Title: A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets
Description: Creates visualizations of intersecting sets using a novel matrix
design, along with visualizations of several common set, element and attribute
related tasks (Conway 2017) <doi:10.1093/bioinformatics/btx364>.
Author: Jake Conway [cre],
Nils Gehlenborg [aut]
Maintainer: Jake Conway <jake_conway@hms.harvard.edu>
Diff between UpSetR versions 1.3.3 dated 2017-03-21 and 1.4.0 dated 2019-05-22
DESCRIPTION | 12 ++-- MD5 | 52 ++++++++--------- NAMESPACE | 2 NEWS | 16 ++++- R/Helper.funcs.R | 5 + R/MainBar.R | 21 +++---- R/Matrix.R | 22 +++---- R/SizeBar.R | 40 +++++++++++-- R/UpSet.plot.R | 93 ++++++++++++++++--------------- R/elements.R | 2 R/histogram.R | 2 R/intersects.R | 4 - R/scatter_plot.R | 10 +-- R/upset.R | 116 +++++++++++++++++++++++++++++---------- README.md | 29 ++++++--- build/vignette.rds |binary inst/doc/attribute.plots.html | 45 +++++++++------ inst/doc/basic.usage.html | 48 +++++++++------- inst/doc/queries.html | 42 ++++++++------ inst/doc/set.metadata.plots.html | 68 ++++++++++++---------- man/elements.Rd | 3 - man/fromExpression.Rd | 1 man/fromList.Rd | 1 man/histogram.Rd | 3 - man/intersects.Rd | 5 - man/scatter_plot.Rd | 3 - man/upset.Rd | 55 ++++++++++-------- 27 files changed, 425 insertions(+), 275 deletions(-)
Title: Traveling Salesperson Problem (TSP)
Description: Basic infrastructure and some algorithms for the traveling
salesperson problem (also traveling salesman problem; TSP).
The package provides some simple algorithms and
an interface to the Concorde TSP solver and its implementation of the
Chained-Lin-Kernighan heuristic. The code for Concorde
itself is not included in the package and has to be obtained separately.
Author: Michael Hahsler [aut, cre, cph],
Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between TSP versions 1.1-6 dated 2018-04-30 and 1.1-7 dated 2019-05-22
DESCRIPTION | 12 ++-- MD5 | 26 +++++----- NEWS.md | 9 +++ R/ATSP.R | 24 +++++---- R/TSP.R | 5 + R/cut_tour.R | 10 +-- R/read_TSPLIB.R | 114 ++++++++++++++++++++------------------------ R/reformulare_ATSP_as_TSP.R | 11 ++-- R/tsp_concorde.R | 1 build/vignette.rds |binary inst/CITATION | 14 +---- inst/doc/TSP.pdf |binary man/ATSP.Rd | 17 +++--- man/TSP.Rd | 9 +-- 14 files changed, 128 insertions(+), 124 deletions(-)
Title: Simulation and Group Sequential Monitoring of Randomized
Two-Stage Treatment Efficacy Trials with Time-to-Event
Endpoints
Description: A modification of the preventive vaccine efficacy trial design of Gilbert, Grove et al. (2011, Statistical Communications in Infectious Diseases) is implemented, with application generally to individual-randomized clinical trials with multiple active treatment groups and a shared control group, and a study endpoint that is a time-to-event endpoint subject to right-censoring. The design accounts for the issues that the efficacy of the treatment/vaccine groups may take time to accrue while the multiple treatment administrations/vaccinations are given; there is interest in assessing the durability of treatment efficacy over time; and group sequential monitoring of each treatment group for potential harm, non-efficacy/efficacy futility, and high efficacy is warranted. The design divides the trial into two stages of time periods, where each treatment is first evaluated for efficacy in the first stage of follow-up, and, if and only if it shows significant treatment efficacy in stage one, it is evaluated for longer-term durability of efficacy in stage two. The package produces plots and tables describing operating characteristics of a specified design including an unconditional power for intention-to-treat and per-protocol/as-treated analyses; trial duration; probabilities of the different possible trial monitoring outcomes (e.g., stopping early for non-efficacy); unconditional power for comparing treatment efficacies; and distributions of numbers of endpoint events occurring after the treatments/vaccinations are given, useful as input parameters for the design of studies of the association of biomarkers with a clinical outcome (surrogate endpoint problem). The code can be used for a single active treatment versus control design and for a single-stage design.
Author: Michal Juraska [aut, cre],
Doug Grove [aut],
Xuesong Yu [ctb],
Peter Gilbert [ctb],
Stephanie Wu [ctb]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between seqDesign versions 1.1 dated 2015-04-27 and 1.2 dated 2019-05-22
seqDesign-1.1/seqDesign/inst/extdata |only seqDesign-1.2/seqDesign/DESCRIPTION | 25 seqDesign-1.2/seqDesign/MD5 | 34 seqDesign-1.2/seqDesign/NAMESPACE | 16 seqDesign-1.2/seqDesign/R/seqDesign.R | 8470 ++++++---- seqDesign-1.2/seqDesign/README.md |only seqDesign-1.2/seqDesign/build/vignette.rds |binary seqDesign-1.2/seqDesign/inst/doc/seqDesignInstructions.R | 131 seqDesign-1.2/seqDesign/inst/doc/seqDesignInstructions.Rnw | 194 seqDesign-1.2/seqDesign/inst/doc/seqDesignInstructions.pdf |binary seqDesign-1.2/seqDesign/inst/doc/seqDesignReportTemplate.pdf |only seqDesign-1.2/seqDesign/inst/doc/seqDesignReportTemplate.pdf.asis |only seqDesign-1.2/seqDesign/man/VEpowerPP.Rd | 183 seqDesign-1.2/seqDesign/man/censTrial.Rd | 168 seqDesign-1.2/seqDesign/man/getBlockSize.Rd | 29 seqDesign-1.2/seqDesign/man/monitorTrial.Rd | 277 seqDesign-1.2/seqDesign/man/rankTrial.Rd | 203 seqDesign-1.2/seqDesign/man/simTrial.Rd | 208 seqDesign-1.2/seqDesign/vignettes/seqDesignInstructions.Rnw | 194 seqDesign-1.2/seqDesign/vignettes/seqDesignReportTemplate.pdf.asis |only 20 files changed, 5971 insertions(+), 4161 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>),
Jeff Allen [ctb],
Barret Schloerke [ctb],
Roy Storey [ctb],
Rob Hyndman [ctb],
Ruben Arslan [ctb],
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Christophe Dervieux [ctb],
Malcolm Barrett [ctb],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/rmd/h/jqueryui-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Greg Franko [ctb, cph] (tocify library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library),
Dave Gandy [ctb, cph] (Font-Awesome),
Ben Sperry [ctb] (Ionicons),
Drifty [cph] (Ionicons),
Aidan Lister [ctb, cph] (jQuery StickyTabs)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 1.12 dated 2019-03-14 and 1.13 dated 2019-05-22
DESCRIPTION | 8 MD5 | 85 +++--- NEWS.md | 20 + R/html_document.R | 36 +- R/html_resources.R | 14 - R/ioslides_presentation.R | 225 +++++++++++++++++- R/jupyter.R |only R/output_format.R | 12 R/params.R | 2 R/pdf_document.R | 10 R/render.R | 128 ++++++++-- R/render_site.R | 16 - R/rmarkdown.R |only R/shiny.R | 2 R/shiny_prerendered.R | 15 - inst/rmd/h/default.html | 2 inst/rmd/h/tocify/jquery.tocify.css | 10 inst/rmd/h/tocify/jquery.tocify.js | 4 man/all_output_formats.Rd | 2 man/beamer_presentation.Rd | 2 man/compile_notebook.Rd | 66 ++--- man/convert_ipynb.Rd |only man/default_output_format.Rd | 2 man/find_external_resources.Rd | 6 man/github_document.Rd | 2 man/html_document.Rd | 38 +-- man/html_document_base.Rd | 4 man/html_fragment.Rd | 6 man/html_notebook.Rd | 4 man/html_vignette.Rd | 2 man/ioslides_presentation.Rd | 447 +++++++++++++++--------------------- man/knit_params_ask.Rd | 3 man/md_document.Rd | 2 man/output_format.Rd | 2 man/pdf_document.Rd | 9 man/powerpoint_presentation.Rd | 6 man/render.Rd | 8 man/render_site.Rd | 12 man/resolve_output_format.Rd | 2 man/rmarkdown-package.Rd | 45 +-- man/rmd_metadata.Rd | 38 +-- man/slidy_presentation.Rd | 6 man/word_document.Rd | 6 man/yaml_front_matter.Rd | 2 tests/testthat/test-formats.R | 2 45 files changed, 804 insertions(+), 509 deletions(-)
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'.
For example, the 'parallelFor()' function can be used to convert the work of
a standard serial "for" loop into a parallel one and the 'parallelReduce()'
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut],
Romain Francois [aut, cph],
Kevin Ushey [aut, cre],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/),
RStudio [cph],
Intel [aut, cph] (Intel TBB library,
https://www.threadingbuildingblocks.org/),
Microsoft [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between RcppParallel versions 4.4.2 dated 2018-12-11 and 4.4.3 dated 2019-05-22
DESCRIPTION | 6 ++-- MD5 | 14 ++++++---- inst/NEWS | 8 ++++++ inst/include/RcppParallel/RMatrix.h | 2 - inst/include/serial |only inst/include/tbb/concurrent_hash_map.h | 2 - src/tbb/include/tbb/concurrent_hash_map.h | 2 - tools/config.R | 39 +++--------------------------- 8 files changed, 26 insertions(+), 47 deletions(-)
Title: Creates and Plots P-Value Functions, S-Value Functions,
Confidence Distributions and Confidence Densities
Description: Contains functions to compute and plot confidence distributions, confidence densities, p-value functions and s-value (surprisal) functions for several commonly used estimates. Instead of just calculating one p-value and one confidence interval, p-value functions display p-values and confidence intervals for many levels thereby allowing to gauge the compatibility of several parameter values with the data. These methods are discussed by Poole C. (1987) <doi:10.2105/AJPH.77.2.195>; Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>; Bender R, Berg G, Zeeb H. (2005) <doi:10.1002/bimj.200410104> ; Singh K, Xie M, Strawderman WE. (2007) <doi:10.1214/074921707000000102>; Rothman KJ, Greenland S, Lash TL. (2008, ISBN:9781451190052); Amrhein V, Trafimow D, Greenland S. (2019) <doi:10.1080/00031305.2018.1543137>; and Greenland S. (2019) <doi:10.1080/00031305.2018.1529625>.
Author: Denis Infanger [aut, cre] (<https://orcid.org/0000-0001-9028-7110>)
Maintainer: Denis Infanger <denis.infanger@unibas.ch>
Diff between pvaluefunctions versions 1.0.0 dated 2019-05-08 and 1.1.0 dated 2019-05-22
pvaluefunctions-1.0.0/pvaluefunctions/vignettes/pvaluefun_files |only pvaluefunctions-1.1.0/pvaluefunctions/DESCRIPTION | 6 pvaluefunctions-1.1.0/pvaluefunctions/MD5 | 28 pvaluefunctions-1.1.0/pvaluefunctions/NEWS | 6 pvaluefunctions-1.1.0/pvaluefunctions/R/confidence_distributions.R | 349 ++++++++-- pvaluefunctions-1.1.0/pvaluefunctions/README.md | 172 ++-- pvaluefunctions-1.1.0/pvaluefunctions/build/vignette.rds |binary pvaluefunctions-1.1.0/pvaluefunctions/inst/doc/pvaluefun.R | 58 + pvaluefunctions-1.1.0/pvaluefunctions/inst/doc/pvaluefun.Rmd | 135 ++- pvaluefunctions-1.1.0/pvaluefunctions/inst/doc/pvaluefun.html | 163 ++-- pvaluefunctions-1.1.0/pvaluefunctions/man/conf_dist.Rd | 36 - pvaluefunctions-1.1.0/pvaluefunctions/vignettes/pvaluefun.Rmd | 135 ++- 12 files changed, 711 insertions(+), 377 deletions(-)
More information about pvaluefunctions at CRAN
Permanent link
Title: Tidy RSS for R
Description: With the objective of including data from RSS feeds into your analysis, 'tidyRSS' parses RSS, Atom XML, JSON and geoRSS feeds and returns a tidy data frame.
Author: Robert Myles McDonnell
Maintainer: Robert Myles McDonnell <robertmylesmcdonnell@gmail.com>
Diff between tidyRSS versions 1.2.10 dated 2019-05-14 and 1.2.11 dated 2019-05-22
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 7 +++++++ R/geo_parse.R | 32 ++++++++++++++++++++------------ R/rss_parse.R | 8 +++----- R/tidyfeed.R | 2 +- README.md | 47 +++++++++++++++++++++++++++++++---------------- data/feeds.rda |binary inst/doc/tidyrss.html | 4 ++-- 9 files changed, 75 insertions(+), 47 deletions(-)
Title: Clean and Analyze Continuous Glucose Monitor Data
Description: This code provides several different functions for cleaning and analyzing continuous glucose monitor data. Currently it works with 'Dexcom' (<https://www.dexcom.com>), 'iPro 2' (<http://professional.medtronicdiabetes.com/ipro2-professional-cgm>), Diasend (<https://diasend.com//us>), Libre (<https://www.freestylelibre.us/>) or Carelink (<https://www.medtronicdiabetes.com/products/carelink-personal-diabetes-software>) data. The cleandata() function takes a directory of CGM data files and prepares them for analysis. cgmvariables() iterates through a directory of cleaned CGM data files and produces a single spreadsheet with data for each file in either rows or columns. The column format of this spreadsheet is compatible with REDCap data upload ("--1" is added to each subject ID automatically for double data entry). cgmreport() also iterates through a directory of cleaned data, and produces PDFs of individual and aggregate AGP plots. Please visit <https://github.com/childhealthbiostatscore/R-Packages/> to download the new-user guide.
Author: Tim Vigers [aut, cre]
Maintainer: Tim Vigers <tim.b.vigers@gmail.com>
Diff between cgmanalysis versions 2.3 dated 2019-03-26 and 2.4 dated 2019-05-22
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/cgmvariables.R | 6 ++++-- 3 files changed, 9 insertions(+), 7 deletions(-)
Title: Regularized Structural Equation Modeling
Description: Uses both ridge and lasso penalties (and extensions) to penalize
specific parameters in structural equation models. The package offers additional
cost functions, cross validation, and other extensions beyond traditional structural
equation models. Also contains a function to perform exploratory mediation (XMed).
Author: Ross Jacobucci[aut,cre],
Kevin J. Grimm [ctb],
Andreas M. Brandmaier [ctb],
Sarfaraz Serang [ctb],
Rogier A. Kievit [ctb],
Florian Scharf [ctb]
Maintainer: Ross Jacobucci <rcjacobuc@gmail.com>
Diff between regsem versions 1.3.8 dated 2019-05-07 and 1.3.9 dated 2019-05-22
DESCRIPTION | 6 MD5 | 100 - NAMESPACE | 68 - R/RAMmult.R | 56 - R/RcppExports.R | 130 +- R/coord_desc.R | 1252 +++++++++++----------- R/cv_regsem.R | 2140 +++++++++++++++++++------------------- R/efaModel.R | 130 +- R/extractMatrices.R | 906 ++++++++-------- R/fiml_calc.R | 182 +-- R/fiml_calc2.R | 204 +-- R/fit_fun.R | 140 +- R/fit_indices.R | 522 ++++----- R/grad_fun.R | 192 +-- R/grad_ram.R | 226 ++-- R/grad_ram_wMean.R | 194 +-- R/hess_ram.R | 112 +- R/hess_ramParallel.R | 138 +- R/hessian.R | 60 - R/hessian_parallel.R | 80 - R/multi_optim.R | 806 +++++++------- R/parse_parameters.R | 48 R/plot.R | 244 ++-- R/ram_calc.R | 154 +- R/regsem.R | 2528 +++++++++++++++++++++++----------------------- R/ret_hess.R | 16 R/soft.R | 132 +- R/summary.cvregsem.R | 104 - R/summary.regsem.R | 78 - R/trace.R | 8 R/xmed.R | 320 ++--- build/vignette.rds |binary inst/doc/short_intro.R | 96 - inst/doc/short_intro.Rmd | 204 +-- inst/doc/short_intro.html | 658 +++++------ man/cv_regsem.Rd | 442 ++++---- man/efaModel.Rd | 88 - man/extractMatrices.Rd | 56 - man/fit_indices.Rd | 74 - man/multi_optim.Rd | 312 ++--- man/parse_parameters.Rd | 42 man/plot.cvregsem.Rd | 94 - man/rcpp_RAMmult.Rd | 60 - man/rcpp_fit_fun.Rd | 62 - man/rcpp_grad_ram.Rd | 74 - man/rcpp_quasi_calc.Rd | 40 man/regsem.Rd | 416 +++---- man/summary.cvregsem.Rd | 32 man/summary.regsem.Rd | 32 man/xmed.Rd | 142 +- vignettes/short_intro.Rmd | 204 +-- 51 files changed, 7202 insertions(+), 7202 deletions(-)
Title: Robust Outliers Detection
Description: Detecting outliers using robust methods,
i.e. the Median Absolute Deviation (MAD) for univariate outliers; Leys, Ley, Klein, Bernard, & Licata (2013) <doi:10.1016/j.jesp.2013.03.013>
and the Mahalanobis-Minimum Covariance Determinant (MMCD) for multivariate outliers; Leys, C., Klein, O., Dominicy, Y. & Ley, C. (2018) <doi:10.1016/j.jesp.2017.09.011>.
There is also the more known but less robust Mahalanobis distance method, only for comparison purposes.
Author: Marie Delacre [aut, cre],
Olivier Klein [aut]
Maintainer: Marie Delacre <marie.delacre@ulb.ac.be>
Diff between Routliers versions 0.0.0.1 dated 2019-04-28 and 0.0.0.2 dated 2019-05-22
DESCRIPTION | 23 ++-- MD5 | 20 +-- NAMESPACE | 1 R/outliers_mahalanobis.R | 5 R/outliers_mcd.R | 6 - R/plot_outliers_mahalanobis.R | 218 +++++++++++++++++++++--------------------- R/plot_outliers_mcd.R | 209 +++++++++++++++++++--------------------- man/Routliers-package.Rd | 4 man/outliers_mahalanobis.Rd | 1 man/outliers_mcd.Rd | 2 man/plot_outliers_mcd.Rd | 6 - 11 files changed, 247 insertions(+), 248 deletions(-)
Title: Estimation and Validation Methods for Subgroup Identification
and Personalized Medicine
Description: Provides functions for fitting and validation of models for subgroup
identification and personalized medicine / precision medicine under the general subgroup
identification framework of Chen et al. (2017) <doi:10.1111/biom.12676>.
This package is intended for use for both randomized controlled trials and
observational studies.
Author: Jared Huling [aut, cre] (<https://orcid.org/0000-0003-0670-4845>),
Aaron Potvien [ctb],
Alexandros Karatzoglou [cph],
Alex Smola [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between personalized versions 0.2.3 dated 2019-02-07 and 0.2.4 dated 2019-05-22
DESCRIPTION | 8 MD5 | 34 +-- NAMESPACE | 1 R/plot_subgroup_validated.R | 15 - R/validate_subgroup.R | 22 +- R/weighted_svm.R | 2 README.md | 78 +++---- build/vignette.rds |binary inst/doc/usage_of_the_personalized_package.html | 214 ++++++++++---------- man/plot.Rd | 4 man/validate.subgroup.Rd | 5 man/weighted.ksvm.Rd | 2 tests/testthat/test-fitsubgroup.R | 250 ++++++++++++------------ tests/testthat/test-plotandplotcompare.R | 87 ++++---- tests/testthat/test-validatesubgroup.R | 25 +- tests/testthat/test-wksvm.R | 104 +++++---- vignettes/usage_overview-1.png |binary vignettes/vis_val-1.png |binary 18 files changed, 441 insertions(+), 410 deletions(-)
Title: Bayesian Continual Reassessment Method for Phase I
Dose-Escalation Trials
Description: Implements a wide variety of one- and two-parameter Bayesian CRM
designs. The program can run interactively, allowing the user to enter outcomes
after each cohort has been recruited, or via simulation to assess operating
characteristics.
Author: Michael Sweeting [aut],
Graham Wheeler [aut, cre]
Maintainer: Graham Wheeler <graham.wheeler@ucl.ac.uk>
Diff between bcrm versions 0.4.7 dated 2018-01-28 and 0.5.1 dated 2019-05-22
bcrm-0.4.7/bcrm/R/bcrm_0.4.7.R |only bcrm-0.4.7/bcrm/inst |only bcrm-0.4.7/bcrm/man/posterior.Rd |only bcrm-0.5.1/bcrm/DESCRIPTION | 28 - bcrm-0.5.1/bcrm/MD5 | 43 + bcrm-0.5.1/bcrm/NAMESPACE | 47 -- bcrm-0.5.1/bcrm/NEWS | 26 + bcrm-0.5.1/bcrm/R/bcrm-package.R |only bcrm-0.5.1/bcrm/R/bcrm.R |only bcrm-0.5.1/bcrm/R/models.R |only bcrm-0.5.1/bcrm/R/nextdose.R |only bcrm-0.5.1/bcrm/R/posteriors.R |only bcrm-0.5.1/bcrm/R/simFun.R |only bcrm-0.5.1/bcrm/R/stopcheck.R |only bcrm-0.5.1/bcrm/R/threep3.R |only bcrm-0.5.1/bcrm/README.md |only bcrm-0.5.1/bcrm/man/Posterior.BRugs.Rd |only bcrm-0.5.1/bcrm/man/Posterior.R2WinBUGS.Rd |only bcrm-0.5.1/bcrm/man/Posterior.exact.Rd |only bcrm-0.5.1/bcrm/man/Posterior.exact.sim.Rd |only bcrm-0.5.1/bcrm/man/Posterior.rjags.Rd |only bcrm-0.5.1/bcrm/man/bcrm-package.Rd | 40 - bcrm-0.5.1/bcrm/man/bcrm.Rd | 658 +++++++++++++++++------------ bcrm-0.5.1/bcrm/man/find.x.Rd | 96 ++-- bcrm-0.5.1/bcrm/man/getprior.Rd | 56 +- bcrm-0.5.1/bcrm/man/plot.bcrm.Rd | 62 +- bcrm-0.5.1/bcrm/man/plot.bcrm.sim.Rd | 66 +- bcrm-0.5.1/bcrm/man/plot.threep3.Rd | 43 + bcrm-0.5.1/bcrm/man/print.bcrm.Rd | 94 ++-- bcrm-0.5.1/bcrm/man/print.threep3.Rd | 64 +- bcrm-0.5.1/bcrm/man/threep3.Rd | 160 ++++--- 31 files changed, 874 insertions(+), 609 deletions(-)
Title: Bayesian Dynamic Factor Analysis (DFA) with 'Stan'
Description: Implements Bayesian dynamic factor analysis with 'Stan'. Dynamic
factor analysis is a dimension reduction tool for multivariate time series.
'bayesdfa' extends conventional dynamic factor models in several ways.
First, extreme events may be estimated in the latent trend by modeling
process error with a student-t distribution. Second, autoregressive and
moving average components can be optionally included. Third, the estimated
dynamic factors can be analyzed with hidden Markov models to evaluate
support for latent regimes.
Author: Eric J. Ward [aut, cre],
Sean C. Anderson [aut],
Luis A. Damiano [aut],
Mary E. Hunsicker, [ctb],
Mike A. Litzow [ctb],
Trustees of Columbia University [cph]
Maintainer: Eric J. Ward <eric.ward@noaa.gov>
Diff between bayesdfa versions 0.1.2 dated 2019-03-05 and 0.1.3 dated 2019-05-22
DESCRIPTION | 10 +- MD5 | 26 +++-- NEWS.md | 4 R/fit_dfa.R | 96 ++++++++++++++------- R/plot_regime_model.R | 2 build/vignette.rds |binary inst/doc/bayesdfa.html | 211 +++++++++++++++++++++++------------------------ inst/doc/covariates.R |only inst/doc/covariates.Rmd |only inst/doc/covariates.html |only man/fit_dfa.Rd | 39 +++++--- man/plot_regime_model.Rd | 2 src/Makevars | 3 src/Makevars.win | 2 src/stan_files/dfa.stan | 30 +++++- vignettes/covariates.Rmd |only 16 files changed, 253 insertions(+), 172 deletions(-)
Title: The IsoSpec Algorithm
Description: IsoSpec is a fine structure calculator used for obtaining the most
probable masses of a chemical compound given the frequencies of the composing
isotopes and their masses. It finds the smallest set of isotopologues with
a given probability. The probability is assumed to be that of the product of
multinomial distributions, each corresponding to one particular element and
parametrized by the frequencies of finding these elements in nature. These
numbers are supplied by IUPAC - the International Union of Pure and Applied
Chemistry.
Author: Mateusz Krzysztof Lacki and Michal Startek
Maintainer: Matteo Lacki <matteo.lacki@gmail.com>
Diff between IsoSpecR versions 1.9.2 dated 2019-01-21 and 2.0.1 dated 2019-05-22
IsoSpecR-1.9.2/IsoSpecR/src/tabulator.cpp |only IsoSpecR-1.9.2/IsoSpecR/src/tabulator.h |only IsoSpecR-2.0.1/IsoSpecR/DESCRIPTION | 12 IsoSpecR-2.0.1/IsoSpecR/MD5 | 70 - IsoSpecR-2.0.1/IsoSpecR/NAMESPACE | 3 IsoSpecR-2.0.1/IsoSpecR/R/IsoSpecR.R | 3 IsoSpecR-2.0.1/IsoSpecR/R/RcppExports.R | 2 IsoSpecR-2.0.1/IsoSpecR/R/add_custom_isotopes.R |only IsoSpecR-2.0.1/IsoSpecR/man/IsoSpecify.Rd | 6 IsoSpecR-2.0.1/IsoSpecR/man/custom_isotopes_example.Rd |only IsoSpecR-2.0.1/IsoSpecR/man/isotopicData.Rd | 1 IsoSpecR-2.0.1/IsoSpecR/src/Rinterface.cpp | 134 +- IsoSpecR-2.0.1/IsoSpecR/src/allocator.cpp | 4 IsoSpecR-2.0.1/IsoSpecR/src/allocator.h | 4 IsoSpecR-2.0.1/IsoSpecR/src/conf.h | 2 IsoSpecR-2.0.1/IsoSpecR/src/cwrapper.cpp | 110 +- IsoSpecR-2.0.1/IsoSpecR/src/cwrapper.h | 63 - IsoSpecR-2.0.1/IsoSpecR/src/dirtyAllocator.cpp | 6 IsoSpecR-2.0.1/IsoSpecR/src/dirtyAllocator.h | 4 IsoSpecR-2.0.1/IsoSpecR/src/element_tables.cpp | 4 IsoSpecR-2.0.1/IsoSpecR/src/element_tables.h | 4 IsoSpecR-2.0.1/IsoSpecR/src/fixedEnvelopes.cpp |only IsoSpecR-2.0.1/IsoSpecR/src/fixedEnvelopes.h |only IsoSpecR-2.0.1/IsoSpecR/src/isoMath.cpp | 60 + IsoSpecR-2.0.1/IsoSpecR/src/isoMath.h | 30 IsoSpecR-2.0.1/IsoSpecR/src/isoSpec++.cpp | 492 +++++----- IsoSpecR-2.0.1/IsoSpecR/src/isoSpec++.h | 163 ++- IsoSpecR-2.0.1/IsoSpecR/src/marginalTrek++.cpp | 117 ++ IsoSpecR-2.0.1/IsoSpecR/src/marginalTrek++.h | 90 + IsoSpecR-2.0.1/IsoSpecR/src/misc.cpp | 6 IsoSpecR-2.0.1/IsoSpecR/src/misc.h | 24 IsoSpecR-2.0.1/IsoSpecR/src/mman.cpp | 52 - IsoSpecR-2.0.1/IsoSpecR/src/mman.h | 6 IsoSpecR-2.0.1/IsoSpecR/src/operators.cpp | 4 IsoSpecR-2.0.1/IsoSpecR/src/operators.h | 10 IsoSpecR-2.0.1/IsoSpecR/src/platform.h | 23 IsoSpecR-2.0.1/IsoSpecR/src/summator.h | 7 IsoSpecR-2.0.1/IsoSpecR/src/unity-build.cpp | 22 IsoSpecR-2.0.1/IsoSpecR/tests/testthat/test-numerical-stability.R | 42 39 files changed, 990 insertions(+), 590 deletions(-)
Title: Import 'OpenStreetMap' Data as Simple Features or Spatial
Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp'
objects. 'OSM' data are extracted from the 'Overpass' web server and
processed with very fast 'C++' routines for return to 'R'.
Author: Mark Padgham [aut, cre],
Bob Rudis [aut],
Robin Lovelace [aut],
Maëlle Salmon [aut],
Andrew Smith [ctb],
James Smith [ctb],
Marcin Kalicinski [ctb, cph] (Author of included RapidXML code),
Finkelstein Noam [ctb, cph] (Author of included stub.R code),
Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between osmdata versions 0.1.0 dated 2019-04-25 and 0.1.1 dated 2019-05-22
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/trim-osmdata.R | 3 +++ inst/doc/osm-sf-translation.html | 4 ++-- inst/doc/osmdata-sc.html | 4 ++-- inst/doc/osmdata.html | 6 +++--- 7 files changed, 25 insertions(+), 16 deletions(-)
Title: A Shiny Application for Automatic Measurements of Tree-Ring
Widths on Digital Images
Description: Use morphological image processing and edge detection algorithms to automatically measure tree ring widths on digital images. Users can also manually mark tree rings on species with complex anatomical structures. The arcs of inner-rings and angles of successive inclined ring boundaries are used to correct ring-width series. The package provides a Shiny-based application, allowing R beginners to easily analyze tree ring images and export ring-width series in standard file formats.
Author: Jingning Shi [aut, cre],
Wei Xiang [aut]
Maintainer: Jingning Shi <snow940220@bjfu.edu.cn>
Diff between MtreeRing versions 1.1 dated 2018-10-16 and 1.3 dated 2019-05-22
MtreeRing-1.1/MtreeRing/R/autoDetect.R |only MtreeRing-1.1/MtreeRing/R/calcRingWidth.R |only MtreeRing-1.1/MtreeRing/R/correct.color.R |only MtreeRing-1.1/MtreeRing/R/create.label.R |only MtreeRing-1.1/MtreeRing/R/createServer.R |only MtreeRing-1.1/MtreeRing/R/createUI.R |only MtreeRing-1.1/MtreeRing/R/f.bor.plot.R |only MtreeRing-1.1/MtreeRing/R/f.border.R |only MtreeRing-1.1/MtreeRing/R/f.combine.R |only MtreeRing-1.1/MtreeRing/R/f.img.middle.R |only MtreeRing-1.1/MtreeRing/R/f.marker.R |only MtreeRing-1.1/MtreeRing/R/f.morphological.R |only MtreeRing-1.1/MtreeRing/R/f.plot.double.R |only MtreeRing-1.1/MtreeRing/R/f.plot.single.R |only MtreeRing-1.1/MtreeRing/R/f.rw.plot.R |only MtreeRing-1.1/MtreeRing/R/f.sort.R |only MtreeRing-1.1/MtreeRing/R/hat.R |only MtreeRing-1.1/MtreeRing/R/imgInput.R |only MtreeRing-1.1/MtreeRing/R/is.early2late.R |only MtreeRing-1.1/MtreeRing/R/launchMtRApp.R |only MtreeRing-1.1/MtreeRing/R/nearPith.R |only MtreeRing-1.1/MtreeRing/R/r.det.R |only MtreeRing-1.1/MtreeRing/R/split.label.R |only MtreeRing-1.1/MtreeRing/R/visualSelect.R |only MtreeRing-1.1/MtreeRing/R/water.im.R |only MtreeRing-1.1/MtreeRing/R/watershed.im.R |only MtreeRing-1.1/MtreeRing/inst/arc.png |only MtreeRing-1.1/MtreeRing/man/autoDetect.Rd |only MtreeRing-1.1/MtreeRing/man/calcRingWidth.Rd |only MtreeRing-1.1/MtreeRing/man/imgInput.Rd |only MtreeRing-1.1/MtreeRing/man/launchMtRApp.Rd |only MtreeRing-1.1/MtreeRing/man/nearPith.Rd |only MtreeRing-1.1/MtreeRing/man/visualSelect.Rd |only MtreeRing-1.3/MtreeRing/DESCRIPTION | 23 ++-- MtreeRing-1.3/MtreeRing/MD5 | 60 ++++------- MtreeRing-1.3/MtreeRing/NAMESPACE | 125 +++++++++++++++++++---- MtreeRing-1.3/MtreeRing/NEWS.md |only MtreeRing-1.3/MtreeRing/R/img_plot.R |only MtreeRing-1.3/MtreeRing/R/morphology_process.R |only MtreeRing-1.3/MtreeRing/R/pith_measure.R |only MtreeRing-1.3/MtreeRing/R/ring_app_launch.R |only MtreeRing-1.3/MtreeRing/R/ring_calculate.R |only MtreeRing-1.3/MtreeRing/R/ring_detect.R |only MtreeRing-1.3/MtreeRing/R/ring_modify.R |only MtreeRing-1.3/MtreeRing/R/ring_read.R |only MtreeRing-1.3/MtreeRing/README.md |only MtreeRing-1.3/MtreeRing/inst/README-img001.png |only MtreeRing-1.3/MtreeRing/inst/README-img002.png |only MtreeRing-1.3/MtreeRing/inst/RingCorrection.png |only MtreeRing-1.3/MtreeRing/inst/missing_pith.png |only MtreeRing-1.3/MtreeRing/inst/mtr_app |only MtreeRing-1.3/MtreeRing/man/MtreeRing-package.Rd | 11 +- MtreeRing-1.3/MtreeRing/man/pith_measure.Rd |only MtreeRing-1.3/MtreeRing/man/ring_app_launch.Rd |only MtreeRing-1.3/MtreeRing/man/ring_calculate.Rd |only MtreeRing-1.3/MtreeRing/man/ring_detect.Rd |only MtreeRing-1.3/MtreeRing/man/ring_modify.Rd |only MtreeRing-1.3/MtreeRing/man/ring_read.Rd |only 58 files changed, 152 insertions(+), 67 deletions(-)
Title: Network Dynamic Temporal Visualizations
Description: Renders dynamic network data from 'networkDynamic' objects as movies, interactive animations, or other representations of changing relational structures and attributes.
Author: Skye Bender-deMoll [cre, aut],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between ndtv versions 0.12.3 dated 2018-10-08 and 0.13.0 dated 2019-05-22
ChangeLog | 3 +++ DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- R/animate.layouts.R | 5 +++-- R/export.movie.R | 4 ++-- R/installers.R | 6 ++++-- R/render.d3_animation.R | 4 ++-- build/vignette.rds |binary inst/doc/ndtv.R | 2 +- inst/doc/ndtv.Rnw | 2 +- inst/doc/ndtv.pdf |binary man/network.layout.animate.Rd | 4 ++-- man/stergm.sim.1.Rd | 2 +- vignettes/ndtv.Rnw | 2 +- 14 files changed, 38 insertions(+), 32 deletions(-)
Title: Generalized Linear Mixed Model Association Tests
Description: Perform association tests using generalized linear mixed models (GLMMs) in genome-wide association studies (GWAS) and sequencing association studies. First, GMMAT fits a GLMM with covariate adjustment and random effects to account for population structure and familial or cryptic relatedness. For GWAS, GMMAT performs score tests for each genetic variant as proposed in Chen et al. (2016) <DOI:10.1016/j.ajhg.2016.02.012>. For candidate gene studies, GMMAT can also perform Wald tests to get the effect size estimate for each genetic variant. For rare variant analysis from sequencing association studies, GMMAT performs the variant Set Mixed Model Association Tests (SMMAT) as proposed in Chen et al. (2019) <DOI:10.1016/j.ajhg.2018.12.012>, including the burden test, the sequence kernel association test (SKAT), SKAT-O and an efficient hybrid test of the burden test and SKAT, based on user-defined variant sets.
Author: Han Chen, Matthew P. Conomos
Maintainer: Han Chen <Han.Chen.2@uth.tmc.edu>
Diff between GMMAT versions 1.0.4 dated 2019-03-06 and 1.1.0 dated 2019-05-22
DESCRIPTION | 11 MD5 | 34 +- NAMESPACE | 1 R/SMMAT.R | 39 +- R/glmm.score.R | 82 +++- R/glmm.wald.R | 22 + R/glmmkin.R | 123 +++++-- build/vignette.rds |binary data/example.rda |binary inst/doc/GMMAT.Rnw | 30 + inst/doc/GMMAT.pdf |binary man/GMMAT-package.Rd | 4 man/glmmkin.Rd | 4 src/fitglmm.cpp | 657 +++++++++++++++++++++++++++++++++++++++ src/registerDynamicSymbol.c | 6 tests/testthat/test_SMMAT.R | 6 tests/testthat/test_SMMAT.meta.R | 2 vignettes/GMMAT.Rnw | 30 + 18 files changed, 929 insertions(+), 122 deletions(-)
Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code or use a easy to remember set of tidy functions for exploratory data analysis. Introduces two main verbs. describe() to describe a variable or table, explore() to graphically explore a variable or table.
Author: Roland Krasser
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between explore versions 0.4.1 dated 2019-05-19 and 0.4.2 dated 2019-05-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/explore.R | 15 ++++++++++++++- inst/doc/explore.html | 4 ++-- man/report.Rd | 4 +++- 5 files changed, 26 insertions(+), 11 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu, Simon Firestone, Ryan Kyle, Johann Popp and Mathew Jay.
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 0.9-99 dated 2018-11-06 and 1.0-2 dated 2019-05-22
epiR-0.9-99/epiR/R/epi.interaction.r |only epiR-1.0-2/epiR/DESCRIPTION | 8 epiR-1.0-2/epiR/MD5 | 22 - epiR-1.0-2/epiR/NEWS | 41 ++ epiR-1.0-2/epiR/R/NEW_epi.2by2_v01.R |only epiR-1.0-2/epiR/R/NEW_epi.2by2_v02.R |only epiR-1.0-2/epiR/R/epi.2by2.R | 633 +++++++++++++++++----------------- epiR-1.0-2/epiR/R/epi.conf.R | 481 +++++++++++++------------ epiR-1.0-2/epiR/R/epi.interaction.R |only epiR-1.0-2/epiR/R/epi.kappa.R | 294 ++++++++------- epiR-1.0-2/epiR/man/epi.2by2.Rd | 59 +-- epiR-1.0-2/epiR/man/epi.conf.Rd | 6 epiR-1.0-2/epiR/man/epi.detectsize.Rd | 4 epiR-1.0-2/epiR/man/epi.kappa.Rd | 4 14 files changed, 822 insertions(+), 730 deletions(-)
Title: General Utility Functions for the 'Agricultural Production
Systems Simulator'
Description: Contains functions designed to facilitate the loading
and transformation of 'Agricultural Production Systems Simulator'
output files <https://www.apsim.info>. Input meteorological data
(also known as "weather" or "met") files can also be generated
from user supplied data.
Author: Justin Fainges
Maintainer: Dean Holzworth <Dean.Holzworth@csiro.au>
Diff between APSIM versions 0.9.2 dated 2017-07-23 and 0.9.3 dated 2019-05-22
DESCRIPTION | 10 MD5 | 40 +- NAMESPACE | 39 +- R/LoadAPSIMouts.R | 318 +++++++++---------- R/LoadNGouts.R | 34 +- R/MetFunctions.R | 818 ++++++++++++++++++++++++------------------------- R/apsim.R | 96 ++--- README.md | 86 ++--- man/GetApsimNGTable.Rd | 44 +- man/apsim.Rd | 56 +-- man/checkCont.Rd | 66 +-- man/checkMet.Rd | 88 ++--- man/getToken.Rd | 68 ++-- man/insertTavAmp.Rd | 56 +-- man/kingsData.Rd | 24 - man/loadApsim.Rd | 114 +++--- man/loadMet.Rd | 52 +-- man/met.Rd | 26 - man/metFile-class.Rd | 56 +-- man/prepareMet.Rd | 120 +++---- man/writeMetFile.Rd | 48 +- 21 files changed, 1132 insertions(+), 1127 deletions(-)
Title: Download and Tidy Time Series Data from the Australian Bureau of
Statistics
Description: Downloads, imports, and tidies time series data from the
Australian Bureau of Statistics <https://www.abs.gov.au/>.
Author: Matt Cowgill [aut, cre],
Zoe Meers [aut],
Jaron Lee [aut]
Maintainer: Matt Cowgill <mattcowgill@gmail.com>
Diff between readabs versions 0.3.0 dated 2019-02-01 and 0.3.1 dated 2019-05-22
DESCRIPTION | 12 +++---- MD5 | 30 ++++++++++--------- NAMESPACE | 1 NEWS.md | 7 ++++ R/get_abs_xml_metadata.R | 13 ++++++-- R/get_xml_df.R | 7 +++- R/read_abs.R | 45 +++++++++++++++++++++++++++-- R/tidy_abs.R | 3 + README.md | 26 ++++++++++++----- build/vignette.rds |binary inst/doc/readabs_vignette.Rmd | 2 - inst/doc/readabs_vignette.html | 62 ++++++++++++++++++++++++++++++----------- man/read_abs.Rd | 5 ++- tests/testthat/data |only tests/testthat/test_readabs.R | 2 - vignettes/readabs_vignette.Rmd | 2 - 16 files changed, 161 insertions(+), 56 deletions(-)
Title: Colors Palettes for R and 'ggplot2', Additional Themes for
'ggplot2'
Description: Contains a selection of color palettes and 'ggplot2' themes designed by the package author.
Author: Jared Huling [aut, cre] (<https://orcid.org/0000-0003-0670-4845>)
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between jcolors versions 0.0.3 dated 2018-08-09 and 0.0.4 dated 2019-05-22
DESCRIPTION | 12 MD5 | 62 +- NAMESPACE | 1 R/ggplot2_themes.R | 9 build/vignette.rds |binary inst/doc/using_the_jcolors_package.html | 449 +++++++++++++++------ vignettes/readme_figs/contin_example-1.png |binary vignettes/readme_figs/contin_example_display-1.png |binary vignettes/readme_figs/darkbg-1.png |binary vignettes/readme_figs/diamonds_light_theme-1.png |binary vignettes/readme_figs/displayall-1.png |binary vignettes/readme_figs/jitterplot-1.png |binary vignettes/readme_figs/moreplots-1.png |binary vignettes/readme_figs/moreplots-2.png |binary vignettes/readme_figs/moreplots-3.png |binary vignettes/readme_figs/moreplots-4.png |binary vignettes/readme_figs/mountain_ex-1.png |binary vignettes/readme_figs/unnamed-chunk-10-1.png |binary vignettes/readme_figs/unnamed-chunk-11-1.png |binary vignettes/readme_figs/unnamed-chunk-12-1.png |binary vignettes/readme_figs/unnamed-chunk-13-1.png |binary vignettes/readme_figs/unnamed-chunk-14-1.png |binary vignettes/readme_figs/unnamed-chunk-15-1.png |binary vignettes/readme_figs/unnamed-chunk-16-1.png |binary vignettes/readme_figs/unnamed-chunk-3-1.png |binary vignettes/readme_figs/unnamed-chunk-3-2.png |binary vignettes/readme_figs/unnamed-chunk-4-1.png |binary vignettes/readme_figs/unnamed-chunk-5-1.png |binary vignettes/readme_figs/unnamed-chunk-6-1.png |binary vignettes/readme_figs/unnamed-chunk-7-1.png |binary vignettes/readme_figs/unnamed-chunk-8-1.png |binary vignettes/readme_figs/unnamed-chunk-9-1.png |binary 32 files changed, 387 insertions(+), 146 deletions(-)