'rquery' for 'data.table'
Description: Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows
for a high-speed in memory implementation of Codd-style data manipulation tools.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rqdatatable versions 1.1.6 dated 2019-05-14 and 1.1.8 dated 2019-06-01
DESCRIPTION | 10 +++++----- MD5 | 29 +++++++++++++++++------------ NEWS.md | 8 ++++++++ R/patch_env.R |only R/relop_extend.R | 2 +- R/relop_natural_join.R | 26 +++++++------------------- R/relop_null_replace.R | 23 ++++++----------------- R/relop_order_expr.R | 2 +- R/relop_project.R | 2 +- R/relop_select_rows.R | 2 +- R/relop_set_indicator.R | 13 ++----------- R/relop_theta_join.R | 2 +- inst/doc/GroupedSampling.html | 4 ++-- inst/doc/logisticexample.html | 4 ++-- inst/unit_tests/test_cross_join.R |only inst/unit_tests/test_null_replace_op.R |only inst/unit_tests/test_set_ind_op.R |only inst/unit_tests/test_space_merge.R |only 18 files changed, 54 insertions(+), 73 deletions(-)
Title: Tutorial Analysis of Some Agricultural Experiments
Description: Example software for the analysis of data from designed
experiments, especially agricultural crop experiments. The basics
of the analysis of designed experiments are discussed
using real examples from agricultural field trials.
A range of statistical methods using a range
of R statistical packages are exemplified . The experimental
data is made available as separate data sets for each example
and the R analysis code is made available as example code.
The example code can be readily extended, as required.
Author: Rodney Edmondson [aut, cre],
Hans-Peter Piepho [aut, ctb],
Muhammad Yaseen [aut, ctb]
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between agriTutorial versions 0.1.4 dated 2018-08-20 and 0.1.5 dated 2019-06-01
DESCRIPTION | 10 ++++----- MD5 | 34 ++++++++++++++++---------------- R/agriTutorial-package.R | 4 +-- R/example1.R | 2 - R/example2.R | 2 - R/example3.R | 2 - R/example4.R | 2 - R/example5.R | 2 - build/vignette.rds |binary inst/doc/agriTutorialVignette.pdf |binary inst/doc/agriTutorialVignette.pdf.asis | 2 - man/agriTutorial.Rd | 4 +-- man/example1.Rd | 2 - man/example2.Rd | 2 - man/example3.Rd | 2 - man/example4.Rd | 2 - man/example5.Rd | 2 - vignettes/agriTutorialVignette.pdf.asis | 2 - 18 files changed, 38 insertions(+), 38 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-16 0.0-4
2012-04-20 0.0-3
Title: Power Analysis Tools for Multilevel Randomized Experiments
Description: Includes tools to calculate statistical power, minimum detectable effect size (MDES), MDES difference (MDESD), and minimum required sample size for various multilevel randomized experiments with continuous outcomes. Some of the functions can assist with planning two- and three-level cluster-randomized trials (CRTs) sensitive to multilevel moderation and mediation (2-1-1, 2-2-1, and 3-2-1). See 'PowerUp!' Excel series at <https://www.causalevaluation.org/>.
Author: Metin Bulus [aut, cre],
Nianbo Dong [aut],
Benjamin Kelcey [aut],
Jessaca Spybrook [aut]
Maintainer: Metin Bulus <bulusmetin@gmail.com>
Diff between PowerUpR versions 1.0.3 dated 2019-03-08 and 1.0.4 dated 2019-06-01
DESCRIPTION | 10 - MD5 | 36 ++-- NAMESPACE | 1 NEWS.md | 4 R/cra2r2.R | 72 ++++---- R/cra3r3.R | 174 ++++++++++++++------- R/error.R | 16 - R/plot.R | 41 +++- R/t1t2.R | 15 + R/utils.R | 50 ++++-- README.md | 11 - inst/CITATION | 4 inst/doc/three_level_cluster_randomized_trial.Rmd | 2 inst/doc/three_level_cluster_randomized_trial.html | 10 - man/PowerUpR-package.Rd | 2 man/cra2r2.Rd | 5 man/cra3r3.Rd | 28 ++- man/plot.Rd | 4 vignettes/three_level_cluster_randomized_trial.Rmd | 2 19 files changed, 315 insertions(+), 172 deletions(-)
Title: Genome and Transcriptome Wide Association Study
Description: Quantitative trait loci mapping and genome wide association analysis are used to find candidate molecular marker or region associated with phenotype based on linkage analysis and linkage disequilibrium. Gene expression quantitative trait loci mapping is used to find candidate molecular marker or region associated with gene expression. In this package, we applied the method in Liu W. (2011) <doi:10.1007/s00122-011-1631-7> and Gusev A. (2016) <doi:10.1038/ng.3506> to genome and transcriptome wide association study, which is aimed at revealing the association relationship between phenotype and molecular markers, expression levels, molecular markers nested within different related expression effect and expression effect nested within different related molecular marker effect. F test based on full and reduced model are performed to obtain p value or likelihood ratio statistic. The best linear model can be obtained by stepwise regression analysis.
Author: JunhuiLi WenxinLiu
Maintainer: JunhuiLi<junhuili@cau.edu.cn>
Diff between gtWAS versions 1.0.0 dated 2018-01-08 and 1.1.0 dated 2019-06-01
gtWAS-1.0.0/gtWAS/R/InfoCriteria.R |only gtWAS-1.0.0/gtWAS/R/gtWAS.R |only gtWAS-1.0.0/gtWAS/R/stepwise.R |only gtWAS-1.0.0/gtWAS/man/InfoCriteria.Rd |only gtWAS-1.0.0/gtWAS/man/gtWAS.Rd |only gtWAS-1.0.0/gtWAS/man/stepwise.Rd |only gtWAS-1.1.0/gtWAS/DESCRIPTION | 8 - gtWAS-1.1.0/gtWAS/MD5 | 26 +-- gtWAS-1.1.0/gtWAS/NAMESPACE | 4 gtWAS-1.1.0/gtWAS/R/Association.R |only gtWAS-1.1.0/gtWAS/R/ModelFit.R |only gtWAS-1.1.0/gtWAS/R/StepOne.R | 243 ++++++++++++++++----------------- gtWAS-1.1.0/gtWAS/R/stp.R |only gtWAS-1.1.0/gtWAS/data/Tdata.rda |binary gtWAS-1.1.0/gtWAS/data/alldata.rda |binary gtWAS-1.1.0/gtWAS/man/Association.Rd |only gtWAS-1.1.0/gtWAS/man/ModelFit.Rd |only gtWAS-1.1.0/gtWAS/man/StepOne.Rd | 2 gtWAS-1.1.0/gtWAS/man/gtWAS-package.Rd | 4 gtWAS-1.1.0/gtWAS/man/stp.Rd |only 20 files changed, 142 insertions(+), 145 deletions(-)
Title: Display and Analyze ROC Curves
Description: Tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). (Partial) area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.
Author: Xavier Robin [cre, aut] (<https://orcid.org/0000-0002-6813-3200>),
Natacha Turck [aut],
Alexandre Hainard [aut],
Natalia Tiberti [aut],
Frédérique Lisacek [aut],
Jean-Charles Sanchez [aut],
Markus Müller [aut],
Stefan Siegert [ctb] (Fast DeLong code),
Matthias Doering [ctb] (Hand & Till Multiclass)
Maintainer: Xavier Robin <pROC-cran@xavier.robin.name>
Diff between pROC versions 1.14.0 dated 2019-03-12 and 1.15.0 dated 2019-06-01
DESCRIPTION | 8 MD5 | 57 NAMESPACE | 10 NEWS | 16 R/are.paired.R | 2 R/bootstrap.R | 48 R/coords.R | 416 +-- R/ggroc.R | 2 R/null.roc.R | 2 R/onLoad.R | 9 R/plot.roc.R | 25 R/roc.R | 129 - R/roc.utils.R | 137 + R/smooth.R | 10 inst/extra/algorithms.speed.test.R | 27 inst/extra/bench |only inst/extra/benchmark.Rmd |only inst/extra/benchmark.md |only man/coords.Rd | 192 + man/coords_transpose.Rd |only man/pROC-package.Rd | 62 man/roc.Rd | 115 - tests/testthat/helper-coords-expected.R | 422 ++- tests/testthat/helper-expect_equal_roc.R |only tests/testthat/helper-roc-expected.R | 3556 ++++++++++++++++++++++++++----- tests/testthat/test-are-paired.R | 60 tests/testthat/test-coords.R | 528 ++++ tests/testthat/test-onload.R |only tests/testthat/test-power.roc.test.R | 40 tests/testthat/test-roc.R | 230 +- tests/testthat/test-roc.utils.R |only tests/testthat/test-roc.utils.percent.R | 19 32 files changed, 5032 insertions(+), 1090 deletions(-)
Title: Advanced Forest Plot Using 'grid' Graphics
Description: A forest plot that allows for
multiple confidence intervals per row,
custom fonts for each text element,
custom confidence intervals,
text mixed with expressions, and more.
The aim is to extend the use of forest plots beyond meta-analyses.
This is a more general version of the original 'rmeta' package's forestplot()
function and relies heavily on the 'grid' package.
Author: Max Gordon [aut, cre],
Thomas Lumley [aut, ctb]
Maintainer: Max Gordon <max@gforge.se>
Diff between forestplot versions 1.7.2 dated 2017-09-16 and 1.8 dated 2019-06-01
forestplot-1.7.2/forestplot/tests/testthat/Rplots.pdf |only forestplot-1.8/forestplot/DESCRIPTION | 10 forestplot-1.8/forestplot/MD5 | 37 forestplot-1.8/forestplot/NEWS | 7 forestplot-1.8/forestplot/R/forestplot.R | 4 forestplot-1.8/forestplot/R/private.R | 38 forestplot-1.8/forestplot/README.md | 2 forestplot-1.8/forestplot/build/vignette.rds |binary forestplot-1.8/forestplot/inst/doc/forestplot.html | 765 ++++++++----- forestplot-1.8/forestplot/man/forestplot.Rd | 21 forestplot-1.8/forestplot/man/fpColors.Rd | 7 forestplot-1.8/forestplot/man/fpDrawCI.Rd | 18 forestplot-1.8/forestplot/man/fpLegend.Rd | 1 forestplot-1.8/forestplot/man/fpTxtGp.Rd | 3 forestplot-1.8/forestplot/man/getTicks.Rd | 3 forestplot-1.8/forestplot/man/prFpDrawLine.Rd | 4 forestplot-1.8/forestplot/man/prFpGetConfintFnList.Rd | 3 forestplot-1.8/forestplot/man/prFpGetGraphTicksAndClips.Rd | 6 forestplot-1.8/forestplot/man/prFpGetLabels.Rd | 3 forestplot-1.8/forestplot/man/prFpXrange.Rd | 2 20 files changed, 592 insertions(+), 342 deletions(-)
Title: Design of Risk Parity Portfolios
Description: Fast design of risk parity portfolios for financial investment.
The goal of the risk parity portfolio formulation is to equalize or distribute
the risk contributions of the different assets, which is missing if we simply
consider the overall volatility of the portfolio as in the mean-variance
Markowitz portfolio. In addition to the vanilla formulation, where the risk
contributions are perfectly equalized subject to no shortselling and budget
constraints, many other formulations are considered that allow for box
constraints and shortselling, as well as the inclusion of additional
objectives like the expected return and overall variance. See vignette for
a detailed documentation and comparison, with several illustrative examples.
The package is based on the papers:
Y. Feng, and D. P. Palomar (2015). SCRIP: Successive Convex Optimization Methods
for Risk Parity Portfolio Design. IEEE Trans. on Signal Processing, vol. 63,
no. 19, pp. 5285-5300. <doi:10.1109/TSP.2015.2452219>.
F. Spinu (2013), An Algorithm for Computing Risk Parity Weights.
<doi:10.2139/ssrn.2297383>.
T. Griveau-Billion, J. Richard, and T. Roncalli (2013). A fast algorithm for computing
High-dimensional risk parity portfolios. <arXiv:1311.4057>.
Author: Ze Vinicius [aut],
Daniel P. Palomar [cre, aut]
Maintainer: Daniel P. Palomar <daniel.p.palomar@gmail.com>
Diff between riskParityPortfolio versions 0.1.1 dated 2019-01-08 and 0.1.2 dated 2019-06-01
DESCRIPTION | 9 +-- MD5 | 22 +++---- NEWS.md | 6 ++ R/riskParityPortfolio-package.R | 8 +- R/riskParityPortfolio.R | 14 +++- README.md | 104 +++++++++++++++++++++++++++---------- build/vignette.rds |binary inst/CITATION | 8 +- man/riskParityPortfolio-package.Rd | 8 +- man/riskParityPortfolio.Rd | 4 - src/cyclical_coordinate_descent.h | 3 - tests/testthat/test-checks.R | 12 ++++ 12 files changed, 137 insertions(+), 61 deletions(-)
More information about riskParityPortfolio at CRAN
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